Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001735.1 Hibiscus syriacus cultivar Beakdansim tig00003506_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: 109095
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2710 original size:21 final size:20
Alignment explanation
Indices: 2656--2710 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 20
2646 AAATAAAAGG
2656 AAAAG-GAAAAAATAATAGAT
1 AAAAGAGAAAAAAT-ATAGAT
* *
2676 AAAA-A-TATAAATATAGAT
1 AAAAGAGAAAAAATATAGAT
2694 CAAAAGAGAAAAAATAT
1 -AAAAGAGAAAAAATAT
2711 TAATAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
18 6 0.22
19 9 0.33
20 5 0.19
21 7 0.26
ACGTcount: A:0.69, C:0.02, G:0.11, T:0.18
Consensus pattern (20 bp):
AAAAGAGAAAAAATATAGAT
Found at i:2775 original size:20 final size:20
Alignment explanation
Indices: 2747--2785 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2737 AAAATAGTTA
*
2747 GAAACAAATGTTAAATAAAT
1 GAAAAAAATGTTAAATAAAT
2767 GAAAAAAATGTTAAATAAA
1 GAAAAAAATGTTAAATAAA
2786 AAAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.64, C:0.03, G:0.10, T:0.23
Consensus pattern (20 bp):
GAAAAAAATGTTAAATAAAT
Found at i:3955 original size:15 final size:14
Alignment explanation
Indices: 3935--3980 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
3925 ACAAAAAATG
3935 AAAATAAATTAATAA
1 AAAATAAA-TAATAA
*
3950 AAAATAAAAAAATAAA
1 AAAAT-AAATAAT-AA
3966 AAAATAAATAATAA
1 AAAATAAATAATAA
3980 A
1 A
3981 GTTAACAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 3 0.11
15 14 0.52
16 10 0.37
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AAAATAAATAATAA
Found at i:3961 original size:23 final size:23
Alignment explanation
Indices: 3935--3980 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3925 ACAAAAAATG
**
3935 AAAATAAATTAATAAAAAATAAA
1 AAAATAAAAAAATAAAAAATAAA
*
3958 AAAATAAAAAAATAAATAATAAA
1 AAAATAAAAAAATAAAAAATAAA
3981 GTTAACAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (23 bp):
AAAATAAAAAAATAAAAAATAAA
Found at i:4074 original size:34 final size:35
Alignment explanation
Indices: 4026--4388 Score: 162
Period size: 32 Copynumber: 10.4 Consensus size: 35
4016 TTTCTGAAAC
* *
4026 CTATATAATTTATATTTTCAAAA-GTATTTTAAAA
1 CTATATTATATATATTTTCAAAATGTATTTTAAAA
* * *
4060 TTATATTATATATATATATATATATATTAAATGT-TTTCAAAA
1 CTATA-T-TATATATAT-T-T-T-CA--AAATGTATTTTAAAA
4102 -T-TA-TATA-AT-TT-TCAAAAATGT-TTTTAAAA
1 CTATATTATATATATTTTCAA-AATGTATTTTAAAA
* *
4131 CTATACTATATA-ATTTTTCAAAATGT-TTTCAAAA
1 CTATATTATATATA-TTTTCAAAATGTATTTTAAAA
* * * *
4165 TTATATAATATATATGTTTTCAAAATGTTTTTTTAAA
1 CTATAT--TATATATATTTTCAAAATGTATTTTAAAA
* *
4202 --A-ACTATATATATTTTCAAAATGT-TTTAAAAA
1 CTATATTATATATATTTTCAAAATGTATTTTAAAA
*
4233 CTATA-TATATATATTTTCAAAA-ATATTTTAAAA
1 CTATATTATATATATTTTCAAAATGTATTTTAAAA
* * *
4266 -AATA-TATATTTATTTTCAAAATAT-TTTTAAAAA
1 CTATATTATATATATTTTCAAAATGTATTTT-AAAA
* *
4299 CTATATAATATATAAATGTTTTCAAATATGT-TTTCAAAA
1 CTATAT--TATAT--ATATTTTCAAA-ATGTATTTTAAAA
* * *
4338 CCATATATTATATGT-TTTT-AAAA-ATATTTTCAAA
1 -C-TATATTATATATATTTTCAAAATGTATTTTAAAA
4372 CTATATACTATATATAT
1 CTATAT--TATATATAT
4389 ATGATAAAAT
Statistics
Matches: 258, Mismatches: 31, Indels: 79
0.70 0.08 0.21
Matches are distributed among these distances:
28 1 0.00
29 12 0.05
30 2 0.01
31 9 0.03
32 52 0.20
33 34 0.13
34 41 0.16
35 11 0.04
36 31 0.12
37 17 0.07
38 1 0.00
39 19 0.07
40 10 0.04
41 6 0.02
42 10 0.04
43 2 0.01
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (35 bp):
CTATATTATATATATTTTCAAAATGTATTTTAAAA
Found at i:4082 original size:42 final size:41
Alignment explanation
Indices: 4027--4107 Score: 94
Period size: 42 Copynumber: 2.0 Consensus size: 41
4017 TTCTGAAACC
* *
4027 TATATAAT-T-TATATTTTCAAAAGTATTTTAAAATTATATTA
1 TATATAATATATATATATT-AAAAGT-TTTCAAAATTATATTA
*
4068 TATATATATATATATATATTAAATGTTTTCAAAATTATAT
1 TATATA-ATATATATATATTAAAAGTTTTCAAAATTATAT
4108 AATTTTCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
41 6 0.18
42 15 0.44
43 6 0.18
44 7 0.21
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (41 bp):
TATATAATATATATATATTAAAAGTTTTCAAAATTATATTA
Found at i:4321 original size:39 final size:38
Alignment explanation
Indices: 4290--4385 Score: 85
Period size: 35 Copynumber: 2.6 Consensus size: 38
4280 TTCAAAATAT
*
4290 TTTTAAAAACTATATAATATATAAATGTTTTC-AAATATG
1 TTTT-AAAACTATATAATATAT-AATGTTTTCAAAATATA
* *
4329 TTTTCAAAACCATAT-AT-TAT-ATGTTTTTAAAA-ATA
1 TTTT-AAAACTATATAATATATAATGTTTTCAAAATATA
* *
4364 TTTTCAAACTATATACTATATA
1 TTTTAAAACTATATAATATATA
4386 TATATGATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
34 8 0.17
35 14 0.30
36 6 0.13
37 3 0.07
38 2 0.04
39 13 0.28
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (38 bp):
TTTTAAAACTATATAATATATAATGTTTTCAAAATATA
Found at i:4409 original size:12 final size:12
Alignment explanation
Indices: 4392--4420 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4382 TATATATATG
4392 ATAAAATAAAAA
1 ATAAAATAAAAA
4404 ATAAAATAAAAA
1 ATAAAATAAAAA
4416 A-AAAA
1 ATAAAA
4421 GAGAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
ATAAAATAAAAA
Found at i:4414 original size:17 final size:18
Alignment explanation
Indices: 4392--4433 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
4382 TATATATATG
*
4392 ATAAAATAAAAAATA-AA
1 ATAAAATAAAAAAGAGAA
4409 ATAAAA-AAAAAAGAGAA
1 ATAAAATAAAAAAGAGAA
4426 A-AAAATAA
1 ATAAAATAA
4434 CTTTGGGCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.83, C:0.00, G:0.05, T:0.12
Consensus pattern (18 bp):
ATAAAATAAAAAAGAGAA
Found at i:6192 original size:26 final size:26
Alignment explanation
Indices: 6163--6217 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
6153 TTAGCATATT
* *
6163 AAAAACAAAGCTTGAAAA-TAAAAGA
1 AAAAATAAAACTTGAAAAGTAAAAGA
*
6188 AAAAATAAAACTTGAAAAGTAAAAGG
1 AAAAATAAAACTTGAAAAGTAAAAGA
6214 AAAA
1 AAAA
6218 CTTTAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.69, C:0.05, G:0.13, T:0.13
Consensus pattern (26 bp):
AAAAATAAAACTTGAAAAGTAAAAGA
Found at i:11490 original size:25 final size:25
Alignment explanation
Indices: 11461--11517 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
11451 TTAACATATT
*
11461 AAAAACAAAGCTTGAAAA-TAAAAGA
1 AAAAACAAAACTTGAAAAGTAAAA-A
*
11486 AAAAAGAAAACTTGAAAAGTAAAAA
1 AAAAACAAAACTTGAAAAGTAAAAA
11511 AGAAAAC
1 A-AAAAC
11518 TTTAATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 18 0.67
26 9 0.33
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.11
Consensus pattern (25 bp):
AAAAACAAAACTTGAAAAGTAAAAA
Found at i:11509 original size:21 final size:20
Alignment explanation
Indices: 11480--11519 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
11470 GCTTGAAAAT
11480 AAAAGAAAAAAGAAAACTTG
1 AAAAGAAAAAAGAAAACTTG
11500 AAAAGTAAAAAAGAAAACTT
1 AAAAG-AAAAAAGAAAACTT
11520 TAATAAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.70, C:0.05, G:0.12, T:0.12
Consensus pattern (20 bp):
AAAAGAAAAAAGAAAACTTG
Found at i:13280 original size:14 final size:14
Alignment explanation
Indices: 13261--13289 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13251 TCGATTATAT
13261 GTTCATTTATGTTC
1 GTTCATTTATGTTC
13275 GTTCATTTATGTTC
1 GTTCATTTATGTTC
13289 G
1 G
13290 AACAGAGGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.17, T:0.55
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:16735 original size:35 final size:35
Alignment explanation
Indices: 16689--16759 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
16679 TAAACAATAG
*
16689 TACTGCACGTGATCATTTATCCTAAAACTACCATT
1 TACTGCACGTGATAATTTATCCTAAAACTACCATT
16724 TACTGCACGTGATAATTTATCCTAAAACTACCATT
1 TACTGCACGTGATAATTTATCCTAAAACTACCATT
16759 T
1 T
16760 TTTCCTGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.35
Consensus pattern (35 bp):
TACTGCACGTGATAATTTATCCTAAAACTACCATT
Found at i:17922 original size:21 final size:21
Alignment explanation
Indices: 17896--17940 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
17886 TAACATGTCA
17896 AAATATACTTCAAAAGAGGTT
1 AAATATACTTCAAAAGAGGTT
17917 AAATATACTTCAAAAGAGGTT
1 AAATATACTTCAAAAGAGGTT
17938 AAA
1 AAA
17941 CATAATCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.27
Consensus pattern (21 bp):
AAATATACTTCAAAAGAGGTT
Found at i:19362 original size:10 final size:10
Alignment explanation
Indices: 19349--19396 Score: 60
Period size: 10 Copynumber: 4.4 Consensus size: 10
19339 TTTTCATTTA
19349 TTATGTTCGT
1 TTATGTTCGT
19359 TTATGTTCGT
1 TTATGTTCGT
19369 TCATATGTGTTCGT
1 T--TA--TGTTCGT
19383 TTATGTTCGT
1 TTATGTTCGT
19393 TTAT
1 TTAT
19397 CATTTAAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 22 0.65
12 4 0.12
14 8 0.24
ACGTcount: A:0.12, C:0.10, G:0.19, T:0.58
Consensus pattern (10 bp):
TTATGTTCGT
Found at i:19384 original size:24 final size:23
Alignment explanation
Indices: 19329--19393 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 23
19319 TTGTTTGTGT
* * *
19329 TGTTCGTTTATTTTCATTTATTA
1 TGTTCGTTTATGTTCGTTCATTA
*
19352 TGTTCGTTTATGTTCGTTCATATG
1 TGTTCGTTTATGTTCGTTCAT-TA
19376 TGTTCGTTTATGTTCGTT
1 TGTTCGTTTATGTTCGTT
19394 TATCATTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 18 0.49
24 19 0.51
ACGTcount: A:0.12, C:0.11, G:0.17, T:0.60
Consensus pattern (23 bp):
TGTTCGTTTATGTTCGTTCATTA
Found at i:33510 original size:3 final size:3
Alignment explanation
Indices: 33502--33548 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
33492 GGGCATCTTC
*
33502 ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
33549 CTCATTTGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:36577 original size:43 final size:43
Alignment explanation
Indices: 36508--36653 Score: 121
Period size: 43 Copynumber: 3.4 Consensus size: 43
36498 AAAATGCTGC
* * * *
36508 ATAGGTTTAGACATATAGCGGGGTTTTTTTTACAAACACCGTA
1 ATAGGTTCAGACATTTAGCAGCGTTTTTTTTACAAACACCGTA
* * ** * * **
36551 ATAGGTTCAGACATTTAGCTGCGTTTTCTCAATAAAGACTATA
1 ATAGGTTCAGACATTTAGCAGCGTTTTTTTTACAAACACCGTA
* * ** *
36594 ATAGGTTCAGACATTTAGCAGTGTTTTTATTACAAATGCCGCA
1 ATAGGTTCAGACATTTAGCAGCGTTTTTTTTACAAACACCGTA
* *
36637 ATAGATTCAAACATTTA
1 ATAGGTTCAGACATTTA
36654 ACACCGCTAA
Statistics
Matches: 78, Mismatches: 25, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
43 78 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (43 bp):
ATAGGTTCAGACATTTAGCAGCGTTTTTTTTACAAACACCGTA
Found at i:37420 original size:25 final size:25
Alignment explanation
Indices: 37392--37444 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
37382 CACATAGAAA
*
37392 TGAAAGAATCGATATACAACTTACT
1 TGAAAGAATCAATATACAACTTACT
37417 TGAAAGAATCAATATACAACTTACT
1 TGAAAGAATCAATATACAACTTACT
37442 TGA
1 TGA
37445 TACTTACTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.28
Consensus pattern (25 bp):
TGAAAGAATCAATATACAACTTACT
Found at i:39015 original size:42 final size:41
Alignment explanation
Indices: 38962--39061 Score: 139
Period size: 40 Copynumber: 2.4 Consensus size: 41
38952 ATAGACAGTT
* *
38962 GTGGCGTTTACAATAAAAACGTTGCTAAAGTATAGGTCGATC
1 GTGGCGTTTACAA-AAAAACGGTGCTAAAGTACAGGTCGATC
*
39004 GTGGCGTTTAC-AAAAAACGGTGCTAAAGTACAGGTCGGTC
1 GTGGCGTTTACAAAAAAACGGTGCTAAAGTACAGGTCGATC
* *
39044 GTGACATTTACAAAAAAA
1 GTGGCGTTTACAAAAAAA
39062 GCCGCCTTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
40 34 0.65
41 7 0.13
42 11 0.21
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (41 bp):
GTGGCGTTTACAAAAAAACGGTGCTAAAGTACAGGTCGATC
Found at i:39374 original size:19 final size:19
Alignment explanation
Indices: 39350--39454 Score: 129
Period size: 19 Copynumber: 5.2 Consensus size: 19
39340 GCGATTTTGA
39350 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
39369 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
39388 AAAATGTGTTGCGATAGTTT
1 AAAATGTGTTGCGATAG-TT
*
39408 GAAAAACGTGTTGTTGCGATAGTG
1 --AAAA--TG-TGTTGCGATAGTT
* *
39432 AAAAAGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTT
39451 AAAA
1 AAAA
39455 ATCCAAAATA
Statistics
Matches: 78, Mismatches: 2, Indels: 12
0.85 0.02 0.13
Matches are distributed among these distances:
19 53 0.68
20 3 0.04
22 8 0.10
24 3 0.04
25 11 0.14
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:39441 original size:44 final size:39
Alignment explanation
Indices: 39347--39449 Score: 127
Period size: 44 Copynumber: 2.5 Consensus size: 39
39337 AACGCGATTT
39347 TGAAAAATGTGTTGCGATAG-TTAAAATGTGTTGCGATAG
1 TGAAAAA-GTGTTGCGATAGTTTAAAATGTGTTGCGATAG
* *
39386 TTAAAATGTGTTGCGATAGTTTGAAAAACGTGTTGTTGCGATAG
1 TGAAAAAGTGTTGCGATAGTTT--AAAA--TG-TGTTGCGATAG
39430 TGAAAAAGTGTTGCGATAGT
1 TGAAAAAGTGTTGCGATAGT
39450 GAAAAATCCA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
38 12 0.22
39 7 0.13
41 4 0.07
43 2 0.04
44 29 0.54
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.34
Consensus pattern (39 bp):
TGAAAAAGTGTTGCGATAGTTTAAAATGTGTTGCGATAG
Found at i:40222 original size:16 final size:16
Alignment explanation
Indices: 40201--40231 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40191 GGTTAGTTTA
*
40201 AAAAAGGAAATAAAAC
1 AAAAAGCAAATAAAAC
40217 AAAAAGCAAATAAAA
1 AAAAAGCAAATAAAA
40232 AATTAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.06, G:0.10, T:0.06
Consensus pattern (16 bp):
AAAAAGCAAATAAAAC
Found at i:40244 original size:16 final size:15
Alignment explanation
Indices: 40225--40301 Score: 59
Period size: 16 Copynumber: 4.9 Consensus size: 15
40215 ACAAAAAGCA
40225 AATAAAAAATTAAAAT
1 AATAAAAAA-TAAAAT
* *
40241 AATATAAAATATATAT
1 AATAAAAAATA-AAAT
*
40257 AATACAAAAA-ATAAGT
1 AATA-AAAAATA-AAAT
40273 AAT-AAAAATAAAAT
1 AATAAAAAATAAAAT
40287 AAATAAATAAATAAA
1 -AATAAA-AAATAAA
40302 TAGTATATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
14 8 0.16
15 6 0.12
16 24 0.49
17 11 0.22
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.25
Consensus pattern (15 bp):
AATAAAAAATAAAAT
Found at i:40285 original size:18 final size:17
Alignment explanation
Indices: 40224--40301 Score: 52
Period size: 18 Copynumber: 4.4 Consensus size: 17
40214 AACAAAAAGC
*
40224 AAATAAAA-AATTAAAA
1 AAATAAAATAAATAAAA
*
40240 TAATATAAAATATATATAATA
1 -AA-ATAAAATA-A-ATAAAA
* *
40261 CAA-AAAATAAGTAATAA
1 AAATAAAATAAATAA-AA
*
40278 AAATAAAATAAATAAAT
1 AAATAAAATAAATAAAA
40295 AAATAAA
1 AAATAAA
40302 TAGTATATAT
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
16 3 0.06
17 14 0.30
18 22 0.47
19 2 0.04
20 2 0.04
21 4 0.09
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAATAAAA
Found at i:40290 original size:22 final size:23
Alignment explanation
Indices: 40257--40301 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
40247 AAATATATAT
*
40257 AATACAAAAAATAAGT-AATAAA
1 AATACAAAAAATAAATAAATAAA
40279 AATA-AAATAAATAAATAAATAAA
1 AATACAAA-AAATAAATAAATAAA
40302 TAGTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 3 0.15
22 11 0.55
23 6 0.30
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (23 bp):
AATACAAAAAATAAATAAATAAA
Found at i:42090 original size:165 final size:165
Alignment explanation
Indices: 41761--42766 Score: 859
Period size: 165 Copynumber: 6.1 Consensus size: 165
41751 TTTTACTGAT
* * * * * * * **
41761 AGATAGCCCTTCTTGCCCTGAGTTATGCTGTAAATGATGTGCCTAAGAGCTGAGCATAGTCGAAC
1 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGACTTGGAGCTGAGCATAGTCGAAC
* ** * * * * * * *
41826 TCGAAGGT-TTTTGTTGGTAGATAACCCTTCTAGCCTTGAGTTACGCTGCAAATGGTGTGCCCTC
66 TCGAAGGTCTTTTGGTGACAAATAACTCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTC
*
41890 GAAGCTGAGTGTAATCGAACTCGAAGGTTTTTGGC
131 GAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGC
* * *
41925 AGACATCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGACTTGGAGCTGAGCGTAGTCGAAC
1 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGACTTGGAGCTGAGCATAGTCGAAC
* * * * *
41990 TCGGAGGTCTTTTGGTGACAAATAACTCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCTC
66 TCGAAGGTCTTTTGGTGACAAATAACTCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTC
* * *
42055 GAAGTTGAGCGTAATCGAACTCGAGGGTCTTTGGC
131 GAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGC
* * * *
42090 AGATAGCCCTTCTCGACTTAAGCTATTCTGTAAATAATGTGCCTTGGAGCTGAGCATAGTCGAAC
1 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGACTTGGAGCTGAGCATAGTCGAAC
* * * ** *
42155 TCGAAGGTC-TTTGGTTGGCAGATAACTCTTCTCGACTTAAGTTATGCTGCAAATGACGTACCCT
66 TCGAAGGTCTTTTGG-TGACAAATAACTCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCT
*
42219 CGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGC
130 CGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGC
*
42255 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGACGTT-GAGCTGAGCGTAGTCGAA
1 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGAC-TTGGAGCTGAGCATAGTCGAA
* * * * *
42319 CTCAAAGGTCTTTTGTTGGA-AAACAAC-CTTCTAGACTTAAGTTGTGTTGCAAATGATATG-CC
65 CTCGAAGGTCTTTTGGT-GACAAATAACTCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCC
* * * *
42381 TTGGAGCTGAGTGTAGTCGAACTCGAAGGTATTTGGTGAC
129 TCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTT-G-G-C
* * * * * * * * * * * * ** *
42421 AGATAACCCTTCTAGCCTTGAGTTAAGTTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAA
1 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-ACTTGGAGCTGAGCATAGTCGAA
* * * * * * * *
42486 CTCGAGGGGC-TTT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCT
65 CTCGAAGGTCTTTTGGTGACAAATAACTCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCT
* * * * * *
42546 TGGAGCTGAGTATAGTCAAACTCGAAGGTCTTTAGTTGGT
130 CGAAGCTGAGTGTAATCGAACTCGAAGGTC--T--TTGGC
* * * * * * *
42586 AGATAACCCTTCTCGACTTAAGTTATGTTACAAATGATGTGTCTTGGAGCTGAGCGTAGTCTAAC
1 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGACTTGGAGCTGAGCATAGTCGAAC
* * * * * * * * *
42651 TCGAAGGTC-TTTGGTTGGCAGATAGCCCTTCTGGCCTTGAGATATGCTGCAAATGATGTG-CCT
66 TCGAAGGTCTTTTGG-TGACAAATAACTCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCT
* * * * *
42714 TGGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTGGTTGGC
130 CGAAGCTGAGTGTAATCGAACTCGAAGGTC--T--TTGGC
42754 AGATAGCCCTTCT
1 AGATAGCCCTTCT
42767 GGCCTTGAGT
Statistics
Matches: 698, Mismatches: 124, Indels: 36
0.81 0.14 0.04
Matches are distributed among these distances:
163 36 0.05
164 179 0.26
165 323 0.46
166 46 0.07
167 25 0.04
168 89 0.13
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (165 bp):
AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGACTTGGAGCTGAGCATAGTCGAAC
TCGAAGGTCTTTTGGTGACAAATAACTCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTC
GAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGC
Found at i:42486 original size:84 final size:83
Alignment explanation
Indices: 41781--42788 Score: 928
Period size: 84 Copynumber: 12.2 Consensus size: 83
41771 TCTTGCCCTG
* ** * * * *
41781 AGTTATGCTGTAAATGATGTGCCTAAGAGCTGAGCATAGTCGAACTCGAAGGTTTTTGTTGGTAG
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAG
* * *
41846 ATAACCCTTCTAGCCTTG
66 ATAACCCTTCTCGACTTA
* * * * * *
41864 AGTTACGCTGCAAATGGTGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGT-TTT--TGGCA
1 AGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCA
* *
41926 GACATCCCTTCTCGACTTA
65 GATAACCCTTCTCGACTTA
* * * *
41945 AGCTATGCTGCAAATGATGTGACTTGGAGCTGAGCGTAGTCGAACTCGGAGGTCTTTTGGTGACA
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGGCA
* * * * *
42010 AATAACTCTTCTAGCCTTG
65 GATAACCCTTCTCGACTTA
* * * * * * * *
42029 AGTTATGTTGTAAATGATATGCCCTCGAAGTTGAGCGTAATCGAACTCGAGGGTC-TT--TGGCA
1 AGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCA
*
42091 GATAGCCCTTCTCGACTTA
65 GATAACCCTTCTCGACTTA
* * * * *
42110 AGCTATTCTGTAAATAATGTGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTTGGCA
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGGCA
*
42175 GATAACTCTTCTCGACTTA
65 GATAACCCTTCTCGACTTA
* * * * * * *
42194 AGTTATGCTGCAAATGACGTACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-TT--TGGCA
1 AGTTATGCTGCAAATGATGT-GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCA
*
42256 GATAGCCCTTCTCGACTTA
65 GATAACCCTTCTCGACTTA
* * * * *
42275 AGCTATGCTGCAAATGATGTGACGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGA
1 AGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGGC
* * *
42339 AAACAA-CCTTCTAGACTTA
64 AGATAACCCTTCTCGACTTA
* * * * * *
42358 AGTTGTGTTGCAAATGATATGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTATTTGGTGACAG
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAG
* * *
42423 ATAACCCTTCTAGCCTTG
66 ATAACCCTTCTCGACTTA
* * * * * * * * * *
42441 AGTTAAGTTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGGC-TT--TGGCA
1 AGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCA
*
42503 GATAGCCCTTCTCGACTTA
65 GATAACCCTTCTCGACTTA
* ** * * *
42522 AGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTATAGTCAAACTCGAAGGTCTTTAGTTGGTA
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GGTGGCA
42587 GATAACCCTTCTCGACTTA
65 GATAACCCTTCTCGACTTA
* * * *
42606 AGTTATGTTACAAATGATGTGTCTTGGAGCTGAGCGTAGTCTAACTCGAAGGTCTTTGGTTGGCA
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGGCA
* * * *
42671 GATAGCCCTTCTGGCCTTG
65 GATAACCCTTCTCGACTTA
* *
42690 AGATATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTGGTTGGCA
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGGCA
* * * *
42755 GATAGCCCTTCTGGCCTTG
65 GATAACCCTTCTCGACTTA
*
42774 AGTTAAGCTGCAAAT
1 AGTTATGCTGCAAAT
42789 AGTTTCTTCA
Statistics
Matches: 745, Mismatches: 156, Indels: 47
0.79 0.16 0.05
Matches are distributed among these distances:
80 102 0.14
81 150 0.20
82 18 0.02
83 109 0.15
84 313 0.42
85 53 0.07
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (83 bp):
AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAG
ATAACCCTTCTCGACTTA
Found at i:42501 original size:247 final size:249
Alignment explanation
Indices: 42129--42706 Score: 820
Period size: 247 Copynumber: 2.3 Consensus size: 249
42119 GTAAATAATG
* * * * *
42129 TGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACTCTTCTCGACTTA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTG
* * *
42194 AGTTATGCTGCAAATGACGTACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGAT
66 AGTTAAGCTGCAAATGACATACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGGCTTTGGCAGAT
* * *
42259 AGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGACGTT-GAGCTGAGCGTAGTCGAACTCA
131 AGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCATAGTCAAACTCA
* * *
42323 AAGGTCTTTTGTTGGAAAACAA-CCTTCTAGACTTAAGTTGTGTTGCAAATGATA
195 AAGGTCTTTAGTTGGAAAACAACCCTTCTAGACTTAAGTTATGTTACAAATGATA
* * *
42377 TGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTATTTGG-TGACAGATAACCCTTCTAGCCTTG
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTG
* * * *
42441 AGTTAAGTTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGGCTTTGGCAGAT
66 AGTTAAGCTGCAAATGACATACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGGCTTTGGCAGAT
* *
42506 AGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTATAGTCAAACTCGA
131 AGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCAAACTCAA
* * * * *
42571 AGGTCTTTAGTTGGTAGATAACCCTTCTCGACTTAAGTTATGTTACAAATGATG
196 AGGTCTTTAGTTGGAAAACAACCCTTCTAGACTTAAGTTATGTTACAAATGATA
* * * *
42625 TGTCTTGGAGCTGAGCGTAGTCTAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTGGCCTTG
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTG
* *
42690 AGATATGCTGCAAATGA
66 AGTTAAGCTGCAAATGA
42707 TGTGCCTTGG
Statistics
Matches: 288, Mismatches: 39, Indels: 5
0.87 0.12 0.02
Matches are distributed among these distances:
246 3 0.01
247 150 0.52
248 101 0.35
249 34 0.12
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (249 bp):
TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTG
AGTTAAGCTGCAAATGACATACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGGCTTTGGCAGAT
AGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCAAACTCAA
AGGTCTTTAGTTGGAAAACAACCCTTCTAGACTTAAGTTATGTTACAAATGATA
Found at i:42501 original size:412 final size:414
Alignment explanation
Indices: 41808--42752 Score: 1222
Period size: 412 Copynumber: 2.3 Consensus size: 414
41798 TGTGCCTAAG
* * * * * * * * * *
41808 AGCTGAGCATAGTCGAACTCGAAGGTTTTTGTTGGTAGATAACCCTTCTAGCCTTGAGTTACGCT
1 AGCTGAGCGTAATCGAACTCGAAGG-TCTTGTTGGCAGATAGCCCTTCTCGACTTAAGATATGCT
* * * * * * * * *
41873 GCAAATGGTGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGG--TTT--TTGGCAGACATCCC
65 GCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGAAAACA-ACC
* * *
41934 TTCTCGACTTAAGCTATGCTGCAAATGATGTGACTTGGAGCTGAGCGTAGTCGAACTCGGAGGTC
128 TTCTAGACTTAAGCTATGCTGCAAATGATATGACTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
* * * *
41999 TTTTGGTGACAAATAACTCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCTCGAAGTTGAG
193 ATTTGGTGACAAATAACCCTTCTAGCCTTGAGTTAAGTTGTAAATGATATGCCCTCGAAGCTGAG
* * *
42064 CGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGTAAATAATG
258 CGTAATCGAACTCGAGGGGCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATG
* * *
42129 TGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACTCTTCTCGACTTA
323 TGCCTTGGAGCTGAGCATAGTCAAACTCGAAGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTA
*
42194 AGTTATGCTGCAAATGACGTACCCTCGA
388 AGTTATGCTACAAATGACGT-CCCTCGA
* * *
42222 AGCTGAGTGTAATCGAACTCGAGGGTC-T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTG
1 AGCTGAGCGTAATCGAACTCGAAGGTCTTGTTGGCAGATAGCCCTTCTCGACTTAAGATATGCTG
* *
42285 CAAATGATGTGACGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGAAAACAACCTT
66 CAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGAAAACAACCTT
* * * * *
42349 CTAGACTTAAGTTGTGTTGCAAATGATATGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGT-AT
130 CTAGACTTAAGCTATGCTGCAAATGATATGACTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCAT
* *
42413 TTGGTGACAGATAACCCTTCTAGCCTTGAGTTAAGTTGTAAATGATATGCCCTCGAAGCTGAGTG
195 TTGGTGACAAATAACCCTTCTAGCCTTGAGTTAAGTTGTAAATGATATGCCCTCGAAGCTGAGCG
*
42478 TAATCGAACTCGAGGGGCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
260 TAATCGAACTCGAGGGGCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATGTG
* *
42543 CCTTGGAGCTGAGTATAGTCAAACTCGAAGGTCTTTAGTTGGTAGATAACCCTTCTCGACTTAAG
325 CCTTGGAGCTGAGCATAGTCAAACTCGAAGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAG
* * ** * *
42608 TTATGTTACAAATGATGTGTCTTGG
390 TTATGCTACAAATGACGTCCCTCGA
* * * * *
42633 AGCTGAGCGTAGTCTAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTGGCCTTGAGATATGC
1 AGCTGAGCGTAATCGAACTCGAAGGTC-TT-GTTGGCAGATAGCCCTTCTCGACTTAAGATATGC
* *
42698 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTGGTTGG
64 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGG
42753 CAGATAGCCC
Statistics
Matches: 457, Mismatches: 65, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
410 22 0.05
411 66 0.14
412 201 0.44
413 60 0.13
414 32 0.07
415 76 0.17
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.30
Consensus pattern (414 bp):
AGCTGAGCGTAATCGAACTCGAAGGTCTTGTTGGCAGATAGCCCTTCTCGACTTAAGATATGCTG
CAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGAAAACAACCTTC
TAGACTTAAGCTATGCTGCAAATGATATGACTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCATT
TGGTGACAAATAACCCTTCTAGCCTTGAGTTAAGTTGTAAATGATATGCCCTCGAAGCTGAGCGT
AATCGAACTCGAGGGGCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATGTGC
CTTGGAGCTGAGCATAGTCAAACTCGAAGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAGT
TATGCTACAAATGACGTCCCTCGA
Found at i:46842 original size:16 final size:16
Alignment explanation
Indices: 46823--46853 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46813 GGTTAGTTTA
*
46823 AAAAAGGAAATAAAAT
1 AAAAAGAAAATAAAAT
46839 AAAAAGAAAATAAAA
1 AAAAAGAAAATAAAA
46854 AAATTAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAAAGAAAATAAAAT
Found at i:46862 original size:19 final size:19
Alignment explanation
Indices: 46834--46872 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
46824 AAAAGGAAAT
46834 AAAATAAAAAGAAAATAAA
1 AAAATAAAAAGAAAATAAA
* * *
46853 AAAATTAAAATAATATAAA
1 AAAATAAAAAGAAAATAAA
46872 A
1 A
46873 TATATATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (19 bp):
AAAATAAAAAGAAAATAAA
Found at i:46881 original size:11 final size:10
Alignment explanation
Indices: 46848--46947 Score: 58
Period size: 9 Copynumber: 10.6 Consensus size: 10
46838 TAAAAAGAAA
*
46848 ATAAAAAAAT
1 ATAAAATAAT
46858 -TAAAATAAT
1 ATAAAATAAT
46867 ATAAAAT-AT
1 ATAAAATAAT
*
46876 ATATAATACA-
1 ATAAAATA-AT
*
46886 AAAAAATAAGT
1 ATAAAATAA-T
46897 AATAAAA-AAT
1 -ATAAAATAAT
46907 -TAAAA-AA-
1 ATAAAATAAT
46914 AT-AAATAA-
1 ATAAAATAAT
46922 AT-AAATAAT
1 ATAAAATAAT
*
46931 ATATATATAAT
1 ATA-AAATAAT
46942 ATAAAA
1 ATAAAA
46948 GAAGTATCAA
Statistics
Matches: 72, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
7 3 0.04
8 18 0.25
9 19 0.26
10 15 0.21
11 12 0.17
12 5 0.07
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.27
Consensus pattern (10 bp):
ATAAAATAAT
Found at i:48708 original size:21 final size:20
Alignment explanation
Indices: 48684--48741 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 20
48674 GTTGCAGAAT
*
48684 TTAAAATGTAATTTTATTGCA
1 TTAAATTGTAATTTTATTG-A
*
48705 TT-AATTGATAATTTTA-CGA
1 TTAAATTG-TAATTTTATTGA
*
48724 TTAAATTATAATTTTATT
1 TTAAATTGTAATTTTATT
48742 ACTTTACTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
19 11 0.37
20 9 0.30
21 10 0.33
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (20 bp):
TTAAATTGTAATTTTATTGA
Found at i:48763 original size:24 final size:24
Alignment explanation
Indices: 48725--48788 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
48715 ATTTTACGAT
* * *
48725 TAAATTATAATTTTATTACTTTAC
1 TAAATAATAAATTTATTACATTAC
* * *
48749 TAGATCATAAATTTATTGCATTAC
1 TAAATAATAAATTTATTACATTAC
*
48773 TAAATAATGAATTTAT
1 TAAATAATAAATTTAT
48789 AGAGGCTTAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.47
Consensus pattern (24 bp):
TAAATAATAAATTTATTACATTAC
Found at i:52816 original size:85 final size:85
Alignment explanation
Indices: 52510--52807 Score: 429
Period size: 85 Copynumber: 3.5 Consensus size: 85
52500 TATGACGGTC
* ** *
52510 ATTTATGACACGCATGTATGACTTACATTGCGAGTCATTAAAGCTTCTGTCATAAATTAATATGA
1 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTAAAGCCCCCGTCATAAATTAATATGA
*
52575 TACACATTTGTGTGTCATAA
66 CACACATTTGTGTGTCATAA
* *
52595 ATTTATGACACGCATGTATGACTTATATTGCGCGTTATTAAAGCCCCCGTCATAAATTAATATGA
1 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTAAAGCCCCCGTCATAAATTAATATGA
*
52660 C-CACATTTGTGCGTCATAA
66 CACACATTTGTGTGTCATAA
* * * *
52679 ATTTATGACACGCATGTATGACTTACATTGCGCGTTATTGAAGCCCCCGTCATAAATCT-GTTTG
1 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTAAAGCCCCCGTCATAAAT-TAATATG
*
52743 ACATACATTTGTGTGTCATAA
65 ACACACATTTGTGTGTCATAA
* * *
52764 ATTTATGACACGCATATATGACTTACATTGCGTGTCATTGAAGC
1 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTAAAGC
52808 ATACGTCATT
Statistics
Matches: 194, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
84 77 0.40
85 117 0.60
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTAAAGCCCCCGTCATAAATTAATATGA
CACACATTTGTGTGTCATAA
Found at i:54385 original size:12 final size:12
Alignment explanation
Indices: 54368--54398 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
54358 ATATATTGAT
54368 AATCAAATGAAA
1 AATCAAATGAAA
54380 AATCAAATGAAA
1 AATCAAATGAAA
*
54392 AAACAAA
1 AATCAAA
54399 CCCGGGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.10, G:0.06, T:0.13
Consensus pattern (12 bp):
AATCAAATGAAA
Found at i:62252 original size:51 final size:50
Alignment explanation
Indices: 62197--62300 Score: 145
Period size: 51 Copynumber: 2.1 Consensus size: 50
62187 CCCTGTGCTA
* *
62197 TACCCCACGTGACGCCAAATCAACGTAAAGCGCGTTGCAGAGGGCGCACCT
1 TACCCCACGTGACGCCAAATCAACGTAAAACGCGCTGCAG-GGGCGCACCT
* * * *
62248 TACCCCACGTGGCGCCATATCAATGTAAAACGCGCTGCAGGGGCGCGCCT
1 TACCCCACGTGACGCCAAATCAACGTAAAACGCGCTGCAGGGGCGCACCT
62298 TAC
1 TAC
62301 TGCAAAGGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 12 0.26
51 35 0.74
ACGTcount: A:0.25, C:0.34, G:0.26, T:0.15
Consensus pattern (50 bp):
TACCCCACGTGACGCCAAATCAACGTAAAACGCGCTGCAGGGGCGCACCT
Found at i:64425 original size:2 final size:2
Alignment explanation
Indices: 64418--64479 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
64408 ATGAACATTC
64418 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
64460 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
64480 TAGTGTTCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67900 original size:20 final size:20
Alignment explanation
Indices: 67875--67988 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 20
67865 AATTGGGAAA
*
67875 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
67895 ATCGCAATGTGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
67915 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
67936 ATCACAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
67956 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
67976 TTCGCAACGCGAT
1 ATCGCAACGCGAT
67989 TTACATAGCG
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
19 2 0.03
20 61 0.79
21 12 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:68601 original size:19 final size:19
Alignment explanation
Indices: 68577--68684 Score: 82
Period size: 20 Copynumber: 5.8 Consensus size: 19
68567 CAACGCGAAA
68577 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
68596 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
* **
68610 TCGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
** *
68629 TTGCGATAGTCATTTCCACG
1 TTGCGATTTTCATTT-CGCG
* *
68649 TTGCGATTCTCATTATCTCG
1 TTGCGATTTTCATT-TCGCG
68669 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
68685 AACCAAAAGA
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
14 9 0.12
16 2 0.03
17 3 0.04
19 26 0.36
20 31 0.43
21 1 0.01
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:70853 original size:42 final size:42
Alignment explanation
Indices: 70782--70940 Score: 194
Period size: 42 Copynumber: 3.8 Consensus size: 42
70772 GCCTGTTATC
* * *
70782 CCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATT
1 CCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTATCATT
* * * * *
70824 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCATC
1 CCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTATCATT
* * *
70866 CCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATT
1 CCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTATCATT
*
70908 CCT-AGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTCA-AGAGTCCACTCCCACCGTTCAAGAGGCC
70941 ATTGTCATCG
Statistics
Matches: 96, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
41 1 0.01
42 95 0.99
ACGTcount: A:0.22, C:0.38, G:0.18, T:0.22
Consensus pattern (42 bp):
CCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTATCATT
Found at i:70958 original size:84 final size:84
Alignment explanation
Indices: 70774--70949 Score: 325
Period size: 84 Copynumber: 2.1 Consensus size: 84
70764 CCCGACTCGC
* *
70774 CTGTTATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTAGAGAGTCCCCT
70839 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
70858 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTAGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTAGAGAGTCCCCT
70923 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
*
70942 TTGTCATC
1 CTGTCATC
70950 GTTGAAGAGG
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 89 1.00
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTAGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:70965 original size:42 final size:41
Alignment explanation
Indices: 70786--70979 Score: 158
Period size: 42 Copynumber: 4.6 Consensus size: 41
70776 GTTATCCCTC
* * * * * *
70786 AAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCG
1 AAGAGTCC-CTCCCACCGTTCAAGAGGCCACTGTCA-TCCTTG
* *
70829 -AGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCATCCCTC
1 AAGAGT-CCCTCCCACCGTTCAAGAGGCCACTGTCATCCTTG
* * * * * *
70870 AAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTAG
1 AAGAGTCC-CTCCCACCGTTCAAGAGGCCACTGTCA-TCCTTG
* *
70913 -AGAGTCCCCTCCCACCGTTCAAGAGGCCATTGTCATCGTTG
1 AAGAGT-CCCTCCCACCGTTCAAGAGGCCACTGTCATCCTTG
*
70954 AAGAGGTCCCTCCCACCATTCAAGAG
1 AAGA-GTCCCTCCCACCGTTCAAGAG
70980 CCTGATTCAC
Statistics
Matches: 119, Mismatches: 25, Indels: 15
0.75 0.16 0.09
Matches are distributed among these distances:
41 9 0.08
42 101 0.85
43 9 0.08
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.23
Consensus pattern (41 bp):
AAGAGTCCCTCCCACCGTTCAAGAGGCCACTGTCATCCTTG
Found at i:70979 original size:84 final size:84
Alignment explanation
Indices: 70774--70979 Score: 270
Period size: 84 Copynumber: 2.5 Consensus size: 84
70764 CCCGACTCGC
* * * * * *
70774 CTGTTATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTAGAGAGTCCCCT
70839 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * * *
70858 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTAGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTAGAGAGTCCCCT
70923 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* ** *
70942 TTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
70980 CCTGATTCAC
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
84 107 0.96
85 4 0.04
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTAGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:71865 original size:18 final size:18
Alignment explanation
Indices: 71839--71883 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
71829 GTCGATCAGA
71839 TGATGGCTCTGAGTGAGG
1 TGATGGCTCTGAGTGAGG
* *
71857 TGATAGCTCTGGGTGAGG
1 TGATGGCTCTGAGTGAGG
71875 TGATGGCTC
1 TGATGGCTC
71884 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.13, G:0.42, T:0.29
Consensus pattern (18 bp):
TGATGGCTCTGAGTGAGG
Found at i:73531 original size:22 final size:22
Alignment explanation
Indices: 73504--73547 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
73494 AGATGGAGAT
73504 AGACGGATTTCGCCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
*
73526 AGACGGATTTCGTCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
73548 GTGAGAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.16, G:0.41, T:0.20
Consensus pattern (22 bp):
AGACGGATTTCGCCGGAGATGG
Found at i:73798 original size:61 final size:61
Alignment explanation
Indices: 73716--73853 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
73706 CGCTTTGAAA
* * * * *
73716 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCACATTGCGAAAGTCAGT
* * * * *
73777 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCACATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCACATTGCGAAAGTCAGT
73838 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
73854 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCACATTGCGAAAGTCAGT
Found at i:73825 original size:20 final size:20
Alignment explanation
Indices: 73716--73850 Score: 94
Period size: 20 Copynumber: 6.7 Consensus size: 20
73706 CGCTTTGAAA
*
73716 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTAAGT
* * * *
73737 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTAAGT
* * *
73757 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
73777 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
73798 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* *
73818 ATCACATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTAAGT
73838 ATCGCATTGCGAT
1 ATCGCATTGCGAT
73851 TTTCCCAATT
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 5 0.05
20 64 0.68
21 23 0.24
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:73961 original size:21 final size:21
Alignment explanation
Indices: 73921--73961 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
73911 ACTGTAAACC
**
73921 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
73942 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
73962 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:74246 original size:30 final size:31
Alignment explanation
Indices: 74176--74247 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
74166 ATTTAAGTAT
74176 TTAAAATA--TTTTTTGATCAAAATAAATAC
1 TTAAAATATTTTTTTTGATCAAAATAAATAC
*
74205 TTAAAGTTATTTTTTTTG-TCAAAATAAATA-
1 TTAAA-ATATTTTTTTTGATCAAAATAAATAC
74235 TCTAAAATATTTT
1 T-TAAAATATTTT
74248 ATGTCAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
29 5 0.14
30 9 0.24
31 16 0.43
32 7 0.19
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (31 bp):
TTAAAATATTTTTTTTGATCAAAATAAATAC
Found at i:74438 original size:31 final size:29
Alignment explanation
Indices: 74353--74486 Score: 98
Period size: 30 Copynumber: 4.5 Consensus size: 29
74343 AATTGAATAC
*
74353 TTTAAGTACCTATTTTGATCAAAAAA-ATA
1 TTTAAGTACTTATTTTGA-CAAAAAATATA
* * *
74382 TTTTAGATACTTATTTTAACCAAAAATATAA
1 TTTAAG-TACTTATTTTGACAAAAAATAT-A
*
74413 GTTTAAGTATTTATTTTGAC-AAAAA-ATA
1 -TTTAAGTACTTATTTTGACAAAAAATATA
* *
74441 CTTAAGATACTT-TTATGA-AAAAATGATATA
1 TTTAAG-TACTTATTTTGACAAAAA--ATATA
74471 CTTTAAGTACTTATTT
1 -TTTAAGTACTTATTT
74487 GTTATATAAT
Statistics
Matches: 82, Mismatches: 12, Indels: 20
0.72 0.11 0.18
Matches are distributed among these distances:
27 14 0.17
28 5 0.06
29 14 0.17
30 25 0.30
31 19 0.23
32 5 0.06
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (29 bp):
TTTAAGTACTTATTTTGACAAAAAATATA
Found at i:76204 original size:13 final size:13
Alignment explanation
Indices: 76186--76212 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
76176 TCCTTACCCC
76186 ATACATATGGGAA
1 ATACATATGGGAA
76199 ATACATATGGGAA
1 ATACATATGGGAA
76212 A
1 A
76213 AAAGGACAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.22
Consensus pattern (13 bp):
ATACATATGGGAA
Found at i:77978 original size:201 final size:199
Alignment explanation
Indices: 77522--78044 Score: 500
Period size: 201 Copynumber: 2.6 Consensus size: 199
77512 ATTTAATCTC
* * * * **
77522 AAAATTTTCGTAATTTATAAGATTAGAGGCGTAGTATTGGA-ATTTATCTTTCAACTGATGCCAA
1 AAAATTTTCGTAATTTATAAGATTAGAGGCGTAGTATT-GATACTTATCTTTCAATTCAGGATAA
* * * * * *
77586 TATCGAG-ACATATGTGATATTGTAAGCGGGTTAAAAATCACATTAAAAATGGTTCCAAAGCTTG
65 TATCG-GCACATACGAGACATTGTAAGCGGG-TAAAAATCACGTTCAAAATGGTTACAAAGCTTG
* ** * * ** * * * *
77650 TTTTGTGTATGAAGAAAATGTTAAAATGGTTTGATAGACATATTCAATGGGTTTTTTTGGGTAGT
128 TTTTCTACATGAAGAAAAAGCTAAAATGACTTGATAGACATATTCAAGGGGTATTTTTCGGAAGT
77715 TAATATG
193 TAATATG
* * * *
77722 AAAATTTTCAG-AATTTATAAGATTATAGACATAATATTG-TAACTTATCTTTCAATTCAGGATA
1 AAAATTTTC-GTAATTTATAAGATTAGAGGCGTAGTATTGAT-ACTTATCTTTCAATTCAGGATA
* *
77785 ATATCGGCACATACGAAACATTGTAAGCAGGGTAAAAATCACGTTCAAAATGGTTACAGAGCTTG
64 ATATCGGCACATACGAGACATTGTAAGC-GGGTAAAAATCACGTTCAAAATGGTTACAAAGCTTG
* * *
77850 ATTTTCTACATGAAGAAAAAGCTAACATGACTTGATAGACATGTTC-GGGGAGTATTTTTCGGAA
128 -TTTTCTACATGAAGAAAAAGCTAAAATGACTTGATAGACATATTCAAGGG-GTATTTTTCGGAA
* *
77914 GTTAGTTTG
191 GTTAATATG
* * * * ** * *
77923 AAATTTTTCGTCATTTATAAGATTAGAGGTGTAGTATTGATACTTATATTTCAATTTTGGTTAGT
1 AAAATTTTCGTAATTTATAAGATTAGAGGCGTAGTATTGATACTTATCTTTCAATTCAGGATAAT
* * * * *
77988 ATCGACACATAGGAGACATTCTAAACGGTGTAAAAATCATGTTCAAAATGGTT-CAAA
66 ATCGGCACATACGAGACATTGTAAGCGG-GTAAAAATCACGTTCAAAATGGTTACAAA
78045 ACCAAAAAAA
Statistics
Matches: 260, Mismatches: 53, Indels: 20
0.78 0.16 0.06
Matches are distributed among these distances:
199 2 0.01
200 107 0.41
201 150 0.58
202 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (199 bp):
AAAATTTTCGTAATTTATAAGATTAGAGGCGTAGTATTGATACTTATCTTTCAATTCAGGATAAT
ATCGGCACATACGAGACATTGTAAGCGGGTAAAAATCACGTTCAAAATGGTTACAAAGCTTGTTT
TCTACATGAAGAAAAAGCTAAAATGACTTGATAGACATATTCAAGGGGTATTTTTCGGAAGTTAA
TATG
Found at i:84074 original size:18 final size:20
Alignment explanation
Indices: 84053--84097 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
84043 AAATCATATT
84053 CAAATAAAAA-AGAAAAA-A
1 CAAATAAAAATAGAAAAAGA
84071 CAAA-AAAAATAGAAAAAGA
1 CAAATAAAAATAGAAAAAGA
84090 -AAATAAAA
1 CAAATAAAA
84098 CAAATGGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.21
18 14 0.58
19 5 0.21
ACGTcount: A:0.82, C:0.04, G:0.07, T:0.07
Consensus pattern (20 bp):
CAAATAAAAATAGAAAAAGA
Found at i:87136 original size:21 final size:22
Alignment explanation
Indices: 87089--87144 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
87079 AATATCGGGC
*
87089 GCTACCTAAAATGTTATTTTTT
1 GCTACCTAAAATGTTATATTTT
*
87111 TCTACC-AGAAATGTTA-ATTTT
1 GCTACCTA-AAATGTTATATTTT
87132 GCTACCTAAAATG
1 GCTACCTAAAATG
87145 AATATTTCTG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (22 bp):
GCTACCTAAAATGTTATATTTT
Found at i:100730 original size:20 final size:20
Alignment explanation
Indices: 100705--100745 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
100695 GGATGAATAA
100705 TCTGTTTACCTTTTCTGGGT
1 TCTGTTTACCTTTTCTGGGT
100725 TCTGTTTACCTTTTCTGGGT
1 TCTGTTTACCTTTTCTGGGT
100745 T
1 T
100746 TTCTTCTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.05, C:0.20, G:0.20, T:0.56
Consensus pattern (20 bp):
TCTGTTTACCTTTTCTGGGT
Done.