Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000556.1 Hibiscus syriacus cultivar Beakdansim tig00001086_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: 359109
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:6152 original size:26 final size:23
Alignment explanation
Indices: 6110--6157 Score: 60
Period size: 26 Copynumber: 2.0 Consensus size: 23
6100 TTAAGTTATT
6110 ATTATTTTTAAAAATTAATAAAC
1 ATTATTTTTAAAAATTAATAAAC
*
6133 ATTATTTAATTAAAATATTATTAAA
1 ATTATTT--TTAAAA-ATTAATAAA
6158 AATATATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
25 6 0.29
26 8 0.38
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTATTTTTAAAAATTAATAAAC
Found at i:6373 original size:22 final size:22
Alignment explanation
Indices: 6348--6394 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
6338 TAGAACCAAA
*
6348 ATAATAATTAGAT-ATTACATCT
1 ATAATAATTAAATAATTACAT-T
6370 ATAATAATTAAATAATTACATT
1 ATAATAATTAAATAATTACATT
6392 ATA
1 ATA
6395 TAAAAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.40
Consensus pattern (22 bp):
ATAATAATTAAATAATTACATT
Found at i:8258 original size:62 final size:62
Alignment explanation
Indices: 8182--8299 Score: 164
Period size: 62 Copynumber: 1.9 Consensus size: 62
8172 TTTAAGAGAC
* * *
8182 AGAAACTAGAATAAAAGCAAGAGCCAAATGTAGCTTTAGAAGTTCACACTTTGATGCGTGGT
1 AGAAACAAGAATAAAAGCAAGAGCCAAATGGAGCTTTAGAAATTCACACTTTGATGCGTGGT
* ** * *
8244 AGAAACAAGAATAAAAGCAAGTGTGAAATGGAGCTTTAGAAATTCATATTTTGATG
1 AGAAACAAGAATAAAAGCAAGAGCCAAATGGAGCTTTAGAAATTCACACTTTGATG
8300 TGTAAAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 48 1.00
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (62 bp):
AGAAACAAGAATAAAAGCAAGAGCCAAATGGAGCTTTAGAAATTCACACTTTGATGCGTGGT
Found at i:20683 original size:12 final size:12
Alignment explanation
Indices: 20657--20689 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
20647 GGAGGGCAAC
20657 AAAAAAA-AATT
1 AAAAAAATAATT
20668 -AAAAAATAATT
1 AAAAAAATAATT
20679 AAAAAAATAAT
1 AAAAAAATAAT
20690 CATAGGTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 6 0.30
11 4 0.20
12 10 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAAAATAATT
Found at i:20876 original size:21 final size:20
Alignment explanation
Indices: 20855--20894 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20845 AATAATTTAT
20855 TTTAT-ATTAAAATATAAATA
1 TTTATAATT-AAATATAAATA
*
20875 TTTATAATTAAATTTAAATA
1 TTTATAATTAAATATAAATA
20895 GTATATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTATAATTAAATATAAATA
Found at i:28671 original size:21 final size:21
Alignment explanation
Indices: 28647--28699 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
28637 ACACTTAGGG
28647 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
28668 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
28689 TACCGATTCCC
1 AACCGATTCCC
28700 CCATGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:28916 original size:13 final size:13
Alignment explanation
Indices: 28895--28949 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
28885 AAGTTCGATA
*
28895 AATTCAAATACTT
1 AATTGAAATACTT
28908 AATTGAAATACTT
1 AATTGAAATACTT
* *
28921 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
28935 AATTGAAATACTT
1 AATTGAAATACTT
28948 AA
1 AA
28950 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:28980 original size:33 final size:32
Alignment explanation
Indices: 28935--29032 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 32
28925 AACTCAACAT
* *
28935 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAA-ACTTCCAAGTTCGATA
28968 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTT-AAAACTTCCAAGTTCGATA
29001 AATTCAAATACTTAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAACTTCCAAGTTCGATA
29032 A
1 A
29033 TTGAAACAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
31 12 0.19
32 7 0.11
33 40 0.65
34 3 0.05
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (32 bp):
AATTCAAATACTTAAAACTTCCAAGTTCGATA
Found at i:31374 original size:11 final size:12
Alignment explanation
Indices: 31353--31398 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
31343 TCCGGATAAA
31353 AACCGGTTTTTT
1 AACCGGTTTTTT
31365 AACCGGTTTTTTT
1 AACCGG-TTTTTT
31378 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
31392 ATCCGGT
1 AACCGGT
31399 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:31383 original size:15 final size:14
Alignment explanation
Indices: 31352--31391 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
31342 TTCCGGATAA
31352 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
31365 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
31378 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
31392 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:33262 original size:18 final size:20
Alignment explanation
Indices: 33225--33262 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
33215 AAATATATAC
*
33225 ATAATTTATTTTAATTTTAT
1 ATAATTTATTTTAATATTAT
33245 ATAATTT-TTTTAA-ATTAT
1 ATAATTTATTTTAATATTAT
33263 CATATTGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATAATTTATTTTAATATTAT
Found at i:38002 original size:36 final size:36
Alignment explanation
Indices: 37961--38045 Score: 143
Period size: 36 Copynumber: 2.4 Consensus size: 36
37951 TGATTCTGTT
*
37961 CAAGTACCGAGTCTGCGTTGCGGTTAATCATGATTG
1 CAAGTACCGAGGCTGCGTTGCGGTTAATCATGATTG
37997 CAAGTACCGAGGCTGCGTTGCGGTTAATCATGATTG
1 CAAGTACCGAGGCTGCGTTGCGGTTAATCATGATTG
* *
38033 CAAATATCGAGGC
1 CAAGTACCGAGGC
38046 ATGAGCAGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (36 bp):
CAAGTACCGAGGCTGCGTTGCGGTTAATCATGATTG
Found at i:42355 original size:59 final size:60
Alignment explanation
Indices: 42271--42414 Score: 166
Period size: 60 Copynumber: 2.4 Consensus size: 60
42261 AAATTGAAAT
* * * * *
42271 ATTCAAAAGTTT-GGAGACCAATTTAGAAAGAGGGTC-TAGTTTAGGGATGAAATTAGAAC
1 ATTCAAAAGTTTAAG-GACTAATTTAGAAAGAGAGTCATAGTATAGGGATGAAATCAGAAC
* * * * * *
42330 ATTCAAAATTTTAAGGACTAGTTTAGAATGAGAGTCATTGTATGGGGATGAAATCAGAAT
1 ATTCAAAAGTTTAAGGACTAATTTAGAAAGAGAGTCATAGTATAGGGATGAAATCAGAAC
42390 ATTCAAAAGTTTAAGGACTAATTTA
1 ATTCAAAAGTTTAAGGACTAATTTA
42415 AAGTGAGGTC
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
59 28 0.40
60 42 0.60
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.31
Consensus pattern (60 bp):
ATTCAAAAGTTTAAGGACTAATTTAGAAAGAGAGTCATAGTATAGGGATGAAATCAGAAC
Found at i:42394 original size:60 final size:59
Alignment explanation
Indices: 42314--42437 Score: 169
Period size: 60 Copynumber: 2.1 Consensus size: 59
42304 GTCTAGTTTA
* * * *
42314 GGGATGAAATTAGAACATTCAAAATTTTAAGGACTAGTTTAGAA-TGAGAGTCATTGTATG
1 GGGATGAAATCAGAACATTCAAAAGTTTAAGGACTAATTTA-AAGTGAG-GTCATAGTATG
* *
42374 GGGATGAAATCAGAATATTCAAAAGTTTAAGGACTAATTTAAAGTGAGGTCATAGTTTG
1 GGGATGAAATCAGAACATTCAAAAGTTTAAGGACTAATTTAAAGTGAGGTCATAGTATG
42433 GGGAT
1 GGGAT
42438 ATATGATGTA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 16 0.28
60 41 0.72
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (59 bp):
GGGATGAAATCAGAACATTCAAAAGTTTAAGGACTAATTTAAAGTGAGGTCATAGTATG
Found at i:43431 original size:6 final size:6
Alignment explanation
Indices: 43420--43451 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
43410 TTCACACGCC
43420 TTGCTT TTGCTT TTGCTT TTGCTT TTGCTT TT
1 TTGCTT TTGCTT TTGCTT TTGCTT TTGCTT TT
43452 ATTTACAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.69
Consensus pattern (6 bp):
TTGCTT
Found at i:46316 original size:21 final size:21
Alignment explanation
Indices: 46222--46316 Score: 52
Period size: 21 Copynumber: 4.6 Consensus size: 21
46212 GCGAAATAAA
**
46222 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
46242 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* ** *
46262 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
46282 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
46304 AATCGCAACGCGA
1 AATCGCAACGCGA
46317 ATATGAAAAT
Statistics
Matches: 54, Mismatches: 17, Indels: 7
0.69 0.22 0.09
Matches are distributed among these distances:
19 1 0.02
20 24 0.44
21 27 0.50
22 2 0.04
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:46351 original size:40 final size:40
Alignment explanation
Indices: 46304--46395 Score: 184
Period size: 40 Copynumber: 2.3 Consensus size: 40
46294 GATTTTCCAG
46304 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
46344 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
46384 AATCGCAACGCG
1 AATCGCAACGCG
46396 TATCCGTAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.43, C:0.26, G:0.18, T:0.12
Consensus pattern (40 bp):
AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
Found at i:46405 original size:20 final size:20
Alignment explanation
Indices: 46304--46532 Score: 160
Period size: 20 Copynumber: 11.4 Consensus size: 20
46294 GATTTTCCAG
* ** *
46304 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
46324 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
* ** *
46344 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
46364 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
46384 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
46404 AACCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
46424 TATCGCAACGCATATCCGTA
1 AATCGCAACGCGTATCCGTA
*
46444 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * **
46464 AATCGCAACGAGAATCTATA
1 AATCGCAACGCGTATCCGTA
*
46484 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
46504 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
46524 AATCACAAC
1 AATCGCAAC
46533 ACTGAAATTT
Statistics
Matches: 165, Mismatches: 36, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
19 4 0.02
20 158 0.96
21 3 0.02
ACGTcount: A:0.40, C:0.26, G:0.17, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:46501 original size:60 final size:60
Alignment explanation
Indices: 46342--46532 Score: 183
Period size: 60 Copynumber: 3.2 Consensus size: 60
46332 CGCGAACACA
* ** * *
46342 TAAATCGCAACGCGAATATGA-AAATCGCAACGCGAA-CACATAAATCGCAACGCGT-ATCCG
1 TAAATCGCAACGCGAATCT-ATAAATCGCAACGATAATC-CGTAAATCGCAACG-ATAATCCG
* * * ** *
46402 TAAACCGCAATGCGTATCCGTATATCGCAACGCAT-ATCCGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGCGAATCTATAAATCGCAACG-ATAATCCGTAAATCGCAACGATAATCCG
* * *
46462 TAAATCGCAACGAGAATCTATAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGAATCTATAAATCGCAACGATAATCCGTAAATCGCAACGATAATCCG
*
46522 TAAATCACAAC
1 TAAATCGCAAC
46533 ACTGAAATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 10
0.77 0.15 0.07
Matches are distributed among these distances:
59 3 0.03
60 101 0.96
61 1 0.01
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (60 bp):
TAAATCGCAACGCGAATCTATAAATCGCAACGATAATCCGTAAATCGCAACGATAATCCG
Found at i:47263 original size:24 final size:24
Alignment explanation
Indices: 47224--47270 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
47214 AAATTTGGTC
47224 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
47248 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
47271 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:47462 original size:12 final size:12
Alignment explanation
Indices: 47445--47469 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47435 ATATAATCCT
47445 GAAGAAGAAAAA
1 GAAGAAGAAAAA
47457 GAAGAAGAAAAA
1 GAAGAAGAAAAA
47469 G
1 G
47470 TCCCGAAGAA
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:49836 original size:19 final size:19
Alignment explanation
Indices: 49767--49975 Score: 243
Period size: 19 Copynumber: 11.7 Consensus size: 19
49757 GCAACGAGAG
49767 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
49786 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
49800 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
49820 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
49839 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
49858 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
49872 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
49892 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
49911 AATCG-AA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
49924 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
49944 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
49963 AATCGCATTGCGA
1 AATCGCAATGCGA
49976 TTCTCTCGTT
Statistics
Matches: 164, Mismatches: 7, Indels: 38
0.78 0.03 0.18
Matches are distributed among these distances:
13 7 0.04
14 25 0.15
15 1 0.01
16 5 0.03
17 5 0.03
18 2 0.01
19 77 0.47
20 42 0.26
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:49860 original size:72 final size:72
Alignment explanation
Indices: 49767--49975 Score: 284
Period size: 72 Copynumber: 2.9 Consensus size: 72
49757 GCAACGAGAG
*
49767 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
49832 AAATGAA
66 AAATGAA
*
49839 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAAAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCGCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
49903 GAAATGAA
65 GAAATGAA
* * * * *
49911 AATCG-AACGAGAGAATCG-CAATGCGGAA-ATGAAAATCGCAATGC-GAAATGAAAATCGCATT
1 AATCGCAATGCGA-AAT-GAAAAT-CGCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAAT
49972 GCGA
63 GCGA
49976 TTCTCTCGTT
Statistics
Matches: 124, Mismatches: 8, Indels: 11
0.87 0.06 0.08
Matches are distributed among these distances:
71 26 0.21
72 92 0.74
73 6 0.05
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:49920 original size:52 final size:52
Alignment explanation
Indices: 49753--49969 Score: 302
Period size: 52 Copynumber: 4.1 Consensus size: 52
49743 CGGAAATTAC
*
49753 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
49800 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
49858 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
49911 AATCG-AACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
49963 AATCGCA
1 AATCGCA
49970 TTGCGATTCT
Statistics
Matches: 154, Mismatches: 3, Indels: 20
0.87 0.02 0.11
Matches are distributed among these distances:
47 8 0.05
49 1 0.01
50 1 0.01
52 66 0.43
53 62 0.40
55 2 0.01
56 1 0.01
58 13 0.08
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:50078 original size:52 final size:53
Alignment explanation
Indices: 49965--50081 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
49955 GAAATGAAAA
49965 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
50018 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
50070 TCGCATTGCGAT
1 TCGCATTGCGAT
50082 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:50089 original size:19 final size:19
Alignment explanation
Indices: 49984--50081 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
49974 GATTCTCTCG
49984 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
50004 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
50023 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
50037 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
50056 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
50075 TTGCGAT
1 TTGCGAT
50082 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:50207 original size:14 final size:14
Alignment explanation
Indices: 50188--50224 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
50178 CATCAATTAC
50188 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
50202 ACAAATCATCTTTT
1 ACAAATCAACTTTT
50216 ACAAATCAA
1 ACAAATCAA
50225 TTAAACAATA
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:52187 original size:19 final size:19
Alignment explanation
Indices: 52145--52317 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
52135 TAGTTTACTT
* *
52145 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
52165 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
52184 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
52203 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
52222 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
52241 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
52255 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
52274 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
52288 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* *
52307 TTGCAATGCGA
1 TCGCAACGCGA
52318 TTTTGGTTTC
Statistics
Matches: 127, Mismatches: 16, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 18 0.14
15 1 0.01
16 7 0.06
17 7 0.06
18 1 0.01
19 81 0.64
20 12 0.09
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:52258 original size:14 final size:14
Alignment explanation
Indices: 52239--52295 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
52229 GCGAAATGAA
*
52239 AATCGCAACGACAG
1 AATCGCAACGAAAG
52253 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
52270 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
52286 AATCGCAACG
1 AATCGCAACG
52296 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:52266 original size:33 final size:33
Alignment explanation
Indices: 52220--52312 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
52210 GCGAAACCAA
52220 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
52253 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
*
52286 AATCGCAACGCGAAATGAAAATTGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
52313 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:52335 original size:19 final size:19
Alignment explanation
Indices: 52313--52371 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
52303 AAAATTGCAA
52313 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
52332 TGCGATTTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
52346 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
52365 TGCGATT
1 TGCGATT
52372 CTCTCGTTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 12 0.34
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 19 0.54
ACGTcount: A:0.07, C:0.15, G:0.31, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:52348 original size:14 final size:14
Alignment explanation
Indices: 52329--52387 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
52319 TTTGGTTTCG
52329 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
52343 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
* *
52360 CGCGTTGCGATTCTCT
1 --CGTTGCGATTTTGT
52376 CGTTGCGATTTT
1 CGTTGCGATTTT
52388 AAGTTTCGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 23 0.62
15 1 0.03
16 1 0.03
17 1 0.03
19 11 0.30
ACGTcount: A:0.07, C:0.19, G:0.27, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:52355 original size:33 final size:33
Alignment explanation
Indices: 52313--52403 Score: 137
Period size: 33 Copynumber: 2.7 Consensus size: 33
52303 AAAATTGCAA
* *
52313 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
52346 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
* *
52379 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
52404 AAGTAAACTA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 40 0.75
34 13 0.25
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
Found at i:52567 original size:83 final size:87
Alignment explanation
Indices: 52451--52723 Score: 315
Period size: 93 Copynumber: 3.1 Consensus size: 87
52441 ATGGATTGCA
* ** *
52451 TTAC-TTCAACCAATAGACAAAACAAAGACAAATACTGACTT-CAG-G-G-TA-TTAGTTTAGCA
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACT-ACTTACAGTGAGATACACAGTTTAACA
52510 GAATTGGCAGCAACCGAACAAAT
65 GAATTGGCAGCAACCGAACAAAT
*
52533 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTT-ACAGTG----AG-ATACACAGTT
52598 TAACAGAATTGGCAGCAACCGAACAAAT
60 TAACAGAATTGGCAGCAACCGAACAAAT
*
52626 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTT-ACAGTG----AG-ATACACAGTT
* *
52691 TAGCAGAATTGGCAGCAACCGAATAAAT
60 TAACAGAATTGGCAGCAACCGAACAAAT
52719 TTACT
1 TTACT
52724 AAGCAATCTA
Statistics
Matches: 172, Mismatches: 7, Indels: 13
0.90 0.04 0.07
Matches are distributed among these distances:
82 7 0.04
83 31 0.18
84 3 0.02
85 1 0.01
90 1 0.01
92 2 0.01
93 127 0.74
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (87 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTTACAGTGAGATACACAGTTTAACAG
AATTGGCAGCAACCGAACAAAT
Found at i:52596 original size:17 final size:17
Alignment explanation
Indices: 52574--52606 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
52564 AATACTATTT
52574 CACAGTGTTAA-AGAATA
1 CACAGT-TTAACAGAATA
52591 CACAGTTTAACAGAAT
1 CACAGTTTAACAGAAT
52607 TGGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.24
Consensus pattern (17 bp):
CACAGTTTAACAGAATA
Found at i:52660 original size:93 final size:93
Alignment explanation
Indices: 52501--52723 Score: 428
Period size: 93 Copynumber: 2.4 Consensus size: 93
52491 TCAGGGTATT
52501 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
52566 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
52594 AGTTTAACAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
52659 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
52687 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
52724 AAGCAATCTA
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 127 1.00
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:54441 original size:20 final size:20
Alignment explanation
Indices: 54410--54506 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
54400 TTTTGGTTGA
54410 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
54430 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
54450 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
54469 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
54484 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
54504 AAT
1 AAT
54507 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:54462 original size:21 final size:21
Alignment explanation
Indices: 54408--54472 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
54398 TCTTTTGGTT
54408 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
54429 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
54449 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
54470 GAA
1 GAA
54473 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:54476 original size:14 final size:14
Alignment explanation
Indices: 54457--54513 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
54447 GAGAAATGAA
54457 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
54471 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
54490 AATCGCAACGAGAG
1 AATCGCAACGAGAG
54504 AATCGCAACG
1 AATCGCAACG
54514 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:54489 original size:33 final size:33
Alignment explanation
Indices: 54408--54529 Score: 163
Period size: 33 Copynumber: 3.5 Consensus size: 33
54398 TCTTTTGGTT
*
54408 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
54449 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
54482 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
54515 GAAATGAAAATCGCA
1 GAAATGAAAATCGCA
54530 TTGTGATTTT
Statistics
Matches: 80, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 49 0.61
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.28
ACGTcount: A:0.46, C:0.19, G:0.25, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:54566 original size:14 final size:14
Alignment explanation
Indices: 54547--54603 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
54537 TTTGGTTTCG
54547 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
54561 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
54580 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
54594 CGTTGCGATT
1 CGTTGCGATT
54604 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:54579 original size:33 final size:33
Alignment explanation
Indices: 54542--54610 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
54532 GTGATTTTGG
54542 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
54575 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
54608 TTT
1 TTT
54611 TTCTCGTTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.09, C:0.23, G:0.20, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:54616 original size:21 final size:21
Alignment explanation
Indices: 54591--54664 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
54581 GTTGCGATTC
54591 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
* **
54612 TCTCGTTACAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
54633 TCACGTTGCGATTTTCATTTC
1 TCTCGTTGCGATTTTCATTTT
54654 TCTCGTTGCGA
1 TCTCGTTGCGA
54665 CTCTTCTGCA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
20 6 0.14
21 30 0.71
22 6 0.14
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:54786 original size:33 final size:33
Alignment explanation
Indices: 54744--54814 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
54734 AATACTAACT
54744 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
54777 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
54810 TGAAA
1 TGAAA
54815 TCTAAGTGAA
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:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:55033 original size:22 final size:22
Alignment explanation
Indices: 55005--55064 Score: 120
Period size: 22 Copynumber: 2.7 Consensus size: 22
54995 GGGATTTCGC
55005 CGGAGATGGGGACGGAAATCTT
1 CGGAGATGGGGACGGAAATCTT
55027 CGGAGATGGGGACGGAAATCTT
1 CGGAGATGGGGACGGAAATCTT
55049 CGGAGATGGGGACGGA
1 CGGAGATGGGGACGGA
55065 TTTCGCCGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.27, C:0.13, G:0.45, T:0.15
Consensus pattern (22 bp):
CGGAGATGGGGACGGAAATCTT
Found at i:55241 original size:20 final size:20
Alignment explanation
Indices: 55216--55388 Score: 197
Period size: 20 Copynumber: 8.6 Consensus size: 20
55206 CTTTAAAAAT
55216 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
55236 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
55256 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
55277 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
55297 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
55317 CACGTTGCGGTTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
55337 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
55357 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
55377 CGCGTTGCGATT
1 CGCGTTGCGATT
55389 CTGGAAAATC
Statistics
Matches: 130, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
20 112 0.86
21 18 0.14
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:56049 original size:35 final size:35
Alignment explanation
Indices: 56003--56078 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
55993 AAAACAGTCC
* *
56003 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
56038 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
56073 TCAATT
1 TCAATT
56079 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:56621 original size:130 final size:130
Alignment explanation
Indices: 56475--56722 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
56465 TATTTATATA
* **
56475 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTAACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTAACATGTG
* *
56540 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
*
56605 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTAACATGTG
* * *
56670 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
56723 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTAACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:56753 original size:130 final size:129
Alignment explanation
Indices: 56489--56753 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
56479 ATTTGGTCCT
* ** *
56489 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTAACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTAACATGTGTTAACACATGATCA
* *** * * **** *
56554 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
*
56619 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTAACATGTGTTAACACATGATCA
* * * *
56684 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
56748 -A
128 CA
56749 AAATT
1 AAATT
56754 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTAACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:57080 original size:28 final size:27
Alignment explanation
Indices: 57049--57111 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
57039 AGTTGATACA
57049 ATATTTTAAAAGAATAAATTTAA-AATTT
1 ATATTTTAAAA-AATAAATTTAATAA-TT
** *
57077 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAATAATT
57105 ATATTTT
1 ATATTTT
57112 TCATATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 3 0.10
28 20 0.67
29 7 0.23
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAATAATT
Found at i:62049 original size:24 final size:23
Alignment explanation
Indices: 62022--62091 Score: 60
Period size: 24 Copynumber: 3.1 Consensus size: 23
62012 ATAACAATCC
62022 ACAAATACACTAAACTAACATATT
1 ACAAATACAC-AAACTAACATATT
* *
62046 AC--A-AC-CAAAGTAACA-ATCC
1 ACAAATACACAAACTAACATAT-T
62065 ACAAATACACCAAACTAACATATT
1 ACAAATACA-CAAACTAACATATT
62089 ACA
1 ACA
62092 TCAATTCTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
18 2 0.06
19 10 0.29
20 1 0.03
21 3 0.09
22 3 0.09
24 14 0.40
25 2 0.06
ACGTcount: A:0.54, C:0.26, G:0.01, T:0.19
Consensus pattern (23 bp):
ACAAATACACAAACTAACATATT
Found at i:62068 original size:43 final size:43
Alignment explanation
Indices: 62007--62091 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
61997 AGTTCAAACT
*
62007 CCAAAATAACAATCCACAAATACACTAAACTAACATATTACAA
1 CCAAAATAACAATCCACAAATACACCAAACTAACATATTACAA
*
62050 CCAAAGTAACAATCCACAAATACACCAAACTAACATATTACA
1 CCAAAATAACAATCCACAAATACACCAAACTAACATATTACA
62092 TCAATTCTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.54, C:0.27, G:0.01, T:0.18
Consensus pattern (43 bp):
CCAAAATAACAATCCACAAATACACCAAACTAACATATTACAA
Found at i:63155 original size:60 final size:60
Alignment explanation
Indices: 63082--63215 Score: 198
Period size: 60 Copynumber: 2.2 Consensus size: 60
63072 ATAAAAGGGT
* * * * *
63082 AAAG-TACACAAATGGTCTCCCGACTATAGAGCATTATTTTTTTAAGTCTCCCGGCTGTTA
1 AAAGTTACA-AAATGGTCCCCCGACTATAAAGCATTATTTTGTTAAGTCTCCCGACTATTA
*
63142 AAAGTTACAAAATGGTCCCCCGACTATAAAGCATTATTTTGTTGAGTCTCCCGACTATTA
1 AAAGTTACAAAATGGTCCCCCGACTATAAAGCATTATTTTGTTAAGTCTCCCGACTATTA
63202 AAAGTTACAAAATG
1 AAAGTTACAAAATG
63216 ATCATCTGAC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 63 0.94
61 4 0.06
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCCCCCGACTATAAAGCATTATTTTGTTAAGTCTCCCGACTATTA
Found at i:63535 original size:60 final size:60
Alignment explanation
Indices: 63432--63544 Score: 136
Period size: 60 Copynumber: 1.9 Consensus size: 60
63422 GTCGAGAGAT
* * * * * *
63432 CATTTTGTAACTTTTAATAGTCGAGGGGCTCAACAAAGCAATGTCCTATAATCAATGGAC
1 CATTTTATAAATTTTAATAGTCGAGAGACTCAACAAAACAATGTCCTAAAATCAATGGAC
* * * *
63492 CATTTTATAAATTTTAATTGTCGAGAGACTCAATAAAATAATGTTCTAAAATC
1 CATTTTATAAATTTTAATAGTCGAGAGACTCAACAAAACAATGTCCTAAAATC
63545 GGGGGCACAT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 43 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (60 bp):
CATTTTATAAATTTTAATAGTCGAGAGACTCAACAAAACAATGTCCTAAAATCAATGGAC
Found at i:63648 original size:31 final size:31
Alignment explanation
Indices: 63613--63701 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 31
63603 TGATAAATTC
*
63613 TCAATAAGTTTAAAGATTATTTTATAATAAT
1 TCAATAAGTTTAAAGATCATTTTATAATAAT
* *
63644 TCAATAAATTTAATA-ATCATTTTGTAATAAT
1 TCAATAAGTTTAA-AGATCATTTTATAATAAT
** *
63675 TTGATAAAGTTTAAGGATCA-TTTATAA
1 TCAAT-AAGTTTAAAGATCATTTTATAA
63702 CATTTAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
31 35 0.74
32 12 0.26
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (31 bp):
TCAATAAGTTTAAAGATCATTTTATAATAAT
Found at i:76279 original size:13 final size:13
Alignment explanation
Indices: 76261--76295 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
76251 AAACAAATGT
76261 GGAAGAAGGGAAA
1 GGAAGAAGGGAAA
76274 GGAAGAAGGGAAA
1 GGAAGAAGGGAAA
76287 GGAAGAAGG
1 GGAAGAAGG
76296 TTGTAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (13 bp):
GGAAGAAGGGAAA
Found at i:90541 original size:24 final size:24
Alignment explanation
Indices: 90514--90594 Score: 63
Period size: 24 Copynumber: 3.4 Consensus size: 24
90504 GATGATGATG
*
90514 AAAATGATGATCAAGATGACAACA
1 AAAACGATGATCAAGATGACAACA
* *** ** **
90538 AAAACGATGTTTGTGATGATGATG
1 AAAACGATGATCAAGATGACAACA
* *
90562 AAAATGATGATCAAGAAGACAACA
1 AAAACGATGATCAAGATGACAACA
90586 AAAACGATG
1 AAAACGATG
90595 GCTGTGATGA
Statistics
Matches: 37, Mismatches: 20, Indels: 0
0.65 0.35 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.49, C:0.10, G:0.21, T:0.20
Consensus pattern (24 bp):
AAAACGATGATCAAGATGACAACA
Found at i:90557 original size:48 final size:48
Alignment explanation
Indices: 90503--90667 Score: 228
Period size: 48 Copynumber: 3.4 Consensus size: 48
90493 TTAGTGACCA
**
90503 TGATGATGATGAAAATGATGATCAAGATGACAACAAAAACGATGTTTG
1 TGATGATGATGAAAATGATGATCAAGATGACAACAAAAACGATGGCTG
*
90551 TGATGATGATGAAAATGATGATCAAGAAGACAACAAAAACGATGGCTG
1 TGATGATGATGAAAATGATGATCAAGATGACAACAAAAACGATGGCTG
90599 TGATGATGATGAAAATGATGATCAAGAT---AACAAAAACGATGGTCATG
1 TGATGATGATGAAAATGATGATCAAGATGACAACAAAAACGATGG-C-TG
90646 ACTATGATGATGATGAAAATGA
1 ----TGATGATGATGAAAATGA
90668 CAGAGAACCG
Statistics
Matches: 107, Mismatches: 4, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
45 14 0.13
46 1 0.01
47 2 0.02
48 72 0.67
51 18 0.17
ACGTcount: A:0.45, C:0.08, G:0.24, T:0.23
Consensus pattern (48 bp):
TGATGATGATGAAAATGATGATCAAGATGACAACAAAAACGATGGCTG
Found at i:93470 original size:16 final size:16
Alignment explanation
Indices: 93451--93484 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
93441 CAATATACGA
93451 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
93467 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
93483 AT
1 AT
93485 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:93558 original size:16 final size:18
Alignment explanation
Indices: 93526--93559 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
93516 TATTAATGTA
93526 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
93544 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
93560 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:94233 original size:130 final size:130
Alignment explanation
Indices: 94029--94276 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
94019 AATTTTCTTC
* * * *
94029 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACAAGTGTCACCAATAACACATATCATGACCATGTGCTAACACATGTCAGAT
** *
94094 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
94159 TAATTAGGTGGTGACAAGTGTCACCAATGACACGTGTCATGACCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACAAGTGTCACCAATAACACATATCATGACCATGTGCTAACACATGTCAGAT
94224 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
94277 TATATAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.35
Consensus pattern (130 bp):
TAATTAGGTGGTGACAAGTGTCACCAATAACACATATCATGACCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:94723 original size:35 final size:35
Alignment explanation
Indices: 94673--94748 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
94663 AATTGAATTT
* * *
94673 AATTGAATTATTTTGGAATTTAGGGTTTATAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
94708 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
94743 AATTGA
1 AATTGA
94749 GGACTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.01, G:0.22, T:0.41
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:98580 original size:50 final size:50
Alignment explanation
Indices: 98521--98662 Score: 284
Period size: 50 Copynumber: 2.8 Consensus size: 50
98511 TATTAGATGT
98521 CGATTTTATATTTGAGGTATGAATTTAAGAAGTTATAATAAATATAAAAC
1 CGATTTTATATTTGAGGTATGAATTTAAGAAGTTATAATAAATATAAAAC
98571 CGATTTTATATTTGAGGTATGAATTTAAGAAGTTATAATAAATATAAAAC
1 CGATTTTATATTTGAGGTATGAATTTAAGAAGTTATAATAAATATAAAAC
98621 CGATTTTATATTTGAGGTATGAATTTAAGAAGTTATAATAAA
1 CGATTTTATATTTGAGGTATGAATTTAAGAAGTTATAATAAA
98663 ATTTAAGGAT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 92 1.00
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.39
Consensus pattern (50 bp):
CGATTTTATATTTGAGGTATGAATTTAAGAAGTTATAATAAATATAAAAC
Found at i:102358 original size:25 final size:26
Alignment explanation
Indices: 102309--102358 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
102299 GCACTCACTC
* *
102309 GCTGAGAGCTGGAACGTCAAGCGGCG
1 GCTGAGAGCTGGAACGCCAAACGGCG
*
102335 GCTG-GAGCTGGAAGGCCAAACGGC
1 GCTGAGAGCTGGAACGCCAAACGGC
102359 TGAGCTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.24, C:0.24, G:0.42, T:0.10
Consensus pattern (26 bp):
GCTGAGAGCTGGAACGCCAAACGGCG
Found at i:102491 original size:25 final size:25
Alignment explanation
Indices: 102456--102532 Score: 127
Period size: 25 Copynumber: 3.1 Consensus size: 25
102446 CGGCTGGAAC
102456 ATTTAGGGTTTGAAACCCTAATCTG
1 ATTTAGGGTTTGAAACCCTAATCTG
*
102481 TTTTAGGGTTTGAAACCCTAATCTG
1 ATTTAGGGTTTGAAACCCTAATCTG
* *
102506 AATTAGGGTTTGAAACCCTAATATG
1 ATTTAGGGTTTGAAACCCTAATCTG
102531 AT
1 AT
102533 GGGTTGATTG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.36
Consensus pattern (25 bp):
ATTTAGGGTTTGAAACCCTAATCTG
Found at i:102627 original size:3 final size:3
Alignment explanation
Indices: 102614--102660 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
102604 TATTTGATAT
102614 TAA TAA T-A TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
102658 TAA
1 TAA
102661 CGATAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:102961 original size:46 final size:45
Alignment explanation
Indices: 102898--103223 Score: 258
Period size: 46 Copynumber: 7.5 Consensus size: 45
102888 TGGTCGGGGA
*
102898 ATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTG
1 ATGACACGGCTCCTACGTGATGAAGAGTTCTGGCCATCT-AAGGTG
* * * * ** *
102944 ATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT-
1 ATGACACGGCTCCTACGTGATGAAGA-GTTCTGGCCATCTAAGGTG
* *
102988 -TGACACGGCTCCTACGTGATGAAGAGATCTGG---TC---GGGG
1 ATGACACGGCTCCTACGTGATGAAGAGTTCTGGCCATCTAAGGTG
*
103026 AATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTG
1 -ATGACACGGCTCCTACGTGATGAAGAGTTCTGGCCATCT-AAGGTG
* * * * ** *
103073 ATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT-
1 ATGACACGGCTCCTACGTGATGAAGA-GTTCTGGCCATCTAAGGTG
*
103117 -TGACACGGCTCCTACGTGATGAAGAGATCTGG---TC---GG-G
1 ATGACACGGCTCCTACGTGATGAAGAGTTCTGGCCATCTAAGGTG
*
103154 AATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTG
1 -ATGACACGGCTCCTACGTGATGAAGAGTTCTGGCCATCT-AAGGTG
* *
103201 ATAACACGGTTCCTACGTGATGA
1 ATGACACGGCTCCTACGTGATGA
103224 GGACGGCTGG
Statistics
Matches: 222, Mismatches: 33, Indels: 50
0.73 0.11 0.16
Matches are distributed among these distances:
37 4 0.02
39 30 0.14
40 34 0.15
42 4 0.02
43 54 0.24
45 8 0.04
46 82 0.37
47 6 0.03
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.25
Consensus pattern (45 bp):
ATGACACGGCTCCTACGTGATGAAGAGTTCTGGCCATCTAAGGTG
Found at i:103060 original size:129 final size:129
Alignment explanation
Indices: 102859--103241 Score: 723
Period size: 129 Copynumber: 3.0 Consensus size: 129
102849 CGTCTAAGGG
* * * *
102859 TGACATGGTTCCTACGTGATGAGGACATCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGA
102924 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
66 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
102988 TGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGA
103053 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
66 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
103117 TGACACGGCTCCTACGTGATGAAGAGATCTGGTC-GGGAATGACACGGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGA
103181 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAT
66 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAT
103242 AGGGATAATG
Statistics
Matches: 250, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
128 91 0.36
129 159 0.64
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (129 bp):
TGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGA
GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
Found at i:103716 original size:64 final size:64
Alignment explanation
Indices: 103636--103795 Score: 173
Period size: 64 Copynumber: 2.5 Consensus size: 64
103626 CAAAGATGGT
*
103636 AAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTC-AAAGAAACTGTCTCGAGAGACACA
1 AAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTCAAAAGAAACTGTCTCAAGAGACA-A
* * * * * * * * *
103700 AAATTTTGTTTCCAAAGAAAGAGATTCAATGATTTTTTTCAAAAGAAATTGTTTCAAGGGATAA
1 AAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTCAAAAGAAACTGTCTCAAGAGACAA
* *
103764 AACA--CTGTTTCCAGAGAAACAAACTCAAAGAT
1 AA-ATTTTGTTTCCAAAGAAACAAACTCAAAGAT
103796 GATCTTGTTT
Statistics
Matches: 78, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
63 22 0.28
64 38 0.49
65 18 0.23
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (64 bp):
AAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTCAAAAGAAACTGTCTCAAGAGACAA
Found at i:103825 original size:15 final size:15
Alignment explanation
Indices: 103801--103845 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
103791 AAGATGATCT
*
103801 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
103816 TGTTTCAAGAGAGAA
1 TGTTTCAAGAGAAAA
*
103831 TGTTTCAAGTGAAAA
1 TGTTTCAAGAGAAAA
103846 GACTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.22, T:0.31
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:104457 original size:67 final size:65
Alignment explanation
Indices: 104285--104596 Score: 409
Period size: 67 Copynumber: 4.8 Consensus size: 65
104275 ATGAACATAT
** * * * * * *
104285 TCAAAGATTTACTTCAAGAGAAACTGTCTCAAGAGATACAAAATTCAT-TTT--AAGAGAAACAG
1 TCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATT-TTGTTTCCAA-AGAAACAA
*
104347 AT
64 AC
*
104349 TCAAAGATTTTTTTCAAAAG-AATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAAC
1 TCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAAC
*
104413 TCAAAGATTTTTGTTTCAACAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
1 TCAAAGA-TTTT-TTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
104478 AC
64 AC
104480 TCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
1 TCAAAGA-TTTT-TTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
104545 AC
64 AC
* * *
104547 TCAAAGATTTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTT
1 TCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTT
104597 TTTAGAAAAA
Statistics
Matches: 226, Mismatches: 16, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
62 1 0.00
63 23 0.10
64 39 0.17
65 35 0.15
66 12 0.05
67 116 0.51
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (65 bp):
TCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAAC
Found at i:104474 original size:37 final size:37
Alignment explanation
Indices: 104421--104542 Score: 134
Period size: 37 Copynumber: 3.5 Consensus size: 37
104411 ACTCAAAGAT
104421 TTTTGTTT-CAACAGAAACTATCTTAAGAGAGACAAAA
1 TTTTGTTTCCAA-AGAAACTATCTTAAGAGAGACAAAA
* * * *
104458 TTTTGTTTCCAAAGAAACAAAC-TCA-A-AG----AT
1 TTTTGTTTCCAAAGAAACTATCTTAAGAGAGACAAAA
*
104488 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAA
1 TTTTGTTTCCAAAGAAACTATCTTAAGAGAGACAAAA
104525 TTTTGTTTCCAAAGAAAC
1 TTTTGTTTCCAAAGAAAC
104543 AAACTCAAAG
Statistics
Matches: 67, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
30 20 0.30
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 34 0.51
38 3 0.04
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (37 bp):
TTTTGTTTCCAAAGAAACTATCTTAAGAGAGACAAAA
Found at i:104969 original size:14 final size:14
Alignment explanation
Indices: 104950--104977 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
104940 TTTATGTATC
104950 ATGTATGTATGTGT
1 ATGTATGTATGTGT
104964 ATGTATGTATGTGT
1 ATGTATGTATGTGT
104978 TCTTAATCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (14 bp):
ATGTATGTATGTGT
Found at i:106159 original size:21 final size:22
Alignment explanation
Indices: 106115--106165 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
106105 TTTGTATGTG
106115 CTCTTTGTCCACTTTCTCTTCTTT
1 CTCTTT-T-CACTTTCTCTTCTTT
* *
106139 TTCTTTTCACTTTGT-TTCTTT
1 CTCTTTTCACTTTCTCTTCTTT
106160 CTCTTT
1 CTCTTT
106166 GCTTTTCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 11 0.46
22 7 0.29
23 1 0.04
24 5 0.21
ACGTcount: A:0.04, C:0.27, G:0.04, T:0.65
Consensus pattern (22 bp):
CTCTTTTCACTTTCTCTTCTTT
Found at i:109255 original size:31 final size:32
Alignment explanation
Indices: 109199--109260 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
109189 TGACAAAATG
109199 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
109231 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
109261 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:112643 original size:25 final size:27
Alignment explanation
Indices: 112591--112643 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
112581 GGCACTCACT
* *
112591 CGGCTGAGAGGCTGGAACGTCAAGCGG
1 CGGCTGAGAGGCTGGAACGCCAAACGG
*
112618 CGGCTG-GA-GCTGGAAGGCCAAACGG
1 CGGCTGAGAGGCTGGAACGCCAAACGG
112643 C
1 C
112644 TGAGCTGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 15 0.65
26 2 0.09
27 6 0.26
ACGTcount: A:0.23, C:0.25, G:0.43, T:0.09
Consensus pattern (27 bp):
CGGCTGAGAGGCTGGAACGCCAAACGG
Found at i:112776 original size:25 final size:25
Alignment explanation
Indices: 112741--112817 Score: 136
Period size: 25 Copynumber: 3.1 Consensus size: 25
112731 CGGCTGGAAC
112741 ATTTAGGGTTTGAAACCCTAATCTG
1 ATTTAGGGTTTGAAACCCTAATCTG
*
112766 TTTTAGGGTTTGAAACCCTAATCTG
1 ATTTAGGGTTTGAAACCCTAATCTG
*
112791 ATTTAGGGTTTGAAACCCTAATATG
1 ATTTAGGGTTTGAAACCCTAATCTG
112816 AT
1 AT
112818 GGGTTGATTG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (25 bp):
ATTTAGGGTTTGAAACCCTAATCTG
Found at i:112912 original size:3 final size:3
Alignment explanation
Indices: 112899--112945 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
112889 TATTTGATAT
112899 TAA TAA T-A TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
112943 TAA
1 TAA
112946 CGATAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:116296 original size:21 final size:21
Alignment explanation
Indices: 116249--116302 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 21
116239 AATTGAAATT
116249 TATAAAT-TAATATTTAATAA
1 TATAAATATAATATTTAATAA
116269 TATAAATATAAT-TTTAAT-A
1 TATAAATATAATATTTAATAA
116288 TATCAAAATATAATA
1 TAT--AAATATAATA
116303 ATATAACATG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.13
20 13 0.43
21 13 0.43
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TATAAATATAATATTTAATAA
Found at i:118102 original size:15 final size:15
Alignment explanation
Indices: 118076--118123 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
118066 TTCAAACATC
*
118076 CAAACAAATCCAAAGT
1 CAAAC-AATCCAAAAT
*
118092 CTAACAATCCACAAAAT
1 CAAACAAT-C-CAAAAT
118109 CAAACAATCCAAAAT
1 CAAACAATCCAAAAT
118124 ATTCAAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 9 0.33
16 6 0.22
17 12 0.44
ACGTcount: A:0.56, C:0.27, G:0.02, T:0.15
Consensus pattern (15 bp):
CAAACAATCCAAAAT
Found at i:127212 original size:15 final size:16
Alignment explanation
Indices: 127191--127232 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
127181 CAAATAAAAA
127191 TAATATTTATTTTATG
1 TAATATTTATTTTATG
127207 -AATATTTA-TTTATG
1 TAATATTTATTTTATG
127221 TAGATATTTATT
1 TA-ATATTTATT
127233 ATAATTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.26
15 9 0.39
16 7 0.30
17 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (16 bp):
TAATATTTATTTTATG
Found at i:129939 original size:34 final size:32
Alignment explanation
Indices: 129869--129947 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 32
129859 TCCGATCTGA
*
129869 TCGGGTCGGATTTTTTTTAAAAAATTTCGGGT
1 TCGGGTCGGGTTTTTTTTAAAAAATTTCGGGT
**
129901 TCGGGTCGGGTTTTTTTTAAATGTATTTTTCGGG-
1 TCGGGTCGGGTTTTTTTTAAA---AAATTTCGGGT
129935 TCGGGTCGGGTTT
1 TCGGGTCGGGTTT
129948 AGGGTGAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
32 20 0.49
34 13 0.32
35 8 0.20
ACGTcount: A:0.14, C:0.10, G:0.30, T:0.46
Consensus pattern (32 bp):
TCGGGTCGGGTTTTTTTTAAAAAATTTCGGGT
Found at i:130104 original size:5 final size:5
Alignment explanation
Indices: 130094--130119 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
130084 TATTATTATT
130094 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
130120 GAAAGCTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:131826 original size:40 final size:40
Alignment explanation
Indices: 131746--131826 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
131736 TTTAAATTTG
* *
131746 AATGATATTTTTAATAAATAATTTAAATTTAAACTTTAAA
1 AATGATATTATTAATAAATAATTTAAATTTAAACTATAAA
131786 AATGATATTATTAA-AAATAATCTTAAATTCTAAAC-ATAAA
1 AATGATATTATTAATAAATAAT-TTAAATT-TAAACTATAAA
131826 A
1 A
131827 TTTAAAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
39 7 0.19
40 25 0.68
41 5 0.14
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (40 bp):
AATGATATTATTAATAAATAATTTAAATTTAAACTATAAA
Found at i:134334 original size:39 final size:39
Alignment explanation
Indices: 134291--134380 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 39
134281 GTATTGAAAA
* * *
134291 TTTAGGAATTTAAGGTTC-TAGTAGATTTATGGATTTAAG
1 TTTAGGGATTTAAGGTTCATA-AAGATATATGGATTTAAG
* * * *
134330 TTTAGGGGTTTAGGGTTCATAAAGATATGTGGTTTTAAG
1 TTTAGGGATTTAAGGTTCATAAAGATATATGGATTTAAG
134369 TTTAGGGATTTA
1 TTTAGGGATTTA
134381 GAGGATTAGG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
39 40 0.95
40 2 0.05
ACGTcount: A:0.28, C:0.02, G:0.27, T:0.43
Consensus pattern (39 bp):
TTTAGGGATTTAAGGTTCATAAAGATATATGGATTTAAG
Found at i:150875 original size:29 final size:29
Alignment explanation
Indices: 150842--150916 Score: 150
Period size: 29 Copynumber: 2.6 Consensus size: 29
150832 GTTACCTATT
150842 AATCATGAATTGTGAATTGTTATAAAAAA
1 AATCATGAATTGTGAATTGTTATAAAAAA
150871 AATCATGAATTGTGAATTGTTATAAAAAA
1 AATCATGAATTGTGAATTGTTATAAAAAA
150900 AATCATGAATTGTGAAT
1 AATCATGAATTGTGAAT
150917 AACAAAAACA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.47, C:0.04, G:0.15, T:0.35
Consensus pattern (29 bp):
AATCATGAATTGTGAATTGTTATAAAAAA
Found at i:151259 original size:173 final size:175
Alignment explanation
Indices: 150961--151312 Score: 528
Period size: 173 Copynumber: 2.0 Consensus size: 175
150951 TTTTACTATG
* *
150961 TATAAAGTGGTTTTGACATAAAATGATTGCATAATATGATTATATGAACGATTTATATTGAAGAT
1 TATAAAGTGGTTTTGACATAAAATGAATGC---A-ATG--TATATGAACGATTTACATTGAAGAT
* *
151026 TTTCCACAGAGTTCAATCTAAAGCTTCAACTGCATATTCATATCAGATGAAATTCTTTTGCAGCG
60 TTTCCACAGAGTTCAACCTAAAGCTTCAACTGCATATTCATATCAGATGAAATGCTTTTGCAGCG
* *
151091 AGTAAAAATTTTCATGTAAAGTTGTTAATTTAAAAGATAAAATATCAGACA
125 AGCAAAAATTTTCATATAAAGTTGTTAATTTAAAAGATAAAATATCAGACA
151142 TATAAAGTGGTTTTGACATAAAATGAATGC-ATG-ATATGAACGATTTACATTGAAGATTTTCCA
1 TATAAAGTGGTTTTGACATAAAATGAATGCAATGTATATGAACGATTTACATTGAAGATTTTCCA
* *
151205 CAGAGTTCAACCTAAAGCTTCAACTGCATATTCATATCAGATTAAATGCTTTTGCAGCGAGCCAA
66 CAGAGTTCAACCTAAAGCTTCAACTGCATATTCATATCAGATGAAATGCTTTTGCAGCGAGCAAA
* * **
151270 AATTTTCATATAAAGTTGTTACTTTGAAAGATAATTTATCAGA
131 AATTTTCATATAAAGTTGTTAATTTAAAAGATAAAATATCAGA
151313 TGTCACACCA
Statistics
Matches: 159, Mismatches: 12, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
173 127 0.80
176 3 0.02
181 29 0.18
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (175 bp):
TATAAAGTGGTTTTGACATAAAATGAATGCAATGTATATGAACGATTTACATTGAAGATTTTCCA
CAGAGTTCAACCTAAAGCTTCAACTGCATATTCATATCAGATGAAATGCTTTTGCAGCGAGCAAA
AATTTTCATATAAAGTTGTTAATTTAAAAGATAAAATATCAGACA
Found at i:153367 original size:8 final size:8
Alignment explanation
Indices: 153354--153381 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
153344 ATTTCTTCAA
153354 AACTTGCC
1 AACTTGCC
153362 AACTTGCC
1 AACTTGCC
153370 AACTTGCC
1 AACTTGCC
153378 AACT
1 AACT
153382 AATCCGGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.29, C:0.36, G:0.11, T:0.25
Consensus pattern (8 bp):
AACTTGCC
Found at i:158474 original size:35 final size:34
Alignment explanation
Indices: 158433--158546 Score: 129
Period size: 35 Copynumber: 3.3 Consensus size: 34
158423 AAAATAGTCC
* * *
158433 TCAATTTCATTCTAAACTCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAAC-CCAAATTCCAAAATAAT
* *
158468 TTAATTTTATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTAATTCTAAACCC-AAATTCCAAAATAAT
* * *
158503 TCAATTAAATTTTAAACCCCAAATTCTAAAATAAT
1 TCAATTTAATTCTAAA-CCCAAATTCCAAAATAAT
158538 TCAATTTAA
1 TCAATTTAA
158547 GGTTTAGAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
34 2 0.03
35 62 0.93
36 3 0.04
ACGTcount: A:0.43, C:0.18, G:0.01, T:0.38
Consensus pattern (34 bp):
TCAATTTAATTCTAAACCCAAATTCCAAAATAAT
Found at i:163925 original size:24 final size:23
Alignment explanation
Indices: 163872--163925 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
163862 TAAGATATAA
* *
163872 AAAATTTATAATAATTTTTTAGG
1 AAAATTTATAATAATTTTTCAAG
* *
163895 AATATTTAATAATAATTTTTCAAT
1 AAAATTT-ATAATAATTTTTCAAG
163919 AAAATTT
1 AAAATTT
163926 CATTGAAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (23 bp):
AAAATTTATAATAATTTTTCAAG
Found at i:168583 original size:3 final size:3
Alignment explanation
Indices: 168575--168602 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
168565 CATGATATTT
168575 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
168603 AACCCAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:184296 original size:20 final size:21
Alignment explanation
Indices: 184273--184311 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
184263 TCAAATTTTC
*
184273 ATTTAATATTTTAA-ATTTGA
1 ATTTAATATATTAACATTTGA
*
184293 ATTTATTATATTAACATTT
1 ATTTAATATATTAACATTT
184312 TAAATTTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (21 bp):
ATTTAATATATTAACATTTGA
Found at i:197156 original size:41 final size:42
Alignment explanation
Indices: 197054--197160 Score: 126
Period size: 42 Copynumber: 2.6 Consensus size: 42
197044 TTCACAATTT
* * * * *
197054 ATAAGTCCTTCGAGCCATCAGTAAGTCTTTCGAGCATGATGC
1 ATAAGTCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATGC
* * *
197096 TTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG-
1 ATAAGTCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATGC
*
197137 ATGAGTCCTTCGGGCCATCTGTAA
1 ATAAGTCCTTCGGGCCATCTGTAA
197161 AACCTTCGGG
Statistics
Matches: 53, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 20 0.38
42 33 0.62
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (42 bp):
ATAAGTCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATGC
Found at i:197317 original size:214 final size:214
Alignment explanation
Indices: 196948--197338 Score: 676
Period size: 214 Copynumber: 1.8 Consensus size: 214
196938 CATCCATAAG
* *
196948 ACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAATGATGTTTTAAGAAGATGGAAT
1 ACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAACGATGTTTTAAGAAGATGAAAT
*
197013 TTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGAGCCATCAGTAA
66 TTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGAGCCATCAGTAA
* * *
197078 GTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATGAGT
131 GTCTTTCGAGCATGATGATTAAATCCTTCGAGTAATCTGTAAGCCTTTAGAGCAAGATGATGAGT
197143 CCTTCGGGCCATCTGTAAA
196 CCTTCGGGCCATCTGTAAA
* *
197162 ACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATGAAAAACGATGTTTTGAGAAGATGAAAT
1 ACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAACGATGTTTTAAGAAGATGAAAT
*
197227 TTTTGAAAACAAATAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG-GTCCATCAGTA
66 TTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGAG-CCATCAGTA
*
197291 AGTCTTTCGAGCATGATGATTAAATCCTTCGAGTAATTTGTAAGCCTT
130 AGTCTTTCGAGCATGATGATTAAATCCTTCGAGTAATCTGTAAGCCTT
197339 CACCGAAGAG
Statistics
Matches: 166, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
213 1 0.01
214 165 0.99
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (214 bp):
ACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAACGATGTTTTAAGAAGATGAAAT
TTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGAGCCATCAGTAA
GTCTTTCGAGCATGATGATTAAATCCTTCGAGTAATCTGTAAGCCTTTAGAGCAAGATGATGAGT
CCTTCGGGCCATCTGTAAA
Found at i:197415 original size:42 final size:41
Alignment explanation
Indices: 197368--197459 Score: 118
Period size: 41 Copynumber: 2.2 Consensus size: 41
197358 AAATTCATCA
*
197368 GTAAGTCTTTCGAGCATGATGATGA-AA-TCCTTCGGGTCATTT
1 GTAAGTCTTTCGAG--TGA-GATGATAAGTCCTTCGGGCCATTT
197410 GTAAGTCTTTCGAGTGAGATGATAAGTCCTTCGGGCCATTT
1 GTAAGTCTTTCGAGTGAGATGATAAGTCCTTCGGGCCATTT
*
197451 -TAAGCCTTT
1 GTAAGTCTTT
197460 TCAGAATAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
39 5 0.11
40 13 0.28
41 14 0.30
42 14 0.30
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (41 bp):
GTAAGTCTTTCGAGTGAGATGATAAGTCCTTCGGGCCATTT
Found at i:197910 original size:53 final size:53
Alignment explanation
Indices: 197830--198079 Score: 387
Period size: 53 Copynumber: 4.7 Consensus size: 53
197820 ATCACACCAG
197830 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAA
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAA
*
197883 AAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAA
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAA
* * *
197936 AAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAA
* *
197989 AAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTA-AGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGA-CAA
* * * *
198042 AAGATTATTCAAATTCTACTCCCTGAA-CAAGAGAGAGC
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGC
198080 ATATCCGTCA
Statistics
Matches: 187, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
52 10 0.05
53 177 0.95
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAA
Found at i:212379 original size:33 final size:33
Alignment explanation
Indices: 212326--212439 Score: 183
Period size: 33 Copynumber: 3.5 Consensus size: 33
212316 CCCGAATCAG
* * *
212326 CTTCTGCCTCCGCCACTGCTTCCTCCAAACCCA
1 CTTCAGCCACCGCCATTGCTTCCTCCAAACCCA
212359 CTTCAGCCACCGCCATTGCTTCCTCCAAACCCA
1 CTTCAGCCACCGCCATTGCTTCCTCCAAACCCA
* *
212392 CTTCAACCACCGCCATTGCTTTCTCCAAACCCA
1 CTTCAGCCACCGCCATTGCTTCCTCCAAACCCA
212425 CTTCAGCCACCGCCA
1 CTTCAGCCACCGCCA
212440 GCTCCGCTAG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 75 1.00
ACGTcount: A:0.20, C:0.49, G:0.09, T:0.22
Consensus pattern (33 bp):
CTTCAGCCACCGCCATTGCTTCCTCCAAACCCA
Found at i:214713 original size:31 final size:31
Alignment explanation
Indices: 214677--214743 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
214667 AGTGATAAAT
*
214677 TTTGATAAATTTAAG-GATTATTTTGTAATAA
1 TTTGATAAATTT-AGTGACTATTTTGTAATAA
* * *
214708 TTTGATAAGTTTAGTGCCTATTTTGTAATAG
1 TTTGATAAATTTAGTGACTATTTTGTAATAA
214739 TTTGA
1 TTTGA
214744 CAAAATTACA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.31, C:0.03, G:0.16, T:0.49
Consensus pattern (31 bp):
TTTGATAAATTTAGTGACTATTTTGTAATAA
Found at i:215798 original size:37 final size:38
Alignment explanation
Indices: 215743--215826 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 38
215733 TGGCAACCAA
215743 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
* *
215780 CTTTGAAAAATA-GTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
*
215817 -GTTGAAAAAT
1 CTTTGAAAAAT
215827 GATAATGAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 9 0.21
37 33 0.77
38 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:218981 original size:18 final size:18
Alignment explanation
Indices: 218958--218994 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
218948 ATTTTCCTTC
*
218958 ATGGTGATTTGGAGGAAG
1 ATGGTGATTTAGAGGAAG
218976 ATGGTGATTTAGAGGAAG
1 ATGGTGATTTAGAGGAAG
218994 A
1 A
218995 AATCTATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.41, T:0.27
Consensus pattern (18 bp):
ATGGTGATTTAGAGGAAG
Found at i:220326 original size:37 final size:37
Alignment explanation
Indices: 220270--220355 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
220260 TGGTAACCAA
*
220270 TTTTGAAAAAAATGATTTTCAAAGTTTGGTAAATGTT
1 TTTTGAAAAATATGATTTTCAAAGTTTGGTAAATGTT
* *
220307 TATTTGAAAAATA-GTTTTTCAAAGTTTGGTAGATGTT
1 T-TTTGAAAAATATGATTTTCAAAGTTTGGTAAATGTT
*
220344 TGTTGAAAAATA
1 TTTTGAAAAATA
220356 ATAATGGGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 10 0.23
37 24 0.55
38 10 0.23
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.43
Consensus pattern (37 bp):
TTTTGAAAAATATGATTTTCAAAGTTTGGTAAATGTT
Found at i:244116 original size:15 final size:15
Alignment explanation
Indices: 244096--244124 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
244086 CATTAAATGC
244096 AATGGAGTAGGAGGT
1 AATGGAGTAGGAGGT
244111 AATGGAGTAGGAGG
1 AATGGAGTAGGAGG
244125 CATTAGAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.48, T:0.17
Consensus pattern (15 bp):
AATGGAGTAGGAGGT
Found at i:244133 original size:15 final size:15
Alignment explanation
Indices: 244094--244141 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
244084 TCCATTAAAT
*
244094 GCAATGGAGTAGGAG
1 GCAATAGAGTAGGAG
* *
244109 GTAATGGAGTAGGAG
1 GCAATAGAGTAGGAG
* *
244124 GCATTAGAGTAGCAG
1 GCAATAGAGTAGGAG
244139 GCA
1 GCA
244142 GAAATCCATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.33, C:0.08, G:0.42, T:0.17
Consensus pattern (15 bp):
GCAATAGAGTAGGAG
Found at i:255125 original size:36 final size:38
Alignment explanation
Indices: 255068--255139 Score: 130
Period size: 37 Copynumber: 1.9 Consensus size: 38
255058 TGTGCAGGGG
255068 GAACAGATTCCCCCCT-GGGGGGGTATCGATTCCCCGT
1 GAACAGATTCCCCCCTGGGGGGGGTATCGATTCCCCGT
255105 GAACAGATT-CCCCCTGGGGGGGGTATCGATTCCCC
1 GAACAGATTCCCCCCTGGGGGGGGTATCGATTCCCC
255140 CCTAAATGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
36 6 0.18
37 28 0.82
ACGTcount: A:0.17, C:0.32, G:0.31, T:0.21
Consensus pattern (38 bp):
GAACAGATTCCCCCCTGGGGGGGGTATCGATTCCCCGT
Found at i:256347 original size:17 final size:19
Alignment explanation
Indices: 256316--256350 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
256306 TATGTAAATT
256316 AAAGTATTTTGTTTTAAAC
1 AAAGTATTTTGTTTTAAAC
256335 AAAGT-TTTT-TTTTAAA
1 AAAGTATTTTGTTTTAAA
256351 TTCCCGGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.51
Consensus pattern (19 bp):
AAAGTATTTTGTTTTAAAC
Found at i:261039 original size:37 final size:36
Alignment explanation
Indices: 260971--261043 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 36
260961 TATGTGCAGG
260971 GGGAACAGATTCCCCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCTGGGGGGTATCGATTCCCC
261007 GGGAACAGATT-CCCCCTGGGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCT--GGGGGGTATCGATTCCCC
261044 CTAAATGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 6 0.17
36 11 0.31
37 18 0.51
ACGTcount: A:0.16, C:0.32, G:0.33, T:0.19
Consensus pattern (36 bp):
GGGAACAGATTCCCCCCTGGGGGGTATCGATTCCCC
Found at i:261660 original size:15 final size:15
Alignment explanation
Indices: 261642--261691 Score: 100
Period size: 15 Copynumber: 3.3 Consensus size: 15
261632 CGAGGGTTCT
261642 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
261657 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
261672 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
261687 GTAGT
1 GTAGT
261692 GGTCCTACGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.14, C:0.24, G:0.34, T:0.28
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:262712 original size:15 final size:13
Alignment explanation
Indices: 262666--262712 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
262656 CATTACACAT
262666 TCACATA-TTCATA
1 TCACATAGTTC-TA
*
262679 TCACATAGTTCTT
1 TCACATAGTTCTA
262692 TCACATAGCTCTCTA
1 TCACATAG-T-TCTA
262707 TCACAT
1 TCACAT
262713 TTCATATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 16 0.55
14 4 0.14
15 9 0.31
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.38
Consensus pattern (13 bp):
TCACATAGTTCTA
Found at i:264885 original size:37 final size:38
Alignment explanation
Indices: 264816--264889 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 38
264806 AAATACTTAG
*
264816 TGATGTTATGATTAGACATTTTTTGTAAAAAAAATTAA
1 TGATGTTATGATTAGACATTTTTTATAAAAAAAATTAA
*
264854 TGATTTTATGATTAGACA-TTTTTATAAAAAAAATTA
1 TGATGTTATGATTAGACATTTTTTATAAAAAAAATTA
264890 TGAACATACC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 17 0.50
38 17 0.50
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (38 bp):
TGATGTTATGATTAGACATTTTTTATAAAAAAAATTAA
Found at i:265522 original size:176 final size:176
Alignment explanation
Indices: 265228--265581 Score: 690
Period size: 176 Copynumber: 2.0 Consensus size: 176
265218 AACCAAAATA
265228 AAAAAGAGAAAAAAATTAAGCTGAGAAACTTGTAATTTACCCAAAAATACACGTGAACATGATTA
1 AAAAAGAGAAAAAAATTAAGCTGAGAAACTTGTAATTTACCCAAAAATACACGTGAACATGATTA
265293 ATCTATGTTTAAACCATTGAAGAGAGAGAAAGTATAAATATATATATAGGACCGAAAATCCGATT
66 ATCTATGTTTAAACCATTGAAGAGAGAGAAAGTATAAATATATATATAGGACCGAAAATCCGATT
*
265358 ACAAATTAAAAGAAAGAAAACAGAATTCCAAAATGACCCATGCACC
131 AAAAATTAAAAGAAAGAAAACAGAATTCCAAAATGACCCATGCACC
*
265404 AAAAAGAGCAAAAAATTAAGCTGAGAAACTTGTAATTTACCCAAAAATACACGTGAACATGATTA
1 AAAAAGAGAAAAAAATTAAGCTGAGAAACTTGTAATTTACCCAAAAATACACGTGAACATGATTA
265469 ATCTATGTTTAAACCATTGAAGAGAGAGAAAGTATAAATATATATATAGGACCGAAAATCCGATT
66 ATCTATGTTTAAACCATTGAAGAGAGAGAAAGTATAAATATATATATAGGACCGAAAATCCGATT
265534 AAAAATTAAAAGAAAGAAAACAGAATTCCAAAATGACCCATGCACC
131 AAAAATTAAAAGAAAGAAAACAGAATTCCAAAATGACCCATGCACC
265580 AA
1 AA
265582 GAAGTTTCAT
Statistics
Matches: 176, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
176 176 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (176 bp):
AAAAAGAGAAAAAAATTAAGCTGAGAAACTTGTAATTTACCCAAAAATACACGTGAACATGATTA
ATCTATGTTTAAACCATTGAAGAGAGAGAAAGTATAAATATATATATAGGACCGAAAATCCGATT
AAAAATTAAAAGAAAGAAAACAGAATTCCAAAATGACCCATGCACC
Found at i:267734 original size:29 final size:29
Alignment explanation
Indices: 267691--267773 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
267681 CTCACCTAAC
*
267691 TAAATTGATGTAAGCATTGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
267721 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
* *
267750 TAAATTATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
267774 ATTTAGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:270424 original size:15 final size:15
Alignment explanation
Indices: 270406--270442 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
270396 TCCAAAATTG
270406 AGATGCCCAAATCGA
1 AGATGCCCAAATCGA
*
270421 AGATGCCCAAATTGA
1 AGATGCCCAAATCGA
270436 AGATGCC
1 AGATGCC
270443 AAAGCCATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (15 bp):
AGATGCCCAAATCGA
Found at i:270454 original size:29 final size:29
Alignment explanation
Indices: 270400--270455 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
270390 TAGACCTCCA
* *
270400 AAATTGAGATGCCCAAATCGAAGATGCCC
1 AAATTGAGATGCCCAAAGCCAAGATGCCC
*
270429 AAATTGAAGATG-CCAAAGCCATGATGC
1 AAATTG-AGATGCCCAAAGCCAAGATGC
270456 ATCTTGTAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 18 0.78
30 5 0.22
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (29 bp):
AAATTGAGATGCCCAAAGCCAAGATGCCC
Found at i:272751 original size:22 final size:21
Alignment explanation
Indices: 272717--272757 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
272707 ATAATTATTT
272717 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
272738 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
272758 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:273468 original size:17 final size:18
Alignment explanation
Indices: 273446--273479 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
273436 TCAGCCGGTC
273446 CGGTTCT-AACGGTTCAG
1 CGGTTCTGAACGGTTCAG
*
273463 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
273480 CTAGTAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.15, C:0.26, G:0.29, T:0.29
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAG
Found at i:276936 original size:2 final size:2
Alignment explanation
Indices: 276931--276956 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
276921 TATAGGTGTC
276931 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
276957 ACAAGAGCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:277739 original size:28 final size:28
Alignment explanation
Indices: 277706--277760 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
277696 AAAATTATAT
277706 TAAAAA-TAAAATATTTTTATTAAACAAA
1 TAAAAAGTAAAATATTTTTA-TAAACAAA
277734 TAAAAAGTAAAATATTTTTATAAACAA
1 TAAAAAGTAAAATATTTTTATAAACAA
277761 TATCCATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (28 bp):
TAAAAAGTAAAATATTTTTATAAACAAA
Found at i:282557 original size:2 final size:2
Alignment explanation
Indices: 282552--282584 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
282542 AGTTTTTTTA
282552 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
282585 CTGTGATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:283521 original size:28 final size:27
Alignment explanation
Indices: 283488--283563 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 27
283478 TATTTTTAAA
*
283488 TAAATATATATATTAATAATTAATTTTT
1 TAAATATATATATTAATAATT-ATATTT
283516 TAAATA-ATATATGT-ATAAATTATATTT
1 TAAATATATATAT-TAAT-AATTATATTT
*
283543 TAAGATATATATTGTTAATAA
1 TAA-ATATATA-TATTAATAA
283564 AATGAATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
27 16 0.40
28 14 0.35
29 6 0.15
30 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (27 bp):
TAAATATATATATTAATAATTATATTT
Found at i:283533 original size:27 final size:30
Alignment explanation
Indices: 283488--283564 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 30
283478 TATTTTTAAA
283488 TAAATATATATATTAAT-AATTA-ATTTTT
1 TAAATATATATATTAATAAATTATATTTTT
283516 TAAATA-ATATATGT-ATAAATTATA--TTT
1 TAAATATATATAT-TAATAAATTATATTTTT
*
283543 TAAGATATATATTGTTAATAAA
1 TAA-ATATATA-TATTAATAAA
283565 ATGAATAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
27 14 0.34
28 15 0.37
29 5 0.12
30 7 0.17
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (30 bp):
TAAATATATATATTAATAAATTATATTTTT
Done.