Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007886.1 Hibiscus syriacus cultivar Beakdansim tig00110266_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: 1254954
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 7
Found at i:1992 original size:24 final size:26
Alignment explanation
Indices: 1960--2011 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
1950 GACTTAAAAT
*
1960 TTCAAAA-CCT-TTCACTTCAAATAA
1 TTCAAAACCCTATTAACTTCAAATAA
*
1984 TTCAAAACCCTATTAACTTCTAATAA
1 TTCAAAACCCTATTAACTTCAAATAA
2010 TT
1 TT
2012 TATTTATGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.29
25 3 0.12
26 14 0.58
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (26 bp):
TTCAAAACCCTATTAACTTCAAATAA
Found at i:10558 original size:3 final size:3
Alignment explanation
Indices: 10539--10588 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
10529 CAGTTTATTT
* *
10539 ATA ACA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
10587 AT
1 AT
10589 TTATTTATAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:17971 original size:43 final size:43
Alignment explanation
Indices: 17904--17989 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
17894 TGACTTCGAA
** *
17904 TTTTTTGATAAGAATTTCAAGCCTCGTTAAAAACCCCCTTCTT
1 TTTTTTGATAAGAATGACAAGCCTCCTTAAAAACCCCCTTCTT
* * *
17947 TTTTTTTATAAGAATGACAGGCCTCCTTAAAAACCTCCTTCTT
1 TTTTTTGATAAGAATGACAAGCCTCCTTAAAAACCCCCTTCTT
17990 GATCAAAGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (43 bp):
TTTTTTGATAAGAATGACAAGCCTCCTTAAAAACCCCCTTCTT
Found at i:23171 original size:16 final size:16
Alignment explanation
Indices: 23150--23180 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23140 CAAGCTATAA
*
23150 TCTTAACTTAGGAAAC
1 TCTTAAATTAGGAAAC
23166 TCTTAAATTAGGAAA
1 TCTTAAATTAGGAAA
23181 GTAACTAATC
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:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (16 bp):
TCTTAAATTAGGAAAC
Found at i:28296 original size:20 final size:21
Alignment explanation
Indices: 28271--28363 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
28261 TTTTCCCAAT
*
28271 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
28291 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
* *
28312 TCGTAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
28332 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
28353 TCGCAATGCGA
1 TCGCAATGCGA
28364 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:28332 original size:41 final size:41
Alignment explanation
Indices: 28271--28363 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
28261 TTTTCCCAAT
28271 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
28312 TCGTAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
28353 TCGCAATGCGA
1 TCGCAATGCGA
28364 TACTGACTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:28376 original size:41 final size:41
Alignment explanation
Indices: 28290--28424 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
28280 GAATAAGTAA
* * *
28290 ATCGCAACGCGAATTGGGAAAATCGTAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
28331 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
28372 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
28413 TTCGCAACGCGA
1 ATCGCAACGCGA
28425 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:28377 original size:20 final size:20
Alignment explanation
Indices: 28352--28466 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
28342 AATTGGGAAA
*
28352 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
28372 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
28393 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
28413 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
28433 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
28453 TTCGCAACGCGATA
1 ATCGCAACGCGATA
28467 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:28425 original size:41 final size:41
Alignment explanation
Indices: 28349--28486 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
28339 GCGAATTGGG
* * *
28349 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
28390 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** *
28432 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
28471 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
28487 TTTCAAAGCG
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.39
41 44 0.56
42 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:28985 original size:20 final size:20
Alignment explanation
Indices: 28960--28997 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28950 CGATTCTCTC
28960 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
28980 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
28998 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:30337 original size:18 final size:18
Alignment explanation
Indices: 30316--30361 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
30306 CTCCACTTCG
*
30316 AGAGCCATCACCTCGCCC
1 AGAGCCATCACCTCACCC
*
30334 AGAGCTATCACCTCACCC
1 AGAGCCATCACCTCACCC
30352 AGAGCCATCA
1 AGAGCCATCA
30362 TCTGATCGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.43, G:0.15, T:0.13
Consensus pattern (18 bp):
AGAGCCATCACCTCACCC
Found at i:30897 original size:19 final size:20
Alignment explanation
Indices: 30843--30909 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
30833 TAGTTTACTT
* *
30843 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
30863 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
30883 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
30902 TCGCAACG
1 TCGCAACG
30910 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:30917 original size:14 final size:14
Alignment explanation
Indices: 30898--30955 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
30888 ATGCGAAATG
30898 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
30912 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
30928 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
30944 AAAATCGCAACG
1 AAAATCGCAACG
30956 CGAAATAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:30927 original size:33 final size:33
Alignment explanation
Indices: 30882--30972 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
30872 GGAAATGGCT
*
30882 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
30915 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
30947 ATCGCAACGCGAAATAAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
30973 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:30966 original size:19 final size:18
Alignment explanation
Indices: 30882--30977 Score: 73
Period size: 19 Copynumber: 5.7 Consensus size: 18
30872 GGAAATGGCT
*
30882 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAAT-AAA
*
30901 ATCGCAA--CG--ACAAA
1 ATCGCAACGCGAAATAAA
*
30915 ATCGCAACGCGAAATGAA
1 ATCGCAACGCGAAATAAA
*
30933 ATCGCAA--CG--ACAAA
1 ATCGCAACGCGAAATAAA
30947 ATCGCAACGCGAAATAAAA
1 ATCGCAACGCGAAAT-AAA
*
30966 ATCGCAATGCGA
1 ATCGCAACGCGA
30978 TTTGTGTTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
14 20 0.33
15 1 0.02
16 6 0.10
17 2 0.03
18 11 0.18
19 21 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (18 bp):
ATCGCAACGCGAAATAAA
Found at i:31008 original size:14 final size:14
Alignment explanation
Indices: 30989--31046 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
30979 TTGTGTTTCG
30989 CGTTGCGATTTTAT
1 CGTTGCGATTTTAT
*
31003 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TAT
*
31019 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTAT
31035 CGTTGCGATTTT
1 CGTTGCGATTTT
31047 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTAT
Found at i:31023 original size:32 final size:33
Alignment explanation
Indices: 30984--31062 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
30974 GCGATTTGTG
30984 TTTCGCGTTGCGATTTTATCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTATCGTTGCGATTTTCA
*
31016 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTATCGTTGCGATTTTCA
*
31049 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
31063 ATCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTATCGTTGCGATTTTCA
Found at i:31112 original size:20 final size:19
Alignment explanation
Indices: 31003--31121 Score: 97
Period size: 20 Copynumber: 6.4 Consensus size: 19
30993 GCGATTTTAT
31003 CGTTGCGAT-TTCATTTCG
1 CGTTGCGATATTCATTTCG
*
31021 CGTTGCGAT-TT--TGT--
1 CGTTGCGATATTCATTTCG
*
31035 CGTTGCGATTTTCATTTCG
1 CGTTGCGATATTCATTTCG
* *
31054 CATTGCGATATCCATTTCCG
1 CGTTGCGATATTCATTT-CG
*
31074 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATATTCA-TTTCG
* *
31094 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATATTCA-TTTCG
*
31114 TGTTGCGA
1 CGTTGCGA
31122 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 13, Indels: 12
0.76 0.12 0.11
Matches are distributed among these distances:
14 9 0.11
15 2 0.02
16 2 0.02
17 2 0.02
18 11 0.14
19 14 0.17
20 38 0.47
21 3 0.04
ACGTcount: A:0.13, C:0.20, G:0.24, T:0.43
Consensus pattern (19 bp):
CGTTGCGATATTCATTTCG
Found at i:32984 original size:13 final size:14
Alignment explanation
Indices: 32968--33002 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
32958 ATTGTTTAAT
32968 TGATTTGTAAA-GA
1 TGATTTGTAAATGA
*
32981 TGATTTGTAAATGT
1 TGATTTGTAAATGA
32995 TGATTTGT
1 TGATTTGT
33003 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.49
Consensus pattern (14 bp):
TGATTTGTAAATGA
Found at i:33128 original size:14 final size:14
Alignment explanation
Indices: 33109--33162 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
33099 CGAAATGGCT
33109 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
33123 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
33142 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
33156 ATCGCAA
1 ATCGCAA
33163 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:33135 original size:33 final size:33
Alignment explanation
Indices: 33090--33167 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
33080 AAAACAGACT
* ***
33090 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
33123 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
33156 ATCGCAATGCGA
1 ATCGCAATGCGA
33168 TTTTCATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:33211 original size:20 final size:20
Alignment explanation
Indices: 33186--33243 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
33176 TTGCATTGCG
*
33186 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
33206 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
33226 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
33244 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:34358 original size:24 final size:24
Alignment explanation
Indices: 34307--34361 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
34297 GTATTCGAAA
* *
34307 TTTGATCTTGGTCAATACCCAGAC
1 TTTGATATTGGTCAATACACAGAC
* *
34331 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACAGAC
34355 TTTGATA
1 TTTGATA
34362 ATGTTTCAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.38
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACAGAC
Found at i:34552 original size:12 final size:12
Alignment explanation
Indices: 34535--34559 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34525 ATATAATCCT
34535 GAAGAAGAAAAA
1 GAAGAAGAAAAA
34547 GAAGAAGAAAAA
1 GAAGAAGAAAAA
34559 G
1 G
34560 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:36305 original size:33 final size:33
Alignment explanation
Indices: 36263--36389 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
36253 GGAAATTACT
*
36263 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
36296 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
36328 TATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
36362 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
36390 CGAATTTAAT
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
32 1 0.01
33 84 0.98
34 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:36319 original size:19 final size:19
Alignment explanation
Indices: 36263--36393 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
36253 GGAAATTACT
36263 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
36282 ATCACAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
36296 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
36315 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
36329 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
36348 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
36362 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
36381 ATCGCAACGCGAA
1 ATCGCAATGCGAA
36394 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:36344 original size:66 final size:66
Alignment explanation
Indices: 36262--36390 Score: 240
Period size: 66 Copynumber: 2.0 Consensus size: 66
36252 CGGAAATTAC
36262 TATCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTA
1 TATCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTA
36327 A
66 A
* *
36328 TATCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGC
1 TATCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGC
36391 GAATTTAATT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (66 bp):
TATCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTA
A
Found at i:36457 original size:19 final size:20
Alignment explanation
Indices: 36418--36465 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
36408 GCGATTCTCT
36418 CGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
36438 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
*
36457 CATTGCGAT
1 CGTTGCGAT
36466 AGTACTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:38044 original size:42 final size:42
Alignment explanation
Indices: 37998--38077 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
37988 CGATGACAAT
* * *
37998 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
38040 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
38078 CAGGCGAGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:40110 original size:20 final size:20
Alignment explanation
Indices: 40081--40143 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
40071 TTTTGGTTGA
40081 AATGAAAATCGCAACGAGAT
1 AATGAAAATCGCAACGAGAT
* *
40101 AATGAGAATCGCAACGCGGA-
1 AATGAAAATCGCAACG-AGAT
**
40121 AATGACTATCGCAACGAGAT
1 AATGAAAATCGCAACGAGAT
40141 AAT
1 AAT
40144 CGCAACGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.06
20 32 0.89
21 2 0.06
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.16
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAT
Found at i:40147 original size:14 final size:14
Alignment explanation
Indices: 40128--40164 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
40118 GGAAATGACT
* *
40128 ATCGCAACGAGATA
1 ATCGCAACGAAAGA
40142 ATCGCAACGAAAGA
1 ATCGCAACGAAAGA
40156 ATCGCAACG
1 ATCGCAACG
40165 CGAAATGACT
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:0.43, C:0.24, G:0.22, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAAAGA
Found at i:40210 original size:19 final size:19
Alignment explanation
Indices: 40079--40238 Score: 98
Period size: 19 Copynumber: 9.1 Consensus size: 19
40069 TCTTTTGGTT
*
40079 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
40098 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
40118 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
40136 G--A-GATAATCGCAA--C
1 GAAATGAAAATCGCAACGC
40150 GAAA-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
40166 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
40184 ---A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
40199 GAAATGAAAATCACAACGC
1 GAAATGAAAATCGCAACGC
*
40218 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
40237 GA
1 GA
40239 TTTTTGTTTC
Statistics
Matches: 112, Mismatches: 15, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
14 28 0.25
15 3 0.03
16 7 0.06
17 2 0.02
18 3 0.03
19 40 0.36
20 27 0.24
21 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:40266 original size:18 final size:19
Alignment explanation
Indices: 40234--40277 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
40224 AAAATCGCAA
*
40234 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
40253 TGCG-TTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
40271 TGCGATT
1 TGCGATT
40278 CTCGTTGCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.07, C:0.16, G:0.25, T:0.52
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:40832 original size:20 final size:20
Alignment explanation
Indices: 40807--40856 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
40797 GCGCTATGTA
40807 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
40827 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
40847 TATCTCGTTG
1 AATCGCGTTG
40857 TGATTTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:40893 original size:20 final size:20
Alignment explanation
Indices: 40868--40921 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
40858 GATTTTGTAT
40868 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
40888 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
40908 TATCGCATTGCGAT
1 TATCGCATTGCGAT
40922 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:40923 original size:61 final size:61
Alignment explanation
Indices: 40808--40924 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
40798 CGCTATGTAA
* * * * * *
40808 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGTGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
40869 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
40925 CCCAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:40940 original size:61 final size:61
Alignment explanation
Indices: 40808--40942 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
40798 CGCTATGTAA
* * * * * * ** *
40808 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGTGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
40869 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
40931 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
40943 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:42350 original size:15 final size:15
Alignment explanation
Indices: 42330--42374 Score: 90
Period size: 15 Copynumber: 3.0 Consensus size: 15
42320 TTTAGCTGGG
42330 CGGGCGGATGCGGGA
1 CGGGCGGATGCGGGA
42345 CGGGCGGATGCGGGA
1 CGGGCGGATGCGGGA
42360 CGGGCGGATGCGGGA
1 CGGGCGGATGCGGGA
42375 TGGGTAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.13, C:0.20, G:0.60, T:0.07
Consensus pattern (15 bp):
CGGGCGGATGCGGGA
Found at i:53733 original size:20 final size:20
Alignment explanation
Indices: 53696--53750 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
53686 CTCTAAATCA
***
53696 TTTTTCAAAATTTTATTTTG
1 TTTTTCAAAATCAAATTTTG
53716 TTTTTCAAAATCAAATTTTG
1 TTTTTCAAAATCAAATTTTG
* *
53736 -CTTTCAAAACCAAAT
1 TTTTTCAAAATCAAAT
53751 CATTTTCAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.04, T:0.49
Consensus pattern (20 bp):
TTTTTCAAAATCAAATTTTG
Found at i:56345 original size:30 final size:30
Alignment explanation
Indices: 56311--56368 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
56301 TTATTTAAAC
*
56311 TTGGTGGCCAAGTCCATGTACTATTTGGCA
1 TTGGTGACCAAGTCCATGTACTATTTGGCA
* *
56341 TTGGTGATCAAGTCCTTGTACTATTTGG
1 TTGGTGACCAAGTCCATGTACTATTTGG
56369 TTCTTAGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (30 bp):
TTGGTGACCAAGTCCATGTACTATTTGGCA
Found at i:56748 original size:24 final size:27
Alignment explanation
Indices: 56692--56746 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
56682 TCAAAAGGTG
*
56692 AAAATGTTTTATGAAAGAATTTTGAAA
1 AAAATGTTTGATGAAAGAATTTTGAAA
*
56719 AAAATGTTTGATG-AAG-TTTTTGAAA
1 AAAATGTTTGATGAAAGAATTTTGAAA
56744 AAA
1 AAA
56747 TGGTGCCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 11 0.42
26 3 0.12
27 12 0.46
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.36
Consensus pattern (27 bp):
AAAATGTTTGATGAAAGAATTTTGAAA
Found at i:56863 original size:26 final size:26
Alignment explanation
Indices: 56832--56889 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
56822 CTCTTTTAAT
*
56832 TTTTCAAAGTTATTATTCATTGACAA
1 TTTTCAAAGTTATTATTCATTAACAA
56858 TTTTCAAAGTTATTATTCATTAACAA
1 TTTTCAAAGTTATTATTCATTAACAA
*
56884 GTTTCA
1 TTTTCA
56890 TGATTTGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (26 bp):
TTTTCAAAGTTATTATTCATTAACAA
Found at i:57953 original size:12 final size:12
Alignment explanation
Indices: 57927--57960 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
57917 AACTGTTGAT
57927 GGTTTAGGCTTAG
1 GGTTTAGG-TTAG
57940 GGTTTAGGTTAG
1 GGTTTAGGTTAG
57952 GG-TTAGGTT
1 GGTTTAGGTT
57961 TAATTAGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.33
12 6 0.29
13 8 0.38
ACGTcount: A:0.15, C:0.03, G:0.41, T:0.41
Consensus pattern (12 bp):
GGTTTAGGTTAG
Found at i:63617 original size:14 final size:13
Alignment explanation
Indices: 63585--63618 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
63575 TATGCTATAG
63585 GGTTTAAGATTTA
1 GGTTTAAGATTTA
63598 GAGTTTAAGATTTAA
1 G-GTTTAAGATTT-A
63613 GGTTTA
1 GGTTTA
63619 GAGTTTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 16 0.84
15 2 0.11
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (13 bp):
GGTTTAAGATTTA
Found at i:70560 original size:24 final size:25
Alignment explanation
Indices: 70505--70561 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
70495 CAGAGAAAAA
70505 AACCAAAATAATACAAGCAATAAAT
1 AACCAAAATAATACAAGCAATAAAT
*
70530 AACCCAAAA-AAT-CGAGCAACTAAAT
1 AA-CCAAAATAATACAAGCAA-TAAAT
70555 AACCAAA
1 AACCAAA
70562 CCACAAGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 11 0.38
25 12 0.41
26 6 0.21
ACGTcount: A:0.61, C:0.21, G:0.05, T:0.12
Consensus pattern (25 bp):
AACCAAAATAATACAAGCAATAAAT
Found at i:71210 original size:19 final size:18
Alignment explanation
Indices: 71178--71233 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
71168 ATAATTTCTA
*
71178 ATTTAATTTTTTTAATTTT
1 ATTT-ATTTATTTAATTTT
*
71197 CTCTTATTTATTTAATATTT
1 AT-TTATTTATTTAAT-TTT
71217 ATTTATTTA-TTAATTTT
1 ATTTATTTATTTAATTTT
71234 TACAATCTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.09
18 5 0.16
19 18 0.56
20 6 0.19
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTATTTATTTAATTTT
Found at i:84750 original size:79 final size:79
Alignment explanation
Indices: 84656--84976 Score: 453
Period size: 79 Copynumber: 4.1 Consensus size: 79
84646 TAATAGCATA
** * * ** * * *
84656 CTTTTATGTTGATAATGCACCCATATGTATTTCAACTTTGACATCATTTCATGTCTATAATGCAC
1 CTTTTATGCCGATAATGCACCCATATGCATTTCAGCTAAGGCATCATTTCATGCCAATAATGCAC
* * *
84721 TCATATGCGTTATT
66 CCATATACATTATT
*
84735 CTTTTATGCCGATAATGCACTCATATGCATTTCAGCTAAGGCATCATTTCATGCCAATAATGCAC
1 CTTTTATGCCGATAATGCACCCATATGCATTTCAGCTAAGGCATCATTTCATGCCAATAATGCAC
84800 CCATATACATTATT
66 CCATATACATTATT
* * * *
84814 CTTTTATGCCGAGAATGCACCCATATGCATTTCAGCTAAGGCATCCTTTCCTGCTAATAATGCAC
1 CTTTTATGCCGATAATGCACCCATATGCATTTCAGCTAAGGCATCATTTCATGCCAATAATGCAC
*
84879 CCATATGCATTATT
66 CCATATACATTATT
** *
84893 CTTTTATGCCGATAATGCATTCATATGCATTTCAGCTAAGGCATCATTTCATGCCAATAATGCAT
1 CTTTTATGCCGATAATGCACCCATATGCATTTCAGCTAAGGCATCATTTCATGCCAATAATGCAC
84958 CCATATACATTATT
66 CCATATACATTATT
84972 CTTTT
1 CTTTT
84977 GATCATTCGT
Statistics
Matches: 215, Mismatches: 27, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 215 1.00
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (79 bp):
CTTTTATGCCGATAATGCACCCATATGCATTTCAGCTAAGGCATCATTTCATGCCAATAATGCAC
CCATATACATTATT
Found at i:84795 original size:45 final size:44
Alignment explanation
Indices: 84734--84968 Score: 168
Period size: 45 Copynumber: 5.7 Consensus size: 44
84724 TATGCGTTAT
* * *
84734 TCTTTTATGCCGATAATGCACTCATATGCATTTCAGCTAAGGCA
1 TCTTTCATGCCAATAATGCACCCATATGCATTTCAGCTAAGGCA
*
84778 TCATTTCATGCCAATAATGCACCCATATACA-TT-A--T------
1 TC-TTTCATGCCAATAATGCACCCATATGCATTTCAGCTAAGGCA
* * *
84813 TCTTTTATGCCGAGAATGCACCCATATGCATTTCAGCTAAGGCA
1 TCTTTCATGCCAATAATGCACCCATATGCATTTCAGCTAAGGCA
* *
84857 TCCTTTCCTGCTAATAATGCACCCATATGCA-TT-A--T------
1 T-CTTTCATGCCAATAATGCACCCATATGCATTTCAGCTAAGGCA
* * **
84892 TCTTTTATGCCGATAATGCATTCATATGCATTTCAGCTAAGGCA
1 TCTTTCATGCCAATAATGCACCCATATGCATTTCAGCTAAGGCA
* *
84936 TCATTTCATGCCAATAATGCATCCATATACATT
1 TC-TTTCATGCCAATAATGCACCCATATGCATT
84969 ATTCTTTTGA
Statistics
Matches: 145, Mismatches: 23, Indels: 45
0.68 0.11 0.21
Matches are distributed among these distances:
34 47 0.32
35 7 0.05
36 2 0.01
38 2 0.01
41 2 0.01
43 2 0.01
44 9 0.06
45 74 0.51
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.34
Consensus pattern (44 bp):
TCTTTCATGCCAATAATGCACCCATATGCATTTCAGCTAAGGCA
Found at i:84944 original size:158 final size:158
Alignment explanation
Indices: 84669--84976 Score: 501
Period size: 158 Copynumber: 1.9 Consensus size: 158
84659 TTATGTTGAT
* ** * *
84669 AATGCACCCATATGTATTTCAACTTTGACATCATTTCATGTCTATAATGCACTCATATGCGTTAT
1 AATGCACCCATATGCATTTCAACTAAGACATCATTTCATGTCTATAATGCACCCATATGCATTAT
84734 TCTTTTATGCCGATAATGCACTCATATGCATTTCAGCTAAGGCATCATTTCATGCCAATAATGCA
66 TCTTTTATGCCGATAATGCACTCATATGCATTTCAGCTAAGGCATCATTTCATGCCAATAATGCA
84799 CCCATATACATTATTCTTTTATGCCGAG
131 CCCATATACATTATTCTTTTATGCCGAG
* * * *
84827 AATGCACCCATATGCATTTCAGCTAAGGCATCCTTTCCTG-CTAATAATGCACCCATATGCATTA
1 AATGCACCCATATGCATTTCAACTAAGACATCATTTCATGTCT-ATAATGCACCCATATGCATTA
*
84891 TTCTTTTATGCCGATAATGCATTCATATGCATTTCAGCTAAGGCATCATTTCATGCCAATAATGC
65 TTCTTTTATGCCGATAATGCACTCATATGCATTTCAGCTAAGGCATCATTTCATGCCAATAATGC
*
84956 ATCCATATACATTATTCTTTT
130 ACCCATATACATTATTCTTTT
84977 GATCATTCGT
Statistics
Matches: 138, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
157 2 0.01
158 136 0.99
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (158 bp):
AATGCACCCATATGCATTTCAACTAAGACATCATTTCATGTCTATAATGCACCCATATGCATTAT
TCTTTTATGCCGATAATGCACTCATATGCATTTCAGCTAAGGCATCATTTCATGCCAATAATGCA
CCCATATACATTATTCTTTTATGCCGAG
Found at i:85410 original size:20 final size:22
Alignment explanation
Indices: 85385--85437 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
85375 TGGTTCCTCA
85385 GTATCGATACCA-C-TACCATG
1 GTATCGATACCACCATACCATG
* *
85405 GTATCGATACTACCATACTATG
1 GTATCGATACCACCATACCATG
*
85427 ATATCGATACC
1 GTATCGATACC
85438 GGTTTTGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 11 0.41
21 1 0.04
22 15 0.56
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.28
Consensus pattern (22 bp):
GTATCGATACCACCATACCATG
Found at i:85486 original size:20 final size:20
Alignment explanation
Indices: 85461--85512 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
85451 GTTTCAAAAT
*
85461 GGTATCGATACAT-TCCCTTC
1 GGTATCGATAC-TCCCCCTTC
*
85481 GGTATCGATACTCCCCCTTT
1 GGTATCGATACTCCCCCTTC
85501 GGTATCGATACT
1 GGTATCGATACT
85513 GATTGAATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.35
Consensus pattern (20 bp):
GGTATCGATACTCCCCCTTC
Found at i:86362 original size:25 final size:24
Alignment explanation
Indices: 86334--86416 Score: 62
Period size: 25 Copynumber: 3.3 Consensus size: 24
86324 ATTCTTGGCT
86334 TATATATAAGCTTATCACGTGTCTG
1 TATATATAAGCTTATCA-GTGTCTG
* * * *
86359 TATATATTAA-CTCA-GATTGTTTGGG
1 TATATA-TAAGCTTATCAGTGTCT--G
86384 TTATATATAAGCTTATCATGTGTCTG
1 -TATATATAAGCTTATCA-GTGTCTG
86410 TATATAT
1 TATATAT
86417 TAACTCAGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
23 4 0.09
24 1 0.02
25 20 0.47
26 13 0.30
27 1 0.02
28 4 0.09
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.45
Consensus pattern (24 bp):
TATATATAAGCTTATCAGTGTCTG
Found at i:86390 original size:26 final size:26
Alignment explanation
Indices: 86359--86437 Score: 69
Period size: 25 Copynumber: 3.1 Consensus size: 26
86349 CACGTGTCTG
86359 TATATATTAACTCAGATTGTTTGGGT
1 TATATATTAACTCAGATTGTTTGGGT
* * *
86385 TATATA-TAAGCTTATCATGTGTCT--G-
1 TATATATTAA-CTCA-GAT-TGTTTGGGT
86410 TATATATTAACTCAGATTG-TTGGGT
1 TATATATTAACTCAGATTGTTTGGGT
86435 TAT
1 TAT
86438 TCCAGCCTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 15
0.66 0.10 0.25
Matches are distributed among these distances:
22 1 0.03
23 2 0.05
24 3 0.08
25 15 0.38
26 13 0.32
27 2 0.05
28 4 0.10
ACGTcount: A:0.28, C:0.09, G:0.18, T:0.46
Consensus pattern (26 bp):
TATATATTAACTCAGATTGTTTGGGT
Found at i:86394 original size:51 final size:50
Alignment explanation
Indices: 86319--86437 Score: 202
Period size: 51 Copynumber: 2.4 Consensus size: 50
86309 GCTGATATGT
* *
86319 CTCAGATTCTTGGCTTATATATAAGCTTATCACGTGTCTGTATATATTAA
1 CTCAGATTGTTGGGTTATATATAAGCTTATCACGTGTCTGTATATATTAA
*
86369 CTCAGATTGTTTGGGTTATATATAAGCTTATCATGTGTCTGTATATATTAA
1 CTCAGATTG-TTGGGTTATATATAAGCTTATCACGTGTCTGTATATATTAA
86420 CTCAGATTGTTGGGTTAT
1 CTCAGATTGTTGGGTTAT
86438 TCCAGCCTTA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
50 17 0.26
51 48 0.74
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.44
Consensus pattern (50 bp):
CTCAGATTGTTGGGTTATATATAAGCTTATCACGTGTCTGTATATATTAA
Found at i:87238 original size:89 final size:89
Alignment explanation
Indices: 87087--87261 Score: 323
Period size: 89 Copynumber: 2.0 Consensus size: 89
87077 GATACCTAGT
87087 TGATTACCCTATATTTAAAAATTAAAAACTTTGAGTTCAAGATTTTATTTAATTTAAAAATCATT
1 TGATTACCCTATATTTAAAAATTAAAAACTTTGAGTTCAAGATTTTATTTAATTTAAAAATCATT
*
87152 ATGTATGCAAAGTTTGGAAAAAGA
66 ATGTATGAAAAGTTTGGAAAAAGA
* *
87176 TGATTACCCTATATTTAAAAATTAGAAACTTTGAGTTCAATATTTTATTTAATTTAAAAATCATT
1 TGATTACCCTATATTTAAAAATTAAAAACTTTGAGTTCAAGATTTTATTTAATTTAAAAATCATT
87241 ATGTATGAAAAGTTTGGAAAA
66 ATGTATGAAAAGTTTGGAAAA
87262 TTATGTGGTT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 83 1.00
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.39
Consensus pattern (89 bp):
TGATTACCCTATATTTAAAAATTAAAAACTTTGAGTTCAAGATTTTATTTAATTTAAAAATCATT
ATGTATGAAAAGTTTGGAAAAAGA
Found at i:88182 original size:45 final size:45
Alignment explanation
Indices: 88095--88195 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 45
88085 GTTAGGCTAA
* * * *
88095 TCCGGGTTTGGTTTGTAAATGGGCTTTTGGGTCTGATGTTGGGCC
1 TCCGGGTCTGGTTTGTAAATGGGCTTCTGGATCTGATATTGGGCC
**
88140 TCCGGGTCTGGTTTGTAAATGGGCTTCTGGATCTTCTATTGGGCC
1 TCCGGGTCTGGTTTGTAAATGGGCTTCTGGATCTGATATTGGGCC
* *
88185 TCTGAGTCTGG
1 TCCGGGTCTGG
88196 GCCTATAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.10, C:0.17, G:0.35, T:0.39
Consensus pattern (45 bp):
TCCGGGTCTGGTTTGTAAATGGGCTTCTGGATCTGATATTGGGCC
Found at i:88232 original size:3 final size:3
Alignment explanation
Indices: 88224--88297 Score: 120
Period size: 3 Copynumber: 26.0 Consensus size: 3
88214 TAGTGTTATT
88224 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
88270 TAA TAA TAA TAA TAA TAA -AA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
88298 AACTGGACAA
Statistics
Matches: 67, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
2 8 0.12
3 59 0.88
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:90259 original size:32 final size:33
Alignment explanation
Indices: 90190--90264 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
90180 TAAAATGGTC
* *
90190 ATTAAATTTTATCGAATAGTTACAAAAATAATT
1 ATTAAATTTTATCAAATAGTTACAAAAATAATA
*
90223 ATTAAATTTTATCAAACT-GTTA-TAAAATAATA
1 ATTAAATTTTATCAAA-TAGTTACAAAAATAATA
90255 ATTAAATTTT
1 ATTAAATTTT
90265 CAAAGTTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 18 0.47
33 19 0.50
34 1 0.03
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (33 bp):
ATTAAATTTTATCAAATAGTTACAAAAATAATA
Found at i:91749 original size:6 final size:6
Alignment explanation
Indices: 91715--91747 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
91705 TAAGCTATGG
91715 TTTTGT TTTTGT TTTTGT TTTTGT TTTT-T TTTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTT
91748 TTATGAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTTTGT
Found at i:95017 original size:14 final size:14
Alignment explanation
Indices: 94994--95031 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
94984 TCTGTCTATA
*
94994 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
95007 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
95022 TGCAGGGATT
1 TGCAGGGATT
95032 ACTTCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:96839 original size:4 final size:4
Alignment explanation
Indices: 96830--97076 Score: 71
Period size: 4 Copynumber: 59.8 Consensus size: 4
96820 AAAATGTAAG
* *
96830 AAAT AAAT AAAT AAATT AAATT AAATT AAAAT GAAG AAA- AAAT AAATT
1 AAAT AAAT AAAT AAA-T AAA-T AAA-T -AAAT AAAT AAAT AAAT AAA-T
* * * * * * *
96878 AAAT AAA- AGAT AAGAT AAAG AAAG CAA- AGAT AAA- ATAGT AAGT AAAAT
1 AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT -AAAT
* * * *
96926 AAAT ATAAA AAAT AAAT -AAT AAAT AAAG AAAA AGAAG AAA- AAA- AAAT
1 AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT
* * *
96973 ATAT AAAT AAAAT AAAT AAAT AAA- ATAAT AAAA AAAGT AAAA ATAAT
1 AAAT AAAT -AAAT AAAT AAAT AAAT A-AAT AAAT AAA-T AAAT A-AAT
* * * * * *
97020 ATAT ATAT ATAT ATAAT AAAT AAAT -AGT AAAT ATATAT ATAT ATAT AAAT
1 AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT A-A-AT AAAT AAAT AAAT
*
97070 TAAT AAA
1 AAAT AAA
97077 ATTATAATAA
Statistics
Matches: 189, Mismatches: 31, Indels: 46
0.71 0.12 0.17
Matches are distributed among these distances:
3 19 0.10
4 119 0.63
5 45 0.24
6 6 0.03
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:96939 original size:13 final size:13
Alignment explanation
Indices: 96921--97007 Score: 52
Period size: 13 Copynumber: 6.3 Consensus size: 13
96911 AATAGTAAGT
96921 AAAATAAATATAA
1 AAAATAAATATAA
96934 AAAATAAATAATAA
1 AAAATAAAT-ATAA
* * *
96948 ATAAAGAAAAAGAA
1 A-AAATAAATATAA
*
96962 GAAAA-AAAAATATA
1 -AAAATAAATATA-A
*
96976 TAAATAAA-ATAA
1 AAAATAAATATAA
96988 ATAAATAAAATAATAA
1 A-AAAT-AAAT-ATAA
97004 AAAA
1 AAAA
97008 AGTAAAAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
12 1 0.02
13 25 0.42
14 18 0.31
15 10 0.17
16 5 0.08
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.18
Consensus pattern (13 bp):
AAAATAAATATAA
Found at i:96972 original size:47 final size:48
Alignment explanation
Indices: 96921--97045 Score: 141
Period size: 47 Copynumber: 2.6 Consensus size: 48
96911 AATAGTAAGT
*
96921 AAAATAAATATAA-AAAATAAAT-AAT-AAATAAAGAAAAAGAAGAAAAA
1 AAAATATATATAATAAAATAAATAAATAAAAT-AAGAAAAA-AAGAAAAA
*
96968 AAAATATATA-AATAAAATAAATAAATAAAATAATAAAAAAAGTAAAAA
1 AAAATATATATAATAAAATAAATAAATAAAATAAGAAAAAAAG-AAAAA
* *
97016 TAATATATATATATATATAATAAATAAATA
1 -AAAATATATATA-ATAAAATAAATAAATA
97046 GTAAATATAT
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
46 2 0.03
47 21 0.31
48 15 0.22
49 13 0.19
50 1 0.01
51 15 0.22
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (48 bp):
AAAATATATATAATAAAATAAATAAATAAAATAAGAAAAAAAGAAAAA
Found at i:97023 original size:2 final size:2
Alignment explanation
Indices: 97018--97066 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
97008 AGTAAAAATA
* * *
97018 AT AT AT AT AT AT AT AT A- AT AA AT AA AT AGT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
97060 AT AT AT A
1 AT AT AT A
97067 AATTAATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:97026 original size:51 final size:50
Alignment explanation
Indices: 96924--97052 Score: 140
Period size: 51 Copynumber: 2.5 Consensus size: 50
96914 AGTAAGTAAA
96924 ATAAATATAAA-AAATAAATAATAAATAAAGAAAAAGAAGAAAAAAAAATAT
1 ATAAATA-AAATAAATAAAT-ATAAATAAAGAAAAAGAAGAAAAAAAAATAT
*
96975 ATAAATAAAATAAATAAATA-AAAT-AATAAAAA-AAGTAAAAATAATATATAT
1 ATAAATAAAATAAATAAATATAAATAAAGAAAAAGAAG-AAAAA-AA-A-ATAT
* *
97026 ATATATATAATAAATAAATAGTAAATA
1 ATAAATAAAATAAATAAATA-TAAATA
97053 TATATATATA
Statistics
Matches: 67, Mismatches: 3, Indels: 13
0.81 0.04 0.16
Matches are distributed among these distances:
47 3 0.04
48 12 0.18
49 6 0.09
50 5 0.07
51 37 0.55
53 4 0.06
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (50 bp):
ATAAATAAAATAAATAAATATAAATAAAGAAAAAGAAGAAAAAAAAATAT
Found at i:97151 original size:73 final size:75
Alignment explanation
Indices: 97011--97151 Score: 168
Period size: 75 Copynumber: 1.9 Consensus size: 75
97001 TAAAAAAAGT
* * *
97011 AAAAATAATATATATATATATATAATAAATAAATAGTAAATATATATATATATATAAATTAATAA
1 AAAAATAATATATATATATATATAATAAATAAATAGTAAATATATATATATAAATAAATAAAGAA
97076 AATTATAATA
66 AATTATAATA
*
97086 AAAAATAATATATATATATATAATATCTAAA-AAA-A-TAAA-A-ATATATACTAAAGTAAA-AA
1 AAAAATAATATATATATATAT-ATA-ATAAATAAATAGTAAATATATATATA-TAAA-TAAATAA
97145 AGAAAAT
62 AGAAAAT
97152 GCATAAAATG
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
72 7 0.12
73 11 0.19
74 8 0.14
75 22 0.38
76 6 0.10
77 4 0.07
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (75 bp):
AAAAATAATATATATATATATATAATAAATAAATAGTAAATATATATATATAAATAAATAAAGAA
AATTATAATA
Found at i:98389 original size:36 final size:37
Alignment explanation
Indices: 98342--98572 Score: 198
Period size: 36 Copynumber: 6.5 Consensus size: 37
98332 TTTTTTTTTC
* *
98342 TTCAAGAGAAACTGTCTCAAGAGTGACAA-AATTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAGAATTTGT
** * *
98378 TTCAAAAGAAACTGTCTCAAGAGAGACAAGACTTAG-
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAGAATTTGT
* * * *
98414 TTCTAAAGAAAACTGTCTCAAGGGAGACGA-AATTTGT
1 TTC-AAGGGAAACTGTCTCAAGAGAGACAAGAATTTGT
* * *** *
98451 TTCAA-GGAAA-AG-----ATATTTA-AAGATTTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAGAATTTGT
*
98480 TTCAAGGGAATCTGTCTCAAGAGAGACAA-AATTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAGAATTTGT
* *
98516 TTCAAGGGAAACTGTCTTAAGAGAGACAAGATTTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAGAATTTGT
98553 TTCAAGGGAAACTGTCTCAA
1 TTCAAGGGAAACTGTCTCAA
98573 AACTCATTTT
Statistics
Matches: 152, Mismatches: 30, Indels: 25
0.73 0.14 0.12
Matches are distributed among these distances:
28 1 0.01
29 13 0.09
30 4 0.03
31 1 0.01
34 1 0.01
35 4 0.03
36 72 0.47
37 56 0.37
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.28
Consensus pattern (37 bp):
TTCAAGGGAAACTGTCTCAAGAGAGACAAGAATTTGT
Found at i:98506 original size:102 final size:102
Alignment explanation
Indices: 98373--98559 Score: 245
Period size: 102 Copynumber: 1.8 Consensus size: 102
98363 AGTGACAAAA
* *
98373 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAGACTTAG-TTCTAAAGAAAACTGTCTCAAGG
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAA-AATTAGTTTC-AAAGAAAACTGTCTCAAGA
98437 GAGACGAA-A-TTTGTTTCAAGGAAAAGATATTTAAAGAT
64 GAGAC-AAGATTTTGTTTCAAGGAAAAGATATTTAAAGAT
** * * * * *
98475 TTTGTTTCAAGGGAATCTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTTAAGAGA
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAAGAAAACTGTCTCAAGAGA
98540 GACAAGATTTTGTTTCAAGG
66 GACAAGATTTTGTTTCAAGG
98560 GAAACTGTCT
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
100 2 0.03
101 25 0.34
102 46 0.63
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.29
Consensus pattern (102 bp):
TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAAGAAAACTGTCTCAAGAGA
GACAAGATTTTGTTTCAAGGAAAAGATATTTAAAGAT
Found at i:98722 original size:36 final size:37
Alignment explanation
Indices: 98646--98722 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
98636 ATGTTTCAGA
** *
98646 GAAACTATCTCAAAGGAGACAAAATGTTGTTTCAATG
1 GAAACTATCTCAAAGGAGACAAAATGTAATTTCAAAG
98683 GAAACTATCTC-AAGAGAGACAAAAT-TAATTTCAAAG
1 GAAACTATCTCAAAG-GAGACAAAATGTAATTTCAAAG
98719 GAAA
1 GAAA
98723 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 15 0.42
37 21 0.58
ACGTcount: A:0.47, C:0.13, G:0.17, T:0.23
Consensus pattern (37 bp):
GAAACTATCTCAAAGGAGACAAAATGTAATTTCAAAG
Found at i:98788 original size:102 final size:102
Alignment explanation
Indices: 98624--98848 Score: 328
Period size: 102 Copynumber: 2.2 Consensus size: 102
98614 AAGGAAAACA
* *
98624 TTTTCAAGGTTTATGTTTC-AGAGAAACTATCTCAAAGGAGACAAAATGTTGTTTCAATGGAAAC
1 TTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAAGGAGACAAAATGTTGTTTCAAGGGAAAC
*
98688 TA-TCTCAAGAGAGACAAAATTAATTTCAAAGGAAATG
66 TACCCT-AAGAGAGACAAAATTAATTTCAAAGGAAATG
* * * *
98725 TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAATTTTGTTTCAAGGGAAAC
1 TTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAAGGAGACAAAATGTTGTTTCAAGGGAAAC
* * * *
98790 TACCCTAAGCGAGATAAAATTTATTTCAAGGGAAATG
66 TACCCTAAGAGAGACAAAATTAATTTCAAAGGAAATG
98827 TTTTCAATGTTTATGTTTCAAG
1 TTTTCAATGTTTATGTTTCAAG
98849 GGAGACAAAA
Statistics
Matches: 111, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
101 18 0.16
102 91 0.82
103 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (102 bp):
TTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAAGGAGACAAAATGTTGTTTCAAGGGAAAC
TACCCTAAGAGAGACAAAATTAATTTCAAAGGAAATG
Found at i:98789 original size:37 final size:36
Alignment explanation
Indices: 98738--98824 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 36
98728 TCAATGTTTA
* ** * *
98738 TGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTACCCTAAGCGAGACAAAA-TT
*
98775 TGTTTCAAGGGAAACTACCCTAAGCGAGATAAAATT
1 TGTTTCAAGGGAAACTACCCTAAGCGAGACAAAATT
*
98811 TATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
98825 TGTTTTCAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 15 0.35
37 28 0.65
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTACCCTAAGCGAGACAAAATT
Found at i:98850 original size:87 final size:87
Alignment explanation
Indices: 98759--98931 Score: 294
Period size: 87 Copynumber: 2.0 Consensus size: 87
98749 AAACTGTCTT
* *
98759 AAGGGAGACAAAATTTTGTTTCAAGGGAAACTACC-CTAAGCGAGATAAAATTTATTTCAAGGGA
1 AAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCTC-AAGCGAGATAAAATTCATTTCAAGGGA
98823 AATGTTTTCAATGTTTATGTTTC
65 AATGTTTTCAATGTTTATGTTTC
* *
98846 AAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGGAA
1 AAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCTCAAGCGAGATAAAATTCATTTCAAGGGAA
98911 ATGTTTTCAATGTTTATGTTT
66 ATGTTTTCAATGTTTATGTTT
98932 TAAGAGAAAC
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
87 80 0.99
88 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.34
Consensus pattern (87 bp):
AAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCTCAAGCGAGATAAAATTCATTTCAAGGGAA
ATGTTTTCAATGTTTATGTTTC
Found at i:99037 original size:189 final size:189
Alignment explanation
Indices: 98655--99040 Score: 474
Period size: 189 Copynumber: 2.0 Consensus size: 189
98645 AGAAACTATC
* *
98655 TCAAAGGAGACAAAATGTTGTTTCAATGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
1 TCAAGGGAGACAAAATGTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
* * * **
98720 AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAATTTTGTTTCAAGG
66 AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAA
* * * ** * * *
98785 GAAACTACCCTAAGCGAGATAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTATGTT
131 GAAAATACCCTAAGCGAGACAAAATTTATTTCAAGGAAAACATATTCAATATTTATATT
** * * *
98844 TCAAGGGAGACAAAAT-TTCGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGG
1 TCAAGGGAGACAAAATGTT-GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAG
*
98908 GAAATGTTTTCAATGTTTATGTTTTAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAA
65 GAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAA
** * * *
98973 AGAAAAT-GTCTCAAGGGAGACGAAA-TTAGTTTCAATGAAAACATATTCAAATATTT-TATT
130 AGAAAATACCCT-AAGCGAGACAAAATTTA-TTTCAAGGAAAACATATTC-AATATTTATATT
99033 TCAAGGGA
1 TCAAGGGA
99041 AACTTGGAAA
Statistics
Matches: 167, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
188 7 0.04
189 154 0.92
190 6 0.04
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (189 bp):
TCAAGGGAGACAAAATGTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAA
GAAAATACCCTAAGCGAGACAAAATTTATTTCAAGGAAAACATATTCAATATTTATATT
Found at i:99384 original size:106 final size:106
Alignment explanation
Indices: 99194--99510 Score: 422
Period size: 106 Copynumber: 3.0 Consensus size: 106
99184 TATTGTCCCA
* * * * * *
99194 AGTCCAATATC-TTCCGCCGTGAAGTTAAAATTGGCC-CTGGAACTAAGAAATTGTTTGTTGACA
1 AGTCCAATATCATT-CGCTGTGAAGTTGAAATT-GCCTCCGAAATTAGGAAATTGTTTGTTGACA
* * * * * *
99257 GCCAGCTGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCG
64 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
* *
99300 AGTCTAATATCATTCGTTGTGAAGTTGAAATTGCCTCCGAAATTAGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCATTCGCTGTGAAGTTGAAATTGCCTCCGAAATTAGGAAATTGTTTGTTGACAAC
* * *
99365 CATCCATCCCTTCGTTGTGAAGTTAAACTTGTGTTGTCTCG
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
* *
99406 AGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCATTCGCTGTGAAGTTGAAATTGCCTCCGAAATTAGGAAATTGTTTGTTGACAAC
*
99471 CAGCCGTCCCTTCGTTGTGGAGTTGAACTTGTGTTGTCTC
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
99511 AGGTGGCACG
Statistics
Matches: 184, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
105 3 0.02
106 179 0.97
107 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (106 bp):
AGTCCAATATCATTCGCTGTGAAGTTGAAATTGCCTCCGAAATTAGGAAATTGTTTGTTGACAAC
CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
Found at i:100178 original size:33 final size:32
Alignment explanation
Indices: 100091--100199 Score: 121
Period size: 32 Copynumber: 3.4 Consensus size: 32
100081 TTTGCATCAG
* * * *
100091 GATGTTGAATTCT-CAAAGATGCCCCAATATTC
1 GATGTTGAA-TCTAAAAAAATGCCCCAACATTT
*
100123 GATGTTGAATCTGAAAAAATGCCCCAACATTT
1 GATGTTGAATCTAAAAAAATGCCCCAACATTT
* * *
100155 AATGTTAAATCTAAAAAAAATGCCTCAACATTT
1 GATGTTGAATCT-AAAAAAATGCCCCAACATTT
100188 GATGTTGAATCT
1 GATGTTGAATCT
100200 TCAAATATGC
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
31 3 0.05
32 34 0.52
33 28 0.43
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (32 bp):
GATGTTGAATCTAAAAAAATGCCCCAACATTT
Found at i:101364 original size:27 final size:26
Alignment explanation
Indices: 101328--101380 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
101318 CTTTTTTTCA
101328 ATTTTCCTTTATTTTTTTCTCTTTTT
1 ATTTTCCTTTATTTTTTTCTCTTTTT
*
101354 ATTTTCTCTTTGTTTTTTTCTCTTTTT
1 ATTTTC-CTTTATTTTTTTCTCTTTTT
101381 GCTTTGATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.06, C:0.15, G:0.02, T:0.77
Consensus pattern (26 bp):
ATTTTCCTTTATTTTTTTCTCTTTTT
Found at i:101369 original size:16 final size:14
Alignment explanation
Indices: 101329--101378 Score: 68
Period size: 13 Copynumber: 3.7 Consensus size: 14
101319 TTTTTTTCAA
*
101329 TTTTC-CTTTATTT
1 TTTTCTCTTTGTTT
*
101342 TTTTCTCTTT-TTA
1 TTTTCTCTTTGTTT
101355 TTTTCTCTTTGTTT
1 TTTTCTCTTTGTTT
101369 TTTTCTCTTT
1 TTTTCTCTTT
101379 TTGCTTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
13 17 0.52
14 16 0.48
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTTCTCTTTGTTT
Found at i:104555 original size:5 final size:5
Alignment explanation
Indices: 104443--104618 Score: 50
Period size: 5 Copynumber: 34.6 Consensus size: 5
104433 AAAATGTAAG
* *
104443 AAAT- AAAT- AAAT- AAATA AAATTA AAACGA AGAA-A AAAT- AAATT
1 AAATA AAATA AAATA AAATA AAA-TA AAA-TA A-AATA AAATA AAATA
* * * * *
104486 AAATAA AAGATA AGATA AGAT- AAAGA AAGTA AAGATA AAATA GTAAGTA
1 AAAT-A AA-ATA AAATA AAATA AAATA AAATA AA-ATA AAATA --AAATA
* * * *
104535 AAATA AATATA AAA-A ATAAAA AAATA AAA-A AAAGA AGAAAA AGAAAA
1 AAATA AA-ATA AAATA A-AATA AAATA AAATA AAATA A-AATA A-AATA
104582 AAATA TAAAT- AAAT- AAAT- AAATA AAATA ATAATA AAA
1 AAATA -AAATA AAATA AAATA AAATA AAATA A-AATA AAA
104619 AAGTAAAAAT
Statistics
Matches: 139, Mismatches: 14, Indels: 37
0.73 0.07 0.19
Matches are distributed among these distances:
4 38 0.27
5 52 0.37
6 41 0.29
7 8 0.06
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:104569 original size:49 final size:48
Alignment explanation
Indices: 104516--104666 Score: 113
Period size: 48 Copynumber: 3.2 Consensus size: 48
104506 TAAAGAAAGT
104516 AAAGATAAAATAGTAAGTAAAATAAATATAAA-AAATAAAAAAATAAAA-A
1 AAAGATAAAA-AGTAAG-AAAA-AAATATAAATAAATAAAAAAATAAAATA
* *
104565 AAAGA-AGAAA--AAGAAAAAAATATAAATAAATAAATAAATAAAATA
1 AAAGATAAAAAGTAAGAAAAAAATATAAATAAATAAAAAAATAAAATA
* * * * * * *
104610 ATA-ATAAAAAAGTAA-AAATAATATATATATATATATATATATAAAA-A
1 AAAGAT-AAAAAGTAAGAAA-AAAATATAAATAAATAAAAAAATAAAATA
104657 AAA-ATAAAAA
1 AAAGATAAAAA
104667 AAATAGTATA
Statistics
Matches: 85, Mismatches: 10, Indels: 17
0.76 0.09 0.15
Matches are distributed among these distances:
43 9 0.11
44 20 0.24
45 6 0.07
46 9 0.11
47 9 0.11
48 27 0.32
49 5 0.06
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (48 bp):
AAAGATAAAAAGTAAGAAAAAAATATAAATAAATAAAAAAATAAAATA
Found at i:104575 original size:26 final size:25
Alignment explanation
Indices: 104545--104632 Score: 86
Period size: 26 Copynumber: 3.3 Consensus size: 25
104535 AAATAAATAT
104545 AAAAAATAAAAAAATAAAAAAAAGA
1 AAAAAATAAAAAAATAAAAAAAAGA
* * *
104570 AGAAAAAGAAAAAAATATAAATAAATA
1 A-AAAAATAAAAAAATA-AAAAAAAGA
* *
104597 AATAAATAAAATAATAATAAAAAAGTA
1 AAAAAATAAAAAAATAA-AAAAAAG-A
104624 AAAATAATA
1 AAAA-AATA
104633 TATATATATA
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
25 2 0.04
26 31 0.63
27 12 0.24
28 4 0.08
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.16
Consensus pattern (25 bp):
AAAAAATAAAAAAATAAAAAAAAGA
Found at i:104627 original size:9 final size:8
Alignment explanation
Indices: 104533--104619 Score: 75
Period size: 9 Copynumber: 10.0 Consensus size: 8
104523 AAATAGTAAG
104533 TAAAATAAA
1 TAAAA-AAA
104542 TATAAAAAA
1 TA-AAAAAA
104551 TAAAAAAA
1 TAAAAAAA
104559 TAAAAAAAA
1 T-AAAAAAA
*
104568 GAAGAAAAA
1 TAA-AAAAA
*
104577 GAAAAAAA
1 TAAAAAAA
104585 TATAAATAAA
1 TA-AAA-AAA
*
104595 TAAATAAA
1 TAAAAAAA
*
104603 TAAAATAA
1 TAAAAAAA
104611 TAATAAAAA
1 TAA-AAAAA
104620 AGTAAAAATA
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
8 27 0.41
9 31 0.47
10 8 0.12
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.17
Consensus pattern (8 bp):
TAAAAAAA
Found at i:104682 original size:42 final size:40
Alignment explanation
Indices: 104607--104746 Score: 160
Period size: 40 Copynumber: 3.5 Consensus size: 40
104597 AATAAATAAA
* *
104607 ATAATAATAAAAAAGTAAAAATAATATATATATATATATAT
1 ATAATAA-AAAAAAATAAAAAAAATATATATATATATATAT
*
104648 AT-ATAAAAAAAAATAAAAAAAATAGTATATATATATAAAT
1 ATAATAAAAAAAAATAAAAAAAATA-TATATATATATATAT
* *
104688 -TAATAAAACTGATAAT-AAAAAAATATATATATATATATAT
1 ATAATAAAA--AAAAATAAAAAAAATATATATATATATATAT
**
104728 ATAATCTAAAAAAATAAAA
1 ATAATAAAAAAAAATAAAA
104747 TATATACTAA
Statistics
Matches: 83, Mismatches: 10, Indels: 13
0.78 0.09 0.12
Matches are distributed among these distances:
39 21 0.25
40 41 0.49
41 17 0.20
42 4 0.05
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (40 bp):
ATAATAAAAAAAAATAAAAAAAATATATATATATATATAT
Found at i:104749 original size:24 final size:24
Alignment explanation
Indices: 104722--104791 Score: 88
Period size: 24 Copynumber: 2.9 Consensus size: 24
104712 ATATATATAT
*
104722 ATATATATAATCTAAAAAAATAAA
1 ATATATATAATGTAAAAAAATAAA
* *
104746 ATATATACTAAAGT-AAAAAAGAAA
1 ATATATA-TAATGTAAAAAAATAAA
*
104770 ATATATAAAATGTAAAAAAATA
1 ATATATATAATGTAAAAAAATA
104792 TTACAAGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
23 4 0.11
24 30 0.79
25 4 0.11
ACGTcount: A:0.67, C:0.03, G:0.04, T:0.26
Consensus pattern (24 bp):
ATATATATAATGTAAAAAAATAAA
Found at i:110224 original size:12 final size:12
Alignment explanation
Indices: 110209--110241 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
110199 CCCCCAACAG
110209 CTCCCACAGCAA
1 CTCCCACAGCAA
*
110221 CTCCCACAGCAG
1 CTCCCACAGCAA
110233 CTCCCACAG
1 CTCCCACAG
110242 ACTTATCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.27, C:0.52, G:0.12, T:0.09
Consensus pattern (12 bp):
CTCCCACAGCAA
Found at i:111672 original size:2 final size:2
Alignment explanation
Indices: 111665--111692 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
111655 AATCGTTTAA
111665 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
111693 GGTCAAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:114317 original size:2 final size:2
Alignment explanation
Indices: 114310--114347 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
114300 ATGTAACATA
114310 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
114348 TAGGGTTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:115324 original size:32 final size:34
Alignment explanation
Indices: 115279--115352 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 34
115269 TTTAGGCGAT
** *
115279 ATGACACGTGTCATGTTATCAGTTT-A-GGTAAC
1 ATGACACACGTCATGCTATCAGTTTAAGGGTAAC
* * *
115311 ATGACACACGTCATGCTATTATTTTAAGGGTGAC
1 ATGACACACGTCATGCTATCAGTTTAAGGGTAAC
115345 ATGACACA
1 ATGACACA
115353 TAATGCATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 20 0.59
33 1 0.03
34 13 0.38
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (34 bp):
ATGACACACGTCATGCTATCAGTTTAAGGGTAAC
Found at i:116327 original size:21 final size:21
Alignment explanation
Indices: 116301--116342 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
116291 AAGAAAGTAA
*
116301 AATTATTTTAT-ATTATATTAT
1 AATTATTTAATAATT-TATTAT
116322 AATTATTTAATAATTTATTAT
1 AATTATTTAATAATTTATTAT
116343 TTTATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AATTATTTAATAATTTATTAT
Found at i:118178 original size:21 final size:21
Alignment explanation
Indices: 118154--118197 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
118144 AGATGCCATT
118154 GCAGCTGAG-TCAGATGACACC
1 GCAGCT-AGTTCAGATGACACC
* *
118175 GCAGCTAGTTTAGATGCCACC
1 GCAGCTAGTTCAGATGACACC
118196 GC
1 GC
118198 CGCAAGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.18
Consensus pattern (21 bp):
GCAGCTAGTTCAGATGACACC
Found at i:126325 original size:27 final size:27
Alignment explanation
Indices: 126294--126379 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
126284 ATTCTGACGT
126294 AACCATTGATTCTATAGCCATCTGCAG
1 AACCATTGATTCTATAGCCATCTGCAG
** *
126321 AACCAGAGA-GC-A-AGACCATTCTG-ACG
1 AACCATTGATTCTATAG-CCA-TCTGCA-G
126347 TAACCATTGATTCTATAGCCATCTGCAG
1 -AACCATTGATTCTATAGCCATCTGCAG
126375 AACCA
1 AACCA
126380 GAGAGTAAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 16
0.67 0.09 0.24
Matches are distributed among these distances:
24 2 0.04
25 5 0.11
26 6 0.13
27 19 0.42
28 6 0.13
29 5 0.11
30 2 0.04
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (27 bp):
AACCATTGATTCTATAGCCATCTGCAG
Found at i:126357 original size:54 final size:54
Alignment explanation
Indices: 126275--126427 Score: 234
Period size: 54 Copynumber: 2.8 Consensus size: 54
126265 ACAACTAGAA
*
126275 AGCAAGATCATTCTGACGTAACCATTGATTCTATAGCCATCTGCAGAACCAGAG
1 AGCAAGACCATTCTGACGTAACCATTGATTCTATAGCCATCTGCAGAACCAGAG
126329 AGCAAGACCATTCTGACGTAACCATTGATTCTATAGCCATCTGCAGAACCAGAG
1 AGCAAGACCATTCTGACGTAACCATTGATTCTATAGCCATCTGCAGAACCAGAG
* * ** * * *
126383 AGTAAGACCATTCTGAAGTAACTGTTAAATCTATAGCCATATGCA
1 AGCAAGACCATTCTGACGTAACCATTGATTCTATAGCCATCTGCA
126428 TTACCTAGTA
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 91 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.25
Consensus pattern (54 bp):
AGCAAGACCATTCTGACGTAACCATTGATTCTATAGCCATCTGCAGAACCAGAG
Found at i:126992 original size:2 final size:2
Alignment explanation
Indices: 126985--127016 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
126975 AAGAGGAATT
*
126985 GA GA GA GA GA GA GA GA GA GA CA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
127017 ACAGGAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:130992 original size:18 final size:18
Alignment explanation
Indices: 130969--131006 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
130959 GATATTTTAT
130969 TTTAATATAGAAAGACTC
1 TTTAATATAGAAAGACTC
130987 TTTAATATAGAAAGACTC
1 TTTAATATAGAAAGACTC
131005 TT
1 TT
131007 CTTCTCCCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (18 bp):
TTTAATATAGAAAGACTC
Found at i:135360 original size:12 final size:12
Alignment explanation
Indices: 135343--135367 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
135333 GGTTGATTTG
135343 GTCACTGTAGGT
1 GTCACTGTAGGT
135355 GTCACTGTAGGT
1 GTCACTGTAGGT
135367 G
1 G
135368 GATGTTCGGT
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:0.16, C:0.16, G:0.36, T:0.32
Consensus pattern (12 bp):
GTCACTGTAGGT
Found at i:135662 original size:3 final size:3
Alignment explanation
Indices: 135654--135705 Score: 72
Period size: 3 Copynumber: 17.3 Consensus size: 3
135644 ATTAATAAAC
135654 ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA AT- ATAA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA AT-A ATA ATA
135699 ATA ATA A
1 ATA ATA A
135706 AAAAGACCCG
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.09
3 36 0.80
4 5 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:135693 original size:12 final size:13
Alignment explanation
Indices: 135656--135706 Score: 81
Period size: 12 Copynumber: 4.2 Consensus size: 13
135646 TAATAAACAT
135656 AATAATAATAAT-
1 AATAATAATAATA
135668 AATAATAATAATA
1 AATAATAATAATA
135681 AATAATAAT-ATA
1 AATAATAATAATA
135693 AATAA-AATAATA
1 AATAATAATAATA
135705 AA
1 AA
135707 AAAGACCCGG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
11 3 0.08
12 25 0.68
13 9 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:135708 original size:9 final size:9
Alignment explanation
Indices: 135646--135708 Score: 58
Period size: 9 Copynumber: 7.0 Consensus size: 9
135636 AATATGTAAT
*
135646 TAATAAACA
1 TAATAAAAA
*
135655 TAATAATAA
1 TAATAAAAA
*
135664 TAATAATAA
1 TAATAAAAA
135673 TAATAATAAA
1 TAATAA-AAA
*
135683 TAAT-AATA
1 TAATAAAAA
135691 TAA-ATAAAA
1 TAATA-AAAA
135700 TAATAAAAA
1 TAATAAAAA
135709 AGACCCGGAC
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
8 5 0.11
9 33 0.73
10 7 0.16
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (9 bp):
TAATAAAAA
Found at i:136038 original size:43 final size:43
Alignment explanation
Indices: 135980--136257 Score: 218
Period size: 43 Copynumber: 6.5 Consensus size: 43
135970 AAAGGTGATA
*
135980 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTATGGTTG
* * * *
136023 ACACGGCTCCTACGTGATAAGGAGATCTGG---TCT-GGGAATG
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTATGG-TTG
*
136063 ACACGGCTCATACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTATGGTTG
* * * * *
136106 ACACGTCTCCTACGTGATAAGGAGATCTGG---TCT-GGGAATG
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTATGG-TTG
* * ** ** * *
136146 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCT-ATGGT--TG
*
136192 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTATGGTTG
*
136235 ACACGGCTCCTACGTGATAAGGA
1 ACACGGCTCCTACGTGATGAGGA
136258 AATCTGGTCT
Statistics
Matches: 184, Mismatches: 34, Indels: 34
0.73 0.13 0.13
Matches are distributed among these distances:
39 4 0.02
40 60 0.33
41 1 0.01
42 2 0.01
43 79 0.43
44 2 0.01
45 6 0.03
46 29 0.16
47 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.26
Consensus pattern (43 bp):
ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTATGGTTG
Found at i:136089 original size:83 final size:83
Alignment explanation
Indices: 135980--136165 Score: 345
Period size: 83 Copynumber: 2.2 Consensus size: 83
135970 AAAGGTGATA
* *
135980 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGG
1 ACACGGCTCATACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGG
136045 AGATCTGGTCTGGGAATG
66 AGATCTGGTCTGGGAATG
*
136063 ACACGGCTCATACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGTCTCCTACGTGATAAGG
1 ACACGGCTCATACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGG
136128 AGATCTGGTCTGGGAATG
66 AGATCTGGTCTGGGAATG
136146 ACACGGCTCATACGTGATGA
1 ACACGGCTCATACGTGATGA
136166 AGAGTTCTGG
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 100 1.00
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (83 bp):
ACACGGCTCATACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGG
AGATCTGGTCTGGGAATG
Found at i:136175 original size:40 final size:40
Alignment explanation
Indices: 136021--136163 Score: 164
Period size: 40 Copynumber: 3.5 Consensus size: 40
136011 TATCTATGGT
*
136021 TGACACGGCTCCTACGTGATAAGGAGATCTGGTCTGGGAA
1 TGACACGGCTCATACGTGATAAGGAGATCTGGTCTGGGAA
* * * *
136061 TGACACGGCTCATACGTGATGAGGACG-GCTGGTTATCTATGG-T
1 TGACACGGCTCATACGTGATAAGGA-GATCTGG---TCT-GGGAA
* *
136104 TGACACGTCTCCTACGTGATAAGGAGATCTGGTCTGGGAA
1 TGACACGGCTCATACGTGATAAGGAGATCTGGTCTGGGAA
136144 TGACACGGCTCATACGTGAT
1 TGACACGGCTCATACGTGAT
136164 GAAGAGTTCT
Statistics
Matches: 83, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
39 2 0.02
40 48 0.58
41 1 0.01
42 1 0.01
43 29 0.35
44 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (40 bp):
TGACACGGCTCATACGTGATAAGGAGATCTGGTCTGGGAA
Found at i:136182 original size:83 final size:83
Alignment explanation
Indices: 135980--136214 Score: 301
Period size: 83 Copynumber: 2.8 Consensus size: 83
135970 AAAGGTGATA
* * * **
135980 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGG
1 ACACGGCTCATACGTGATGAAGACGGCTGGCCATCTATGGTTGACACGGCTCCTACGTGATAAGG
136045 AGATCTGGTCTGGGAATG
66 AGATCTGGTCTGGGAATG
* ** *
136063 ACACGGCTCATACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGTCTCCTACGTGATAAGG
1 ACACGGCTCATACGTGATGAAGACGGCTGGCCATCTATGGTTGACACGGCTCCTACGTGATAAGG
136128 AGATCTGGTCTGGGAATG
66 AGATCTGGTCTGGGAATG
* * * *
136146 ACACGGCTCATACGTGATGAAGA-GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
1 ACACGGCTCATACGTGATGAAGACG-GCTGGCCATCT-ATGGT--TGACACGGCTCCTACGTGAT
*
136210 GAGGA
62 AAGGA
136215 CGGCTGGTTA
Statistics
Matches: 136, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
82 1 0.01
83 110 0.81
84 4 0.03
86 21 0.15
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.26
Consensus pattern (83 bp):
ACACGGCTCATACGTGATGAAGACGGCTGGCCATCTATGGTTGACACGGCTCCTACGTGATAAGG
AGATCTGGTCTGGGAATG
Found at i:136268 original size:212 final size:212
Alignment explanation
Indices: 135901--136303 Score: 725
Period size: 212 Copynumber: 1.9 Consensus size: 212
135891 TTAACGCGGT
*
135901 TCCTACGTGATGAGGACATCTGGTCGGGGAATGACACGACTCATACGTGATGAAGAGTTCTGGCC
1 TCCTACGTGATAAGGACATCTGGTCGGGGAATGACACGACTCATACGTGATGAAGAGTTCTGGCC
135966 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCT
66 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCT
* *
136031 CCTACGTGATAAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAGGACGGCTGGTTA
131 CCTACGTGATAAGGAAATCTGGTCTGGGAATGACACGGCTCATACATGATGAGGACGGCTGGTTA
136096 TCTATGGTTGACACGTC
196 TCTATGGTTGACACGTC
* * *
136113 TCCTACGTGATAAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCC
1 TCCTACGTGATAAGGACATCTGGTCGGGGAATGACACGACTCATACGTGATGAAGAGTTCTGGCC
136178 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCT
66 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCT
* * *
136243 CCTACGTGATAAGGAAATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGACGGCTG
131 CCTACGTGATAAGGAAATCTGGTCTGGGAATGACACGGCTCATACATGATGAGGACGGCTG
136304 TCCATCTTTA
Statistics
Matches: 182, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
212 182 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (212 bp):
TCCTACGTGATAAGGACATCTGGTCGGGGAATGACACGACTCATACGTGATGAAGAGTTCTGGCC
ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCT
CCTACGTGATAAGGAAATCTGGTCTGGGAATGACACGGCTCATACATGATGAGGACGGCTGGTTA
TCTATGGTTGACACGTC
Found at i:136874 original size:31 final size:30
Alignment explanation
Indices: 136810--136884 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
136800 ATAGAAAATG
*
136810 TTTCAAGTGAAACGACTCAAAAATGGTTTTA
1 TTTCAAGTGAAACAACTCAAAAAT-GTTTTA
*
136841 TTTCAAGTGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGTGAAAC-AACTCAAAAATGTTT-TA
* *
136872 TTTCTAGAGAAAC
1 TTTCAAGTGAAAC
136885 TGCCTCAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 26 0.68
32 9 0.24
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (30 bp):
TTTCAAGTGAAACAACTCAAAAATGTTTTA
Found at i:136977 original size:40 final size:40
Alignment explanation
Indices: 136917--136996 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
136907 GTTTTAATAA
136917 AAACAATCTCAAAGGTGGGTAGTTTT-AAAAGAAATTGTCT
1 AAACAATCTCAAAGGTGGGTA-TTTTCAAAAGAAATTGTCT
* * *
136957 AAACGATCTCAAATGTGGGTATTTTCAAAAGAAGTTGTCT
1 AAACAATCTCAAAGGTGGGTATTTTCAAAAGAAATTGTCT
136997 CGAGAGACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (40 bp):
AAACAATCTCAAAGGTGGGTATTTTCAAAAGAAATTGTCT
Found at i:137051 original size:63 final size:64
Alignment explanation
Indices: 136978--137102 Score: 189
Period size: 64 Copynumber: 2.0 Consensus size: 64
136968 AATGTGGGTA
* * * *
136978 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTT
1 TTTTCAAAAGAAATTGTCTTCAAGAGAAAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
* *
137041 TTTTCAAAAGAAATTGTCTTTAAGAGAAAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TTTTCAAAAGAAATTGTCTTCAAGAGAAAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
137103 GGATCACATC
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
63 17 0.31
64 38 0.69
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.30
Consensus pattern (64 bp):
TTTTCAAAAGAAATTGTCTTCAAGAGAAAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
Found at i:137221 original size:120 final size:119
Alignment explanation
Indices: 137001--137223 Score: 274
Period size: 120 Copynumber: 1.9 Consensus size: 119
136991 TTGTCTCGAG
* *
137001 AGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTCTTTAAGA
1 AGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTGTCTTCAAGA
137066 GAAAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCACATCTTAAGTC
66 GAAAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCACATCTTAAGTC
* * * **
137120 AGACCAAA-TTTGTTTCAAATGAAACAATCTCAAA-AGTTAGTTTTTCATTAGAAACTGTC-TCA
1 AGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGA-TT--TTTTTCAAAAGAAACTGTCTTCA
* ** *
137182 AGAGAGACAACA-TTTGTTTTTAAAGAAATAGACTCAAAGATG
63 AGAGA-A-AAAATTTTGTTTCAAAAGAAACAGACTCAAAGATG
137224 ATTTTGTTAA
Statistics
Matches: 88, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
117 1 0.01
118 26 0.30
119 14 0.16
120 44 0.50
121 3 0.03
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (119 bp):
AGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTGTCTTCAAGA
GAAAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCACATCTTAAGTC
Found at i:137350 original size:64 final size:64
Alignment explanation
Indices: 137270--137494 Score: 265
Period size: 67 Copynumber: 3.5 Consensus size: 64
137260 ATGAACATAT
** * * * * * *
137270 TCAAAGATTTACTTCAAGAGAAACTGTCTCAAGAGATACAAAATTCAT-TTT-AAGAGAAACAGA
1 TCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATT-TTGTTTCAA-AGAAACAAA
*
137333 T
64 C
* *
137334 TCAAAGATTTTTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCCAAAGAAACAAAC
1 TCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTT-CAAAGAAACAAAC
*
137399 TCAAAGATTTTTGTTTTAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
1 TCAAAGA-TTTT-TTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTT-CAAAGAAACAA
137464 AC
63 AC
*
137466 TCAAAGATTTTTTTCAAAAGAAACAATCT
1 TCAAAGATTTTTTTCAAAAGAAACTATCT
137495 CAAAGATTTT
Statistics
Matches: 140, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
63 1 0.01
64 40 0.29
65 31 0.22
66 10 0.07
67 58 0.41
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (64 bp):
TCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCAAAGAAACAAAC
Found at i:137391 original size:37 final size:37
Alignment explanation
Indices: 137335--137461 Score: 108
Period size: 37 Copynumber: 3.6 Consensus size: 37
137325 GAAACAGATT
*
137335 CAAAGATTTT-TTTCAAAAGAAATTATCTTAAAAGAGA
1 CAAA-ATTTTGTTTCAAAAGAAACTATCTTAAAAGAGA
* * * *
137372 CAAAATTTTGTTTCCAAAGAAACAAAC-T-CAA-AG-
1 CAAAATTTTGTTTCAAAAGAAACTATCTTAAAAGAGA
* * *
137405 ---ATTTTTGTTTTAAAAGAAACTATCTTAAGAGAGA
1 CAAAATTTTGTTTCAAAAGAAACTATCTTAAAAGAGA
*
137439 CAAAATTTTGTTTCCAAAGAAAC
1 CAAAATTTTGTTTCAAAAGAAAC
137462 AAACTCAAAG
Statistics
Matches: 67, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
30 19 0.28
31 1 0.01
32 1 0.01
33 2 0.03
34 2 0.03
35 2 0.03
36 6 0.09
37 34 0.51
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (37 bp):
CAAAATTTTGTTTCAAAAGAAACTATCTTAAAAGAGA
Found at i:137442 original size:67 final size:65
Alignment explanation
Indices: 137324--137494 Score: 270
Period size: 67 Copynumber: 2.6 Consensus size: 65
137314 TCATTTTAAG
* * *
137324 AGAAACAGATTCAAAGATTTTTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCCAA
1 AGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTATCTTAAAAGAGACAAAATTTTGTTTCCAA
* *
137389 AGAAACAAACTCAAAGATTTTTGTTTTAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGA-TTTT-TTTCAAAAGAAACTATCTTAAAAGAGACAAAATTTTGTTTCC
137454 AA
64 AA
*
137456 AGAAACAAACTCAAAGATTTTTTTCAAAAGAAACAATCT
1 AGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTATCT
137495 CAAAGATTTT
Statistics
Matches: 97, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
65 31 0.32
66 8 0.08
67 58 0.60
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (65 bp):
AGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTATCTTAAAAGAGACAAAATTTTGTTTCCAA
Found at i:137504 original size:27 final size:28
Alignment explanation
Indices: 137439--137507 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
137429 TTAAGAGAGA
*
137439 CAAA-ATTTTGTTTCCAAAGAAACAAACT
1 CAAAGATTTT-TTTCAAAAGAAACAAACT
*
137467 CAAAGATTTTTTTCAAAAGAAACAATCT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
137495 CAAAGATTTTTTT
1 CAAAGATTTTTTT
137508 TCACAAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 33 0.87
29 5 0.13
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.35
Consensus pattern (28 bp):
CAAAGATTTTTTTCAAAAGAAACAAACT
Found at i:137640 original size:25 final size:25
Alignment explanation
Indices: 137593--137686 Score: 89
Period size: 27 Copynumber: 3.5 Consensus size: 25
137583 CAAAACTTTG
* *
137593 TTTCAAAATAAATAGACTCAAAGATT
1 TTTCAAAAGAAACA-ACTCAAAGATT
137619 TTTCAAAAGAAACAACTCAAAGATATT
1 TTTCAAAAGAAACAACTCAAAG--ATT
* *
137646 TATTCAAAAGGAACAAACTCCAAGATTT
1 T-TTCAAAAGAAAC-AACTCAAAGA-TT
*
137674 TTTCAAGAGAAAC
1 TTTCAAAAGAAAC
137687 TGTCTCAAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
25 8 0.14
26 12 0.21
27 15 0.26
28 14 0.25
29 8 0.14
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.27
Consensus pattern (25 bp):
TTTCAAAAGAAACAACTCAAAGATT
Found at i:138012 original size:36 final size:35
Alignment explanation
Indices: 137928--138025 Score: 126
Period size: 36 Copynumber: 2.8 Consensus size: 35
137918 GAGAAAATGA
* *
137928 TGTCTCAAGCGAGACAAAATTTG-CTTTAAGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
* **
137962 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTA-AGAAAT
*
137998 TGTCTCAAGCGAGACAAAGTTTGTTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTTT
138026 GAGGAAACGA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
34 20 0.38
35 4 0.08
36 29 0.55
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
Found at i:138040 original size:36 final size:36
Alignment explanation
Indices: 137929--138047 Score: 120
Period size: 36 Copynumber: 3.4 Consensus size: 36
137919 AGAAAATGAT
* * *
137929 GTCTCAAGCGAGACAAAATTTG-CTTTA-AGATATA
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAATC
** *
137963 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAATC
*
137999 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGGAAA-C
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGA-GAAATC
*
138034 GATCTCAAGTGAGA
1 G-TCTCAAGCGAGA
138048 TCAACTTTGT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
34 20 0.28
35 7 0.10
36 44 0.62
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (36 bp):
GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAATC
Found at i:138245 original size:36 final size:36
Alignment explanation
Indices: 138205--138286 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
138195 AAAGGAAAAA
* * *
138205 TGTCTCAAGCGAGACGAAGTTTG-TTTTAAGAGAATT
1 TGTCTCAAGCGAGACAAACTTTGTTTTTAA-AGAAAT
* * *
138241 TGTCTTAAGTGATACAAACTTTGTTTTTAAAGAAAT
1 TGTCTCAAGCGAGACAAACTTTGTTTTTAAAGAAAT
138277 TGTCTCAAGC
1 TGTCTCAAGC
138287 AAAACAAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
36 31 0.84
37 6 0.16
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAACTTTGTTTTTAAAGAAAT
Found at i:138294 original size:36 final size:36
Alignment explanation
Indices: 138205--138299 Score: 93
Period size: 36 Copynumber: 2.6 Consensus size: 36
138195 AAAGGAAAAA
* * * *
138205 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAGCGAAACAAAATTTGTTTTAAGAGAAAT
* * * *
138241 TGTCTTAAGTGATACAAACTTTGTTTTTAA-AGAAAT
1 TGTCTCAAGCGAAACAAAATTTG-TTTTAAGAGAAAT
*
138277 TGTCTCAAGCAAAACAAAATTTG
1 TGTCTCAAGCGAAACAAAATTTG
138300 AGAAAACGAT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
36 41 0.87
37 6 0.13
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.35
Consensus pattern (36 bp):
TGTCTCAAGCGAAACAAAATTTGTTTTAAGAGAAAT
Found at i:138429 original size:36 final size:35
Alignment explanation
Indices: 138389--138506 Score: 148
Period size: 36 Copynumber: 3.3 Consensus size: 35
138379 AGTGAGGCGG
138389 AATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAA
1 AATTTGTTTTT-AAGAAATTGTCTCAAACGAGACAA
* *
138425 AATTTGTTTTT-AGAAAGCTGTCTCAATCGAGACAA
1 AATTTGTTTTTAAGAAA-TTGTCTCAAACGAGACAA
** *
138460 AATTTGCTTTGAAAGAAATTGTCTCAAGCGAGACAAA
1 AATTTG-TTTTTAAGAAATTGTCTCAAACGAGAC-AA
138497 AATTTGTTTT
1 AATTTGTTTT
138507 AAAATTCTCA
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
34 5 0.07
35 22 0.31
36 31 0.44
37 13 0.18
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (35 bp):
AATTTGTTTTTAAGAAATTGTCTCAAACGAGACAA
Found at i:139101 original size:4 final size:4
Alignment explanation
Indices: 139052--139089 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
139042 TTTATGTATC
*
139052 ATGT ATGT ATG- -TGT ATGT ATGT ATAT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
139090 GTTGATGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 2 0.07
4 28 0.93
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:140304 original size:14 final size:14
Alignment explanation
Indices: 140268--140308 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
140258 TCTTTGTCCA
140268 CTTTCTCTTCT-TTT
1 CTTTCTCTT-TGTTT
*
140282 -TTTCACTTTGTTT
1 CTTTCTCTTTGTTT
140295 CTTTCTCTTTGTTT
1 CTTTCTCTTTGTTT
140309 TTCTTTTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 12 0.52
ACGTcount: A:0.02, C:0.22, G:0.05, T:0.71
Consensus pattern (14 bp):
CTTTCTCTTTGTTT
Found at i:142180 original size:31 final size:32
Alignment explanation
Indices: 142124--142185 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
142114 TGACAAAATG
142124 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
142156 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
142186 CATGTAGAAT
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:145948 original size:3 final size:3
Alignment explanation
Indices: 145940--146001 Score: 72
Period size: 3 Copynumber: 19.3 Consensus size: 3
145930 ATTAATAAAC
145940 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATAA ATA ATA ATA A-A TATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA -ATA
145987 TATAA ATA ATA ATA A
1 -AT-A ATA ATA ATA A
146002 AAAAAGACCC
Statistics
Matches: 54, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 1 0.02
3 40 0.74
4 12 0.22
5 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Done.