Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002580.1 Hibiscus syriacus cultivar Beakdansim tig00005225_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: 90128
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:9301 original size:19 final size:19
Alignment explanation
Indices: 9277--9327 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
9267 AACGATGATG
*
9277 TGGCTGACGACTGTTGACA
1 TGGCTGACGACTGTCGACA
* *
9296 TGGCTGATGACTGTCGACG
1 TGGCTGACGACTGTCGACA
9315 TGGCTGACGACTG
1 TGGCTGACGACTG
9328 CCGATGTAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.18, C:0.22, G:0.35, T:0.25
Consensus pattern (19 bp):
TGGCTGACGACTGTCGACA
Found at i:9991 original size:16 final size:17
Alignment explanation
Indices: 9972--10008 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
9962 TATGATATTT
*
9972 ACACTTTAATTTC-ATG
1 ACACTTTAATATCTATG
9988 ACACTTTAATATCTATG
1 ACACTTTAATATCTATG
10005 ACAC
1 ACAC
10009 ATGTAACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (17 bp):
ACACTTTAATATCTATG
Found at i:10511 original size:20 final size:20
Alignment explanation
Indices: 10486--10524 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
10476 AATTTGTATT
10486 GAAAGGTTAAGACCTTTAAG
1 GAAAGGTTAAGACCTTTAAG
10506 GAAAGGTTAAGACCTTTAA
1 GAAAGGTTAAGACCTTTAA
10525 ATGAAATGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (20 bp):
GAAAGGTTAAGACCTTTAAG
Found at i:15886 original size:24 final size:23
Alignment explanation
Indices: 15859--15909 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
15849 ACTTTTGGGG
*
15859 TGAAATGAAATAATTAATTTTTCA
1 TGAAAAGAAATAATT-ATTTTTCA
** *
15883 TGAAAAGACTTGATTATTTTTCA
1 TGAAAAGAAATAATTATTTTTCA
15906 TGAA
1 TGAA
15910 TAGTCATGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (23 bp):
TGAAAAGAAATAATTATTTTTCA
Found at i:15919 original size:23 final size:23
Alignment explanation
Indices: 15875--15919 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
15865 GAAATAATTA
*
15875 ATTTTTCATGAAAAGACTTGATT
1 ATTTTTCATGAAAAGACATGATT
* *
15898 ATTTTTCATGAATAGTCATGAT
1 ATTTTTCATGAAAAGACATGAT
15920 CAATTCATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.44
Consensus pattern (23 bp):
ATTTTTCATGAAAAGACATGATT
Found at i:19238 original size:2 final size:2
Alignment explanation
Indices: 19231--19271 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
19221 TTTATTTTTC
19231 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19272 TAAATAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20130 original size:84 final size:84
Alignment explanation
Indices: 19989--20156 Score: 309
Period size: 84 Copynumber: 2.0 Consensus size: 84
19979 ATCACTTTAA
* *
19989 AATGTTTATATTGTGGGGATGGCTGTCAATCCTGTTTCCAACCATCTGGCAGTACATTTATCTTG
1 AATGTTTATATTGTGGGGATGGCTGTCAATCCTGTTTCCAACCACCTGGCAGTACATTTATCTGG
*
20054 GCATTCCACCAAAGAAAAT
66 GCATTCCACCAAACAAAAT
20073 AATGTTTATATTGTGGGGATGGCTGTCAATCCTGTTTCCAACCACCTGGCAGTACATTTATCTGG
1 AATGTTTATATTGTGGGGATGGCTGTCAATCCTGTTTCCAACCACCTGGCAGTACATTTATCTGG
20138 GCATTCCACCAAACAAAAT
66 GCATTCCACCAAACAAAAT
20157 TTGTGCTATA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (84 bp):
AATGTTTATATTGTGGGGATGGCTGTCAATCCTGTTTCCAACCACCTGGCAGTACATTTATCTGG
GCATTCCACCAAACAAAAT
Found at i:25886 original size:20 final size:20
Alignment explanation
Indices: 25861--25953 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
25851 TTTTCTCTAT
25861 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
25881 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
25901 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
25922 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
25943 TCGCAATGCGA
1 TCGCAATGCGA
25954 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:25904 original size:41 final size:41
Alignment explanation
Indices: 25859--25953 Score: 181
Period size: 41 Copynumber: 2.3 Consensus size: 41
25849 GATTTTCTCT
25859 ATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
1 ATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
25900 ATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
1 ATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
*
25941 AATCGCAATGCGA
1 ATTCGCAATGCGA
25954 TACTGACTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
ATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
Found at i:25907 original size:21 final size:20
Alignment explanation
Indices: 25861--25953 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
25851 TTTTCTCTAT
*
25861 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
25881 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
25901 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
25922 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
25943 TCGCAATGCGA
1 TCGCAATGCGA
25954 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:26147 original size:21 final size:21
Alignment explanation
Indices: 26127--26227 Score: 100
Period size: 20 Copynumber: 4.9 Consensus size: 21
26117 ATTCGCGTTG
*
26127 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGATAGTTC
* ** *
26148 AAAATCGCGTTGCGAT-TTTC
1 CATTTCGCGTTGCGATAGTTC
*
26168 CATTTCGCGTTGCGATAGTCTA
1 CATTTCGCGTTGCGATAGT-TC
* *
26190 CA-GTCGCGTTGCGAT-TTTC
1 CATTTCGCGTTGCGATAGTTC
26209 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
26228 CTACAGTTGT
Statistics
Matches: 61, Mismatches: 15, Indels: 8
0.73 0.18 0.10
Matches are distributed among these distances:
19 3 0.05
20 28 0.46
21 27 0.44
22 3 0.05
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.37
Consensus pattern (21 bp):
CATTTCGCGTTGCGATAGTTC
Found at i:26172 original size:41 final size:41
Alignment explanation
Indices: 26127--26252 Score: 182
Period size: 41 Copynumber: 3.0 Consensus size: 41
26117 ATTCGCGTTG
26127 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCT-AAAATCGCGTTGCGATTTTC
* *
26168 CATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTAAAATCGCGTTGCGATTTTC
* * *
26209 CATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTAAAATCG-CGTTGCGATTTTC
26251 CA
1 CA
26253 AATTCGTTGT
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
41 64 0.80
42 16 0.20
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTCTAAAATCGCGTTGCGATTTTC
Found at i:26377 original size:10 final size:11
Alignment explanation
Indices: 26346--26379 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
26336 GACACGTATT
26346 ACCACGACCACG
1 ACCACGACC-CG
26358 ACCACGACCCG
1 ACCACGACCCG
26369 ACC-CGACCCG
1 ACCACGACCCG
26379 A
1 A
26380 GACAGACGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 5 0.23
12 9 0.41
ACGTcount: A:0.29, C:0.53, G:0.18, T:0.00
Consensus pattern (11 bp):
ACCACGACCCG
Found at i:26906 original size:6 final size:6
Alignment explanation
Indices: 26864--26984 Score: 186
Period size: 6 Copynumber: 21.5 Consensus size: 6
26854 GTCCGTCTCG
26864 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT -GTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
26906 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT -GTCGT -GTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
26952 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
26985 AATACGTGTC
Statistics
Matches: 113, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
5 40 0.35
6 73 0.65
ACGTcount: A:0.00, C:0.17, G:0.51, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:26981 original size:46 final size:46
Alignment explanation
Indices: 26864--26982 Score: 201
Period size: 46 Copynumber: 2.7 Consensus size: 46
26854 GTCCGTCTCG
*
26864 GGTCG-GGTCG-GGTCG-GGTCG-GGTCGGGTCGTGTCGTGGTCGT
1 GGTCGTGGTCGTGGTCGTGGTCGTGGTCGTGTCGTGTCGTGGTCGT
26906 GGTCGTGGTCGTGGTCGTGGTCGTGGTCGTGTCGTGTCGTGGTCGT
1 GGTCGTGGTCGTGGTCGTGGTCGTGGTCGTGTCGTGTCGTGGTCGT
26952 GGTCGTGGTCGTGGTCGTGGTCGTGGTCGTG
1 GGTCGTGGTCGTGGTCGTGGTCGTGGTCGTG
26983 GTAATACGTG
Statistics
Matches: 72, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
42 5 0.07
43 5 0.07
44 5 0.07
45 5 0.07
46 52 0.72
ACGTcount: A:0.00, C:0.18, G:0.51, T:0.31
Consensus pattern (46 bp):
GGTCGTGGTCGTGGTCGTGGTCGTGGTCGTGTCGTGTCGTGGTCGT
Found at i:27120 original size:21 final size:21
Alignment explanation
Indices: 27094--27170 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
27084 ACAACTGTAG
27094 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
** **
27115 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGATTTTCA
* *
27136 A-AATCACAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
27156 ACTATCGCAACGCGA
1 ACTATCGCAACGCGA
27171 AATGCAACGC
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 14 0.33
21 29 0.67
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (21 bp):
ACTATCGCAACGCGATTTTCA
Found at i:27300 original size:21 final size:21
Alignment explanation
Indices: 27214--27300 Score: 77
Period size: 21 Copynumber: 4.2 Consensus size: 21
27204 GTTGCAATTT
** *
27214 CAACTATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATG
27235 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * ** *
27256 GAA-AAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
27276 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
27297 CAAC
1 CAAC
27301 GTGAATTTGC
Statistics
Matches: 49, Mismatches: 16, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
20 14 0.29
21 35 0.71
ACGTcount: A:0.37, C:0.29, G:0.17, T:0.17
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:27311 original size:122 final size:122
Alignment explanation
Indices: 27094--27325 Score: 394
Period size: 122 Copynumber: 1.9 Consensus size: 122
27084 ACAACTGTAG
* * *
27094 ACTATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTTCAACT
1 ACTATCGCAACGCGATCTCCAACTATCGCAACGCGAAATGGAAAAACACAACGCGATTTTCAACT
27159 ATCGCAACGCGAAATGCAACGCGAATTTGCGAT-GATGGAGATCGCGTTGCAATTTCA
66 ATCGCAACGCGAAATGCAACGCGAATTTGCGATAG-TGGAGATCGCGTTGCAATTTCA
*
27216 ACTATCGCAACGCGATCTCCAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTTCAACT
1 ACTATCGCAACGCGATCTCCAACTATCGCAACGCGAAATGGAAAAACACAACGCGATTTTCAACT
* *
27281 ATCGCAATGCGAAATGCAACGTGAATTTGCGATAGTGGAGATCGC
66 ATCGCAACGCGAAATGCAACGCGAATTTGCGATAGTGGAGATCGC
27326 AATGCGAATT
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
122 102 0.99
123 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (122 bp):
ACTATCGCAACGCGATCTCCAACTATCGCAACGCGAAATGGAAAAACACAACGCGATTTTCAACT
ATCGCAACGCGAAATGCAACGCGAATTTGCGATAGTGGAGATCGCGTTGCAATTTCA
Found at i:27470 original size:20 final size:20
Alignment explanation
Indices: 27445--27497 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
27435 CTCTAAAAAA
* *
27445 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
27465 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
27485 TCGCAACGCGATA
1 TCGCAACGCGATA
27498 ATACATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:27713 original size:22 final size:22
Alignment explanation
Indices: 27685--27728 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
27675 CACTCTCTCA
27685 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
**
27707 CCCATCTCCGGTGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
27729 TATCTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:28017 original size:20 final size:20
Alignment explanation
Indices: 27992--28029 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27982 CGATTCTCTC
27992 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
28012 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
28030 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:29370 original size:18 final size:18
Alignment explanation
Indices: 29349--29393 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
29339 TCCACTTCGG
*
29349 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
29367 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
29385 GAGCCATCA
1 GAGCCATCA
29394 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:29920 original size:19 final size:20
Alignment explanation
Indices: 29866--29932 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
29856 TAGTTTACTT
* *
29866 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
29886 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
29906 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
29925 TCGCAACG
1 TCGCAACG
29933 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:29940 original size:14 final size:14
Alignment explanation
Indices: 29921--29978 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
29911 ATGCGAAATG
29921 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
29935 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
29951 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
29967 AAAATCGCAACG
1 AAAATCGCAACG
29979 CGAAATGAAA
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:29963 original size:32 final size:33
Alignment explanation
Indices: 29905--29995 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
29895 GGAAATGGCT
*
29905 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
29938 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
29970 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
29996 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:29989 original size:19 final size:19
Alignment explanation
Indices: 29866--30000 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
29856 TAGTTTACTT
* **
29866 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
29886 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
29906 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
29925 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
29939 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
29957 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
29971 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
29990 TCGCAATGCGA
1 TCGCAACGCGA
30001 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 27 0.29
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:30031 original size:14 final size:14
Alignment explanation
Indices: 30012--30069 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
30002 TTGTGTTTCG
30012 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
30026 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
30042 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
30058 CGTTGCGATTTT
1 CGTTGCGATTTT
30070 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:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:30046 original size:32 final size:33
Alignment explanation
Indices: 30007--30085 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
29997 GCGATTTGTG
30007 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
30039 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
30072 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
30086 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:30084 original size:19 final size:19
Alignment explanation
Indices: 30026--30143 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
30016 GCGATTTTGT
30026 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
30044 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
30058 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
30077 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
30097 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
30116 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
30136 TGTTGCGA
1 CGTTGCGA
30144 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:32012 original size:14 final size:14
Alignment explanation
Indices: 31993--32028 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
31983 ATTGTTTAAT
31993 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
32007 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
32021 TGATTTGT
1 TGATTTGT
32029 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:32154 original size:14 final size:15
Alignment explanation
Indices: 32135--32211 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
32125 CGAAATAGCT
32135 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
32149 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
32167 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
32186 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
32200 ATCGCAATGCGA
1 ATCGCAA-GCGA
32212 TTATCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:32167 original size:19 final size:19
Alignment explanation
Indices: 32145--32211 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
32135 ATCGCAACGA
32145 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
32164 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
32182 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
32196 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
32212 TTATCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:32287 original size:20 final size:20
Alignment explanation
Indices: 32237--32287 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
32227 GCGATATTCT
*
32237 CGTTGCGATAACCATTTTCA
1 CGTTGCGATAGCCATTTTCA
32257 CGTTGCGATAGCCATTTTCA
1 CGTTGCGATAGCCATTTTCA
32277 CGTTGCGATAG
1 CGTTGCGATAG
32288 TCAAATGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCA
Found at i:32654 original size:14 final size:14
Alignment explanation
Indices: 32635--32670 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
32625 ATTGTTTAAT
32635 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
32649 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
32663 TGATTTGT
1 TGATTTGT
32671 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:33969 original size:24 final size:24
Alignment explanation
Indices: 33913--33971 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
33903 AGTCAGTATT
* *
33913 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
33937 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
33961 CGAATTTTGAT
1 CGAAATTTGAT
33972 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:34163 original size:12 final size:12
Alignment explanation
Indices: 34146--34170 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34136 ATATAATCCT
34146 GAAGAAGAAAAA
1 GAAGAAGAAAAA
34158 GAAGAAGAAAAA
1 GAAGAAGAAAAA
34170 G
1 G
34171 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:36488 original size:19 final size:19
Alignment explanation
Indices: 36466--36563 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
36456 GGAAATTACT
36466 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
36485 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
36499 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
36518 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
36532 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
36551 ATCGCAACGCGAA
1 ATCGCAATGCGAA
36564 TTTAATTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:36508 original size:33 final size:33
Alignment explanation
Indices: 36466--36559 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
36456 GGAAATTACT
36466 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
36499 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
36532 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
36560 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:36581 original size:19 final size:20
Alignment explanation
Indices: 36559--36601 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
36549 AAATCGCAAC
36559 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
36578 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
36598 GCGA
1 GCGA
36602 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:36586 original size:14 final size:14
Alignment explanation
Indices: 36587--36620 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
36577 TGCGATTTTC
36587 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
36601 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
36615 ATTTTC
1 ATTTTC
36621 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:36761 original size:14 final size:14
Alignment explanation
Indices: 36742--36778 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
36732 CATCAATTAA
36742 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
36756 ACAAATCACCTTTT
1 ACAAATCAACTTTT
36770 ACAAATCAA
1 ACAAATCAA
36779 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:38202 original size:21 final size:21
Alignment explanation
Indices: 38136--38202 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
38126 GTGAATCGGG
*
38136 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
38156 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
38178 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
38199 CTCT
1 CTCT
38203 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:38221 original size:42 final size:41
Alignment explanation
Indices: 38136--38258 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
38126 GTGAATCGGG
* * * * *
38136 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
38178 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
38220 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
38259 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:40308 original size:19 final size:19
Alignment explanation
Indices: 40258--40355 Score: 151
Period size: 19 Copynumber: 5.1 Consensus size: 19
40248 TCTTTTGGTT
*
40258 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
40277 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
40297 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
40316 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
*
40335 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
40354 GA
1 GA
40356 TTTTGGTTTC
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
19 57 0.77
20 17 0.23
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:40384 original size:19 final size:19
Alignment explanation
Indices: 40351--40395 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
40341 AAAATCGCAA
*
40351 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
40370 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
40389 TGCGATT
1 TGCGATT
40396 ATCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:41042 original size:20 final size:20
Alignment explanation
Indices: 40949--41042 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
40939 CGCTAAGTAA
*
40949 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
40969 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
40989 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
41010 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
41030 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
41043 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:41061 original size:41 final size:41
Alignment explanation
Indices: 40970--41104 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
40960 AAAGTCAGTA
* * * ** *
40970 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
41010 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
41052 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
41093 TCGCGTTGCGAT
1 TCGCGTTGCGAT
41105 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:41075 original size:20 final size:20
Alignment explanation
Indices: 41031--41123 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
41021 ATAGTCAGTA
* **
41031 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
41052 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
41072 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
41093 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
41113 TCGCATTGCGA
1 TCGCATTGCGA
41124 ATTGGTAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:41105 original size:41 final size:41
Alignment explanation
Indices: 41031--41126 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
41021 ATAGTCAGTA
*
41031 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
41072 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
41113 TCGCATTGCGAATT
1 TCGCATTGCGAATT
41127 GGTAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:41770 original size:13 final size:13
Alignment explanation
Indices: 41752--41777 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41742 CATAGTTGAA
41752 CAGTCTTCATATG
1 CAGTCTTCATATG
41765 CAGTCTTCATATG
1 CAGTCTTCATATG
41778 AGCGTTTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:42234 original size:22 final size:22
Alignment explanation
Indices: 42204--42253 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
42194 AGTCTTCCCA
*
42204 CTTCCGCCTTGGTCGTCCTCTC
1 CTTCTGCCTTGGTCGTCCTCTC
42226 CTTCTGCCTTGGTCGTCCTCTC
1 CTTCTGCCTTGGTCGTCCTCTC
42248 CTTCTG
1 CTTCTG
42254 GCACCGTCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.00, C:0.42, G:0.18, T:0.40
Consensus pattern (22 bp):
CTTCTGCCTTGGTCGTCCTCTC
Found at i:42262 original size:22 final size:22
Alignment explanation
Indices: 42215--42262 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
42205 TTCCGCCTTG
***
42215 GTCGTCCTCTCCTTCTGCCTTG
1 GTCGTCCTCTCCTTCTGCCACC
*
42237 GTCGTCCTCTCCTTCTGGCACC
1 GTCGTCCTCTCCTTCTGCCACC
42259 GTCG
1 GTCG
42263 ACTGTAATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.02, C:0.42, G:0.21, T:0.35
Consensus pattern (22 bp):
GTCGTCCTCTCCTTCTGCCACC
Found at i:43242 original size:24 final size:24
Alignment explanation
Indices: 43232--43277 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
43222 GTAAACGAAC
43232 GAATATAAACAAACACAAACAAAA
1 GAATATAAACAAACACAAACAAAA
*
43256 GAATGTAAACAAACACAAACAA
1 GAATATAAACAAACACAAACAA
43278 CGTAAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.67, C:0.17, G:0.07, T:0.09
Consensus pattern (24 bp):
GAATATAAACAAACACAAACAAAA
Found at i:43509 original size:14 final size:14
Alignment explanation
Indices: 43490--43520 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
43480 GATTGAACTA
*
43490 AATATAAATGAATG
1 AATATAAACGAATG
43504 AATATAAACGAATG
1 AATATAAACGAATG
43518 AAT
1 AAT
43521 TATTGAACGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.13, T:0.26
Consensus pattern (14 bp):
AATATAAACGAATG
Found at i:44087 original size:20 final size:20
Alignment explanation
Indices: 44062--44337 Score: 135
Period size: 20 Copynumber: 13.7 Consensus size: 20
44052 GATTTTCCAT
**
44062 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGAA
**
44082 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATCCGA-A
* * *
44102 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGAATCCGAA
* * *
44122 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATCCG-AA
* * * *
44143 AATCGTAACGTGTATCCGTA
1 AATCGCAACGCGAATCCGAA
*
44163 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCG-AA
* * *
44184 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATCCGAA
* * ** *
44204 AATCACAACGAGAATATGTA
1 AATCGCAACGCGAATCCGAA
* *
44224 AATCGCAACGCGTAT-CTATA
1 AATCGCAACGCGAATCCGA-A
** * *
44244 AATCGCAACAAGAATACGTA
1 AATCGCAACGCGAATCCGAA
* * *
44264 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
* *
44284 AATCGCAATGCGAATACGTAA
1 AATCGCAACGCGAATCCG-AA
* * * *
44305 AATTGCAACGCGTATCTGTA
1 AATCGCAACGCGAATCCGAA
44325 AATCGCAACGCGA
1 AATCGCAACGCGA
44338 TTTTTAAAGC
Statistics
Matches: 189, Mismatches: 58, Indels: 18
0.71 0.22 0.07
Matches are distributed among these distances:
19 1 0.01
20 140 0.74
21 48 0.25
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGAA
Found at i:44145 original size:61 final size:61
Alignment explanation
Indices: 44080--44334 Score: 175
Period size: 61 Copynumber: 4.2 Consensus size: 61
44070 CGCGAATATG
* * * **
44080 AAAATCGCAACGCGAACATATAAATCGCAACGCGATTC-TGACTATCGCAACGAGTATCCGT
1 AAAATCGCAACGAGAACATGTAAATCGCAACGCGATACGT-AAAATCGCAACGAGTATCCGT
* * * * * *
44141 AAAATCGTAACGTGTATC-CGTAAATCGCAACGACAATACGTAAAATCGCAACGTGTATCCGT
1 AAAATCGCAACGAG-AACATGTAAATCGCAACG-CGATACGTAAAATCGCAACGAGTATCCGT
* * * * *
44203 -AAATCACAACGAGAATATGTAAATCGCAACGCG-TATC-TATAAATCGCAACAAGAATACGT
1 AAAATCGCAACGAGAACATGTAAATCGCAACGCGATA-CGTA-AAATCGCAACGAGTATCCGT
* * * * * * * *
44263 -AAATCGCAATGCGTATC-CGTAAATCGCAATGCGAATACGTAAAATTGCAACGCGTATCTGT
1 AAAATCGCAACGAG-AACATGTAAATCGCAACGCG-ATACGTAAAATCGCAACGAGTATCCGT
44324 -AAATCGCAACG
1 AAAATCGCAACG
44335 CGATTTTTAA
Statistics
Matches: 149, Mismatches: 35, Indels: 20
0.73 0.17 0.10
Matches are distributed among these distances:
59 4 0.03
60 43 0.29
61 73 0.49
62 28 0.19
63 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (61 bp):
AAAATCGCAACGAGAACATGTAAATCGCAACGCGATACGTAAAATCGCAACGAGTATCCGT
Found at i:44152 original size:21 final size:21
Alignment explanation
Indices: 44123--44334 Score: 152
Period size: 20 Copynumber: 10.4 Consensus size: 21
44113 GATTCTGACT
44123 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGTATCCGTAAA
* *
44144 ATCGTAACGTGTATCCGT-AA
1 ATCGCAACGAGTATCCGTAAA
** *
44164 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGTAAA
*
44185 ATCGCAACGTGTATCCGT-AA
1 ATCGCAACGAGTATCCGTAAA
* * **
44205 ATCACAACGAGAATATGT-AA
1 ATCGCAACGAGTATCCGTAAA
*
44225 ATCGCAACGCGTAT-C-TATAA
1 ATCGCAACGAGTATCCGTA-AA
* * *
44245 ATCGCAACAAGAATACGT-AA
1 ATCGCAACGAGTATCCGTAAA
* *
44265 ATCGCAATGCGTATCCGT-AA
1 ATCGCAACGAGTATCCGTAAA
* * * *
44285 ATCGCAATGCGAATACGTAAA
1 ATCGCAACGAGTATCCGTAAA
* * *
44306 ATTGCAACGCGTATCTGT-AA
1 ATCGCAACGAGTATCCGTAAA
44326 ATCGCAACG
1 ATCGCAACG
44335 CGATTTTTAA
Statistics
Matches: 149, Mismatches: 36, Indels: 13
0.75 0.18 0.07
Matches are distributed among these distances:
18 1 0.01
20 99 0.66
21 48 0.32
22 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAGTATCCGTAAA
Found at i:44239 original size:40 final size:41
Alignment explanation
Indices: 44123--44334 Score: 266
Period size: 41 Copynumber: 5.2 Consensus size: 41
44113 GATTCTGACT
* * * *
44123 ATCGCAACGAGTATCCGTAAAATCGTAACGTGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
44164 ATCGCAACGACAATACGTAAAATCGCAACGTGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * **
44205 ATCACAACGAGAATATGT-AAATCGCAACGCGTATCTATAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
44245 ATCGCAACAAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * * *
44285 ATCGCAATGCGAATACGTAAAATTGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
44326 ATCGCAACG
1 ATCGCAACG
44335 CGATTTTTAA
Statistics
Matches: 147, Mismatches: 23, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
40 68 0.46
41 79 0.54
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:44246 original size:81 final size:81
Alignment explanation
Indices: 44062--44334 Score: 266
Period size: 81 Copynumber: 3.4 Consensus size: 81
44052 GATTTTCCAT
* * * * ** * *
44062 AATCGCAACGCGAATATGAAAATCGCAACG-CGAACATATAAATCGCAACGCG-ATTC-TGACTA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAC-AATACGTAAATCGCAACGCGTATCCGT-A-AA
* * *
44124 TCGCAACGAGTATCCGTAA
63 TCACAACGAGAATACGTAA
* * * *
44143 AATCGTAACGTGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGTGTATCCGTAAATC
1 AATCGCAACGCGTATCTGTAAATCGCAACGACAATACGT-AAATCGCAACGCGTATCCGTAAATC
*
44208 ACAACGAGAATATGT-A
65 ACAACGAGAATACGTAA
* * * * *
44224 AATCGCAACGCGTATCTATAAATCGCAACAAGAATACGTAAATCGCAATGCGTATCCGTAAATCG
1 AATCGCAACGCGTATCTGTAAATCGCAACGACAATACGTAAATCGCAACGCGTATCCGTAAATCA
* *
44289 CAATGCGAATACGTAA
66 CAACGAGAATACGTAA
*
44305 AATTGCAACGCGTATCTGTAAATCGCAACG
1 AATCGCAACGCGTATCTGTAAATCGCAACG
44335 CGATTTTTAA
Statistics
Matches: 156, Mismatches: 31, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
80 34 0.22
81 90 0.58
82 27 0.17
83 4 0.03
84 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (81 bp):
AATCGCAACGCGTATCTGTAAATCGCAACGACAATACGTAAATCGCAACGCGTATCCGTAAATCA
CAACGAGAATACGTAA
Found at i:44976 original size:21 final size:20
Alignment explanation
Indices: 44898--44969 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
44888 TTCTAAACTT
*
44898 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
*
44918 AAAATCGCAACACGAAATTG
1 AAAATCGCAACACGAAAATG
**
44938 ACTATCGCAACGA-GAGAAATG
1 AAAATCGCAAC-ACGA-AAATG
44959 AAAATCGCAAC
1 AAAATCGCAAC
44970 GAGAGAATCG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.50, C:0.19, G:0.17, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:44980 original size:14 final size:14
Alignment explanation
Indices: 44958--45022 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
44948 CGAGAGAAAT
44958 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
44972 GAGAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
44990 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
45005 GATAATCGCAACGC
1 GAAAATCGCAACGA
45019 GAAA
1 GAAA
45023 CCAAAATCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 25 0.61
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.24
ACGTcount: A:0.46, C:0.22, G:0.23, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:44994 original size:33 final size:33
Alignment explanation
Indices: 44953--45033 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
44943 CGCAACGAGA
44953 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
44986 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
45019 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
45034 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:45081 original size:33 final size:33
Alignment explanation
Indices: 45034--45155 Score: 145
Period size: 33 Copynumber: 3.5 Consensus size: 33
45024 CAAAATCGCA
*
45034 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
45067 TTGCAATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
45100 TTGCGATAGTCATTTCCGCGTTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATTT-CGCGTTGCG------ATTCTCTCG
45140 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
45156 AACCAAAAGA
Statistics
Matches: 75, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
33 43 0.57
34 9 0.12
39 1 0.01
40 22 0.29
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:45132 original size:20 final size:19
Alignment explanation
Indices: 45029--45155 Score: 112
Period size: 20 Copynumber: 7.1 Consensus size: 19
45019 GAAACCAAAA
*
45029 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
45048 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
*
45064 T--CGTTGCAATTTTCATT
1 TCGCGTTGCGATTTTCATT
45081 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
45095 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
45114 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
45134 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
45154 TC
1 TC
45156 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 9, Indels: 24
0.73 0.08 0.20
Matches are distributed among these distances:
14 17 0.20
16 8 0.09
17 9 0.10
19 20 0.23
20 32 0.37
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:46029 original size:19 final size:19
Alignment explanation
Indices: 46005--46066 Score: 115
Period size: 19 Copynumber: 3.3 Consensus size: 19
45995 ACACTCGTTA
46005 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
*
46024 CGATTTTCATTTCACATTG
1 CGATTTTCATTTCGCATTG
46043 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
46062 CGATT
1 CGATT
46067 CTCTCGTTGC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.47
Consensus pattern (19 bp):
CGATTTTCATTTCGCATTG
Found at i:46096 original size:20 final size:20
Alignment explanation
Indices: 46071--46125 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
46061 GCGATTCTCT
*
46071 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
46091 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
**
46111 TATTGCGATAGTCAA
1 CGTTGCGATAGTCAA
46126 ATGAATGTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTCCG
Found at i:48602 original size:24 final size:24
Alignment explanation
Indices: 48551--48602 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
48541 ATCCGAGTAT
** *
48551 TGACCAAGATCAAAGTACGGGTAT
1 TGACCAAGATCAAAGTACGAATAC
* *
48575 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTACGAATAC
48599 TGAC
1 TGAC
48603 TAGCACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTACGAATAC
Found at i:49463 original size:20 final size:20
Alignment explanation
Indices: 49440--49619 Score: 56
Period size: 20 Copynumber: 9.0 Consensus size: 20
49430 TTGCGATAGT
49440 CAGAATCTCGTTGCGATTTA
1 CAGAATCTCGTTGCGATTTA
* * *
49460 CAGATTCGCATTGCGATTTA
1 CAGAATCTCGTTGCGATTTA
* *
49480 C-GTAT-TCGCATTACGATTTA
1 CAGAATCTCG--TTGCGATTTA
*
49500 C-GTAT-TCGCATTGCGATTTA
1 CAGAATCTCG--TTGCGATTTA
* * *
49520 CAG-ATACGCATTGTGATTTA
1 CAGAAT-CTCGTTGCGATTTA
* *
49540 C-GTATTCTCATTGCGATTTA
1 CAG-AATCTCGTTGCGATTTA
** *
49560 CAG-ATACGAGTTTCGATTTA
1 CAGAAT-CTCGTTGCGATTTA
* *
49580 C-GTATTCTCGTTGCGATAGT-
1 CAG-AATCTCGTTGCGAT-TTA
49600 CAGAATCGT-GTTGCGATTTA
1 CAGAATC-TCGTTGCGATTTA
49620 TATGTTCGCA
Statistics
Matches: 118, Mismatches: 27, Indels: 30
0.67 0.15 0.17
Matches are distributed among these distances:
18 1 0.01
19 6 0.05
20 103 0.87
21 7 0.06
22 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (20 bp):
CAGAATCTCGTTGCGATTTA
Found at i:49497 original size:40 final size:40
Alignment explanation
Indices: 49453--49596 Score: 177
Period size: 40 Copynumber: 3.6 Consensus size: 40
49443 AATCTCGTTG
*
49453 CGATTTACAG-ATTCGCATTGCGATTTAC-GTATTCGCATTA
1 CGATTTAC-GTATTCGCATTGCGATTTACAG-ATACGCATTA
*
49493 CGATTTACGTATTCGCATTGCGATTTACAGATACGCATTG
1 CGATTTACGTATTCGCATTGCGATTTACAGATACGCATTA
* * *
49533 TGATTTACGTATTCTCATTGCGATTTACAGATACG-AGTTT
1 CGATTTACGTATTCGCATTGCGATTTACAGATACGCA-TTA
* *
49573 CGATTTACGTATTCTCGTTGCGAT
1 CGATTTACGTATTCGCATTGCGAT
49597 AGTCAGAATC
Statistics
Matches: 94, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
39 2 0.02
40 91 0.97
41 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (40 bp):
CGATTTACGTATTCGCATTGCGATTTACAGATACGCATTA
Found at i:49617 original size:40 final size:40
Alignment explanation
Indices: 49449--49619 Score: 147
Period size: 40 Copynumber: 4.3 Consensus size: 40
49439 TCAGAATCTC
* * *
49449 GTTGCGATTTACAG-ATTCGCATTGCGATTTAC-GTATTCGCA
1 GTTGCGATTTAC-GTATTCTCATTGCGATGTACAG-ATACG-A
* * *
49490 -TTACGATTTACGTATTCGCATTGCGATTTACAGATACGCA
1 GTTGCGATTTACGTATTCTCATTGCGATGTACAGATACG-A
* *
49530 -TTGTGATTTACGTATTCTCATTGCGATTTACAGATACGA
1 GTTGCGATTTACGTATTCTCATTGCGATGTACAGATACGA
* * *
49569 GTTTCGATTTACGTATTCTCGTTGCGATAGT-CAGA-ATCGT
1 GTTGCGATTTACGTATTCTCATTGCGAT-GTACAGATA-CGA
49609 GTTGCGATTTA
1 GTTGCGATTTA
49620 TATGTTCGCA
Statistics
Matches: 114, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
39 3 0.03
40 109 0.96
41 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (40 bp):
GTTGCGATTTACGTATTCTCATTGCGATGTACAGATACGA
Found at i:49745 original size:20 final size:21
Alignment explanation
Indices: 49700--49749 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
49690 TTCATAATCG
* *
49700 CGTTGCGATTCTGGGAGCTGA
1 CGTTGCGATTCTGGGAGATCA
*
49721 -TTTGCGATTCT-GGAGATCA
1 CGTTGCGATTCTGGGAGATCA
49740 CGTTGCGATT
1 CGTTGCGATT
49750 TTTATTTCGC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.16, C:0.18, G:0.32, T:0.34
Consensus pattern (21 bp):
CGTTGCGATTCTGGGAGATCA
Found at i:50196 original size:23 final size:23
Alignment explanation
Indices: 50161--50208 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
50151 ATCAAGTACA
*
50161 ATAATATATTAGGTAACGCTTAT
1 ATAATATAATAGGTAACGCTTAT
* *
50184 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAACGCTTAT
50207 AT
1 AT
50209 TGACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAACGCTTAT
Found at i:51052 original size:57 final size:57
Alignment explanation
Indices: 50963--51078 Score: 205
Period size: 57 Copynumber: 2.0 Consensus size: 57
50953 TAACTTCTTT
* *
50963 TCTTTTAAATTCTAAAAGTGTCGATACCTATAATAAAGTATCGACACTTTCAACATA
1 TCTTTTAAATTCCAAAAGTGTCGATACCTATAATAAAATATCGACACTTTCAACATA
*
51020 TCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAATATCGACACTTTCAACATA
1 TCTTTTAAATTCCAAAAGTGTCGATACCTATAATAAAATATCGACACTTTCAACATA
51077 TC
1 TC
51079 CGATAGCTCT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (57 bp):
TCTTTTAAATTCCAAAAGTGTCGATACCTATAATAAAATATCGACACTTTCAACATA
Found at i:51479 original size:112 final size:112
Alignment explanation
Indices: 51234--51584 Score: 560
Period size: 112 Copynumber: 3.1 Consensus size: 112
51224 GATACTTATA
* * * * *
51234 ATAAAGTATCGACACTATCAACATATCTAGTAGCGCTTTACCTGTTTTGTCATTTATAGACTGAT
1 ATAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
51299 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
51347 ATAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * **
51412 TTTGTCATTTTTTTACATGTTATATTATTATAAATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
51459 ATAAAGTATCGACACTTTCAATATATCCAATAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
** *
51524 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATTAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
51570 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
51585 AAACCGACAA
Statistics
Matches: 220, Mismatches: 18, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
111 47 0.21
112 106 0.48
113 67 0.30
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:52873 original size:3 final size:3
Alignment explanation
Indices: 52865--52902 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
52855 CTGGTCGCAC
* *
52865 GAA GAA GAA GAA AAA GAA GGA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
52903 CTACGACGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:58929 original size:22 final size:22
Alignment explanation
Indices: 58898--58962 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
58888 GGATGGGATG
58898 GGATG-GGGAGTGTGAACGGTC
1 GGATGAGGGAGTGTGAACGGTC
*
58919 GGATGAGGGAGTGTGAACGGTA
1 GGATGAGGGAGTGTGAACGGTC
* *
58941 GGATGAGAGAGTGTGAATGGTC
1 GGATGAGGGAGTGTGAACGGTC
58963 CAGATTAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 5 0.13
22 34 0.87
ACGTcount: A:0.25, C:0.06, G:0.49, T:0.20
Consensus pattern (22 bp):
GGATGAGGGAGTGTGAACGGTC
Found at i:60328 original size:16 final size:16
Alignment explanation
Indices: 60307--60341 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
60297 TATATACATA
60307 TATATAATAATAATAT
1 TATATAATAATAATAT
* *
60323 TATATATTATTAATAT
1 TATATAATAATAATAT
60339 TAT
1 TAT
60342 TATTTACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATATAATAATAATAT
Found at i:61344 original size:24 final size:20
Alignment explanation
Indices: 61317--61374 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
61307 GTATGGGTAG
61317 TGCATCAATGCACATGTTAAAGAA
1 TGCATCAATGCAC-TG-T--AGAA
*
61341 TGCATCAATACACTGTAGAA
1 TGCATCAATGCACTGTAGAA
*
61361 TGTATCAATGCACT
1 TGCATCAATGCACT
61375 TCAAGGGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (20 bp):
TGCATCAATGCACTGTAGAA
Found at i:64373 original size:26 final size:26
Alignment explanation
Indices: 64330--64379 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
64320 AAAGGATCAG
*
64330 ATATGATAAAGGTTATATGGAAGTGT
1 ATATGATAAAGGTTATATAGAAGTGT
*
64356 ATATGAT-AAGTTTGATATAGAAGT
1 ATATGATAAAGGTT-ATATAGAAGT
64380 AAGAGAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (26 bp):
ATATGATAAAGGTTATATAGAAGTGT
Found at i:68460 original size:20 final size:20
Alignment explanation
Indices: 68437--68506 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
68427 TCTTAGAGCT
*
68437 CATATAGATGTATTTAGGAG
1 CATATAGTTGTATTTAGGAG
68457 CATATAGTTGTATTTAGGAG
1 CATATAGTTGTATTTAGGAG
68477 CATATAGTTGTATTTAGGAG
1 CATATAGTTGTATTTAGGAG
68497 CATATAGTTG
1 CATATAGTTG
68507 CATGTGGTGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.31, C:0.06, G:0.24, T:0.39
Consensus pattern (20 bp):
CATATAGTTGTATTTAGGAG
Found at i:73305 original size:17 final size:18
Alignment explanation
Indices: 73283--73316 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
73273 GCAGTGTTAA
73283 CAAAAAGAAAAA-AAAAG
1 CAAAAAGAAAAAGAAAAG
73300 CAAAAAGAAAAAGAAAA
1 CAAAAAGAAAAAGAAAA
73317 CAATGCGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (18 bp):
CAAAAAGAAAAAGAAAAG
Found at i:73710 original size:20 final size:20
Alignment explanation
Indices: 73681--73719 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
73671 AGAGCTCATA
*
73681 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
73701 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
73720 GTGGTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:83519 original size:27 final size:27
Alignment explanation
Indices: 83466--83520 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
83456 CACTATCACT
* *
83466 ACTTTGAACTTGAAACTCCATAGCATC
1 ACTTTGAACTTGAAACTCCACAACATC
*
83493 ACTTTGAACTTGAAAGTCCACAACATC
1 ACTTTGAACTTGAAACTCCACAACATC
83520 A
1 A
83521 AGATCTTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.27
Consensus pattern (27 bp):
ACTTTGAACTTGAAACTCCACAACATC
Found at i:89764 original size:22 final size:22
Alignment explanation
Indices: 89719--89764 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
89709 TAATCGCGAG
*
89719 TTTAGAAGATACGATTCTGGGC
1 TTTAGAAGATACGATTCTGAGC
* *
89741 TTTAGCAGATACGATTTTGAGC
1 TTTAGAAGATACGATTCTGAGC
89763 TT
1 TT
89765 ATTTAGGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (22 bp):
TTTAGAAGATACGATTCTGAGC
Done.