Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005460.1 Hibiscus syriacus cultivar Beakdansim tig00012503_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: 128298
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2963 original size:21 final size:22
Alignment explanation
Indices: 2939--2985 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
2929 TGGATATGCA
2939 GATGAG-GGTGATGGTGAGGGT
1 GATGAGTGGTGATGGTGAGGGT
* *
2960 GATG-GTGGTGGTGGTGATGGT
1 GATGAGTGGTGATGGTGAGGGT
2981 GATGA
1 GATGA
2986 TGTTGAGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.17, C:0.00, G:0.55, T:0.28
Consensus pattern (22 bp):
GATGAGTGGTGATGGTGAGGGT
Found at i:2999 original size:12 final size:12
Alignment explanation
Indices: 2941--2966 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2931 GATATGCAGA
2941 TGAGGGTGATGG
1 TGAGGGTGATGG
2953 TGAGGGTGATGG
1 TGAGGGTGATGG
2965 TG
1 TG
2967 GTGGTGGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.58, T:0.27
Consensus pattern (12 bp):
TGAGGGTGATGG
Found at i:3377 original size:5 final size:5
Alignment explanation
Indices: 3367--3438 Score: 80
Period size: 5 Copynumber: 14.4 Consensus size: 5
3357 AGTTCACGGG
3367 CATAA CATAA CATCTAA CAAATAA CATAA CATAA -A-AA CATAA CATAA
1 CATAA CATAA CA--TAA C--ATAA CATAA CATAA CATAA CATAA CATAA
3414 CATAA CAT-A CATAA CAT-A CATAA CA
1 CATAA CATAA CATAA CATAA CATAA CA
3439 GACTGACTCT
Statistics
Matches: 59, Mismatches: 0, Indels: 16
0.79 0.00 0.21
Matches are distributed among these distances:
3 2 0.03
4 10 0.17
5 38 0.64
7 8 0.14
9 1 0.02
ACGTcount: A:0.60, C:0.21, G:0.00, T:0.19
Consensus pattern (5 bp):
CATAA
Found at i:3392 original size:19 final size:19
Alignment explanation
Indices: 3367--3431 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
3357 AGTTCACGGG
*
3367 CATAACATAACATCTAACAA
1 CATAACATAACAT-TAAAAA
3387 -ATAACATAACA-TAAAAA
1 CATAACATAACATTAAAAA
*
3404 CATAACATAACA-TAACATA
1 CATAACATAACATTAA-AAA
3423 CATAACATA
1 CATAACATA
3432 CATAACAGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
17 5 0.12
18 14 0.34
19 22 0.54
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (19 bp):
CATAACATAACATTAAAAA
Found at i:3417 original size:23 final size:23
Alignment explanation
Indices: 3367--3438 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
3357 AGTTCACGGG
*
3367 CATAACATAACAT-C-TAACA-A
1 CATAACATAACATACAAAACATA
3387 -ATAACATAACATA-AAAACATAA
1 CATAACATAACATACAAAACAT-A
*
3409 CATAACATAACATACATAACATA
1 CATAACATAACATACAAAACATA
3432 CATAACA
1 CATAACA
3439 GACTGACTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
19 12 0.27
20 4 0.09
22 1 0.02
23 21 0.48
24 6 0.14
ACGTcount: A:0.60, C:0.21, G:0.00, T:0.19
Consensus pattern (23 bp):
CATAACATAACATACAAAACATA
Found at i:3428 original size:37 final size:35
Alignment explanation
Indices: 3367--3436 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 35
3357 AGTTCACGGG
3367 CATAACATAACATCTAACAAATAACATAACATAAAAA
1 CATAACATAACA-CTAACAAATAACAT-ACATAAAAA
3404 CATAACATAACA-TAACATACATAACATACATAA
1 CATAACATAACACTAACA-A-ATAACATACATAA
3437 CAGACTGACT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
35 5 0.16
36 7 0.23
37 19 0.61
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (35 bp):
CATAACATAACACTAACAAATAACATACATAAAAA
Found at i:3437 original size:18 final size:18
Alignment explanation
Indices: 3367--3438 Score: 94
Period size: 18 Copynumber: 3.9 Consensus size: 18
3357 AGTTCACGGG
3367 CATAACATAACATCTAACAA
1 CATAACATAACA--TAACAA
*
3387 -ATAACATAACATAAAAA
1 CATAACATAACATAACAA
3404 CATAACATAACATAACATA
1 CATAACATAACATAACA-A
3423 CATAACAT-ACATAACA
1 CATAACATAACATAACA
3439 GACTGACTCT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
17 5 0.10
18 23 0.48
19 20 0.42
ACGTcount: A:0.60, C:0.21, G:0.00, T:0.19
Consensus pattern (18 bp):
CATAACATAACATAACAA
Found at i:4870 original size:18 final size:18
Alignment explanation
Indices: 4845--4888 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
4835 TTCTTATGGG
*
4845 GAGTATCGATACTACCCTT
1 GAGTATCGATACT-CCCAT
4864 G-GTATCGATACTCCCAT
1 GAGTATCGATACTCCCAT
4881 GAGTATCG
1 GAGTATCG
4889 GTACCAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 17 0.74
19 1 0.04
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (18 bp):
GAGTATCGATACTCCCAT
Found at i:9349 original size:325 final size:326
Alignment explanation
Indices: 8773--9404 Score: 1187
Period size: 325 Copynumber: 1.9 Consensus size: 326
8763 ATAGTTTTTA
8773 TATTACTTTATGAATGTCTAAATTCAGAGATTTACAAGCAATTTTAAAAGAAAATTTTGGGTCAC
1 TATTACTTTATGAATGTCTAAATTCAGAGATTTACAAGCAATTTTAAAAGAAAATTTTGGGTCAC
8838 TATTTCGGTAATCCTGTGTAACATTGTAATCCATGGAACTTTGAGTCTAACTGGATTAGGGCATT
66 TATTTCGGTAATCCTGTGTAACATTGTAATCCATGGAACTTTGAGTCTAACTGGATTAGGGCATT
*
8903 ACAAAAGTAGTACCCTACAAGGTTTAATAAATTATGCACCTCAGAGAAATTATTAGGTAGTTCCC
131 ACAAAAGTAGTACCCTACAAGGTTTAATAAATTATGCACCTCAGAGAAATTATTAGGTACTTCCC
*
8968 ACTCAAAGATTACTTTAATCTTTTGGGGGTTTACTCAGATACCGTTGTCTATTACTACATTACCC
196 ACTCAAAGATTACTTTAATCTTTTAGGGGTTTACTCAGATACCGTTGTCTATTACTACATTACCC
9033 AAAAATGCAACTTCGGTCAACCAGAATTCACACTTCCTAAACTTGGCTAGATTATTATTAAGTGT
261 AAAAATGCAACTTCGGTCAACCAGAATTCACACTTCCTAAACTTGGCTAGATTATTATTAAGTGT
9098 T
326 T
*
9099 TATTACTTTATGAATGTCTAAATTTCAGAGATTTACAAGCAATTTTAAAAGAAACTTTTGGGTCA
1 TATTACTTTATGAATGTCTAAA-TTCAGAGATTTACAAGCAATTTTAAAAGAAAATTTTGGGTCA
*
9164 CTATTTCGGTAAT-CTGTGTAACATTGTAATCCATGGAACTTTGGGTCTAACTGGATTAGGGCAT
65 CTATTTCGGTAATCCTGTGTAACATTGTAATCCATGGAACTTTGAGTCTAACTGGATTAGGGCAT
*
9228 TACAAAAGTAGTA-CCTACAAGGTTTAATAAATTATGCACCTCAGAGAAATTATTAGGTACTTCT
130 TACAAAAGTAGTACCCTACAAGGTTTAATAAATTATGCACCTCAGAGAAATTATTAGGTACTTCC
*
9292 CACTCGAAGATTACTTTAATCTTTTAGGGGTTTACTCAGATACCGTTGTCTATTACTACATTACC
195 CACTCAAAGATTACTTTAATCTTTTAGGGGTTTACTCAGATACCGTTGTCTATTACTACATTACC
9357 CAAAAATGCAACTTCGGTCAACCAGAATTCACACTTCCTAAACTTGGC
260 CAAAAATGCAACTTCGGTCAACCAGAATTCACACTTCCTAAACTTGGC
9405 ATATAGTTGA
Statistics
Matches: 299, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
325 160 0.54
326 85 0.28
327 54 0.18
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Consensus pattern (326 bp):
TATTACTTTATGAATGTCTAAATTCAGAGATTTACAAGCAATTTTAAAAGAAAATTTTGGGTCAC
TATTTCGGTAATCCTGTGTAACATTGTAATCCATGGAACTTTGAGTCTAACTGGATTAGGGCATT
ACAAAAGTAGTACCCTACAAGGTTTAATAAATTATGCACCTCAGAGAAATTATTAGGTACTTCCC
ACTCAAAGATTACTTTAATCTTTTAGGGGTTTACTCAGATACCGTTGTCTATTACTACATTACCC
AAAAATGCAACTTCGGTCAACCAGAATTCACACTTCCTAAACTTGGCTAGATTATTATTAAGTGT
T
Found at i:12969 original size:20 final size:19
Alignment explanation
Indices: 12933--12979 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
12923 TCAGTGGTGG
*
12933 TATCGATATTATGCTTGCAA
1 TATCGATATTATCCTTG-AA
*
12953 TATCGATATTCA-CCTTGAG
1 TATCGATATT-ATCCTTGAA
12972 TATCGATA
1 TATCGATA
12980 CCAAAAATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.38
20 14 0.58
21 1 0.04
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (19 bp):
TATCGATATTATCCTTGAA
Found at i:13145 original size:20 final size:20
Alignment explanation
Indices: 13120--13168 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
13110 TTGTCATCGA
13120 TATCGATACT-ACCCTCTGAG
1 TATCGATACTGACCC-CTGAG
**
13140 TATCGATACTGGGCCCTGAG
1 TATCGATACTGACCCCTGAG
13160 TATCGATAC
1 TATCGATAC
13169 CCCTTTCTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (20 bp):
TATCGATACTGACCCCTGAG
Found at i:13196 original size:21 final size:21
Alignment explanation
Indices: 13157--13196 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13147 ACTGGGCCCT
* *
13157 GAGTATCGATACCCCTTTCTG
1 GAGTATCAATACCCATTTCTG
*
13178 GAGTATCAATACTCATTTC
1 GAGTATCAATACCCATTTC
13197 ATAATTTGCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (21 bp):
GAGTATCAATACCCATTTCTG
Found at i:16253 original size:13 final size:13
Alignment explanation
Indices: 16216--16255 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
16206 CTTTTGAATC
16216 ATTTAACAAAATA
1 ATTTAACAAAATA
*
16229 ATATTAACAAAATT
1 AT-TTAACAAAATA
*
16243 ATTTAATAAAATA
1 ATTTAACAAAATA
16256 GTATCTATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (13 bp):
ATTTAACAAAATA
Found at i:20322 original size:6 final size:6
Alignment explanation
Indices: 20311--20337 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
20301 AGATAAGCAT
20311 ATGGAG ATGGAG ATGGAG ATGGAG ATG
1 ATGGAG ATGGAG ATGGAG ATGGAG ATG
20338 AGAAAATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.48, T:0.19
Consensus pattern (6 bp):
ATGGAG
Found at i:22402 original size:12 final size:12
Alignment explanation
Indices: 22387--22414 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
22377 TTCAATTAGA
22387 ATTTAGAATATT
1 ATTTAGAATATT
22399 ATTTAGAATATT
1 ATTTAGAATATT
22411 ATTT
1 ATTT
22415 TATTTTATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (12 bp):
ATTTAGAATATT
Found at i:23019 original size:18 final size:18
Alignment explanation
Indices: 22977--23019 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
22967 CTTTAGATTA
* *
22977 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATAT
*
22995 TTCATTTAATTATTATAT
1 TTTATTTAATTATTATAT
23013 TTTATTT
1 TTTATTT
23020 TAAAAACAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTTAATTATTATAT
Found at i:23198 original size:40 final size:36
Alignment explanation
Indices: 23145--23263 Score: 100
Period size: 40 Copynumber: 3.1 Consensus size: 36
23135 TTCCCAATTC
23145 TTTTTTATTTTATTTTATTTTTATTTTCTCTTTTAACAT
1 TTTTTTATTTTA-TTTATTTTT-TTTT-TCTTTTAACAT
** *
23184 TTTTTATATTTTA-TTATTTTTCTTTTATGAAATTTAATAT
1 TTTTT-TATTTTATTTATTTTT-TTTT-T--CTTTTAACAT
*
23224 TTTTTTCA-TTTATTTA-ATTTTTTTTCTTTTAACAT
1 TTTTTT-ATTTTATTTATTTTTTTTTTCTTTTAACAT
23259 TTTTT
1 TTTTT
23264 ATATAACATT
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
35 12 0.18
37 1 0.02
38 17 0.26
39 13 0.20
40 23 0.35
ACGTcount: A:0.21, C:0.06, G:0.01, T:0.72
Consensus pattern (36 bp):
TTTTTTATTTTATTTATTTTTTTTTTCTTTTAACAT
Found at i:23245 original size:19 final size:20
Alignment explanation
Indices: 23215--23254 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
23205 CTTTTATGAA
23215 ATTTAATATTTTTTTCATTT
1 ATTTAATATTTTTTTCATTT
*
23235 ATTTAAT-TTTTTTTCTTTT
1 ATTTAATATTTTTTTCATTT
23254 A
1 A
23255 ACATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (20 bp):
ATTTAATATTTTTTTCATTT
Found at i:24869 original size:53 final size:53
Alignment explanation
Indices: 24737--24854 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
24727 CCATCAGGCA
* *
24737 TGTATTGATACCTGTAAACATCGAAGTTAATTTGGGTACCGATACCTCAGTAG
1 TGTATCGATACCTGTAAACATCGAAGTTAATTTGGGTACCGATACCCCAGTAG
24790 TGTATCGATACCTGTAAACATCGAAGTTAATTTGGGTACCGATACCCCAGTAG
1 TGTATCGATACCTGTAAACATCGAAGTTAATTTGGGTACCGATACCCCAGTAG
24843 TGTATCGATACC
1 TGTATCGATACC
24855 GTTTTGAAAG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 63 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (53 bp):
TGTATCGATACCTGTAAACATCGAAGTTAATTTGGGTACCGATACCCCAGTAG
Found at i:25259 original size:59 final size:59
Alignment explanation
Indices: 25187--25361 Score: 314
Period size: 59 Copynumber: 3.0 Consensus size: 59
25177 TTACCAAAGG
*
25187 GCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGA
1 GCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGA
* * *
25246 GCACTTTGTGTGCTAAAATGGTAAGGAAATCATTCTAAGTGTATGAATTTCCAAATAGG
1 GCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGA
25305 GCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATA
1 GCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATA
25362 CTAAAATGGT
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 110 1.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (59 bp):
GCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGA
Found at i:25389 original size:45 final size:45
Alignment explanation
Indices: 25317--25406 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
25307 ACTTTGTGTG
*
25317 CTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATA
1 CTAAAATGGTAAGGAAATCATACTAAGTGTATCAATTTCCAGATA
* * *
25362 CTAAAATGGTAAGGAAATTATAGTAAGTGTTTCAATTTCCAGATA
1 CTAAAATGGTAAGGAAATCATACTAAGTGTATCAATTTCCAGATA
25407 GGGCACTTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (45 bp):
CTAAAATGGTAAGGAAATCATACTAAGTGTATCAATTTCCAGATA
Found at i:29883 original size:13 final size:13
Alignment explanation
Indices: 29865--29907 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
29855 GTCATAACCC
*
29865 GACCCGACCTGTT
1 GACCCGACCCGTT
29878 GACCCGACCCGTT
1 GACCCGACCCGTT
29891 GACCCGACCCGTT
1 GACCCGACCCGTT
29904 GACC
1 GACC
29908 GTTGACCGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.16, C:0.44, G:0.23, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:32473 original size:24 final size:24
Alignment explanation
Indices: 32446--32564 Score: 150
Period size: 24 Copynumber: 5.0 Consensus size: 24
32436 TTCGATTTGA
32446 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
* *
32470 ATTCTAATCTGATA-TCTGAAATGG
1 ATTCTGATCTGATACT-TGACATGG
* *
32494 ATTCTGACCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
32518 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
32542 ATTTTGATATGATACTTGACATG
1 ATTCTGATCTGATACTTGACATG
32565 AATTATGTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 1 0.01
24 81 0.98
25 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.39
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:32743 original size:43 final size:43
Alignment explanation
Indices: 32682--32776 Score: 181
Period size: 43 Copynumber: 2.2 Consensus size: 43
32672 GGGCCTTACT
*
32682 TGGTGTGTTGGTGGGTGTATGGTTCTGGGGAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
32725 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
32768 TGGTGTGTT
1 TGGTGTGTT
32777 CGGTTGGAGG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.16, C:0.11, G:0.37, T:0.37
Consensus pattern (43 bp):
TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
Found at i:36148 original size:53 final size:53
Alignment explanation
Indices: 36082--36199 Score: 193
Period size: 53 Copynumber: 2.2 Consensus size: 53
36072 CCATCAGGCA
*
36082 TGTATCGATACCTGTAAACATCGAAGTTAATTTGGGTACCGATA-CCTCAGTAG
1 TGTATCGATACCTGTAAACATCGAAGTTAATTTGGGTACCAATACCCT-AGTAG
* *
36135 TTTATCGATACCTGTAAACATCGAAGTTAATTTGGGTACTAATACCCTAGTAG
1 TGTATCGATACCTGTAAACATCGAAGTTAATTTGGGTACCAATACCCTAGTAG
36188 TGTATCGATACC
1 TGTATCGATACC
36200 GTTCTGAAGG
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
53 57 0.95
54 3 0.05
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (53 bp):
TGTATCGATACCTGTAAACATCGAAGTTAATTTGGGTACCAATACCCTAGTAG
Found at i:36803 original size:59 final size:59
Alignment explanation
Indices: 36512--36780 Score: 493
Period size: 59 Copynumber: 4.6 Consensus size: 59
36502 AAATTACCAA
*
36512 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
36571 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
36630 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAATTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
36689 AGGGCACTTTGTGTACTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
36748 AGGGCACTTTGTGTGCTAAAATGGAAAGAAAAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAAT
36781 ATTATTGATT
Statistics
Matches: 203, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 203 1.00
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.30
Consensus pattern (59 bp):
AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
Found at i:37856 original size:14 final size:13
Alignment explanation
Indices: 37829--37854 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37819 ATTTCACTAA
37829 CATTTTTTCCTTT
1 CATTTTTTCCTTT
37842 CATTTTTTCCTTT
1 CATTTTTTCCTTT
37855 TCCTTTCATT
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:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (13 bp):
CATTTTTTCCTTT
Found at i:39801 original size:20 final size:20
Alignment explanation
Indices: 39776--39813 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39766 TTCCCCTTGA
39776 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
*
39796 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
39814 TTAATATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:45608 original size:123 final size:123
Alignment explanation
Indices: 45344--45577 Score: 292
Period size: 123 Copynumber: 1.9 Consensus size: 123
45334 GTCAATGTCT
* * * * * * * * *
45344 ACTTCACAGCGAATGATATTAAACTC-GAGCCAATGCAATTTTCATGATTGGATTTCAACTTCAT
1 ACTTCAAAGCGAAAGATATTAATCTCAAAG-CGATTCAATTTACAAGATTGGATTTCAACTTCAC
* * * *
45408 AACGAAGGACATCTAATTCAAAGCTCAACTTCACAGCAAAGGAGCCATCCACAATTTCA
65 AACCAAGGACATCCAATTCAAAACTCAACTTCACAACAAAGGAGCCATCCACAATTTCA
* *
45467 AGTTCAAAGCGAAAGATATTAATCTCAAAGCGATTCAATTTACAAGATTGGATTTCAAGTTCACA
1 ACTTCAAAGCGAAAGATATTAATCTCAAAGCGATTCAATTTACAAGATTGGATTTCAACTTCACA
*
45532 ACCAAGGATATCCAATTCAAAACTCAACTTCACAACGAAA-GAGCCA
66 ACCAAGGACATCCAATTCAAAACTCAACTTCACAAC-AAAGGAGCCA
45578 CCTATGATTT
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
123 88 0.95
124 5 0.05
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (123 bp):
ACTTCAAAGCGAAAGATATTAATCTCAAAGCGATTCAATTTACAAGATTGGATTTCAACTTCACA
ACCAAGGACATCCAATTCAAAACTCAACTTCACAACAAAGGAGCCATCCACAATTTCA
Found at i:46035 original size:270 final size:270
Alignment explanation
Indices: 45547--46149 Score: 901
Period size: 270 Copynumber: 2.2 Consensus size: 270
45537 GGATATCCAA
* * * * *
45547 TTCAAAACTCAACTTCACAACGAAAGAGCCACCTATGATTTCGACTTC-TCAATTAAGGATATCG
1 TTCAAAGCTCAACTTCACAACGAAGGAGCCACCTATGATTTAGACTTCAT-AATGAAGGATATCA
*
45611 TACCCAAAAGATTGACCCAACTTCACGACGAAGGAGTCATCTGTAACACAACAATGAAAAACCAG
65 TACCCAAAAGATTGACCCAACTTCACGACGAAGGAGTCATCTGTAACACAACAATGAAAAACCAA
* *
45676 TTTCATACCAAAGTCTTCAGGTCAAATTTTAGCTTCACGACGAAGTATATTGGGCTAGAAGACGA
130 TTTCATAACAAAGTCTTCAGGTCAAATTTCAGCTTCACGACGAAGTATATTGGGCTAGAAGACGA
* * * **
45741 TCCAGGAGTGACTTTTCAATGCTTTAAGCCCTG-TTTCAACTTCACGACAAATGATATTGTACTC
195 TCCAGGAGTGACTTTCCAATGCTTTAAGCCCAGCTTT-AACTTCACGACAAACGATATCATACTC
45805 AGGATTTTTCAG
259 AGGATTTTTCAG
45817 TTCAAAGCTCAACTTCACAACGAAGGAGCCACCTATGATTTAGACTTCATAATGAAGGATATCAT
1 TTCAAAGCTCAACTTCACAACGAAGGAGCCACCTATGATTTAGACTTCATAATGAAGGATATCAT
* *
45882 ACCCAAAAGATTGACCCAACTTCGCGACGAATGAGTCATCTGTAACACAACAATGAAAAACCAAT
66 ACCCAAAAGATTGACCCAACTTCACGACGAAGGAGTCATCTGTAACACAACAATGAAAAACCAAT
* *
45947 TTCATAACAAAGTTTTCAGGTCAAATTTCAGCTTCACGACGAAGTATATTGGTCTAGAAGACGAT
131 TTCATAACAAAGTCTTCAGGTCAAATTTCAGCTTCACGACGAAGTATATTGGGCTAGAAGACGAT
* * * * *
46012 CTATGAGTGACTTTCCAATGCTTTGAGCCCAGCTTTAACTTCACGACGAACGATATCATGCTCAG
196 CCAGGAGTGACTTTCCAATGCTTTAAGCCCAGCTTTAACTTCACGACAAACGATATCATACTCAG
*
46077 GATTTTTTAG
261 GATTTTTCAG
* *
46087 TTCAAAGCACAACTTCACAACGAAGGAGCCA-CTCACGATTTCA-ACTTCACTAA-GAAGGATAT
1 TTCAAAGCTCAACTTCACAACGAAGGAGCCACCT-ATGATTT-AGACTTCA-TAATGAAGGATAT
46149 C
63 C
46150 GTGCCCAATG
Statistics
Matches: 303, Mismatches: 25, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
269 2 0.01
270 293 0.97
271 8 0.03
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (270 bp):
TTCAAAGCTCAACTTCACAACGAAGGAGCCACCTATGATTTAGACTTCATAATGAAGGATATCAT
ACCCAAAAGATTGACCCAACTTCACGACGAAGGAGTCATCTGTAACACAACAATGAAAAACCAAT
TTCATAACAAAGTCTTCAGGTCAAATTTCAGCTTCACGACGAAGTATATTGGGCTAGAAGACGAT
CCAGGAGTGACTTTCCAATGCTTTAAGCCCAGCTTTAACTTCACGACAAACGATATCATACTCAG
GATTTTTCAG
Found at i:47285 original size:19 final size:19
Alignment explanation
Indices: 47261--47303 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
47251 AGATTATTTA
*
47261 TTTAATTATTTTCTTTCAT
1 TTTAATTATTATCTTTCAT
* *
47280 TTTAATTCTTATCTTTTAT
1 TTTAATTATTATCTTTCAT
47299 TTTAA
1 TTTAA
47304 AAACAACTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTAATTATTATCTTTCAT
Found at i:47446 original size:6 final size:6
Alignment explanation
Indices: 47426--47524 Score: 73
Period size: 6 Copynumber: 16.5 Consensus size: 6
47416 AAATTTAACA
* *
47426 TTTATT TTT-TAT TTTATT TTTATT TTTATT TTTCTA TTTA-- TTTATT
1 TTTATT TTTAT-T TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
* * *
47472 TTTA-T TTT-GT TTTATT TTTATT TTCTCTT TTAATATTT TTTATT TTTCTT
1 TTTATT TTTATT TTTATT TTTATT TT-TATT TT--TA-TT TTTATT TTTATT
47522 TTT
1 TTT
47525 TGAAATTTAA
Statistics
Matches: 76, Mismatches: 8, Indels: 18
0.75 0.08 0.18
Matches are distributed among these distances:
4 4 0.05
5 9 0.12
6 50 0.66
7 8 0.11
8 1 0.01
9 4 0.05
ACGTcount: A:0.15, C:0.04, G:0.01, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:47485 original size:32 final size:32
Alignment explanation
Indices: 47428--47490 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
47418 ATTTAACATT
*
47428 TATTTTTTATTTTATTTTTATTTTTATTTTTC
1 TATTTTTTATTTTATTTTTAGTTTTATTTTTC
47460 TATTTATTTATTTT-TATTTT-GTTTTATTTTT
1 TATTT-TTTATTTTAT-TTTTAGTTTTATTTTT
47491 ATTTTCTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.81
Consensus pattern (32 bp):
TATTTTTTATTTTATTTTTAGTTTTATTTTTC
Found at i:47487 original size:44 final size:44
Alignment explanation
Indices: 47432--47523 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
47422 AACATTTATT
**
47432 TTTTATTTTATTTTTATTTT-TATTTTTCTATTTATTTATTTTTA
1 TTTTATTTTATTTTTATTTTCTATTTTAATATTT-TTTATTTTTA
* * *
47476 TTTTGTTTTATTTTTATTTTCTCTTTTAATATTTTTTATTTTTC
1 TTTTATTTTATTTTTATTTTCTATTTTAATATTTTTTATTTTTA
47520 TTTT
1 TTTT
47524 TTGAAATTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 32 0.76
45 10 0.24
ACGTcount: A:0.15, C:0.04, G:0.01, T:0.79
Consensus pattern (44 bp):
TTTTATTTTATTTTTATTTTCTATTTTAATATTTTTTATTTTTA
Found at i:47518 original size:16 final size:15
Alignment explanation
Indices: 47428--47518 Score: 69
Period size: 16 Copynumber: 5.9 Consensus size: 15
47418 ATTTAACATT
*
47428 TATTTTTTATTTTATT
1 TATTTTTTATTTT-TA
* *
47444 TTTATTTTTATTTTTC
1 TAT-TTTTTATTTTTA
47460 TATTTATTTATTTTTA
1 TATTT-TTTATTTTTA
*
47476 TTTTGTTTTA-TTTT-
1 TATT-TTTTATTTTTA
* * *
47490 TATTTTCTCTTTTAA
1 TATTTTTTATTTTTA
47505 TATTTTTTATTTTT
1 TATTTTTTATTTTT
47519 CTTTTTTGAA
Statistics
Matches: 58, Mismatches: 12, Indels: 11
0.72 0.15 0.14
Matches are distributed among these distances:
13 3 0.05
14 6 0.10
15 17 0.29
16 21 0.36
17 11 0.19
ACGTcount: A:0.16, C:0.03, G:0.01, T:0.79
Consensus pattern (15 bp):
TATTTTTTATTTTTA
Found at i:47593 original size:30 final size:29
Alignment explanation
Indices: 47559--47640 Score: 87
Period size: 31 Copynumber: 2.8 Consensus size: 29
47549 ATTTTTTTTC
* *
47559 TTTAACATTTTTATATAATATTTTTTAAAA
1 TTTAA-ATTTTTATTTGATATTTTTTAAAA
*
47589 TTTAATATTTCCTTCTTTGAT-TTTTTTAAAA
1 TTTAA-ATTT--TTATTTGATATTTTTTAAAA
47620 TTT-AATTTTTATTTGATATTT
1 TTTAAATTTTTATTTGATATTT
47641 CTTTTATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
27 8 0.18
28 3 0.07
29 4 0.09
30 10 0.23
31 13 0.30
32 6 0.14
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.62
Consensus pattern (29 bp):
TTTAAATTTTTATTTGATATTTTTTAAAA
Found at i:49224 original size:9 final size:9
Alignment explanation
Indices: 49201--49232 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
49191 CGAAATATAC
49201 ATATATATT
1 ATATATATT
49210 -TATATATT
1 ATATATATT
49218 ATATATATT
1 ATATATATT
49227 ATATAT
1 ATATAT
49233 GTATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATATATATT
Found at i:50282 original size:2 final size:2
Alignment explanation
Indices: 50273--50314 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
50263 TTTATTACAT
50273 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
50314 T
1 T
50315 TATTCCCTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50607 original size:17 final size:19
Alignment explanation
Indices: 50594--50628 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
50584 ATTTATTTTG
50594 TTTTT-ATTTATATTTATA
1 TTTTTAATTTATATTTATA
50612 TTTTTAATTTAT-TTTAT
1 TTTTTAATTTATATTTAT
50629 TTCTTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTAATTTATATTTATA
Found at i:52445 original size:13 final size:13
Alignment explanation
Indices: 52428--52460 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
52418 TTTCACATTA
52428 TTTTTTCTTTT-T
1 TTTTTTCTTTTCT
52440 TCTTTTTCTTTTCT
1 T-TTTTTCTTTTCT
52454 TTTTTTC
1 TTTTTTC
52461 ATTACATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.05
13 16 0.84
14 2 0.11
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTCTTTTCT
Found at i:54400 original size:64 final size:64
Alignment explanation
Indices: 54296--54718 Score: 677
Period size: 64 Copynumber: 6.6 Consensus size: 64
54286 TGCTGCTTTT
* * * * * * *
54296 AGAGTCAATTTCAACTTCATAGCGAAAGATATTTGTCTCAATAAATAACTTTCCAATTTCATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
*
54360 AGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* *
54424 AGAGTCAATTTCAACTTCATAGCGAAGGATATTAGACTCAACAAACAACTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* *
54488 AGAGTCAATTTCAACTTCACAGCTAAGGATATTGGACTCAACAAACAACTTTCCAGATTCATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
54552 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGA-TACAACAAACAACTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACT-CAACAAACAACTTTCCAGTTTCATTC
* * *
54616 ATAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTACAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
**
54680 AGAGTCAATTTCAACTTCACAATGAAGGATATTGGACTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTC
54719 GAAACAATGC
Statistics
Matches: 335, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
63 1 0.00
64 333 0.99
65 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (64 bp):
AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
Found at i:54886 original size:116 final size:116
Alignment explanation
Indices: 54742--54952 Score: 307
Period size: 116 Copynumber: 1.8 Consensus size: 116
54732 TTACACAAGC
** *
54742 TTGGATTTCAACTTCACGACGAATGATATCAAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
1 TTGGATTTCAACTTCAAAACGAAAGATATCAAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
*
54807 CCACTATTTCA-ACTTCACAACAAAGGATATAATGCCCACAAGCAACATCCA
66 CCACGATTT-AGACTTCACAACAAAGGATATAATGCCCACAAGCAACATCCA
* * * *
54858 TTGGATTTCAACTTCAAAATGAAAGATATCCAATTCAAAGCTCAACTTCACGATGAAGGAGCCAT
1 TTGGATTTCAACTTCAAAACGAAAGATATCAAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
* **
54923 CTACGATTTAGACTTCACAATGAAGGATAT
66 CCACGATTTAGACTTCACAACAAAGGATAT
54953 CATACCCTAA
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
115 1 0.01
116 82 0.99
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (116 bp):
TTGGATTTCAACTTCAAAACGAAAGATATCAAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
CCACGATTTAGACTTCACAACAAAGGATATAATGCCCACAAGCAACATCCA
Found at i:55382 original size:7 final size:7
Alignment explanation
Indices: 55364--55553 Score: 330
Period size: 7 Copynumber: 27.0 Consensus size: 7
55354 AAATATACAC
55364 ATATATTT
1 ATATA-TT
55372 ATATATT
1 ATATATT
55379 ATATATT
1 ATATATT
55386 ATATATT
1 ATATATT
55393 ATATATT
1 ATATATT
55400 ATATATT
1 ATATATT
55407 ATATATT
1 ATATATT
55414 ATATATT
1 ATATATT
55421 ATATATT
1 ATATATT
55428 ATATATT
1 ATATATT
55435 ATATATT
1 ATATATT
55442 ATATATT
1 ATATATT
55449 ATATATT
1 ATATATT
55456 ATATATT
1 ATATATT
55463 ATATATT
1 ATATATT
55470 ATATATT
1 ATATATT
55477 ATATATT
1 ATATATT
55484 ATATATT
1 ATATATT
55491 ATATATT
1 ATATATT
55498 ATATATT
1 ATATATT
55505 ATATATT
1 ATATATT
55512 ATAT-TT
1 ATATATT
55518 ATATATAT
1 ATATAT-T
55526 ATATATAT
1 ATATAT-T
55534 ATATATT
1 ATATATT
*
55541 ATGTATT
1 ATATATT
55548 AT-TATT
1 ATATATT
55554 TTATTAACCA
Statistics
Matches: 179, Mismatches: 1, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
6 10 0.06
7 149 0.83
8 20 0.11
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (7 bp):
ATATATT
Found at i:56845 original size:27 final size:26
Alignment explanation
Indices: 56810--56865 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
56800 TGTCTAATTT
* *
56810 TTTAATTCA-TATTTTTTATTATTTTA
1 TTTAATTCACCATTTCTTATT-TTTTA
56836 TTTAATTTCACCATTTCTTATTTTTTA
1 TTTAA-TTCACCATTTCTTATTTTTTA
56863 TTT
1 TTT
56866 TTGTTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 5 0.19
27 12 0.46
28 9 0.35
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTAATTCACCATTTCTTATTTTTTA
Found at i:61447 original size:26 final size:26
Alignment explanation
Indices: 61395--61447 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
61385 ACGATCTAAT
* *
61395 GTGGCAGTTTCTAGAAGGTTCAGTCA
1 GTGGCAGTTTCTAGAAGATTCACTCA
*
61421 GTGGTAGTTTCTAGAAGA-TCTACTCA
1 GTGGCAGTTTCTAGAAGATTC-ACTCA
61447 G
1 G
61448 CGCGCCTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (26 bp):
GTGGCAGTTTCTAGAAGATTCACTCA
Found at i:64671 original size:21 final size:21
Alignment explanation
Indices: 64645--64696 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
64635 TTTAACTATG
64645 GAATTTGACGGTGAGATAGTT
1 GAATTTGACGGTGAGATAGTT
64666 GAATTTGACGGTGAGATAGTT
1 GAATTTGACGGTGAGATAGTT
*
64687 AAATTTGACG
1 GAATTTGACG
64697 TGTATAAGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.33
Consensus pattern (21 bp):
GAATTTGACGGTGAGATAGTT
Found at i:66963 original size:23 final size:23
Alignment explanation
Indices: 66937--66983 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
66927 GTCACCACAA
*
66937 CACATATAAACGCACCGAAGTGC
1 CACATAGAAACGCACCGAAGTGC
** *
66960 CACATAGAATTGCATCGAAGTGC
1 CACATAGAAACGCACCGAAGTGC
66983 C
1 C
66984 GCGTAGAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (23 bp):
CACATAGAAACGCACCGAAGTGC
Found at i:67006 original size:23 final size:23
Alignment explanation
Indices: 66952--66996 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
66942 ATAAACGCAC
66952 CGAAGTGCCACATAGAATTGCAT
1 CGAAGTGCCACATAGAATTGCAT
* *
66975 CGAAGTGCCGCGTAGAATTGCA
1 CGAAGTGCCACATAGAATTGCA
66997 CTGTAGTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (23 bp):
CGAAGTGCCACATAGAATTGCAT
Found at i:67276 original size:31 final size:30
Alignment explanation
Indices: 67232--67291 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
67222 TATTGTATAG
*
67232 ACATATAATTTCCAT-ACCTTTATCACATAA
1 ACATATAATTTCCATCA-CTTTAACACATAA
*
67262 ACATATCATGTTCCATCACTTTAACACATA
1 ACATATAAT-TTCCATCACTTTAACACATA
67292 GCTTATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 17 0.65
32 1 0.04
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (30 bp):
ACATATAATTTCCATCACTTTAACACATAA
Found at i:67687 original size:45 final size:45
Alignment explanation
Indices: 67634--67735 Score: 125
Period size: 45 Copynumber: 2.3 Consensus size: 45
67624 AATGAAGGTA
* *
67634 TGCATCGATGCATAAATCCTATTCGATGTTTATA-TTTAAAGGGGG
1 TGCATCGATGCATAAATCCTATTCGATGTTTATATTTTAAA-AGAG
** ** *
67679 TGCATCGATGCATTGATGGTATTCGATGTTTGTATTTTAAAAGAG
1 TGCATCGATGCATAAATCCTATTCGATGTTTATATTTTAAAAGAG
67724 TGCATCGATGCA
1 TGCATCGATGCA
67736 CTTCATGTGC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
45 43 0.88
46 6 0.12
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (45 bp):
TGCATCGATGCATAAATCCTATTCGATGTTTATATTTTAAAAGAG
Found at i:73892 original size:23 final size:23
Alignment explanation
Indices: 73834--73884 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
73824 CATATAAACA
73834 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
73857 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
73880 CACCG
1 CACCG
73885 TAGGGCCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.16
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTG
Found at i:74145 original size:30 final size:31
Alignment explanation
Indices: 74111--74174 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
74101 TTTATATTGT
*
74111 ATAAACATATAAT-TTCCAT-ACCTTTATCAC
1 ATAAACATATAATGTTCCATCA-ATTTATCAC
*
74141 ATAAACATATCATGTTCCATCAATTTATCAC
1 ATAAACATATAATGTTCCATCAATTTATCAC
74172 ATA
1 ATA
74175 GCTTATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 12 0.40
31 17 0.57
32 1 0.03
ACGTcount: A:0.41, C:0.22, G:0.02, T:0.36
Consensus pattern (31 bp):
ATAAACATATAATGTTCCATCAATTTATCAC
Found at i:79716 original size:26 final size:26
Alignment explanation
Indices: 79666--79716 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
79656 TCTGATGTGG
* *
79666 CAGTTTCTAGAAGGTCCAGTCAGCGA
1 CAGTTTCTAGAAGATCCACTCAGCGA
* *
79692 CAGTTTCTAGAAGATCTACTTAGCG
1 CAGTTTCTAGAAGATCCACTCAGCG
79717 CGCCTTCTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (26 bp):
CAGTTTCTAGAAGATCCACTCAGCGA
Found at i:79950 original size:19 final size:19
Alignment explanation
Indices: 79926--79967 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
79916 TAAAGCTTTC
*
79926 TTTTTT-ATTTTATTTTTTA
1 TTTTTTCATTTT-TCTTTTA
79945 TTTTTTCATTTTTCTTTTA
1 TTTTTTCATTTTTCTTTTA
79964 TTTT
1 TTTT
79968 CAAGCTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTTCATTTTTCTTTTA
Found at i:103181 original size:7 final size:8
Alignment explanation
Indices: 103164--103188 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
103154 CATTATTTTG
103164 TTTTTATT
1 TTTTTATT
103172 TTTTTATT
1 TTTTTATT
103180 TTTTTATT
1 TTTTTATT
103188 T
1 T
103189 GATATATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTATT
Found at i:105725 original size:19 final size:18
Alignment explanation
Indices: 105701--105752 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
105691 ATTCTACTAT
105701 TTTTAATAAATAAATATAA
1 TTTTAA-AAATAAATATAA
**
105720 TTTTAAAATATATTTATAA
1 TTTTAAAA-ATAAATATAA
105739 TTTTAAAAATAAAT
1 TTTTAAAAATAAAT
105753 TCTGAAATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTTAAAAATAAATATAA
Found at i:111364 original size:21 final size:21
Alignment explanation
Indices: 111338--111393 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
111328 ATTTGCCCCA
111338 AAGGACCTCATGTATATCCCG
1 AAGGACCTCATGTATATCCCG
* * * *
111359 AAGGACCTCGTATATGTTCCG
1 AAGGACCTCATGTATATCCCG
111380 AAGGACCTCATGTA
1 AAGGACCTCATGTA
111394 ACCCTCGACT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (21 bp):
AAGGACCTCATGTATATCCCG
Found at i:114646 original size:12 final size:12
Alignment explanation
Indices: 114615--114652 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
114605 TTATGTAATT
114615 TTATTTATTTTTA
1 TTATTTA-TTTTA
*
114628 GTA-TTATTTTA
1 TTATTTATTTTA
114639 TTATTTATTTTA
1 TTATTTATTTTA
114651 TT
1 TT
114653 TTCTTTCTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 7 0.32
12 13 0.59
13 2 0.09
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (12 bp):
TTATTTATTTTA
Found at i:114652 original size:20 final size:22
Alignment explanation
Indices: 114602--114652 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 22
114592 TTAATTTCTA
114602 ATTTTATGTAATTTTATTTATTT
1 ATTTTAT-TAATTTTATTTATTT
*
114625 -TTAGTATT-ATTTTA-TTATTT
1 ATT-TTATTAATTTTATTTATTT
114645 ATTTTATT
1 ATTTTATT
114653 TTCTTTCTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
20 10 0.42
21 8 0.33
22 3 0.12
23 3 0.12
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (22 bp):
ATTTTATTAATTTTATTTATTT
Found at i:119670 original size:319 final size:325
Alignment explanation
Indices: 119082--119733 Score: 941
Period size: 319 Copynumber: 2.0 Consensus size: 325
119072 AGCTCCATGA
*
119082 TTAATCCACTAGTTTTGTAAGATAAAATTTGTAAATGGTCACTAAATTATGTTAAAATAATCTTT
1 TTAATCCACTAATTTTGTAAGATAAAATTTGTAAATGGTCACTAAATTATGTT--AATAATCTTT
* *
119147 TTAGATATTAAACTTTCAAAAATTATATAATACATATTAAATGGGTGAAGTAAGATATTAAATTA
64 TTAGATATTAAACTTTCAAAAATTATATAATACATA-TAAATGGGTGAAGTAACATACTAAATTA
* * * *
119212 ATAAAATGATCTCATTTACCCCTCAAGTATAAATAAAGTTTTATTTTTTATAATTTTTCAACATT
128 ATAAAATAATCTCATTTAACCCTCAAGTATAAATAAAGTTTCAATTTTTATAATTTTTCAACATT
* * * *
119277 TATAAGTAATAGTTCTAATTTTTTTTAAAAAAATAATAAAAATTAACCATTTATTTTTATACATT
193 TATAAGTAATAATCCTAATTTTTTTT-AAAAAATAATAAAAATTAACAATTTATTTTTATAAATT
*
119342 ATAAAATATTTTCT-AATTTATCACTTTATGAATTTGTTAATTTATC-AATTTATTTTATAA-TT
257 ATAAAATATTTT-TAAATTTATAACTTTATGAATTTGTTAATTTATCAAATTT-TTTTATAATTT
119404 TTTTAT
320 TTTTAT
*
119410 TTAATCCACTAATTTTGTAAGATAAAATTTGTAAATGGTCACTAAATTATGTT-ATAATTTTTTT
1 TTAATCCACTAATTTTGTAAGATAAAATTTGTAAATGGTCACTAAATTATGTTAATAATCTTTTT
* *
119474 AGATATTAAACTTTC-AAAATT-TAT-ATA-ATA-AAATGGGTGTAGTGACATACTAAATTAATA
66 AGATATTAAACTTTCAAAAATTATATAATACATATAAATGGGTGAAGTAACATACTAAATTAATA
* *
119534 AAATAATCTCATTTAACCCTCAATTATAAATAAAGTTTCAATTTTTATAATTTTTCAACATTTCT
131 AAATAATCTCATTTAACCCTCAAGTATAAATAAAGTTTCAATTTTTATAATTTTTCAACATTTAT
** *
119599 AAGTAATAATCCTAAAATATATTTTTT-AAATGTAA-AAAAATTCACAATTTATTTTTA-AAATT
196 AAGTAATAATCCT--AAT-T-TTTTTTAAAAAATAATAAAAATTAACAATTTATTTTTATAAATT
119661 ATAAAATATTTTTAAAATTTATAACTTTATGAATTTGTTAATTTATCAAATTTTTTTATAATTTT
257 ATAAAATATTTTT-AAATTTATAACTTTATGAATTTGTTAATTTATCAAATTTTTTTATAATTTT
119726 TTTAT
321 TTTAT
119731 TTA
1 TTA
119734 GGTATGATTC
Statistics
Matches: 296, Mismatches: 20, Indels: 23
0.87 0.06 0.07
Matches are distributed among these distances:
318 1 0.00
319 112 0.38
320 59 0.20
321 28 0.09
322 4 0.01
323 9 0.03
324 6 0.02
325 25 0.08
328 52 0.18
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.46
Consensus pattern (325 bp):
TTAATCCACTAATTTTGTAAGATAAAATTTGTAAATGGTCACTAAATTATGTTAATAATCTTTTT
AGATATTAAACTTTCAAAAATTATATAATACATATAAATGGGTGAAGTAACATACTAAATTAATA
AAATAATCTCATTTAACCCTCAAGTATAAATAAAGTTTCAATTTTTATAATTTTTCAACATTTAT
AAGTAATAATCCTAATTTTTTTTAAAAAATAATAAAAATTAACAATTTATTTTTATAAATTATAA
AATATTTTTAAATTTATAACTTTATGAATTTGTTAATTTATCAAATTTTTTTATAATTTTTTTAT
Found at i:120189 original size:16 final size:17
Alignment explanation
Indices: 120162--120195 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
120152 GTTTAGTGAT
*
120162 TATTTGTAATTTTATTA
1 TATTTGTAATTTAATTA
120179 TATTT-TAATTTAATTA
1 TATTTGTAATTTAATTA
120195 T
1 T
120196 TAATGAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TATTTGTAATTTAATTA
Found at i:121961 original size:2 final size:2
Alignment explanation
Indices: 121954--122003 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
121944 TTATTAAATA
121954 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
121996 AT AT AT AT
1 AT AT AT AT
122004 GAATGGTGAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.