Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017101.1 Corchorus olitorius cultivar O-4 contig17134, 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: 130255
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6218 original size:46 final size:46
Alignment explanation
Indices: 6151--6243 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
6141 GACCCAATAA
6151 TTTGAATTAAATGAAAATTAAAATCTTAAGCATATTACTAATTTTG
1 TTTGAATTAAATGAAAATTAAAATCTTAAGCATATTACTAATTTTG
6197 TTTGAATTAAATGAAAATTAAAATCTTAAGCATATTACTAATTTTG
1 TTTGAATTAAATGAAAATTAAAATCTTAAGCATATTACTAATTTTG
6243 T
1 T
6244 CCTAAAGAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (46 bp):
TTTGAATTAAATGAAAATTAAAATCTTAAGCATATTACTAATTTTG
Found at i:6449 original size:16 final size:16
Alignment explanation
Indices: 6408--6451 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
6398 ACTTGAAACG
6408 ACCTGAACCCAAAATA
1 ACCTGAACCCAAAATA
* * *
6424 ACCCGGACCCAAAATT
1 ACCTGAACCCAAAATA
*
6440 ACTTGAACCCAA
1 ACCTGAACCCAA
6452 TCAACCCGAG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.43, C:0.34, G:0.09, T:0.14
Consensus pattern (16 bp):
ACCTGAACCCAAAATA
Found at i:19014 original size:33 final size:34
Alignment explanation
Indices: 18976--19052 Score: 90
Period size: 33 Copynumber: 2.3 Consensus size: 34
18966 CGGGCTTGCT
* *
18976 TGCTGATGTCGT-GTGCTGGTGCGC-GCGATGG-C
1 TGCTGATGTCCTGGTGCTGATGCGCAGC-ATGGCC
19008 TGGCTGATG-CCTGGTGCTGATGCGCAGCATGGCC
1 T-GCTGATGTCCTGGTGCTGATGCGCAGCATGGCC
19042 TGCTGATGTCC
1 TGCTGATGTCC
19053 GGCCTTTGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
32 3 0.08
33 29 0.76
34 6 0.16
ACGTcount: A:0.09, C:0.25, G:0.39, T:0.27
Consensus pattern (34 bp):
TGCTGATGTCCTGGTGCTGATGCGCAGCATGGCC
Found at i:24443 original size:16 final size:17
Alignment explanation
Indices: 24417--24448 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
24407 AGTGCAAATT
24417 AAAATAGAAAAATAAAG
1 AAAATAGAAAAATAAAG
24434 AAAA-AGAAAAATAAA
1 AAAATAGAAAAATAAA
24449 ACGCAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAATAGAAAAATAAAG
Found at i:33839 original size:23 final size:22
Alignment explanation
Indices: 33789--33829 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
33779 AGAATCATAA
33789 TAAC-ATAACAAGATTTTTTAG
1 TAACAATAACAAGATTTTTTAG
33810 TAACAATAACAAGATTTTTT
1 TAACAATAACAAGATTTTTT
33830 GGTCCACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (22 bp):
TAACAATAACAAGATTTTTTAG
Found at i:36143 original size:18 final size:18
Alignment explanation
Indices: 36122--36174 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
36112 CCAGCACCGC
36122 TACCACTTGCACCCCCAT
1 TACCACTTGCACCCCCAT
*
36140 TACCA---GCA-CCGC--
1 TACCACTTGCACCCCCAT
36152 TACCACTTGCACCCCCAT
1 TACCACTTGCACCCCCAT
36170 TACCA
1 TACCA
36175 GCACCGCTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
12 5 0.19
14 3 0.11
15 6 0.22
16 3 0.11
18 10 0.37
ACGTcount: A:0.25, C:0.49, G:0.08, T:0.19
Consensus pattern (18 bp):
TACCACTTGCACCCCCAT
Found at i:36144 original size:30 final size:30
Alignment explanation
Indices: 36110--36302 Score: 185
Period size: 30 Copynumber: 6.8 Consensus size: 30
36100 CCTCCACCAG
36110 TACCAGCACCGCTACCACTTGCACCCCCAT
1 TACCAGCACCGCTACCACTTGCACCCCCAT
36140 TACCAGCACCGCTACCACTTGCACCCCCAT
1 TACCAGCACCGCTACCACTTGCACCCCCAT
* *
36170 TACCAGCACCGCTACCGCTTGCACCACC--
1 TACCAGCACCGCTACCACTTGCACCCCCAT
* * ** *
36198 -GCCAACA-C-C-ACCAGATGCACCCGCAT
1 TACCAGCACCGCTACCACTTGCACCCCCAT
* *
36224 TACCAGCACCGCTACCGCTTGCACCACC--
1 TACCAGCACCGCTACCACTTGCACCCCCAT
* * **
36252 -GCCAGCA-C-C-ACCAGTTGCACCTGCAT
1 TACCAGCACCGCTACCACTTGCACCCCCAT
36278 TACCAGCACCGCTACCACTTGCACC
1 TACCAGCACCGCTACCACTTGCACC
36303 ACCACCAACA
Statistics
Matches: 128, Mismatches: 23, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
24 21 0.16
25 2 0.02
26 2 0.02
27 22 0.17
28 2 0.02
29 2 0.02
30 77 0.60
ACGTcount: A:0.24, C:0.48, G:0.13, T:0.15
Consensus pattern (30 bp):
TACCAGCACCGCTACCACTTGCACCCCCAT
Found at i:36301 original size:84 final size:84
Alignment explanation
Indices: 36110--36302 Score: 185
Period size: 84 Copynumber: 2.3 Consensus size: 84
36100 CCTCCACCAG
* **
36110 TACCAGCACCGCTACCACTTGCACCCCCATTACCAGCACCGCTACCACTTGCACCCCCATTACCA
1 TACCAGCACCGCTACCACTTGCACCCCCATTACCAGCACCGCTACCACTTGCACCACCACCACCA
*
36175 GCACCGCTACCGCTTGCAC
66 CCACCGCTACCGCTTGCAC
* * * * ** * * * *
36194 CACC-GCCAACACCACCAGATGCACCCGCATTACCAGCACCGCTACCGCTTGCACCACCGCCAGC
1 TACCAG-CACCGCTACCACTTGCACCCCCATTACCAGCACCGCTACCACTTGCACCACCACCACC
* * *
36258 ACCACCAGTTGCAC-C-TGCAT
65 ACCACC-GCTAC-CGCTTGCAC
36278 TACCAGCACCGCTACCACTTGCACC
1 TACCAGCACCGCTACCACTTGCACC
36303 ACCACCAACA
Statistics
Matches: 82, Mismatches: 23, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
83 1 0.01
84 75 0.91
85 5 0.06
86 1 0.01
ACGTcount: A:0.24, C:0.48, G:0.13, T:0.15
Consensus pattern (84 bp):
TACCAGCACCGCTACCACTTGCACCCCCATTACCAGCACCGCTACCACTTGCACCACCACCACCA
CCACCGCTACCGCTTGCAC
Found at i:36324 original size:54 final size:54
Alignment explanation
Indices: 36110--36341 Score: 268
Period size: 54 Copynumber: 4.2 Consensus size: 54
36100 CCTCCACCAG
* * * *
36110 TACCAGCACCGCTACCACTTGCACCCCCATTACCAGCACCGCTACCACTTGCACCCCCAT
1 TACCAGCACCGCTACCACTTGCACCACC---ACCAACA-C-C-ACCAGTTGCACCCGCAT
* * *
36170 TACCAGCACCGCTACCGCTTGCACCACCGCCAACACCACCAGATGCACCCGCAT
1 TACCAGCACCGCTACCACTTGCACCACCACCAACACCACCAGTTGCACCCGCAT
* * * *
36224 TACCAGCACCGCTACCGCTTGCACCACCGCCAGCACCACCAGTTGCACCTGCAT
1 TACCAGCACCGCTACCACTTGCACCACCACCAACACCACCAGTTGCACCCGCAT
* **
36278 TACCAGCACCGCTACCACTTGCACCACCACCAACACCACC-GCTTGCACCTGCGC
1 TACCAGCACCGCTACCACTTGCACCACCACCAACACCACCAG-TTGCACCCGCAT
36332 TACCAGCACC
1 TACCAGCACC
36342 ACCACTAGGA
Statistics
Matches: 156, Mismatches: 15, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
53 1 0.01
54 122 0.78
55 1 0.01
56 1 0.01
57 5 0.03
60 26 0.17
ACGTcount: A:0.24, C:0.49, G:0.13, T:0.14
Consensus pattern (54 bp):
TACCAGCACCGCTACCACTTGCACCACCACCAACACCACCAGTTGCACCCGCAT
Found at i:36345 original size:30 final size:28
Alignment explanation
Indices: 36110--36346 Score: 86
Period size: 30 Copynumber: 8.5 Consensus size: 28
36100 CCTCCACCAG
* * * *
36110 TACCAGCACCGCTACCACTTGCACCCCC
1 TACCAGCACCACCACCGCTTGCACCACC
* * * *
36138 ATTACCAGCACCGCTACCACTTGCACCCCC
1 --TACCAGCACCACCACCGCTTGCACCACC
* *
36168 ATTACCAGCACCGCTACCGCTTGCACCACC
1 --TACCAGCACCACCACCGCTTGCACCACC
* * *
36198 -GCCAACACCACCA--G-ATGCACC-CGC
1 TACCAGCACCACCACCGCTTGCACCAC-C
* *
36222 ATTACCAGCACCGCTACCGCTTGCACCACC
1 --TACCAGCACCACCACCGCTTGCACCACC
* * *
36252 -GCCAGCACCACCA--G-TTGCACCTGCAT
1 TACCAGCACCACCACCGCTTGCACC-AC-C
* * *
36278 TACCAGCACCGCTACCACTTGCACCACC
1 TACCAGCACCACCACCGCTTGCACCACC
*
36306 -ACCA--A-CACCACCGCTTGCACCTGCGC
1 TACCAGCACCACCACCGCTTGCACC-AC-C
36332 TACCAGCACCACCAC
1 TACCAGCACCACCAC
36347 TAGGAGTAGG
Statistics
Matches: 160, Mismatches: 27, Indels: 40
0.70 0.12 0.18
Matches are distributed among these distances:
23 1 0.01
24 27 0.17
25 5 0.03
26 1 0.01
27 46 0.29
29 3 0.02
30 76 0.47
31 1 0.01
ACGTcount: A:0.24, C:0.49, G:0.13, T:0.14
Consensus pattern (28 bp):
TACCAGCACCACCACCGCTTGCACCACC
Found at i:36370 original size:27 final size:27
Alignment explanation
Indices: 36340--36444 Score: 141
Period size: 27 Copynumber: 4.1 Consensus size: 27
36330 GCTACCAGCA
*
36340 CCACCACTAGGAGTAGGAGTAGCACCG
1 CCACCACTAGGAGTAGGAGTAGCACTG
36367 CCACCACTAGGAGTAGGAGTAGCACTG
1 CCACCACTAGGAGTAGGAGTAGCACTG
*
36394 ----C-C-AGGGGTAGGAGTAGCACTG
1 CCACCACTAGGAGTAGGAGTAGCACTG
*
36415 CCGCCACTAGGAGTAGGAGTAGCACTG
1 CCACCACTAGGAGTAGGAGTAGCACTG
36442 CCA
1 CCA
36445 GGAGTAGGAG
Statistics
Matches: 68, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
21 18 0.26
22 1 0.01
23 1 0.01
25 1 0.01
26 1 0.01
27 46 0.68
ACGTcount: A:0.28, C:0.27, G:0.32, T:0.13
Consensus pattern (27 bp):
CCACCACTAGGAGTAGGAGTAGCACTG
Found at i:36403 original size:21 final size:21
Alignment explanation
Indices: 36375--36487 Score: 127
Period size: 21 Copynumber: 5.1 Consensus size: 21
36365 CGCCACCACT
36375 AGGAGTAGGAGTAGCACTGCC
1 AGGAGTAGGAGTAGCACTGCC
*
36396 AGGGGTAGGAGTAGCACTGCCGCCAC
1 AGGAGTAGGAGTAGCACT---G-C-C
36422 TAGGAGTAGGAGTAGCACTGCC
1 -AGGAGTAGGAGTAGCACTGCC
*
36444 AGGAGTAGGAGTAGCACCGCC
1 AGGAGTAGGAGTAGCACTGCC
* * *
36465 AGGAGTGGGAGTAGAACCGCC
1 AGGAGTAGGAGTAGCACTGCC
36486 AG
1 AG
36488 TGACAGCACC
Statistics
Matches: 81, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
21 58 0.72
22 1 0.01
23 1 0.01
24 2 0.02
25 1 0.01
26 1 0.01
27 17 0.21
ACGTcount: A:0.27, C:0.21, G:0.39, T:0.12
Consensus pattern (21 bp):
AGGAGTAGGAGTAGCACTGCC
Found at i:36404 original size:48 final size:48
Alignment explanation
Indices: 36348--36465 Score: 209
Period size: 48 Copynumber: 2.5 Consensus size: 48
36338 CACCACCACT
36348 AGGAGTAGGAGTAGCACCGCCACCACTAGGAGTAGGAGTAGCACTGCC
1 AGGAGTAGGAGTAGCACCGCCACCACTAGGAGTAGGAGTAGCACTGCC
* * *
36396 AGGGGTAGGAGTAGCACTGCCGCCACTAGGAGTAGGAGTAGCACTGCC
1 AGGAGTAGGAGTAGCACCGCCACCACTAGGAGTAGGAGTAGCACTGCC
36444 AGGAGTAGGAGTAGCACCGCCA
1 AGGAGTAGGAGTAGCACCGCCA
36466 GGAGTGGGAG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 64 1.00
ACGTcount: A:0.28, C:0.24, G:0.36, T:0.13
Consensus pattern (48 bp):
AGGAGTAGGAGTAGCACCGCCACCACTAGGAGTAGGAGTAGCACTGCC
Found at i:36478 original size:27 final size:24
Alignment explanation
Indices: 36343--36465 Score: 123
Period size: 27 Copynumber: 5.1 Consensus size: 24
36333 ACCAGCACCA
*
36343 CCACTAGGAGTAGGAGTAGCACCG
1 CCACTAGGAGTAGGAGTAGCACTG
36367 CCACCACTAGGAGTAGGAGTAGCACTG
1 ---CCACTAGGAGTAGGAGTAGCACTG
*
36394 -C-C-AGGGGTAGGAGTAGCACTGCCG
1 CCACTAGGAGTAGGAGTAGCACT---G
36418 CCACTAGGAGTAGGAGTAGCACTG
1 CCACTAGGAGTAGGAGTAGCACTG
*
36442 -C-C-AGGAGTAGGAGTAGCACCG
1 CCACTAGGAGTAGGAGTAGCACTG
36463 CCA
1 CCA
36466 GGAGTGGGAG
Statistics
Matches: 84, Mismatches: 4, Indels: 20
0.78 0.04 0.19
Matches are distributed among these distances:
21 35 0.42
22 3 0.04
23 2 0.02
24 2 0.02
25 1 0.01
26 1 0.01
27 40 0.48
ACGTcount: A:0.28, C:0.25, G:0.34, T:0.13
Consensus pattern (24 bp):
CCACTAGGAGTAGGAGTAGCACTG
Found at i:48202 original size:1 final size:1
Alignment explanation
Indices: 48196--48237 Score: 75
Period size: 1 Copynumber: 42.0 Consensus size: 1
48186 ACATTTATTT
*
48196 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
48238 GAAGAAGAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.98, C:0.00, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:48238 original size:6 final size:6
Alignment explanation
Indices: 48196--48275 Score: 62
Period size: 6 Copynumber: 14.2 Consensus size: 6
48186 ACATTTATTT
*
48196 AAAAA- AAAAA- AAAAA- AAAAA- AAAAA- AAAAAA AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* * * * * *
48239 AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
48276 TAGAGAGAGA
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
5 25 0.35
6 47 0.65
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:48242 original size:3 final size:3
Alignment explanation
Indices: 48230--48275 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
48220 AAAAAAAAAA
*
48230 AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
48276 TAGAGAGAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:54826 original size:121 final size:126
Alignment explanation
Indices: 54680--54928 Score: 366
Period size: 121 Copynumber: 2.0 Consensus size: 126
54670 CATTGTTTAA
* *
54680 ACTTTTATAGTTTCACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT-CTT-TA-T
1 ACTTTTACAGTTTCACTCAACTAAAAACTCTATTTTGATTTAATTAAATCTAATATCCTTATACT
*
54742 A-ATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATAT-T-AGAATTTTTTAAATAT
66 ATATTTTTACCATTTTAATATTTTAATT-AAAAACTTATATATATAAGAATTTTTTAAATAT
* *
54801 ACTTTTACAGTTTTATTCAACTAAAAACTCTATTTTGATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTCACTCAACTAAAAACTCTATTTTGATTTAATTAAATCTAATATCCTTATA-C
54866 TATTTTATTTTTACCATTTTAATATTTTAATTAAAAACTTATATATATAAGAATTTTTTAAAT
65 TA---TATTTTTACCATTTTAATATTTTAATTAAAAACTTATATATATAAGAATTTTTTAAAT
54929 TTATTTCTTA
Statistics
Matches: 113, Mismatches: 5, Indels: 11
0.88 0.04 0.09
Matches are distributed among these distances:
121 52 0.46
122 3 0.03
123 2 0.02
125 2 0.02
128 14 0.12
129 26 0.23
130 14 0.12
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (126 bp):
ACTTTTACAGTTTCACTCAACTAAAAACTCTATTTTGATTTAATTAAATCTAATATCCTTATACT
ATATTTTTACCATTTTAATATTTTAATTAAAAACTTATATATATAAGAATTTTTTAAATAT
Found at i:55222 original size:15 final size:15
Alignment explanation
Indices: 55177--55223 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
55167 CTCATCATTT
55177 TTTAAAAC-TAATTAA
1 TTTAAAACTTAATT-A
* * *
55192 GTTAAAATTTATTTA
1 TTTAAAACTTAATTA
55207 TTTAAAACTTAATTA
1 TTTAAAACTTAATTA
55222 TT
1 TT
55224 GTGATTAACC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (15 bp):
TTTAAAACTTAATTA
Found at i:60449 original size:5 final size:5
Alignment explanation
Indices: 60439--60467 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
60429 CAAGTATTGG
60439 AGATT AGATT AGATT AGATT AGATT AGAT
1 AGATT AGATT AGATT AGATT AGATT AGAT
60468 CCCAGTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (5 bp):
AGATT
Found at i:61381 original size:23 final size:25
Alignment explanation
Indices: 61340--61385 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
61330 TTCTGGGTTT
*
61340 TTTTTTTTTCAATTATCTTTTTAGA
1 TTTTCTTTTCAATTATCTTTTTAGA
61365 TTTTCTTTT-AATT-TCTTTTTA
1 TTTTCTTTTCAATTATCTTTTTA
61386 TCTTTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 4 0.20
25 8 0.40
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (25 bp):
TTTTCTTTTCAATTATCTTTTTAGA
Found at i:61902 original size:29 final size:29
Alignment explanation
Indices: 61860--61920 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
61850 AATCTAGACT
61860 AAATCACATAGATAATCATATATTTATTC
1 AAATCACATAGATAATCATATATTTATTC
61889 AAATCACATAGATAATCATATATTTATTC
1 AAATCACATAGATAATCATATATTTATTC
61918 AAA
1 AAA
61921 AACTCTACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.36
Consensus pattern (29 bp):
AAATCACATAGATAATCATATATTTATTC
Found at i:62045 original size:22 final size:22
Alignment explanation
Indices: 62017--62083 Score: 118
Period size: 22 Copynumber: 3.1 Consensus size: 22
62007 AAATCGTATC
62017 TTAATTATTAAGGTCCTTAATT
1 TTAATTATTAAGGTCCTTAATT
62039 TTAATTATTAAGGTCCTTAATT
1 TTAATTATTAAGGTCCTTAATT
*
62061 TT-TTTATTAAGGTCCTTAATT
1 TTAATTATTAAGGTCCTTAATT
62082 TT
1 TT
62084 TTTAAAAGGA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
21 20 0.45
22 24 0.55
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (22 bp):
TTAATTATTAAGGTCCTTAATT
Found at i:62069 original size:21 final size:21
Alignment explanation
Indices: 62021--62087 Score: 116
Period size: 21 Copynumber: 3.1 Consensus size: 21
62011 CGTATCTTAA
*
62021 TTATTAAGGTCCTTAATTTTAA
1 TTATTAAGGTCCTTAATTTT-T
62043 TTATTAAGGTCCTTAATTTTT
1 TTATTAAGGTCCTTAATTTTT
62064 TTATTAAGGTCCTTAATTTTT
1 TTATTAAGGTCCTTAATTTTT
62085 TTA
1 TTA
62088 AAAGGAAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
21 24 0.55
22 20 0.45
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.55
Consensus pattern (21 bp):
TTATTAAGGTCCTTAATTTTT
Found at i:62132 original size:1 final size:1
Alignment explanation
Indices: 62126--62155 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
62116 CAGTCAACAG
62126 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
62156 AAACCCCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:70650 original size:11 final size:11
Alignment explanation
Indices: 70630--70658 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
70620 ATTATACCAT
70630 AAAATA-ATAA
1 AAAATACATAA
70640 AAAATACATAA
1 AAAATACATAA
70651 AAAATACA
1 AAAATACA
70659 ATGAAATCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATACATAA
Found at i:72205 original size:182 final size:176
Alignment explanation
Indices: 71840--72382 Score: 596
Period size: 180 Copynumber: 3.0 Consensus size: 176
71830 TGTTTGTTGG
* * *
71840 TGGATAATGGATCTAAGAATAGTGTTTTTCCCAAAGTTCCTAAATGCTCTCG-TCTATCCATTCA
1 TGGATAATGGATCCAAGAATAATGTTTTTCCCAAAGTTCCTAAATGCCCTCGAT-TATCCATT-A
* *
71904 AATAACAAAAAAACCAAGCATAAAATGACCCAAATATTCCTCCCCATTTGTCTTTGGATCAATGT
64 AA-AA-AAAAAAA-CAAGCATAAAATGACCCAAATATCCCTCCCAATTTGTCTTTGGATCAATGT
* *
71969 GGTGAGATTTCTTAAATGGTTTTTTCGGTACTTTTACTTGTATATTTTAGA
126 AGTGAGATTTCTCAAATGGTTTTTTCGGTACTTTTACTTGTATATTTTAGA
* *
72020 TGGATAATGGATCCAGGAATAATGTTTTTCCCAAAGTTCCTAAATACCCTCGATTATCCATT-AA
1 TGGATAATGGATCCAAGAATAATGTTTTTCCCAAAGTTCCTAAATGCCCTCGATTATCCATTAAA
* * *
72084 GAAAAAAAA-AAGCATAAAATGACCCAAATATCCCTCCCAATTTATTTTTGGATGATTGAATCAA
66 AAAAAAAAACAAGCATAAAATGACCCAAATATCCCTCCCAATTT-GTCTT---TG---G-ATCAA
* * * *
72148 TGTAGTTAGATTTCTCAAATGTTTTTTTTGGTACTTTTATTTGTATATTTTAGA
123 TGTAGTGAGATTTCTCAAATGGTTTTTTCGGTACTTTTACTTGTATATTTTAGA
* * * * *
72202 TGGATAATGGAT-CAAAAATAATGTTTTTCCCAAAGTTTCTAAATGCCCTTGACTATCTATTCAA
1 TGGATAATGGATCCAAGAATAATGTTTTTCCCAAAGTTCCTAAATGCCCTCGATTATCCATT-AA
* * * *
72266 ATAACCAAAAAATCAAACATAAAATGACCCAAATATCCCTTTCC-ATTTGT-TCTTAGATCAATG
65 A-AA--AAAAAAACAAGCATAAAATGACCCAAATATCCC-TCCCAATTTGTCT-TTGGATCAATG
* **
72329 TGGTGAGATTTCTCAAATGGTTTTTT-TATACTTTTACTTGTATATATTTTAGA
125 TAGTGAGATTTCTCAAATGGTTTTTTCGGTACTTTTACTTG--TATATTTTAGA
72382 T
1 T
72383 ATTGTTACAA
Statistics
Matches: 309, Mismatches: 35, Indels: 38
0.81 0.09 0.10
Matches are distributed among these distances:
174 32 0.10
175 3 0.01
176 7 0.02
177 1 0.00
178 15 0.05
179 30 0.10
180 68 0.22
181 44 0.14
182 65 0.21
183 3 0.01
184 1 0.00
185 1 0.00
186 8 0.03
187 28 0.09
188 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (176 bp):
TGGATAATGGATCCAAGAATAATGTTTTTCCCAAAGTTCCTAAATGCCCTCGATTATCCATTAAA
AAAAAAAAACAAGCATAAAATGACCCAAATATCCCTCCCAATTTGTCTTTGGATCAATGTAGTGA
GATTTCTCAAATGGTTTTTTCGGTACTTTTACTTGTATATTTTAGA
Found at i:90043 original size:6 final size:6
Alignment explanation
Indices: 90032--90077 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
90022 AAGATTGATA
90032 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCT
90078 TTTGAGCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (6 bp):
ATCTAT
Found at i:93870 original size:22 final size:22
Alignment explanation
Indices: 93843--94033 Score: 116
Period size: 22 Copynumber: 8.7 Consensus size: 22
93833 TGACAATCAA
* *
93843 ACCAAAATTACATAGAAAGATT
1 ACCAAAATTTCATAGAAAGGTT
* ***
93865 ATCAAAATTTCATAGTGTGGTT
1 ACCAAAATTTCATAGAAAGGTT
* * *
93887 ACCAAAATTTCACATAGAGGTT
1 ACCAAAATTTCATAGAAAGGTT
* * **
93909 ATCAAAACTTCATAGTGTA-GTT
1 ACCAAAATTTCATAG-AAAGGTT
* * * *
93931 ATCAAAATTTCATACAGAGATT
1 ACCAAAATTTCATAGAAAGGTT
*
93953 ACCAAAATTTCATAAAAAGGTT
1 ACCAAAATTTCATAGAAAGGTT
* ** *
93975 ACCAAAATTTCTTAGGGATGTT
1 ACCAAAATTTCATAGAAAGGTT
**
93997 AATAAAATTTCATATGAAA-GTT
1 ACCAAAATTTCATA-GAAAGGTT
* *
94019 AACAAAATTACATAG
1 ACCAAAATTTCATAG
94034 GGAGGGAGGT
Statistics
Matches: 128, Mismatches: 38, Indels: 7
0.74 0.22 0.04
Matches are distributed among these distances:
21 2 0.02
22 123 0.96
23 3 0.02
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (22 bp):
ACCAAAATTTCATAGAAAGGTT
Found at i:93893 original size:44 final size:43
Alignment explanation
Indices: 93843--93966 Score: 142
Period size: 44 Copynumber: 2.8 Consensus size: 43
93833 TGACAATCAA
*
93843 ACCAAAATTACATAGAAAGATTATCAAAATTTCATAGTGTGGTT
1 ACCAAAATTACATAG-AAGATTATCAAAATTTCATAGTGTAGTT
* *
93887 ACCAAAATTTCACATAG-AGGTTATCAAAACTTCATAGTGTAGTT
1 ACCAAAA-TT-ACATAGAAGATTATCAAAATTTCATAGTGTAGTT
* * * *
93931 ATCAAAATTTCATACAGAGATTACCAAAATTTCATA
1 ACCAAAATTACATAGA-AGATTATCAAAATTTCATA
93967 AAAAGGTTAC
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
42 4 0.06
43 2 0.03
44 53 0.79
45 2 0.03
46 6 0.09
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (43 bp):
ACCAAAATTACATAGAAGATTATCAAAATTTCATAGTGTAGTT
Found at i:94004 original size:66 final size:66
Alignment explanation
Indices: 93863--94010 Score: 165
Period size: 66 Copynumber: 2.2 Consensus size: 66
93853 CATAGAAAGA
** * * * * * *
93863 TTATCAAAATTTCATAGTGTGGTTACCAAAATTTCACATAGAGGTTATCAAAACTTCATAGTGTA
1 TTATCAAAATTTCATACAGAGATTACCAAAATTTCACAAAAAGGTTACCAAAACTTCATAGGGTA
93928 G
66 G
* * *
93929 TTATCAAAATTTCATACAGAGATTACCAAAATTTCATAAAAAGGTTACCAAAATTTCTTAGGG-A
1 TTATCAAAATTTCATACAGAGATTACCAAAATTTCACAAAAAGGTTACCAAAACTTCATAGGGTA
93993 TG
66 -G
93995 TTAAT-AAAATTTCATA
1 TT-ATCAAAATTTCATA
94011 TGAAAGTTAA
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
65 1 0.01
66 66 0.96
67 2 0.03
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (66 bp):
TTATCAAAATTTCATACAGAGATTACCAAAATTTCACAAAAAGGTTACCAAAACTTCATAGGGTA
G
Found at i:94098 original size:22 final size:22
Alignment explanation
Indices: 94073--94114 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
94063 CAAAACTTCC
94073 TAGGGAGGTTAACAAAATTTAA
1 TAGGGAGGTTAACAAAATTTAA
* **
94095 TAGGTAGGTTATGAAAATTT
1 TAGGGAGGTTAACAAAATTT
94115 TATGGAGAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.33
Consensus pattern (22 bp):
TAGGGAGGTTAACAAAATTTAA
Found at i:94198 original size:22 final size:21
Alignment explanation
Indices: 94173--94407 Score: 121
Period size: 22 Copynumber: 10.7 Consensus size: 21
94163 CTCATAGGAA
*
94173 GGTTATCGAAATTTCATGATGT
1 GGTTATCAAAATTTCAT-ATGT
*
94195 GGTTATCAAAATTTTCATATGC
1 GGTTATCAAAA-TTTCATATGT
* * *
94217 GGTTA-CCAATTTTAATTAGTGT
1 GGTTATCAAAATTTCA-TA-TGT
* * * * *
94239 GATTATTAAAATTTTATAGGCA
1 GGTTATCAAAATTTCATATG-T
* * *
94261 GATTATCAAAATTTCACACTGA
1 GGTTATCAAAATTTCATA-TGT
* *
94283 GGTTATCGAAATTTCATTGTGT
1 GGTTATCAAAATTTCA-TATGT
* * *
94305 GGTTACCAAAATTACACAGTGT
1 GGTTATCAAAATTTCATA-TGT
* * * *
94327 GGTTATCATATTTTCATAGGGA
1 GGTTATCAAAATTTCATA-TGT
* *
94349 GGTTATCGAAATTTCATAATGA
1 GGTTATCAAAATTTCAT-ATGT
* *
94371 GGTTATCAAATTTTCAAAATGT
1 GGTTATCAAAATTTC-ATATGT
*
94393 GGTTATCAATATTTC
1 GGTTATCAAAATTTC
94408 TACATTGTAG
Statistics
Matches: 159, Mismatches: 44, Indels: 20
0.71 0.20 0.09
Matches are distributed among these distances:
20 4 0.03
21 6 0.04
22 134 0.84
23 15 0.09
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (21 bp):
GGTTATCAAAATTTCATATGT
Found at i:94333 original size:66 final size:66
Alignment explanation
Indices: 94263--94407 Score: 164
Period size: 66 Copynumber: 2.2 Consensus size: 66
94253 TATAGGCAGA
* ** * * *
94263 TTATCAAAATTTCACACTGAGGTTATCGAAATTTCATTGTGTGGTTACCAAAATTACACAGTGTG
1 TTATCAAAATTTCACACGGAGGTTATCGAAATTTCATAATGAGGTTACCAAAATTACAAAATGTG
94328 G
66 G
* * * * * * *
94329 TTATCATATTTTCATAGGGAGGTTATCGAAATTTCATAATGAGGTTATCAAATTTTCAAAATGTG
1 TTATCAAAATTTCACACGGAGGTTATCGAAATTTCATAATGAGGTTACCAAAATTACAAAATGTG
94394 G
66 G
*
94395 TTATCAATATTTC
1 TTATCAAAATTTC
94408 TACATTGTAG
Statistics
Matches: 63, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (66 bp):
TTATCAAAATTTCACACGGAGGTTATCGAAATTTCATAATGAGGTTACCAAAATTACAAAATGTG
G
Found at i:94385 original size:44 final size:44
Alignment explanation
Indices: 94164--94386 Score: 148
Period size: 44 Copynumber: 5.1 Consensus size: 44
94154 AATTTCATTC
* * *
94164 TCATAGGAAGGTTATCGAAATTTCATGATGTGGTTATCAAAATTT
1 TCATAGGGAGGTTATCAAAATTTCATAATGTGGTTATC-AAATTT
* * * * * * * *
94209 TCATA-TGCGGTTA-CCAATTTTAATTAGTGTGATTATTAAAATTT
1 TCATAGGGAGGTTATCAAAATTTCA-TAATGTGGTTA-TCAAATTT
* * * * *
94253 T-ATAGGCAGATTATCAAAATTTCACACTGAGGTTATCGAAA-TT
1 TCATAGGGAGGTTATCAAAATTTCATAATGTGGTTATC-AAATTT
* * * * * * * *
94296 TCATTGTGTGGTTACCAAAATTACACAGTGTGGTTATCATATTT
1 TCATAGGGAGGTTATCAAAATTTCATAATGTGGTTATCAAATTT
* *
94340 TCATAGGGAGGTTATCGAAATTTCATAATGAGGTTATCAAATTT
1 TCATAGGGAGGTTATCAAAATTTCATAATGTGGTTATCAAATTT
94384 TCA
1 TCA
94387 AAATGTGGTT
Statistics
Matches: 129, Mismatches: 42, Indels: 15
0.69 0.23 0.08
Matches are distributed among these distances:
43 16 0.12
44 100 0.78
45 13 0.10
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (44 bp):
TCATAGGGAGGTTATCAAAATTTCATAATGTGGTTATCAAATTT
Found at i:94394 original size:88 final size:90
Alignment explanation
Indices: 94164--94397 Score: 246
Period size: 88 Copynumber: 2.7 Consensus size: 90
94154 AATTTCATTC
* * * **
94164 TCATAGGAAGGTTATCGAAATTTCATGATGTGGTTATCAAAATTTTC-ATATGCGGTTACCAATT
1 TCATAGGAAGGTTATCGAAATTTCATAATGAGGTTATCAAAATTTTCAATATGTGGTTACCAAAA
*
94228 TTAATTAGTGTGATTATTAAAATTT
66 TTAATCAGTGTGATTATTAAAATTT
* * * * * * * *
94253 T-ATAGGCAGATTATCAAAATTTCACACTGAGGTTATCGAAA-TTTCATTGTGTGGTTACCAAAA
1 TCATAGGAAGGTTATCGAAATTTCATAATGAGGTTATCAAAATTTTCAATATGTGGTTACCAAAA
* * *
94316 TTACA-CAGTGTGGTTA-TCATATTT
66 TTA-ATCAGTGTGATTATTAAAATTT
* *
94340 TCATAGGGAGGTTATCGAAATTTCATAATGAGGTTATC-AAATTTTCAAAATGTGGTTA
1 TCATAGGAAGGTTATCGAAATTTCATAATGAGGTTATCAAAATTTTCAATATGTGGTTA
94398 TCAATATTTC
Statistics
Matches: 116, Mismatches: 25, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
87 14 0.12
88 100 0.86
89 2 0.02
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (90 bp):
TCATAGGAAGGTTATCGAAATTTCATAATGAGGTTATCAAAATTTTCAATATGTGGTTACCAAAA
TTAATCAGTGTGATTATTAAAATTT
Found at i:94397 original size:44 final size:44
Alignment explanation
Indices: 94263--94407 Score: 148
Period size: 44 Copynumber: 3.3 Consensus size: 44
94253 TATAGGCAGA
* *
94263 TTATCAAAATTTCACACTGAGGTTATCGAAA-TTTCATTGTGTGG
1 TTATCAAAATTTCACAATGAGGTTATC-AAATTTTCATAGTGTGG
* * * * * * *
94307 TTACCAAAATTACACAGTGTGGTTATCATATTTTCATAGGGAGG
1 TTATCAAAATTTCACAATGAGGTTATCAAATTTTCATAGTGTGG
* * * *
94351 TTATCGAAATTTCATAATGAGGTTATCAAATTTTCAAAATGTGG
1 TTATCAAAATTTCACAATGAGGTTATCAAATTTTCATAGTGTGG
*
94395 TTATCAATATTTC
1 TTATCAAAATTTC
94408 TACATTGTAG
Statistics
Matches: 79, Mismatches: 21, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
43 2 0.03
44 77 0.97
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (44 bp):
TTATCAAAATTTCACAATGAGGTTATCAAATTTTCATAGTGTGG
Found at i:97496 original size:210 final size:211
Alignment explanation
Indices: 97081--97515 Score: 493
Period size: 210 Copynumber: 2.1 Consensus size: 211
97071 GATGACTCAT
* *
97081 AAAGGTATGAAACC-AGATGTCATCACCTATAATTGTATAATCCAAGGATTTTGTCATTCAAGTC
1 AAAGGTATGAAACCTAGATGTCATCACATATAATTCTATAATCCAAGGATTTTGTCATTCAAGTC
* ** * **
97145 AATGGAAAGAAGTGAAAAGCTTGTTTGACAGAATGGTGGATGAAGGAGTGCAACCGGATATGGTA
66 AATGGAAAGAAGTGAAAAGCTTGTTTGACAGAATGATAAATGAAGGAGTGCAACCAGATATCATA
* * * * *
97210 ACTTTCAGCTCCATAATTGATGCTCTTTGCAAGGAAAGGAGAACTGAAGAGGCAATTGATGTATT
131 ACTTTCAACTCCATAATTGATGCTCTTTGCAAGGAAAAGAGAACTGAAGAAGCAATCGAGGTATT
*
97275 CAATCTAATGGCTGGA
196 CAATCTAATGGCTGAA
* * * * * * *
97291 AGAGGTATGAAACCTA-ATGTCATCACATATAGTTCTATAATCCACGGCTTTTTTCGTTCAGGTC
1 AAAGGTATGAAACCTAGATGTCATCACATATAATTCTATAATCCAAGGATTTTGTCATTCAAGTC
* * * *
97355 AATGGAAAG-TG-GCAATGAGCTT-TTTGGACAGAATGATAAATGAAGGAGTGCAGCCAGATGTC
66 AATGGAAAGAAGTG-AA-AAGCTTGTTT-GACAGAATGATAAATGAAGGAGTGCAACCAGATATC
* ** * *
97417 ATAACTTTCAACTCTATAATTGATGCTCTTTGCAAGGAAAAGTTAGCTGAAGAAGCCATCGAGGT
128 ATAACTTTCAACTCCATAATTGATGCTCTTTGCAAGGAAAAGAGAACTGAAGAAGCAATCGAGGT
* ** *
97482 TTTGGATTTAATGGCTGAA
193 ATTCAATCTAATGGCTGAA
*
97501 AAAGGTGTGAAACCT
1 AAAGGTATGAAACCT
97516 GACATTGTAA
Statistics
Matches: 185, Mismatches: 36, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
208 1 0.01
209 6 0.03
210 177 0.96
211 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (211 bp):
AAAGGTATGAAACCTAGATGTCATCACATATAATTCTATAATCCAAGGATTTTGTCATTCAAGTC
AATGGAAAGAAGTGAAAAGCTTGTTTGACAGAATGATAAATGAAGGAGTGCAACCAGATATCATA
ACTTTCAACTCCATAATTGATGCTCTTTGCAAGGAAAAGAGAACTGAAGAAGCAATCGAGGTATT
CAATCTAATGGCTGAA
Found at i:105499 original size:29 final size:28
Alignment explanation
Indices: 105442--105499 Score: 64
Period size: 29 Copynumber: 2.0 Consensus size: 28
105432 TAACTATCCA
** *
105442 TTTTGGGACAAATTGACCCATTAATTTT
1 TTTTGGGACAAATAAACCCATTAACTTT
105470 TTTTGGGGACAAATAAATCCCA-TAACTTT
1 TTTT-GGGACAAATAAA-CCCATTAACTTT
105499 T
1 T
105500 AAAAATAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
28 4 0.16
29 17 0.68
30 4 0.16
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.40
Consensus pattern (28 bp):
TTTTGGGACAAATAAACCCATTAACTTT
Found at i:110351 original size:20 final size:18
Alignment explanation
Indices: 110314--110354 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
110304 CTCTTGAAAT
*
110314 AATTCTTCAATGATCTTC
1 AATTCTTCAATAATCTTC
110332 AATTCTTCAAATAAATCTTC
1 AATTCTTC-AAT-AATCTTC
110352 AAT
1 AAT
110355 AAGTCTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 3 0.15
20 9 0.45
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.41
Consensus pattern (18 bp):
AATTCTTCAATAATCTTC
Found at i:110351 original size:30 final size:31
Alignment explanation
Indices: 110305--110364 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
110295 AATTTTTGCC
* * *
110305 TCTTGAAATAATTCTTCAATGA-TCTTCAAT
1 TCTTCAAATAAATCTTCAATAAGTCTTCAAT
110335 TCTTCAAATAAATCTTCAATAAGTCTTCAA
1 TCTTCAAATAAATCTTCAATAAGTCTTCAA
110365 ACACGAACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (31 bp):
TCTTCAAATAAATCTTCAATAAGTCTTCAAT
Found at i:112758 original size:10 final size:10
Alignment explanation
Indices: 112743--112794 Score: 77
Period size: 10 Copynumber: 5.2 Consensus size: 10
112733 TTTAATTTAA
112743 TATGGATATT
1 TATGGATATT
112753 TATGGATATT
1 TATGGATATT
**
112763 TACAGATATT
1 TATGGATATT
112773 TATGGATATT
1 TATGGATATT
*
112783 TACGGATATT
1 TATGGATATT
112793 TA
1 TA
112795 CAAATATATC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 37 1.00
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (10 bp):
TATGGATATT
Found at i:112772 original size:20 final size:20
Alignment explanation
Indices: 112747--112794 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
112737 ATTTAATATG
112747 GATATTTATGGATATTTACA
1 GATATTTATGGATATTTACA
*
112767 GATATTTATGGATATTTACG
1 GATATTTATGGATATTTACA
112787 GATATTTA
1 GATATTTA
112795 CAAATATATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
GATATTTATGGATATTTACA
Found at i:112779 original size:30 final size:30
Alignment explanation
Indices: 112743--112801 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
112733 TTTAATTTAA
* *
112743 TATGGATATTTATGGATATTTACAGATATT
1 TATGGATATTTACGGATATTTACAAATATT
112773 TATGGATATTTACGGATATTTACAAATAT
1 TATGGATATTTACGGATATTTACAAATAT
112802 ATCGAAGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (30 bp):
TATGGATATTTACGGATATTTACAAATATT
Found at i:112801 original size:10 final size:10
Alignment explanation
Indices: 112747--112801 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
112737 ATTTAATATG
**
112747 GATATTTATG
1 GATATTTACA
112757 GATATTTACA
1 GATATTTACA
**
112767 GATATTTATG
1 GATATTTACA
*
112777 GATATTTACG
1 GATATTTACA
112787 GATATTTACA
1 GATATTTACA
*
112797 AATAT
1 GATAT
112802 ATCGAAGTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 38 1.00
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (10 bp):
GATATTTACA
Found at i:115331 original size:29 final size:29
Alignment explanation
Indices: 115289--115347 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
115279 ATTTTCACCA
115289 ATGAAACATAATCTACATAACTATCTAAG
1 ATGAAACATAATCTACATAACTATCTAAG
115318 ATGAAACATAATCTACATAACTATCTAAG
1 ATGAAACATAATCTACATAACTATCTAAG
115347 A
1 A
115348 CATAATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.17, G:0.07, T:0.27
Consensus pattern (29 bp):
ATGAAACATAATCTACATAACTATCTAAG
Found at i:116777 original size:130 final size:130
Alignment explanation
Indices: 116552--116793 Score: 371
Period size: 130 Copynumber: 1.9 Consensus size: 130
116542 CTTCATTCAA
* * *
116552 TTTTACTCAATTAAAAACTCTATTTTTATTTACTTAAATCTAATATCTTTATAACAATTTAATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACAATTTAATTT
* * *
116617 TTACCATTTTTACTATTTTAATTAAAAACTTATATATATTAGAATTTTTAAATATACTTTTATAG
66 TTACCATTTTTACTAATTTAATTAAAAACTTAGATATATTAAAATTTTTAAATATACTTTTATAG
* *
116682 TTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTTATATCCTTATACCTAATTT-AT
1 TTTTACTCAACTAAAAACTCTA-TTTTTATTTAATTAAATCTAATATCCTTATAAC-AATTTAAT
*
116746 TTTTATCA-TTTTACTAATTTAATTAAAAACTTAGATATATTAAAATTT
64 TTTTACCATTTTTACTAATTTAATTAAAAACTTAGATATATTAAAATTT
116794 GAATAATGAT
Statistics
Matches: 101, Mismatches: 9, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
130 58 0.57
131 38 0.38
132 5 0.05
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.50
Consensus pattern (130 bp):
TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACAATTTAATTT
TTACCATTTTTACTAATTTAATTAAAAACTTAGATATATTAAAATTTTTAAATATACTTTTATAG
Found at i:119675 original size:36 final size:37
Alignment explanation
Indices: 119625--119696 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
119615 CATTTATAAG
*
119625 GCTACTTTCTCTTCCA-TCTCGAACCAACTGGCTTGA
1 GCTACTTTCCCTTCCATTCTCGAACCAACTGGCTTGA
* *
119661 GCTACTTTCCCTTCCATTTTCGAACCAATTGGCTTG
1 GCTACTTTCCCTTCCATTCTCGAACCAACTGGCTTG
119697 GAACTCTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 15 0.47
37 17 0.53
ACGTcount: A:0.18, C:0.32, G:0.14, T:0.36
Consensus pattern (37 bp):
GCTACTTTCCCTTCCATTCTCGAACCAACTGGCTTGA
Found at i:119706 original size:37 final size:36
Alignment explanation
Indices: 119626--119706 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 36
119616 ATTTATAAGG
* *
119626 CTACTTTCTCTTCCATCTCGAACCAACTGGCTTGAG
1 CTACTTTCCCTTCCATCTCGAACCAACTGGCTTGAA
* *
119662 CTACTTTCCCTTCCATTTTCGAACCAATTGGCTTGGAA
1 CTACTTTCCCTTCCA-TCTCGAACCAACTGGCTT-GAA
119700 CT-CTTTC
1 CTACTTTC
119707 ACCTGTTGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
36 14 0.36
37 21 0.54
38 4 0.10
ACGTcount: A:0.19, C:0.32, G:0.12, T:0.37
Consensus pattern (36 bp):
CTACTTTCCCTTCCATCTCGAACCAACTGGCTTGAA
Found at i:119803 original size:72 final size:72
Alignment explanation
Indices: 119718--119857 Score: 253
Period size: 72 Copynumber: 1.9 Consensus size: 72
119708 CCTGTTGCAT
* *
119718 TTGGACTTATATTGCTTCAAGTGGGCTGATCATTTCTTGGCATTGTCTGCTTGGGCTTGTATTGT
1 TTGGACTTATATTGCTTCAAGTGGGCTGATCATTTCTTGGCATTATCTGCTTGGCCTTGTATTGT
119783 TAACATC
66 TAACATC
*
119790 TTGGACTTATATTGCTTCAAGTGGGCTGATCATTTCTTGGCATTATTTGCTTGGCCTTGTATTGT
1 TTGGACTTATATTGCTTCAAGTGGGCTGATCATTTCTTGGCATTATCTGCTTGGCCTTGTATTGT
119855 TAA
66 TAA
119858 TGTCCTGGAC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.17, C:0.16, G:0.23, T:0.44
Consensus pattern (72 bp):
TTGGACTTATATTGCTTCAAGTGGGCTGATCATTTCTTGGCATTATCTGCTTGGCCTTGTATTGT
TAACATC
Found at i:123440 original size:51 final size:52
Alignment explanation
Indices: 123378--123613 Score: 339
Period size: 52 Copynumber: 4.5 Consensus size: 52
123368 GTTTAAGTTC
* * *
123378 TCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGCAATCAATCTAGCTCTTTT
1 TCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTCTTTT
*
123430 T-AAATTGGGAAAGTTCCCACCAGTCTTCAAAGTATTCAATTTAGCTCTTTT
1 TCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTCTTTT
* *
123481 TCAAATCGGGAAAGTTCCCACCAGTCTTCAAAGTATTCAATTTAGCTCTTTT
1 TCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTCTTTT
* * * **
123533 TCAAATCGGGAAAGTTCCCAGCAATTTTCAAAGTATTCAATTTAGCTGGTTT
1 TCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTCTTTT
* *
123585 TCAAAGTGGGAAAGTTCCCATCAAGTTTT
1 TCAAATTGGGAAAGTTCCCA-CCAGTTTT
123614 AGTTTTCAAT
Statistics
Matches: 167, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
51 47 0.28
52 115 0.69
53 5 0.03
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (52 bp):
TCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTCTTTT
Found at i:126039 original size:69 final size:69
Alignment explanation
Indices: 125928--126066 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
125918 TATCTGCTTC
*
125928 TTATGCTTTTGTTTCCTTCATTGCCCTGGTATGCTTCTTTCTTCCATTCCTTTTACTCACCTGCA
1 TTATGCTTTTGTTTCCTTCATTGCCCAGGTATGCTTCTTTCTTCCATTCCTTTTACTCACCTGCA
125993 TATT
66 TATT
125997 TTATGCTTTTGTTTCCTTCATTGCCCAGGTATGCTTCTTTCTTCCATTCCTTTTACTCACCTGCA
1 TTATGCTTTTGTTTCCTTCATTGCCCAGGTATGCTTCTTTCTTCCATTCCTTTTACTCACCTGCA
126062 TATT
66 TATT
126066 T
1 T
126067 GGCGCCTTTT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.12, C:0.27, G:0.10, T:0.50
Consensus pattern (69 bp):
TTATGCTTTTGTTTCCTTCATTGCCCAGGTATGCTTCTTTCTTCCATTCCTTTTACTCACCTGCA
TATT
Found at i:130035 original size:21 final size:21
Alignment explanation
Indices: 130011--130077 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
130001 GTAACATAAA
130011 TAATAACTAAAATACTTACAT
1 TAATAACTAAAATACTTACAT
* ** *
130032 TAATTAAATGTAATA-ATAC-T
1 TAA-TAACTAAAATACTTACAT
*
130052 ATAATAACTAAAACACTTACAT
1 -TAATAACTAAAATACTTACAT
130074 TAAT
1 TAAT
130078 TAAATTCTTA
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
20 8 0.24
21 16 0.48
22 9 0.27
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.34
Consensus pattern (21 bp):
TAATAACTAAAATACTTACAT
Done.