Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019753.1 Corchorus olitorius cultivar O-4 contig19786, 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: 102597
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5426 original size:46 final size:46
Alignment explanation
Indices: 5369--5461 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
5359 GGAGCTCCGT
5369 TCCTTTCAAGTAAGGTTTCCAGTTCAAATATTATGAATGGAGAAAA
1 TCCTTTCAAGTAAGGTTTCCAGTTCAAATATTATGAATGGAGAAAA
* *
5415 TCCTTTTAAGTAAGGTTTCCGGTTCAAATATTATGAATGGAGAAAA
1 TCCTTTCAAGTAAGGTTTCCAGTTCAAATATTATGAATGGAGAAAA
5461 T
1 T
5462 AGATGCCGTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.34
Consensus pattern (46 bp):
TCCTTTCAAGTAAGGTTTCCAGTTCAAATATTATGAATGGAGAAAA
Found at i:13924 original size:15 final size:15
Alignment explanation
Indices: 13904--13938 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
13894 GGGTTAAGAG
13904 TTTCTCTACAGTTAT
1 TTTCTCTACAGTTAT
* *
13919 TTTCTCTACGGTTTT
1 TTTCTCTACAGTTAT
13934 TTTCT
1 TTTCT
13939 TACCTTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.11, C:0.20, G:0.09, T:0.60
Consensus pattern (15 bp):
TTTCTCTACAGTTAT
Found at i:21600 original size:6 final size:6
Alignment explanation
Indices: 21589--21615 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
21579 GATTGAAACT
21589 TAAAGA TAAAGA TAAAGA TAAAGA TAA
1 TAAAGA TAAAGA TAAAGA TAAAGA TAA
21616 GAGAGAAGAA
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:0.67, C:0.00, G:0.15, T:0.19
Consensus pattern (6 bp):
TAAAGA
Found at i:31281 original size:31 final size:31
Alignment explanation
Indices: 31245--31310 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
31235 TAGGAGATGT
31245 AAATTTGTTCTAGCACTACATGCCTCGGTGC
1 AAATTTGTTCTAGCACTACATGCCTCGGTGC
31276 AAATTTGTTCTAGCACTACATGCCTCGGTGC
1 AAATTTGTTCTAGCACTACATGCCTCGGTGC
31307 AAAT
1 AAAT
31311 AAGAGCCTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (31 bp):
AAATTTGTTCTAGCACTACATGCCTCGGTGC
Found at i:31698 original size:26 final size:26
Alignment explanation
Indices: 31669--31719 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
31659 TGACAGTTCT
* *
31669 TGTGGCAAGACCCTGTGGAAATACCC
1 TGTGGCAACACCCTATGGAAATACCC
*
31695 TGTGGCAACATCCTATGGAAATACC
1 TGTGGCAACACCCTATGGAAATACC
31720 TTATGCTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (26 bp):
TGTGGCAACACCCTATGGAAATACCC
Found at i:33069 original size:46 final size:46
Alignment explanation
Indices: 32998--33086 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
32988 CTTTGCAAGA
* *
32998 AGCTACCGTATAGAGCATTCCTTCTGAAGATGGGTGCTCACATAAT
1 AGCTACCATATAGAGCATTCCTTCTGAAGAAGGGTGCTCACATAAT
* *
33044 AGCTACCATATAGAGTATTCTTTCTGAAGAAGGGTGCTCACAT
1 AGCTACCATATAGAGCATTCCTTCTGAAGAAGGGTGCTCACAT
33087 GAAATGCATC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (46 bp):
AGCTACCATATAGAGCATTCCTTCTGAAGAAGGGTGCTCACATAAT
Found at i:33304 original size:36 final size:36
Alignment explanation
Indices: 33262--33418 Score: 233
Period size: 36 Copynumber: 4.4 Consensus size: 36
33252 AGGCCAGCAA
33262 CATTATAGCCAAATATTGGGCGACTAAGGCCATCGG
1 CATTATAGCCAAATATTGGGCGACTAAGGCCATCGG
* * *
33298 CTTTATAGCCAATTATTGGGCGACTTAGGCCATCGG
1 CATTATAGCCAAATATTGGGCGACTAAGGCCATCGG
* *
33334 CATTATAGCCAAGTATTGGGCGACTAAGGCCAACGG
1 CATTATAGCCAAATATTGGGCGACTAAGGCCATCGG
* * * *
33370 CTTTATAGCCAATTATTAGGCGACTTAGGCCATCGG
1 CATTATAGCCAAATATTGGGCGACTAAGGCCATCGG
33406 CATTATAGCCAAA
1 CATTATAGCCAAA
33419 GACAGAGCAA
Statistics
Matches: 107, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 107 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (36 bp):
CATTATAGCCAAATATTGGGCGACTAAGGCCATCGG
Found at i:33371 original size:72 final size:72
Alignment explanation
Indices: 33262--33418 Score: 287
Period size: 72 Copynumber: 2.2 Consensus size: 72
33252 AGGCCAGCAA
* *
33262 CATTATAGCCAAATATTGGGCGACTAAGGCCATCGGCTTTATAGCCAATTATTGGGCGACTTAGG
1 CATTATAGCCAAATATTGGGCGACTAAGGCCAACGGCTTTATAGCCAATTATTAGGCGACTTAGG
33327 CCATCGG
66 CCATCGG
*
33334 CATTATAGCCAAGTATTGGGCGACTAAGGCCAACGGCTTTATAGCCAATTATTAGGCGACTTAGG
1 CATTATAGCCAAATATTGGGCGACTAAGGCCAACGGCTTTATAGCCAATTATTAGGCGACTTAGG
33399 CCATCGG
66 CCATCGG
33406 CATTATAGCCAAA
1 CATTATAGCCAAA
33419 GACAGAGCAA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 81 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (72 bp):
CATTATAGCCAAATATTGGGCGACTAAGGCCAACGGCTTTATAGCCAATTATTAGGCGACTTAGG
CCATCGG
Found at i:33648 original size:32 final size:31
Alignment explanation
Indices: 33570--33657 Score: 122
Period size: 31 Copynumber: 2.8 Consensus size: 31
33560 GATAGTTTGC
* *
33570 CAACACCATGTGGAAGATGGTGTACTTCTTA
1 CAACACCATATGGAAGAGGGTGTACTTCTTA
*
33601 CAACATCATATGGAAGAGGGTGTACTTCTTGA
1 CAACACCATATGGAAGAGGGTGTACTTCTT-A
* *
33633 TAACACCATATGGAAGAGGATGTAC
1 CAACACCATATGGAAGAGGGTGTAC
33658 CCTTCGATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
31 27 0.54
32 23 0.46
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (31 bp):
CAACACCATATGGAAGAGGGTGTACTTCTTA
Found at i:33802 original size:51 final size:50
Alignment explanation
Indices: 33664--33805 Score: 212
Period size: 51 Copynumber: 2.8 Consensus size: 50
33654 GTACCCTTCG
* * * *
33664 ATATTGGAAGAAGGTGATAGTTTGCCAACGCCATATACAAAAAACTTCATA
1 ATATTGGAAG-AGGTGATATTTTGCGAACACCATATGCAAAAAACTTCATA
*
33715 ATATTGGAAGGAGGTGATATTTTGCGAACACCATATGCAAAAGACTTCATA
1 ATATTGGAA-GAGGTGATATTTTGCGAACACCATATGCAAAAAACTTCATA
33766 ATATTGGATAGAGGTGATATTTTGCGAACACCATATGCAA
1 ATATTGGA-AGAGGTGATATTTTGCGAACACCATATGCAA
33806 GAGGAGGACG
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 82 0.98
52 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (50 bp):
ATATTGGAAGAGGTGATATTTTGCGAACACCATATGCAAAAAACTTCATA
Found at i:33852 original size:30 final size:30
Alignment explanation
Indices: 33816--33876 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
33806 GAGGAGGACG
*
33816 TTGGAAGGAGGTGAG-ACTTCGCTAACACCA
1 TTGGAAGGAGGTG-GTACTTCGCGAACACCA
33846 TTGGAAGGAGGTGGTACTTCGCGAACACCA
1 TTGGAAGGAGGTGGTACTTCGCGAACACCA
33876 T
1 T
33877 ATGCTTTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.28, C:0.20, G:0.31, T:0.21
Consensus pattern (30 bp):
TTGGAAGGAGGTGGTACTTCGCGAACACCA
Found at i:33917 original size:44 final size:44
Alignment explanation
Indices: 33863--34014 Score: 180
Period size: 44 Copynumber: 3.7 Consensus size: 44
33853 GAGGTGGTAC
* *
33863 TTCGCGAACACCATATGCTTTTGACATTGAAAGAGGGTGATAGT
1 TTCGCAAACACCATATGCCTTTGACATTGAAAGAGGGTGATAGT
33907 TTCGCAAACACCATATGCCTTTGACATTGAAAGA----G---G-
1 TTCGCAAACACCATATGCCTTTGACATTGAAAGAGGGTGATAGT
* *
33943 --CACAAACACCATATGTCTTTGACATTGAAAGAGGGTGATAGT
1 TTCGCAAACACCATATGCCTTTGACATTGAAAGAGGGTGATAGT
* *
33985 CTCGCGAACACCATATGCCTTTGACATTGA
1 TTCGCAAACACCATATGCCTTTGACATTGA
34015 CATTGAAAGA
Statistics
Matches: 91, Mismatches: 7, Indels: 20
0.77 0.06 0.17
Matches are distributed among these distances:
34 30 0.33
37 1 0.01
38 1 0.01
40 1 0.01
41 1 0.01
44 57 0.63
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (44 bp):
TTCGCAAACACCATATGCCTTTGACATTGAAAGAGGGTGATAGT
Found at i:33954 original size:34 final size:34
Alignment explanation
Indices: 33911--33976 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
33901 GATAGTTTCG
33911 CAAACACCATATGCCTTTGACATTGAAAGAGGCA
1 CAAACACCATATGCCTTTGACATTGAAAGAGGCA
*
33945 CAAACACCATATGTCTTTGACATTGAAAGAGG
1 CAAACACCATATGCCTTTGACATTGAAAGAGG
33977 GTGATAGTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (34 bp):
CAAACACCATATGCCTTTGACATTGAAAGAGGCA
Found at i:33964 original size:78 final size:78
Alignment explanation
Indices: 33869--34014 Score: 258
Period size: 78 Copynumber: 1.9 Consensus size: 78
33859 GTACTTCGCG
*
33869 AACACCATATGCTTTTGACATTGAAAGAGGGTGATAGTTTCGCAAACACCATATGCCTTTGACAT
1 AACACCATATGCTTTTGACATTGAAAGAGGGTGATAGTCTCGCAAACACCATATGCCTTTGACAT
33934 TGAAAGAGGCACA
66 TGAAAGAGGCACA
*
33947 AACACCATATG-TCTTTGACATTGAAAGAGGGTGATAGTCTCGCGAACACCATATGCCTTTGACA
1 AACACCATATGCT-TTTGACATTGAAAGAGGGTGATAGTCTCGCAAACACCATATGCCTTTGACA
34011 TTGA
65 TTGA
34015 CATTGAAAGA
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
77 1 0.02
78 64 0.98
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (78 bp):
AACACCATATGCTTTTGACATTGAAAGAGGGTGATAGTCTCGCAAACACCATATGCCTTTGACAT
TGAAAGAGGCACA
Found at i:34246 original size:19 final size:18
Alignment explanation
Indices: 34222--34288 Score: 59
Period size: 19 Copynumber: 3.8 Consensus size: 18
34212 GCCTTTAGTG
34222 TCGCGAATACCATACCATA
1 TCGCGAATACCATACCA-A
* *
34241 TCGCGAGTACCAT-GC--
1 TCGCGAATACCATACCAA
*
34256 TCTCGAATACCATACCACA
1 TCGCGAATACCATACCA-A
*
34275 TCGCGAGTACCATA
1 TCGCGAATACCATA
34289 TGCCATCTCC
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
15 11 0.30
16 1 0.03
18 1 0.03
19 24 0.65
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (18 bp):
TCGCGAATACCATACCAA
Found at i:35193 original size:115 final size:114
Alignment explanation
Indices: 35009--35226 Score: 366
Period size: 115 Copynumber: 1.9 Consensus size: 114
34999 TATTAAGCTG
* * *
35009 CATAGGCTAGAAGTATCAACAAGGAAGGGCACTCCTGGAGGTGCAACCAGTGCAGCACTCCTAAG
1 CATAGGCCAGAAGTATCAACAAGGAAGGGCACTCCTAGAGGTGCAACCAGTGCAACACTCCTAAG
35074 GGTGCACTCACTCCAAGTCAAAATATAGATTCTTTTTTTGTAATGGGCTA
66 GGTGCACTCACTCCAAGTCAAAATATAGATT-TTTTTTTGTAATGGGCTA
* *
35124 CATAGGCCAGAA-TCATCAACAAGGAAGGGCACTTCTAGAGGTGCAACTAGTGCAACACTCCTAA
1 CATAGGCCAGAAGT-ATCAACAAGGAAGGGCACTCCTAGAGGTGCAACCAGTGCAACACTCCTAA
35188 GGGTGCACTCACTCCAAGTCAAAATATAGATTTTTTTTT
65 GGGTGCACTCACTCCAAGTCAAAATATAGATTTTTTTTT
35227 AATAGGCTAC
Statistics
Matches: 97, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
114 8 0.08
115 89 0.92
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (114 bp):
CATAGGCCAGAAGTATCAACAAGGAAGGGCACTCCTAGAGGTGCAACCAGTGCAACACTCCTAAG
GGTGCACTCACTCCAAGTCAAAATATAGATTTTTTTTTGTAATGGGCTA
Found at i:37084 original size:19 final size:20
Alignment explanation
Indices: 37060--37097 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
37050 TTTATTCTCT
37060 AATGGGTAG-TTTTATTTTA
1 AATGGGTAGTTTTTATTTTA
37079 AATGGGTAGTTTTTATTTT
1 AATGGGTAGTTTTTATTTT
37098 GTTTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (20 bp):
AATGGGTAGTTTTTATTTTA
Found at i:37367 original size:60 final size:60
Alignment explanation
Indices: 37274--37393 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
37264 GGTAAGTCCC
37274 ATATTAAGACATTGATTTGATAGGTTTTAATAATTATACGAAAAATCCAAATTGTCACAA
1 ATATTAAGACATTGATTTGATAGGTTTTAATAATTATACGAAAAATCCAAATTGTCACAA
37334 ATATTAAGACATTGATTTGATAGGTTTTAATAATTATACGAAAAATCCAAATTGTCACAA
1 ATATTAAGACATTGATTTGATAGGTTTTAATAATTATACGAAAAATCCAAATTGTCACAA
37394 TTCTTTTGGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (60 bp):
ATATTAAGACATTGATTTGATAGGTTTTAATAATTATACGAAAAATCCAAATTGTCACAA
Found at i:37942 original size:28 final size:28
Alignment explanation
Indices: 37902--37955 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
37892 ATTTTGAAGT
*
37902 ATTTATTACGGGGAGTGCTGTTAGAAAG
1 ATTTATTACGGGGAGTGCTGTAAGAAAG
37930 ATTTATTACGGGGAGTGCTGTAAGAA
1 ATTTATTACGGGGAGTGCTGTAAGAA
37956 TCTGCAGTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.07, G:0.31, T:0.31
Consensus pattern (28 bp):
ATTTATTACGGGGAGTGCTGTAAGAAAG
Found at i:40254 original size:2 final size:2
Alignment explanation
Indices: 40249--40293 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
40239 ACATTGTCTA
*
40249 AT AT AT AC 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
40291 AT A
1 AT A
40294 ATACTCTGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:41209 original size:151 final size:151
Alignment explanation
Indices: 40975--41559 Score: 741
Period size: 151 Copynumber: 3.9 Consensus size: 151
40965 ATAATATAAG
* * * * * * ** * * *
40975 TATTTAATAGGTTGTCGATGGAGATGGCAAGAAACATTTTCCCTTGGAGGAGGATTATGTCCGGA
1 TATTTAACAGGTTATCAATGGAGATGGCAAAAAAAATGTTCCAGTGGAGGAGAATCATGTCCGTA
* * *
41040 GCTCTCCAAACTGTAAGGTATGATTTG-TATATG-TTTTTTTT-CTTTTGTTTTATTCAAATTTA
66 GCTCTCCTAACTCTAAGGTATGA-TTGATATATGTTTTTTTTTCCTTTTGTCTTATTCAAATTTA
41102 TAATGTTTACAAGTAGTACACA
130 TAATGTTTACAAGTAGTACACA
*
41124 TATTTAACAGGTTATCAATGGAGATGGCAGGAAAAAAATATTCCAGTGGAGGAGAATCATGTCCG
1 TATTTAACAGGTTATCAATGGAGATGGCA--AAAAAAATGTTCCAGTGGAGGAGAATCATGTCCG
41189 TAGCTCTCCTAACTCTAAGGTATGATTGATGA-ATG-TTTTTTTTCCTTTTGTCTTATTCAAATT
64 TAGCTCTCCTAACTCTAAGGTATGATTGAT-ATATGTTTTTTTTTCCTTTTGTCTTATTCAAATT
*
41252 TATATTGTTTACAAGTAGT--ACA
128 TATAATGTTTACAAGTAGTACACA
* *
41274 -A-GT---A--TTATCAATGGAGATGGCAAAAAAAAAATGTTCCAGTGGAGGAGAATCATGTTCG
1 TATTTAACAGGTTATCAATGGAGATGGC--AAAAAAAATGTTCCAGTGGAGGAGAATCATGTCCG
*
41332 TAGCTCTCCTAACTCTAAGGTATGATTGATGTATGTTTTTTTTTCCTTTTGTCTTATTCAAATTT
64 TAGCTCTCCTAACTCTAAGGTATGATTGATATATGTTTTTTTTTCCTTTTGTCTTATTCAAATTT
41397 ATAATGTTTACAAGTAGTACA-A
129 ATAATGTTTACAAGTAGTACACA
* * * * *
41419 GTATTTAACATGATATAAACGGAGATGGCAAACAAAATGTTCCAGTGGAGGAGAATCATGTCCGT
1 -TATTTAACAGGTTATCAATGGAGATGGCAAAAAAAATGTTCCAGTGGAGGAGAATCATGTCCGT
* * * *
41484 AGCTCTCCTAAGTCTCAGGTATGATTGATCTATGTTTTTTTTTTCATTTTGTCTTATTCAAATTT
65 AGCTCTCCTAACTCTAAGGTATGATTGATATATG-TTTTTTTTTCCTTTTGTCTTATTCAAATTT
41549 ATAATGTTTAC
129 ATAATGTTTAC
41560 GACCAAAATA
Statistics
Matches: 386, Mismatches: 30, Indels: 37
0.85 0.07 0.08
Matches are distributed among these distances:
143 82 0.21
144 46 0.12
145 3 0.01
146 1 0.00
147 1 0.00
148 2 0.01
149 27 0.07
150 6 0.02
151 127 0.33
152 77 0.20
153 14 0.04
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.39
Consensus pattern (151 bp):
TATTTAACAGGTTATCAATGGAGATGGCAAAAAAAATGTTCCAGTGGAGGAGAATCATGTCCGTA
GCTCTCCTAACTCTAAGGTATGATTGATATATGTTTTTTTTTCCTTTTGTCTTATTCAAATTTAT
AATGTTTACAAGTAGTACACA
Found at i:41470 original size:294 final size:294
Alignment explanation
Indices: 41019--41559 Score: 820
Period size: 294 Copynumber: 1.8 Consensus size: 294
41009 CATTTTCCCT
* * *
41019 TGGAGGAGGATTATGTCCGGAGCTCTCCAAACTGTAAGGTATGATTTGTATATGTTTTTTTTCTT
1 TGGAGGAGAATCATGTCCGGAGCTCTCCAAACTCTAAGGTATGATTTGTATATGTTTTTTTTCTT
* * * *
41084 TTGTTTTATTCAAATTTATAATGTTTACAAGTAGTACACATATTTAACAGGTTATCAATGGAGAT
66 TTGTCTTATTCAAATTTATAATGTTTACAAGTAGTACACATATTTAACAGGATATAAACGGAGAT
41149 GGCAGGAAAAAAATATTCCAGTGGAGGAGAATCATGTCCGTAGCTCTCCTAACTCTAAGGTATGA
131 GGCA-GAAAAAAATATTCCAGTGGAGGAGAATCATGTCCGTAGCTCTCCTAACTCTAAGGTATGA
* * *
41214 TTGATGAATG-TTTTTTTTCCTTTTGTCTTATTCAAATTTATATTGTTTACAAGTAGTACAAGTA
195 TTGATCAATGTTTTTTTTTCATTTTGTCTTATTCAAATTTATAATGTTTACAAGTAGTACAAGTA
41278 TTATCAATGGAGATGGCAAAAAAAAAATGTTCCAG
260 TTATCAATGGAGATGGCAAAAAAAAAATGTTCCAG
* * * *
41313 TGGAGGAGAATCATGTTCGTAGCTCTCCTAACTCTAAGGTATGA-TTGATGTATGTTTTTTTTTC
1 TGGAGGAGAATCATGTCCGGAGCTCTCCAAACTCTAAGGTATGATTTG-TATATG-TTTTTTTT-
*
41377 CTTTTGTCTTATTCAAATTTATAATGTTTACAAGTAGTACA-AGTATTTAACATGATATAAACGG
63 CTTTTGTCTTATTCAAATTTATAATGTTTACAAGTAGTACACA-TATTTAACAGGATATAAACGG
* * * *
41441 AGATGGCA-AACAAAATGTTCCAGTGGAGGAGAATCATGTCCGTAGCTCTCCTAAGTCTCAGGTA
127 AGATGGCAGAAAAAAATATTCCAGTGGAGGAGAATCATGTCCGTAGCTCTCCTAACTCTAAGGTA
*
41505 TGATTGATCTATGTTTTTTTTTTCATTTTGTCTTATTCAAATTTATAATGTTTAC
192 TGATTGATCAATG-TTTTTTTTTCATTTTGTCTTATTCAAATTTATAATGTTTAC
41560 GACCAAAATA
Statistics
Matches: 221, Mismatches: 20, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
293 3 0.01
294 106 0.48
295 9 0.04
296 103 0.47
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (294 bp):
TGGAGGAGAATCATGTCCGGAGCTCTCCAAACTCTAAGGTATGATTTGTATATGTTTTTTTTCTT
TTGTCTTATTCAAATTTATAATGTTTACAAGTAGTACACATATTTAACAGGATATAAACGGAGAT
GGCAGAAAAAAATATTCCAGTGGAGGAGAATCATGTCCGTAGCTCTCCTAACTCTAAGGTATGAT
TGATCAATGTTTTTTTTTCATTTTGTCTTATTCAAATTTATAATGTTTACAAGTAGTACAAGTAT
TATCAATGGAGATGGCAAAAAAAAAATGTTCCAG
Found at i:41575 original size:296 final size:293
Alignment explanation
Indices: 41019--41575 Score: 796
Period size: 296 Copynumber: 1.9 Consensus size: 293
41009 CATTTTCCCT
* * *
41019 TGGAGGAGGATTATGTCCGGAGCTCTCCAAACTGTAAGGTATGATTTGTATATGTTTTTTTTCTT
1 TGGAGGAGAATCATGTCCGGAGCTCTCCAAACTCTAAGGTATGATTTGTATATGTTTTTTTTCTT
* * * *
41084 TTGTTTTATTCAAATTTATAATGTTTACAAGTAGTACACATATTTAACAGGTTATCAATGGAGAT
66 TTGTCTTATTCAAATTTATAATGTTTACAAGTAGTACACATATTTAACAGGATATAAACGGAGAT
41149 GGCAGGAAAAAAATATTCCAGTGGAGGAGAATCATGTCCGTAGCTCTCCTAACTCTAAGGTATGA
131 GGCA-GAAAAAAATATTCCAGTGGAGGAGAATCATGTCCGTAGCTCTCCTAACTCTAAGGTATGA
* * * ** **
41214 TTGATGAATGTTTTTTTTCCTTTTGTCTTATTCAAATTTATATTGTTTACAAGTAGTACAAGTAT
195 TTGATCAATGTTTTTTTTCATTTTGTCTTATTCAAATTTATAATGTTTACAACCAAAACAAGTAT
41279 TATCAATGGAGATGGCAAAAAAAAAATGTTCCAG
260 TATCAATGGAGATGGCAAAAAAAAAATGTTCCAG
* * * *
41313 TGGAGGAGAATCATGTTCGTAGCTCTCCTAACTCTAAGGTATGA-TTGATGTATGTTTTTTTTTC
1 TGGAGGAGAATCATGTCCGGAGCTCTCCAAACTCTAAGGTATGATTTG-TATATG-TTTTTTTT-
*
41377 CTTTTGTCTTATTCAAATTTATAATGTTTACAAGTAGTACA-AGTATTTAACATGATATAAACGG
63 CTTTTGTCTTATTCAAATTTATAATGTTTACAAGTAGTACACA-TATTTAACAGGATATAAACGG
* * * *
41441 AGATGGCA-AACAAAATGTTCCAGTGGAGGAGAATCATGTCCGTAGCTCTCCTAAGTCTCAGGTA
127 AGATGGCAGAAAAAAATATTCCAGTGGAGGAGAATCATGTCCGTAGCTCTCCTAACTCTAAGGTA
* * *
41505 TGATTGATCTATGTTTTTTTTTTCATTTTGTCTTATTCAAATTTATAATGTTTACGACCAAAATA
192 TGATTGATCAATG--TTTTTTTTCATTTTGTCTTATTCAAATTTATAATGTTTACAACCAAAACA
41570 AGTATT
255 AGTATT
41576 GAATAGGGTT
Statistics
Matches: 231, Mismatches: 26, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
293 3 0.01
294 106 0.46
295 9 0.04
296 113 0.49
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (293 bp):
TGGAGGAGAATCATGTCCGGAGCTCTCCAAACTCTAAGGTATGATTTGTATATGTTTTTTTTCTT
TTGTCTTATTCAAATTTATAATGTTTACAAGTAGTACACATATTTAACAGGATATAAACGGAGAT
GGCAGAAAAAAATATTCCAGTGGAGGAGAATCATGTCCGTAGCTCTCCTAACTCTAAGGTATGAT
TGATCAATGTTTTTTTTCATTTTGTCTTATTCAAATTTATAATGTTTACAACCAAAACAAGTATT
ATCAATGGAGATGGCAAAAAAAAAATGTTCCAG
Found at i:41656 original size:152 final size:151
Alignment explanation
Indices: 41286--41662 Score: 391
Period size: 152 Copynumber: 2.5 Consensus size: 151
41276 TATTATCAAT
* *
41286 GGAGATGGCAAAAAAAAAATGTTCCAGTGGAGGAGAATCATGTTCGTAGCTCTCCTAACT-CTAA
1 GGAGATGGC--AAACAAAATGTTCCAATGGAGGAGAATCATGTTCGTAGCTCTCCT-ACTGCTAA
* * ** **
41350 GGTATGATTGATGTATGTTTTTTTTTCCTTTTGTCTTATTCAAATTTATAATGTTTACAAGTAGT
63 GGTATGATTGATCTATGTTTTTTTTTCATTTTGTCTTATTCAAATTTATAATGTTTACAACCAAA
* *
41415 ACAAGTATTTAACATGATATAAAC
128 ACAAGTATTGAACAGGATATAAAC
* * * *
41439 GGAGATGGCAAACAAAATGTTCCAGTGGAGGAGAATCATGTCCGTAGCTCTCCTA-AGTCTCAGG
1 GGAGATGGCAAACAAAATGTTCCAATGGAGGAGAATCATGTTCGTAGCTCTCCTACTG-CTAAGG
*
41503 TATGATTGATCTATGTTTTTTTTTTCATTTTGTCTTATTCAAATTTATAATGTTTACGACCAAAA
65 TATGATTGATCTATG-TTTTTTTTTCATTTTGTCTTATTCAAATTTATAATGTTTACAACCAAAA
* * * ** *
41568 TAAGTATTGAATAGGGT-TGTGAT
129 CAAGTATTGAACAGGATAT-AAAC
* ** * * * * * * * *
41591 GGATATGGCAATGAATATTTTTCAATGGAGGAGGATTATGTTCGTAGGTATCCTACTGCGAAGGT
1 GGAGATGGCAAACAAAATGTTCCAATGGAGGAGAATCATGTTCGTAGCTCTCCTACTGCTAAGGT
41656 ATGATTG
66 ATGATTG
41663 TTAATTGTTT
Statistics
Matches: 185, Mismatches: 34, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
150 1 0.01
151 63 0.34
152 111 0.60
153 10 0.05
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (151 bp):
GGAGATGGCAAACAAAATGTTCCAATGGAGGAGAATCATGTTCGTAGCTCTCCTACTGCTAAGGT
ATGATTGATCTATGTTTTTTTTTCATTTTGTCTTATTCAAATTTATAATGTTTACAACCAAAACA
AGTATTGAACAGGATATAAAC
Found at i:50913 original size:2 final size:2
Alignment explanation
Indices: 50908--50966 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
50898 TATATATATA
50908 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
50950 TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG T
50967 ATGTATACTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:52695 original size:20 final size:20
Alignment explanation
Indices: 52666--52704 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52656 TACGGTCAAT
*
52666 TAAAACGCCATGTCACCTAC
1 TAAAACGCCAGGTCACCTAC
*
52686 TAAAAGGCCAGGTCACCTA
1 TAAAACGCCAGGTCACCTA
52705 TTACTTTAGA
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:0.36, C:0.31, G:0.15, T:0.18
Consensus pattern (20 bp):
TAAAACGCCAGGTCACCTAC
Found at i:56715 original size:16 final size:16
Alignment explanation
Indices: 56694--56734 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
56684 TATATATATA
* *
56694 ATATATATTTATGCAT
1 ATATATATATATCCAT
56710 ATATATATATATCCAT
1 ATATATATATATCCAT
*
56726 TTATATATA
1 ATATATATA
56735 AATATTTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.49
Consensus pattern (16 bp):
ATATATATATATCCAT
Found at i:65209 original size:2 final size:2
Alignment explanation
Indices: 65202--65230 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
65192 TGATCGGTTT
65202 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
65231 GAGATGACCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:65725 original size:2 final size:2
Alignment explanation
Indices: 65718--65745 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
65708 TATGAAATTG
65718 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
65746 TTCCCCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66524 original size:30 final size:31
Alignment explanation
Indices: 66464--66524 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
66454 GATAATATGC
* * * *
66464 ATCAGGTAATGGGATGGTTTTTTATTAAATT
1 ATCAAGTAATGAGATGATTTTTTATAAAATT
66495 ATCAAGTAATGAGATGATTTTTTA-AAAATT
1 ATCAAGTAATGAGATGATTTTTTATAAAATT
66525 TGTAGAATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.43
Consensus pattern (31 bp):
ATCAAGTAATGAGATGATTTTTTATAAAATT
Found at i:72092 original size:41 final size:42
Alignment explanation
Indices: 72023--72104 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 42
72013 CAAAATACTT
72023 ACCTGTTAAACTATTCTATCTTTATTTGCTTCAATAATTTTG
1 ACCTGTTAAACTATTCTATCTTTATTTGCTTCAATAATTTTG
* *
72065 ACCTGTTAAACTA-TCTATCTTTCTTTGCTTTAATAATTTT
1 ACCTGTTAAACTATTCTATCTTTATTTGCTTCAATAATTTT
72105 TAATATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 25 0.66
42 13 0.34
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (42 bp):
ACCTGTTAAACTATTCTATCTTTATTTGCTTCAATAATTTTG
Found at i:75015 original size:26 final size:24
Alignment explanation
Indices: 74973--75020 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
74963 ATATTAAATA
**
74973 TATTTTAAAATGTATAAATAATAAT
1 TATTTTAAAATAAAT-AATAATAAT
74998 TATTTATAAAATAAATAATAATA
1 TATTT-TAAAATAAATAATAATA
75021 TAAAAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
TATTTTAAAATAAATAATAATAAT
Found at i:75027 original size:19 final size:21
Alignment explanation
Indices: 74986--75028 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
74976 TTTAAAATGT
*
74986 ATAAATAATAATTATTTATAAA
1 ATAAATAATAATTA-TTAAAAA
75008 ATAAATAATAA-TA-TAAAAA
1 ATAAATAATAATTATTAAAAA
75027 AT
1 AT
75029 CAATTATAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 7 0.35
21 2 0.10
22 11 0.55
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAAATAATAATTATTAAAAA
Found at i:78156 original size:18 final size:18
Alignment explanation
Indices: 78133--78167 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
78123 AATTACCCAC
*
78133 ATAAAATATTCTTAGTAA
1 ATAAAATATTCATAGTAA
78151 ATAAAATATTCATAGTA
1 ATAAAATATTCATAGTA
78168 TACAGTATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (18 bp):
ATAAAATATTCATAGTAA
Found at i:80277 original size:47 final size:47
Alignment explanation
Indices: 80176--80324 Score: 158
Period size: 47 Copynumber: 3.2 Consensus size: 47
80166 AACAGGGTAC
* * * * * * * *
80176 AAGAAAGGGTCGGCGGCAGAAGATA-ATATGAGAACAAAGGTGGAAC
1 AAGAAAGGGTAGGCCGCAGAAGAAAGAAAAGAGGACAAAAGTGGAAG
** *
80222 AAGAAAGGGT-GTGCCGCAGAAGGGAGAAAAGAGGAGAAAAGTGGAAG
1 AAGAAAGGGTAG-GCCGCAGAAGAAAGAAAAGAGGACAAAAGTGGAAG
* *
80269 AAGAAAGGGTAGGTCGCAGAAGAAAGAAAAGAGGACAAAAGTGGGAG
1 AAGAAAGGGTAGGCCGCAGAAGAAAGAAAAGAGGACAAAAGTGGAAG
80316 AAGAAAGGG
1 AAGAAAGGG
80325 CTATTTTTTT
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
45 1 0.01
46 20 0.23
47 64 0.74
48 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.39, T:0.07
Consensus pattern (47 bp):
AAGAAAGGGTAGGCCGCAGAAGAAAGAAAAGAGGACAAAAGTGGAAG
Found at i:80575 original size:16 final size:17
Alignment explanation
Indices: 80554--80594 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
80544 AATAAACCAA
*
80554 AATTATAT-TATTATAT
1 AATTATATATATAATAT
80570 AATTAT-TATATAATAT
1 AATTATATATATAATAT
*
80586 AATAATATA
1 AATTATATA
80595 CCAACATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 1 0.05
16 18 0.86
17 2 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTATATATATAATAT
Found at i:81258 original size:21 final size:21
Alignment explanation
Indices: 81233--81274 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
81223 TAGAATTGAT
81233 GGTGGATTATACAGTCCGACG
1 GGTGGATTATACAGTCCGACG
*
81254 GGTGGATTATACAGTGCGACG
1 GGTGGATTATACAGTCCGACG
81275 TTGTTTTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.24
Consensus pattern (21 bp):
GGTGGATTATACAGTCCGACG
Found at i:82151 original size:19 final size:20
Alignment explanation
Indices: 82117--82154 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
82107 GAAGAATAAG
82117 GAAAGAAAAGATAAAGGAAT
1 GAAAGAAAAGATAAAGGAAT
*
82137 GAAATAAAA-ATAAAGGAA
1 GAAAGAAAAGATAAAGGAA
82155 AAAAAAGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.11
Consensus pattern (20 bp):
GAAAGAAAAGATAAAGGAAT
Found at i:83549 original size:51 final size:51
Alignment explanation
Indices: 83403--83559 Score: 221
Period size: 48 Copynumber: 3.1 Consensus size: 51
83393 TGGCAACCTA
*
83403 CAAAGTTTGATAGTCAAACCACAAAAAAATCATTGTACATGCATGGTCAAACTC
1 CAAAGTTTAATAGTC-AA--ACAAAAAAATCATTGTACATGCATGGTCAAACTC
* *
83457 TAAAGTTTAATAGT--AA-AAAAACATCATTGTACATGCATGGTCAAACTC
1 CAAAGTTTAATAGTCAAACAAAAAAATCATTGTACATGCATGGTCAAACTC
* *
83505 CAAAGTTTAATAGTCAAACAAAAAAATCAGTGTACATGCATGGTCAAACCC
1 CAAAGTTTAATAGTCAAACAAAAAAATCATTGTACATGCATGGTCAAACTC
83556 CAAA
1 CAAA
83560 AGATTATGGT
Statistics
Matches: 93, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
48 44 0.47
49 1 0.01
50 2 0.02
51 34 0.37
54 12 0.13
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (51 bp):
CAAAGTTTAATAGTCAAACAAAAAAATCATTGTACATGCATGGTCAAACTC
Found at i:83583 original size:72 final size:71
Alignment explanation
Indices: 83493--83630 Score: 204
Period size: 71 Copynumber: 1.9 Consensus size: 71
83483 TTGTACATGC
* * * *
83493 ATGGTCAAACTCCAAAGTTTAATAGTCAAACAAAAAAATCAGTGTACATGCATGGTCAAACCCCA
1 ATGGTCAAACCCCAAAGTTTAATAATCAAA-AAAAAAATCAGTATACATGCATGGTCAAACCACA
83558 AAAGATT
65 AAAGATT
* * *
83565 ATGGTCAAACCCCAAAGTTTAATAATCAAAAAAAATATCATTATACATGCATGGTTAAACCACAA
1 ATGGTCAAACCCCAAAGTTTAATAATCAAAAAAAAAATCAGTATACATGCATGGTCAAACCACAA
83630 A
66 A
83631 TTTTGATAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
71 31 0.53
72 28 0.47
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (71 bp):
ATGGTCAAACCCCAAAGTTTAATAATCAAAAAAAAAATCAGTATACATGCATGGTCAAACCACAA
AAGATT
Found at i:83796 original size:55 final size:55
Alignment explanation
Indices: 83724--83828 Score: 151
Period size: 55 Copynumber: 1.9 Consensus size: 55
83714 AAAAAGCGTT
83724 TCATTGTACATGCATGGTCAAACTCC-AAAGT-TTAATAGTCAAACCACAAAAAACA
1 TCATTGTACATGCATGGTCAAAC-CCTAAA-TATTAATAGTCAAACCACAAAAAACA
* * *
83779 TCATTGTACATGTATGGTCAAACCCTAAATATTGATAGTCAAACCCCAAA
1 TCATTGTACATGCATGGTCAAACCCTAAATATTAATAGTCAAACCACAAA
83829 TTTTGGTCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
54 3 0.07
55 42 0.93
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.26
Consensus pattern (55 bp):
TCATTGTACATGCATGGTCAAACCCTAAATATTAATAGTCAAACCACAAAAAACA
Found at i:83819 original size:21 final size:20
Alignment explanation
Indices: 83795--83882 Score: 90
Period size: 21 Copynumber: 4.3 Consensus size: 20
83785 TACATGTATG
*
83795 GTCAAACCCTAAATATTGATA
1 GTCAAACCCCAAAT-TTGATA
*
83816 GTCAAACCCCAAATTT--TG
1 GTCAAACCCCAAATTTGATA
* *
83834 GTCAAACCCAAAATATTAATA
1 GTCAAACCCCAAAT-TTGATA
83855 GTCAAACCCCCAAAGTTTGATA
1 GTCAAA-CCCCAAA-TTTGATA
83877 GTCAAA
1 GTCAAA
83883 TCACGTTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
18 14 0.25
19 2 0.04
20 2 0.04
21 20 0.36
22 17 0.30
23 1 0.02
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (20 bp):
GTCAAACCCCAAATTTGATA
Found at i:83848 original size:39 final size:40
Alignment explanation
Indices: 83793--83873 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
83783 TGTACATGTA
* * *
83793 TGGTCAAACCCTAAATATTGATAGTCAAA-CCCCAAATTT
1 TGGTCAAACCCAAAATATTAATAGTCAAACCCCCAAAGTT
83832 TGGTCAAACCCAAAATATTAATAGTCAAACCCCCAAAGTT
1 TGGTCAAACCCAAAATATTAATAGTCAAACCCCCAAAGTT
83872 TG
1 TG
83874 ATAGTCAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 27 0.71
40 11 0.29
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (40 bp):
TGGTCAAACCCAAAATATTAATAGTCAAACCCCCAAAGTT
Found at i:85337 original size:16 final size:17
Alignment explanation
Indices: 85305--85351 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
85295 GGTATAAAAT
*
85305 AGATTT-TATAGAGCAA
1 AGATTTGTAAAGAGCAA
85321 AGATTTGTAAAGA-CAA
1 AGATTTGTAAAGAGCAA
*
85337 ATATTTGTAAA-AGCA
1 AGATTTGTAAAGAGCA
85352 CACGAATCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 21 0.78
17 5 0.19
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.30
Consensus pattern (17 bp):
AGATTTGTAAAGAGCAA
Found at i:85878 original size:25 final size:25
Alignment explanation
Indices: 85844--85904 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
85834 ACTGCCTTTT
*
85844 GTCATAAAAATGTTTGATTTAATGG
1 GTCATAAAAATGTATGATTTAATGG
* *
85869 GTCATAAAAAGGTATGATTTGATGG
1 GTCATAAAAATGTATGATTTAATGG
85894 GTCATAAAAAT
1 GTCATAAAAAT
85905 CTAGCAAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.34
Consensus pattern (25 bp):
GTCATAAAAATGTATGATTTAATGG
Found at i:85920 original size:34 final size:34
Alignment explanation
Indices: 85876--85948 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
85866 TGGGTCATAA
*
85876 AAAGGTATGATTTGATGGGTCATAAAAATCTAGC
1 AAAGTTATGATTTGATGGGTCATAAAAATCTAGC
85910 AAAGTTATGATTTGATGGGTCATAAAAATCTAGC
1 AAAGTTATGATTTGATGGGTCATAAAAATCTAGC
*
85944 CAAGT
1 AAAGT
85949 CAAGATTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (34 bp):
AAAGTTATGATTTGATGGGTCATAAAAATCTAGC
Found at i:85956 original size:34 final size:34
Alignment explanation
Indices: 85884--85956 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
85874 AAAAAGGTAT
* *
85884 GATTTGATGGGTCATAAAAATCTAGCAAAGTTAT
1 GATTTGATGGGTCATAAAAATCTAGCAAAGTCAA
*
85918 GATTTGATGGGTCATAAAAATCTAGCCAAGTCAA
1 GATTTGATGGGTCATAAAAATCTAGCAAAGTCAA
85952 GATTT
1 GATTT
85957 TAACTTTCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (34 bp):
GATTTGATGGGTCATAAAAATCTAGCAAAGTCAA
Found at i:87185 original size:105 final size:105
Alignment explanation
Indices: 86962--87324 Score: 538
Period size: 105 Copynumber: 3.5 Consensus size: 105
86952 TTTTTATTCT
* *
86962 TTTTATTAAGTTTAGCCCCAAATTAA-ATTTTTATTTTTATTTTAAGGGTAAATTTCA-AATTAA
1 TTTTACTAAGTTTAGCCCCAAATTAAGA-TTTTATTTTTATTTTAAGGGTAAATTCCATAATTAA
*
87025 TAATTTATTGCTATAGGGTTTTAGAAATAAAATACAAAACTAA
65 TAA--TATTGTTATAGGGTTTTAGAAATAAAATACAAAACTAA
*
87068 TTTTACTAAGTTTAGCCCCAAATTAAGATTTTATTTTTATTTTACGGGTAAATTCCATAATTAAT
1 TTTTACTAAGTTTAGCCCCAAATTAAGATTTTATTTTTATTTTAAGGGTAAATTCCATAATTAAT
*
87133 AATATTGTTATATGGTTTTAGAAATAAAATACAAAACTAA
66 AATATTGTTATAGGGTTTTAGAAATAAAATACAAAACTAA
87173 TTTTACTAAGTTTAGCCCCAAATTAAGATTTTATTTTTATTTTACA-GGTAAATTCCATAATTAA
1 TTTTACTAAGTTTAGCCCCAAATTAAGATTTTATTTTTATTTTA-AGGGTAAATTCCATAATTAA
* * *
87237 TAATATTGTTATAGGGTTTTAGAAATAAAATATATAATTAA
65 TAATATTGTTATAGGGTTTTAGAAATAAAATACAAAACTAA
* * ** *
87278 -TTCACTAAGTTTAG-CCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TTTTACTAAGTTTAGCCCCAAATTAAGATTTTATTTTTATTTTAAGGGT
87325 TAGAAAAATT
Statistics
Matches: 238, Mismatches: 15, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
102 1 0.00
103 27 0.11
104 13 0.05
105 135 0.57
106 52 0.22
107 10 0.04
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.43
Consensus pattern (105 bp):
TTTTACTAAGTTTAGCCCCAAATTAAGATTTTATTTTTATTTTAAGGGTAAATTCCATAATTAAT
AATATTGTTATAGGGTTTTAGAAATAAAATACAAAACTAA
Found at i:88444 original size:2 final size:2
Alignment explanation
Indices: 88437--88495 Score: 65
Period size: 2 Copynumber: 32.0 Consensus size: 2
88427 ATTGATTCAC
* *
88437 TA TA TA TA TA -A TA TA -A TA TA TA TA TA TA TA TA TA TT TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
88477 TA TA TA T- TA TA -A TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
88496 GCATGATACT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
1 5 0.10
2 43 0.90
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:88458 original size:16 final size:15
Alignment explanation
Indices: 88437--88495 Score: 74
Period size: 14 Copynumber: 4.3 Consensus size: 15
88427 ATTGATTCAC
88437 TATATATATAATATA
1 TATATATATAATATA
88452 -ATATATAT-ATATA
1 TATATATATAATATA
*
88465 TATATATTTAA-ATA
1 TATATATATAATATA
88479 TATAT-TATAATA-A
1 TATATATATAATATA
88492 TATA
1 TATA
88496 GCATGATACT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
13 14 0.36
14 24 0.62
15 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATATATAATATA
Found at i:98306 original size:130 final size:131
Alignment explanation
Indices: 98092--98354 Score: 411
Period size: 130 Copynumber: 2.0 Consensus size: 131
98082 GCCATTAGAC
98092 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
* * * * *
98157 TTTAATTTTTACCAGTTTACTATTTTAATT-AAAAACTTATATATATTAGAATTTTTTAAATATA
66 TTTAATTTTTACCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAAATTTTAAAATATA
98221 T
131 T
* * * * *
98222 TTTTATAGTTTTACTCAACTAAAAACTCTTTTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
* *
98287 TTTTATTTTTATCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAAATTTTAAAATATA
66 TTTAATTTTTACCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAAATTTTAAAATATA
98352 T
131 T
98353 TT
1 TT
98355 CTTAAATGAC
Statistics
Matches: 120, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
130 86 0.72
131 34 0.28
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.49
Consensus pattern (131 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
TTTAATTTTTACCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAAATTTTAAAATATA
T
Found at i:100582 original size:29 final size:29
Alignment explanation
Indices: 100540--100629 Score: 171
Period size: 29 Copynumber: 3.1 Consensus size: 29
100530 ATGTTAGTTT
100540 AGTTTATTTGTTTGTTTGGTAGTTTGGTA
1 AGTTTATTTGTTTGTTTGGTAGTTTGGTA
*
100569 AGTTTATTTATTTGTTTGGTAGTTTGGTA
1 AGTTTATTTGTTTGTTTGGTAGTTTGGTA
100598 AGTTTATTTGTTTGTTTGGTAGTTTGGTA
1 AGTTTATTTGTTTGTTTGGTAGTTTGGTA
100627 AGT
1 AGT
100630 ATGTTATTTA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.16, C:0.00, G:0.27, T:0.58
Consensus pattern (29 bp):
AGTTTATTTGTTTGTTTGGTAGTTTGGTA
Found at i:100603 original size:25 final size:26
Alignment explanation
Indices: 100550--100638 Score: 97
Period size: 29 Copynumber: 3.1 Consensus size: 26
100540 AGTTTATTTG
100550 TTTGTTTGGTAGTTTGGTAAGTTTATTTA
1 TTTGTTTGGTAGTTTGGTAAG--T-TTTA
*
100579 TTTGTTTGGTAGTTTGGTAAGTTTATTTG
1 TTTGTTTGGTAGTTTGGTAAG--T-TTTA
100608 TTTGTTTGGTAGTTTGGTAAGTATGTTA
1 TTTGTTTGGTAGTTTGGTAAGT-T-TTA
100636 TTT
1 TTT
100639 AAGGTAATTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
27 3 0.05
28 5 0.09
29 49 0.86
ACGTcount: A:0.16, C:0.00, G:0.26, T:0.58
Consensus pattern (26 bp):
TTTGTTTGGTAGTTTGGTAAGTTTTA
Found at i:100607 original size:21 final size:20
Alignment explanation
Indices: 100583--100622 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
100573 TATTTATTTG
100583 TTTGGTAGTTTGGTAAGTTTA
1 TTTGGTAGTTTGGT-AGTTTA
* *
100604 TTTGTTTGTTTGGTAGTTT
1 TTTGGTAGTTTGGTAGTTT
100623 GGTAAGTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.12, C:0.00, G:0.28, T:0.60
Consensus pattern (20 bp):
TTTGGTAGTTTGGTAGTTTA
Found at i:101756 original size:26 final size:25
Alignment explanation
Indices: 101719--101774 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 25
101709 TTTATCCACG
101719 ATTTC-TTTATTCCTTATTTCTAAA
1 ATTTCTTTTATTCCTTATTTCTAAA
101743 ATTTCTTTTCATTCCTTATTTCTAAA
1 ATTTCTTTT-ATTCCTTATTTCTAAA
101769 ATTTCT
1 ATTTCT
101775 AAAAGAAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 5 0.17
25 3 0.10
26 22 0.73
ACGTcount: A:0.23, C:0.18, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTTCTTTTATTCCTTATTTCTAAA
Done.