Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024254.1 Corchorus olitorius cultivar O-4 contig24287, 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: 47110
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:1105 original size:83 final size:83
Alignment explanation
Indices: 961--1125 Score: 321
Period size: 83 Copynumber: 2.0 Consensus size: 83
951 ATTAGTGGCA
*
961 ACTCCATTTCAAACGTCGTTTCGACAGGGTTCGGAACCCGGACCCGAACGTTTCAACACCATGAA
1 ACTCAATTTCAAACGTCGTTTCGACAGGGTTCGGAACCCGGACCCGAACGTTTCAACACCATGAA
1026 CCTGCACTTGCCAACAAG
66 CCTGCACTTGCCAACAAG
1044 ACTCAATTTCAAACGTCGTTTCGACAGGGTTCGGAACCCGGACCCGAACGTTTCAACACCATGAA
1 ACTCAATTTCAAACGTCGTTTCGACAGGGTTCGGAACCCGGACCCGAACGTTTCAACACCATGAA
1109 CCTGCACTTGCCAACAA
66 CCTGCACTTGCCAACAA
1126 CTTTCCACCA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (83 bp):
ACTCAATTTCAAACGTCGTTTCGACAGGGTTCGGAACCCGGACCCGAACGTTTCAACACCATGAA
CCTGCACTTGCCAACAAG
Found at i:8892 original size:19 final size:19
Alignment explanation
Indices: 8868--8904 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
8858 TGTATCTGTA
8868 ACCGTTTCACCACCGTTTG
1 ACCGTTTCACCACCGTTTG
8887 ACCGTTTCACCACCGTTT
1 ACCGTTTCACCACCGTTT
8905 TGGGTCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.38, G:0.14, T:0.32
Consensus pattern (19 bp):
ACCGTTTCACCACCGTTTG
Found at i:12992 original size:24 final size:25
Alignment explanation
Indices: 12946--12996 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
12936 ATTGGAGTAT
*
12946 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
12971 TTATTT-TCTTGTTTATTTATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
12995 TT
1 TT
12997 GTTCACATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:15546 original size:191 final size:190
Alignment explanation
Indices: 15223--15599 Score: 711
Period size: 191 Copynumber: 2.0 Consensus size: 190
15213 CCCCATCCCT
*
15223 TTGACAATAATAATAATCAAGGAAGAGGAGCACTGAAAAAGAAAATTAAATAATTTTGATTAGGG
1 TTGACAATAATAATAATCAAGGAAGAGGAGCACCGAAAAAGAAAATTAAATAATTTTGATTAGGG
15288 AAAAAAACACTTTTGGATATTAGTGGTAATGCAACTAATTCAATCAAAACTTTGGACCATAATTA
66 AAAAAAACACTTTTGGATATTAGTGGTAATGCAACTAATTCAATCAAAACTTTGGACCATAATTA
15353 CTAGCTAGAAAAAAAAGGATGTTTTACAGTGGAATAGCCACTTTGCCTCTTAAATTGACA
131 CTAGCTAGAAAAAAAAGGATGTTTTACAGTGGAATAGCCACTTTGCCTCTTAAATTGACA
*
15413 TTGACAATAATAATAATCAAGGAGGAGGAGCACCGAAAAAGAAAAATTAAATAATTTTGATTAGG
1 TTGACAATAATAATAATCAAGGAAGAGGAGCACCGAAAAAG-AAAATTAAATAATTTTGATTAGG
15478 GAAAAAAAACACTTTTGGATATTAGTGGTAA-GCAACTAATTCAATCAAAACTTTGGACCATAAT
65 G-AAAAAAACACTTTTGGATATTAGTGGTAATGCAACTAATTCAATCAAAACTTTGGACCATAAT
15542 TACTAGCTAGAAAAAAAAGGATGTTTTACAGTGGAATAGCCACTTTGCCTCTTAAATT
129 TACTAGCTAGAAAAAAAAGGATGTTTTACAGTGGAATAGCCACTTTGCCTCTTAAATT
15600 TTGTAAATCT
Statistics
Matches: 183, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
190 39 0.21
191 115 0.63
192 29 0.16
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (190 bp):
TTGACAATAATAATAATCAAGGAAGAGGAGCACCGAAAAAGAAAATTAAATAATTTTGATTAGGG
AAAAAAACACTTTTGGATATTAGTGGTAATGCAACTAATTCAATCAAAACTTTGGACCATAATTA
CTAGCTAGAAAAAAAAGGATGTTTTACAGTGGAATAGCCACTTTGCCTCTTAAATTGACA
Found at i:16604 original size:106 final size:105
Alignment explanation
Indices: 16375--16631 Score: 281
Period size: 106 Copynumber: 2.4 Consensus size: 105
16365 AAGATTTACT
*
16375 CTTTTAAAAAATAAAAGTATTTTTATAATTGGGGCTAATCCTTATTGATAAGTGTTTAAACTTAT
1 CTTTT-AAAAATAAAA-TATTTTTATAATTGGGGCTAAACCTTATTGATAAGTGTTTAAACTTAT
* * * *
16440 TTTTCTAAAATCCATGATGAGTTTCAAAATTTGAGACTTAAC
64 TTTTCTAAAATCAATAATGAGTTTCAAAAGTTAAGACTTAAC
*
16482 CTTTTAAAAAATTAAAATA-TTTTATAATTGGGG-TCAAAGCTTATTGATAAGTGTTTAAACTTA
1 CTTTT-AAAAA-TAAAATATTTTTATAATTGGGGCT-AAACCTTATTGATAAGTGTTTAAACTTA
* * * *
16545 TTTTTCTAAACTCTATAATAATGGGTCTT-AAAAGTTAATA-TTTAC
63 TTTTTCTAAAATC---AATAATGAGT-TTCAAAAGTTAAGACTTAAC
* *
16590 CATTTT-AAAATAAAACATTTTTATAATTGGGGATAAACCTTA
1 C-TTTTAAAAATAAAATATTTTTATAATTGGGGCTAAACCTTA
16632 ATTTCATAAA
Statistics
Matches: 129, Mismatches: 12, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
105 1 0.01
106 58 0.45
107 38 0.29
108 11 0.09
109 19 0.15
110 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.41
Consensus pattern (105 bp):
CTTTTAAAAATAAAATATTTTTATAATTGGGGCTAAACCTTATTGATAAGTGTTTAAACTTATTT
TTCTAAAATCAATAATGAGTTTCAAAAGTTAAGACTTAAC
Found at i:17053 original size:84 final size:82
Alignment explanation
Indices: 16944--17272 Score: 439
Period size: 84 Copynumber: 3.9 Consensus size: 82
16934 CCAATAACCA
16944 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTTTCTTTCTAAAGTCCTCAAACACATTTAT
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAA--TTCTTTCTAAAGTCCTCAAACACATTTAT
17009 AACACAGAAGCATCATATC
64 AACACAGAAGCATCATATC
* *
17028 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTATTCCAAAGTTCTCAAACACATTTATA
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCT-TTCTAAAGTCCTCAAACACATTTATA
17093 ACACAG-AGACATCTATATC
65 ACACAGAAG-CATC-ATATC
* * *
17112 AAAGTCCCCAAACACATTTATAACACAGGGGCAATCCTCTCTAAAAGTCCTCAAACACATTTATA
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTTTCT-AAAGTCCTCAAACACATTTATA
* *
17177 ACATAGAGGCATCCATA-C
65 ACACAGAAGCAT-CATATC
* ** *
17195 TAAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATT-TCAAAGTCCTCAAATACATTTA
1 -AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCT-TTCT-AAAGTCCTCAAACACATTTA
*
17259 TAACACAGAGGCAT
63 TAACACAGAAGCAT
17273 TTCTCTTTAT
Statistics
Matches: 221, Mismatches: 16, Indels: 16
0.87 0.06 0.06
Matches are distributed among these distances:
82 6 0.03
83 37 0.17
84 175 0.79
85 3 0.01
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24
Consensus pattern (82 bp):
AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTTTCTAAAGTCCTCAAACACATTTATAA
CACAGAAGCATCATATC
Found at i:17083 original size:43 final size:43
Alignment explanation
Indices: 16944--17276 Score: 310
Period size: 43 Copynumber: 7.9 Consensus size: 43
16934 CCAATAACCA
* * * *
16944 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTTTCT-TTCT
1 AAAGTCCTCAAACACATTTATAACACAGAGGCAA--TTCTATTCC
*
16988 AAAGTCCTCAAACACATTTATAACACAGAAGC-A-TC-ATAT-C
1 AAAGTCCTCAAACACATTTATAACACAGAGGCAATTCTAT-TCC
* * *
17028 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTATTCC
1 AAAGTCCTCAAACACATTTATAACACAGAGGCAATTCTATTCC
* *
17071 AAAGTTCTCAAACACATTTATAACACAGAGAC-A-TCTATAT-C
1 AAAGTCCTCAAACACATTTATAACACAGAGGCAATTCTAT-TCC
* * * * *
17112 AAAGTCCCCAAACACATTTATAACACAGGGGCAATCCT-CTCTA
1 AAAGTCCTCAAACACATTTATAACACAGAGGCAATTCTATTC-C
* * * *
17155 AAAGTCCTCAAACACATTTATAACATAGAGGC-A-TCCATACT
1 AAAGTCCTCAAACACATTTATAACACAGAGGCAATTCTATTCC
* * ** *
17196 AAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTTC
1 AAAGTCCTCAAACACATTTATAACACAGAGGCAATTCTATTCC
* *
17239 AAAGTCCTCAAATACATTTATAACACAGAGGCATTTCT
1 AAAGTCCTCAAACACATTTATAACACAGAGGCAATTCT
17277 CTTTATGGCA
Statistics
Matches: 233, Mismatches: 42, Indels: 29
0.77 0.14 0.10
Matches are distributed among these distances:
40 31 0.13
41 67 0.29
42 8 0.03
43 99 0.42
44 28 0.12
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24
Consensus pattern (43 bp):
AAAGTCCTCAAACACATTTATAACACAGAGGCAATTCTATTCC
Found at i:17222 original size:168 final size:167
Alignment explanation
Indices: 16944--17268 Score: 501
Period size: 168 Copynumber: 1.9 Consensus size: 167
16934 CCAATAACCA
* *
16944 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTTTCTTTCTAAAGTCCTCAAACACATTTAT
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAA-TTCCTCTCTAAAGTCCTCAAACACATTTAT
*
17009 AACACAGAAGCATCATATCAAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTATTCCAAA
65 AACACAGAAGCATCATATCAAAGTCCCCAAACACAATTATAACACAGGGGCAACTCTATTCCAAA
*
17074 GTTCTCAAACACATTTATAACACAGAGACATCTATATC
130 GTCCTCAAACACATTTATAACACAGAGACATCTATATC
*
17112 AAAGTCCCCAAACACATTTATAACACAGGGGCAA-TCCTCTCTAAAAGTCCTCAAACACATTTAT
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCCTCTCT-AAAGTCCTCAAACACATTTAT
* * * * *
17176 AACATAGAGGCATCCATA-CTAAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTTCA
65 AACACAGAAGCAT-CATATC-AAAGTCCCCAAACACAATTATAACACAGGGGCAACTCTATTCCA
*
17240 AAGTCCTCAAATACATTTATAACACAGAG
128 AAGTCCTCAAACACATTTATAACACAGAG
17269 GCATTTCTCT
Statistics
Matches: 143, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
166 6 0.04
167 33 0.23
168 104 0.73
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24
Consensus pattern (167 bp):
AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCCTCTCTAAAGTCCTCAAACACATTTATA
ACACAGAAGCATCATATCAAAGTCCCCAAACACAATTATAACACAGGGGCAACTCTATTCCAAAG
TCCTCAAACACATTTATAACACAGAGACATCTATATC
Found at i:17674 original size:58 final size:58
Alignment explanation
Indices: 17581--17907 Score: 546
Period size: 58 Copynumber: 5.6 Consensus size: 58
17571 CATGAATTGC
* * *
17581 CTTCAGATCCATCTGTGAGCTGTCTTTAGTTTTAATCTTAAAATCTTTTAGGAACTGT
1 CTTCAGATCCATCTGTGAGCTGTCTTCAGTCTCAATCTTAAAATCTTTTAGGAACTGT
* * * * *
17639 CTTCAGATCCATATGTGAGCTGTCTTCAGCCTTAATCTTAAAACCTTTTAGGAATTGT
1 CTTCAGATCCATCTGTGAGCTGTCTTCAGTCTCAATCTTAAAATCTTTTAGGAACTGT
* *
17697 CTTGAGATTCATCTGTGAGCTGTCTTCAGTCTCAATCTTAAAATCTTTTAGGAACTGT
1 CTTCAGATCCATCTGTGAGCTGTCTTCAGTCTCAATCTTAAAATCTTTTAGGAACTGT
* *
17755 CTTCAGATCCATATGTGAGCTGTCTTCAGTCTCAATCTCAAAATCTTTTAGGAACTGT
1 CTTCAGATCCATCTGTGAGCTGTCTTCAGTCTCAATCTTAAAATCTTTTAGGAACTGT
17813 CTTCAGATCCATCTGTGAGCTGTCTTCAGTCTCAATCTTAAAATCTTTTAGGAACTGT
1 CTTCAGATCCATCTGTGAGCTGTCTTCAGTCTCAATCTTAAAATCTTTTAGGAACTGT
17871 CTTCAGATCCATCTGTGAGCTGTCTTCAGTCTCAATC
1 CTTCAGATCCATCTGTGAGCTGTCTTCAGTCTCAATC
17908 CAGAATCTTT
Statistics
Matches: 250, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 250 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (58 bp):
CTTCAGATCCATCTGTGAGCTGTCTTCAGTCTCAATCTTAAAATCTTTTAGGAACTGT
Found at i:17998 original size:54 final size:54
Alignment explanation
Indices: 17914--18304 Score: 446
Period size: 54 Copynumber: 7.6 Consensus size: 54
17904 AATCCAGAAT
* * ** * *
17914 CTTTCTTGACTGACCACACTGGATTGCTTGAAGAAAAACTTAAACCACTATAAA
1 CTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCACTGTAAA
** * *
17968 CTTGATTAATTGACCGCACTGGATCACTT---G--AAAC---CACCA--G-AAA
1 CTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCACTGTAAA
*
18011 CTTTCTTGATTGACCACACTGGATCACTTGAAGATAAACTTAAACCACTGTAAA
1 CTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCACTGTAAA
* *
18065 CTTTCTTGATTGATCGCACTGGATCACTT-----T-GA---AAACCACTGTAAA
1 CTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCACTGTAAA
*
18110 CTTTCTTGATTGACCGCACTGGATCACCTTGAAGATAAACTTAAACCACTGAAAA
1 CTTTCTTGATTGACCGCACTGGATCA-CTTGAAGATAAACTTAAACCACTGTAAA
* *
18165 CTTTCTTGATTGACCGCGCTGGATCACTTGAAAATAAACTTAAACCACTTGTAAA
1 CTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCAC-TGTAAA
* *
18220 ATTTCTTGATTGACCGCACTGGATCACTTTGAAGATAAACTTATACCACTGTAAA
1 CTTTCTTGATTGACCGCACTGGATCAC-TTGAAGATAAACTTAAACCACTGTAAA
18275 -TTTCTTGATTGACCGCACTGGATCACTTGA
1 CTTTCTTGATTGACCGCACTGGATCACTTGA
18305 GGTAAATTGA
Statistics
Matches: 287, Mismatches: 27, Indels: 47
0.80 0.07 0.13
Matches are distributed among these distances:
43 28 0.10
45 38 0.13
46 8 0.03
48 5 0.02
49 5 0.02
51 6 0.02
52 1 0.00
53 5 0.02
54 99 0.34
55 73 0.25
56 19 0.07
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (54 bp):
CTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCACTGTAAA
Found at i:18077 original size:97 final size:99
Alignment explanation
Indices: 17914--18304 Score: 484
Period size: 97 Copynumber: 3.9 Consensus size: 99
17904 AATCCAGAAT
* ** * * ** *
17914 CTTTCTTGACTGACCACACTGGATTGCTTGAAGAAAAACTTAAACCACTATAAACTTGATTAATT
1 CTTTCTTGATTGACCACACTGGATCACTTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATT
17979 GACCGCACTGGATCACTTG-AAACCACCAG-AAA
66 GACCGCACTGGATCACTTGAAAACCACCAGTAAA
18011 CTTTCTTGATTGACCACACTGGATCACTTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATT
1 CTTTCTTGATTGACCACACTGGATCACTTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATT
* *
18076 GATCGCACTGGATCACTTTGAAAACCA-CTGTAAA
66 GACCGCACTGGATCAC-TTGAAAACCACCAGTAAA
* *
18110 CTTTCTTGATTGACCGCACTGGATCACCTTGAAGATAAACTTAAACCACTGAAAACTTTCTTGAT
1 CTTTCTTGATTGACCACACTGGATCA-CTTGAAGATAAACTTAAACCACTGTAAACTTTCTTGAT
* *
18175 TGACCGCGCTGGATCACTTGAAAATAAACTTAAACCACTTGTAAA
65 TGACCGCACTGGATCACTTG---A-AAAC---CACCA---GTAAA
* * *
18220 ATTTCTTGATTGACCGCACTGGATCACTTTGAAGATAAACTTATACCACTGTAAA-TTTCTTGAT
1 CTTTCTTGATTGACCACACTGGATCAC-TTGAAGATAAACTTAAACCACTGTAAACTTTCTTGAT
18284 TGACCGCACTGGATCACTTGA
65 TGACCGCACTGGATCACTTGA
18305 GGTAAATTGA
Statistics
Matches: 258, Mismatches: 20, Indels: 23
0.86 0.07 0.08
Matches are distributed among these distances:
97 72 0.28
98 5 0.02
99 37 0.14
100 52 0.20
102 1 0.00
103 4 0.02
106 2 0.01
107 1 0.00
109 29 0.11
110 55 0.21
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (99 bp):
CTTTCTTGATTGACCACACTGGATCACTTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATT
GACCGCACTGGATCACTTGAAAACCACCAGTAAA
Found at i:18116 original size:45 final size:45
Alignment explanation
Indices: 18052--18142 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
18042 AGATAAACTT
* *
18052 AAACCACTGTAAACTTTCTTGATTGATCGCACTGGATCACTTTGA
1 AAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACCTTGA
18097 AAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACCTTGA
1 AAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACCTTGA
18142 A
1 A
18143 GATAAACTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (45 bp):
AAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACCTTGA
Found at i:18181 original size:55 final size:53
Alignment explanation
Indices: 18097--18304 Score: 317
Period size: 55 Copynumber: 3.8 Consensus size: 53
18087 ATCACTTTGA
*
18097 AAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACCTTGAAGATAAACTT
1 AAACCACTG-AAAATTTCTTGATTGACCGCACTGGATCA-CTTGAAGATAAACTT
* *
18152 AAACCACTGAAAACTTTCTTGATTGACCGCGCTGGATCACTTGAAAATAAACTT
1 AAACCACTGAAAA-TTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTT
18206 AAACCACTTGTAAAATTTCTTGATTGACCGCACTGGATCACTTTGAAGATAAACTT
1 AAACCAC-TG-AAAATTTCTTGATTGACCGCACTGGATCAC-TTGAAGATAAACTT
* *
18262 ATACCACTGTAAATTTCTTGATTGACCGCACTGGATCACTTGA
1 AAACCACTGAAAATTTCTTGATTGACCGCACTGGATCACTTGA
18305 GGTAAATTGA
Statistics
Matches: 142, Mismatches: 7, Indels: 10
0.89 0.04 0.06
Matches are distributed among these distances:
53 4 0.03
54 53 0.37
55 62 0.44
56 23 0.16
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (53 bp):
AAACCACTGAAAATTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTT
Found at i:18336 original size:16 final size:17
Alignment explanation
Indices: 18311--18344 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
18301 TTGAGGTAAA
*
18311 TTGAAGCATTG-AAGAT
1 TTGAAACATTGAAAGAT
18327 TTGAAACATTGAAAGAT
1 TTGAAACATTGAAAGAT
18344 T
1 T
18345 GAAGAATTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (17 bp):
TTGAAACATTGAAAGAT
Found at i:18337 original size:24 final size:23
Alignment explanation
Indices: 18310--18380 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 23
18300 CTTGAGGTAA
18310 ATTGAAGCATTGAAGATTTGAAAC
1 ATTGAAG-ATTGAAGATTTGAAAC
* * *
18334 ATTGAAAGATTGAAGAATTGGAGC
1 ATTG-AAGATTGAAGATTTGAAAC
*
18358 ATTGAATATTTGAAGAATTTGAA
1 ATTGAAGA-TTGAAG-ATTTGAA
18381 TAATTTGAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
23 3 0.08
24 27 0.71
25 8 0.21
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.31
Consensus pattern (23 bp):
ATTGAAGATTGAAGATTTGAAAC
Found at i:18379 original size:9 final size:9
Alignment explanation
Indices: 18359--18394 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
18349 AATTGGAGCA
18359 TTGAAT-AT
1 TTGAATAAT
*
18367 TTGAAGAAT
1 TTGAATAAT
18376 TTGAATAAT
1 TTGAATAAT
18385 TTGAATAAT
1 TTGAATAAT
18394 T
1 T
18395 GGAGAAAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 5 0.20
9 20 0.80
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (9 bp):
TTGAATAAT
Found at i:20182 original size:10 final size:10
Alignment explanation
Indices: 20167--20197 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
20157 ATTCCTATCT
20167 TATAAATATA
1 TATAAATATA
20177 TATAAATATA
1 TATAAATATA
*
20187 TATATATATA
1 TATAAATATA
20197 T
1 T
20198 GTGTGTAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
TATAAATATA
Found at i:40483 original size:31 final size:31
Alignment explanation
Indices: 40443--40529 Score: 156
Period size: 31 Copynumber: 2.8 Consensus size: 31
40433 CCGTACCGGA
*
40443 TCGGTCGGTTAAACCGGGAACCGATTGAACC
1 TCGGCCGGTTAAACCGGGAACCGATTGAACC
*
40474 TCGGCCGGTTAAATCGGGAACCGATTGAACC
1 TCGGCCGGTTAAACCGGGAACCGATTGAACC
40505 TCGGCCGGTTAAACCGGGAACCGAT
1 TCGGCCGGTTAAACCGGGAACCGAT
40530 ATCCAGTCCG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.25, C:0.26, G:0.30, T:0.18
Consensus pattern (31 bp):
TCGGCCGGTTAAACCGGGAACCGATTGAACC
Found at i:45133 original size:16 final size:17
Alignment explanation
Indices: 45112--45147 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
45102 ACATAACCAT
45112 ATAACAATAATAT-ATA
1 ATAACAATAATATAATA
45128 ATAACAATAATATAATA
1 ATAACAATAATATAATA
45145 ATA
1 ATA
45148 TTAACTTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
ATAACAATAATATAATA
Done.