Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018901.1 Corchorus olitorius cultivar O-4 contig18934, 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: 70675
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Found at i:1952 original size:2 final size:2
Alignment explanation
Indices: 1947--1971 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1937 AAAAATTAAC
1947 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1972 GTAAAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4079 original size:131 final size:130
Alignment explanation
Indices: 3835--4384 Score: 710
Period size: 131 Copynumber: 4.1 Consensus size: 130
3825 GCGCAACGAC
* * * * *
3835 TTATAAAGTTGTTACAAATAGATTATGATTTCGCAACAACTTAAAAATTTGTTGTTACGAATATA
1 TTATAAAGTTGTTACGAAT-GTTTATGATTTCACAACAACTTAAGAAGTTGTTGTTACG-A-ATA
* * * * * *
3900 CTGTAAATATTGACAACAACTAAAAAGGTGTTGTGTAAAATACCATCAAAATCACTTAGGCACCA
63 CTGTAAACATTGGCAACAACTAAAAAAGTGTTGTATAAAATACCATCAAAATCACTTAGACAACA
3965 TTT
128 TTT
* *
3968 TTATAAAGTTGTTACGAATGTTTTATGATTTCACAGCAATTTAAGAAGTTGTTGTTACGAATACT
1 TTATAAAGTTGTTACGAATG-TTTATGATTTCACAACAACTTAAGAAGTTGTTGTTACGAATACT
*
4033 GTAAACATTGGCAACAACTAAAAAAGTGTTGTATAAAATACAATCAAAATCACTTAGACAACATT
65 GTAAACATTGGCAACAACTAAAAAAGTGTTGTATAAAATACCATCAAAATCACTTAGACAACATT
4098 T
130 T
* * * * *
4099 TTTTAAAGCTGTTACGGATGATTTATGATTTCACAGCAACTTAAGAAGTTGTTGTTACGAATACA
1 TTATAAAGTTGTTACGAATG-TTTATGATTTCACAACAACTTAAGAAGTTGTTGTTACGAATACT
* * *
4164 ATAAACATTGGCAACAACTAAAAAAGTGTTGTGT--AA-ACCATCAAAATCACTTATAGGCAACA
65 GTAAACATTGGCAACAACTAAAAAAGTGTTGTATAAAATACCATCAAAATCAC-T-TAGACAAC-
4226 TTTTTAATTT
127 ------ATTT
* * *
4236 TTATAAAGTTGTAACAAATGGTTTATGATTTCGCAACAACTTAAGAAGTTGTTGTTACGAATACT
1 TTATAAAGTTGTTACGAAT-GTTTATGATTTCACAACAACTTAAGAAGTTGTTGTTACGAATACT
*
4301 GTAAACATTGGCAACGACTAAAAAAGTGTTGTATAAAATACCATCAAAATCACTTAGACAACATT
65 GTAAACATTGGCAACAACTAAAAAAGTGTTGTATAAAATACCATCAAAATCACTTAGACAACATT
4366 T
130 T
4367 TTATAAAGTTGTTACGAA
1 TTATAAAGTTGTTACGAA
4385 GAAGAAGTTG
Statistics
Matches: 365, Mismatches: 38, Indels: 30
0.84 0.09 0.07
Matches are distributed among these distances:
128 13 0.04
129 3 0.01
130 7 0.02
131 175 0.48
132 2 0.01
133 50 0.14
137 90 0.25
138 8 0.02
139 3 0.01
140 14 0.04
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (130 bp):
TTATAAAGTTGTTACGAATGTTTATGATTTCACAACAACTTAAGAAGTTGTTGTTACGAATACTG
TAAACATTGGCAACAACTAAAAAAGTGTTGTATAAAATACCATCAAAATCACTTAGACAACATTT
Found at i:4330 original size:268 final size:263
Alignment explanation
Indices: 3835--4382 Score: 755
Period size: 268 Copynumber: 2.1 Consensus size: 263
3825 GCGCAACGAC
* ** * *
3835 TTATAAAGTTGTTACAAATAGA-TTATGATTTCGCAACAACTTAAAAATTTGTTGTTACGAATAT
1 TTATAAAGCTGTTACGGAT-GATTTATGATTTCACAACAACTTAAAAAGTTGTTGTTACGAATAT
** * * *
3899 ACTGTAAATATTGACAACAACTAAAAAGGTGTTGTGTAAAATACCATCAAAATCACTTAGGCACC
65 ACAATAAACATTGACAACAACTAAAAAAGTGTTGTGT-AAATACCATCAAAATCACTTAGGCACA
* * * * *
3964 ATTTTTATAAAGTTGTTACGAATGTTTTATGATTTCACAGCAATTTAAGAAGTTGTTGTTACGAA
129 ATTTTTATAAAGTTGTAACAAATGGTTTATGATTTCACAACAACTTAAGAAGTTGTTGTTACGAA
4029 TACTGTAAACATTGGCAACAACTAAAAAAGTGTTGTATAAAATACAATCAAAATCACTTAGACAA
194 TACTGTAAACATTGGCAACAACTAAAAAAGTGTTGTATAAAATACAATCAAAATCACTTAGACAA
4094 CATTT
259 CATTT
* * *
4099 TTTTAAAGCTGTTACGGATGATTTATGATTTCACAGCAACTTAAGAAGTTGTTGTTACG-A-ATA
1 TTATAAAGCTGTTACGGATGATTTATGATTTCACAACAACTTAAAAAGTTGTTGTTACGAATATA
*
4162 CAATAAACATTGGCAACAACTAAAAAAGTGTTGTGT-AA-ACCATCAAAATCACTTATAGGCAAC
66 CAATAAACATTGACAACAACTAAAAAAGTGTTGTGTAAATACCATCAAAATCAC-T-TAGGC-AC
*
4225 ATTTTTAATTTTTATAAAGTTGTAACAAATGGTTTATGATTTCGCAACAACTTAAGAAGTTGTTG
128 ------AATTTTTATAAAGTTGTAACAAATGGTTTATGATTTCACAACAACTTAAGAAGTTGTTG
* *
4290 TTACGAATACTGTAAACATTGGCAACGACTAAAAAAGTGTTGTATAAAATACCATCAAAATCACT
187 TTACGAATACTGTAAACATTGGCAACAACTAAAAAAGTGTTGTATAAAATACAATCAAAATCACT
4355 TAGACAACATTT
252 TAGACAACATTT
*
4367 TTATAAAGTTGTTACG
1 TTATAAAGCTGTTACG
4383 AAGAAGAAGT
Statistics
Matches: 250, Mismatches: 24, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
259 14 0.06
260 3 0.01
261 5 0.02
262 36 0.14
263 3 0.01
264 48 0.19
268 141 0.56
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (263 bp):
TTATAAAGCTGTTACGGATGATTTATGATTTCACAACAACTTAAAAAGTTGTTGTTACGAATATA
CAATAAACATTGACAACAACTAAAAAAGTGTTGTGTAAATACCATCAAAATCACTTAGGCACAAT
TTTTATAAAGTTGTAACAAATGGTTTATGATTTCACAACAACTTAAGAAGTTGTTGTTACGAATA
CTGTAAACATTGGCAACAACTAAAAAAGTGTTGTATAAAATACAATCAAAATCACTTAGACAACA
TTT
Found at i:4620 original size:131 final size:128
Alignment explanation
Indices: 4423--5109 Score: 758
Period size: 131 Copynumber: 5.3 Consensus size: 128
4413 ACATTGGCAA
* *
4423 TTGTGTAAAATACCATCAAAATCACTTAGGCAACTTTTTATAAAGTTGTTACAAATAGTTTATGA
1 TTGTGTAAAATACCATCAAAATCACTTAGGCAACCTTTTATAAAGTTGTTACGAATAGTTTATGA
**** * *
4488 TTTCGCAACAACTTAAGAAGCTGTTGTTACGAATACTGTAACTATTGGTAACAACTAAAAAAGTG
66 TTTCGCAACAACTT-AGTTTTTGTTGTTACGAAAACTGTAAC-ATTGGCAACAACTAAAAAAGTG
* *
4553 TTGTGTAAAATACCATCAAAATCACTTAGGTAACGCTTTTATAAAGTTGTTACGAATAGATTATG
1 TTGTGTAAAATACCATCAAAATCACTTAGGCAAC-CTTTTATAAAGTTGTTACGAATAGTTTATG
* *** * *
4618 ATTTCGCAGCAACTTAAGAAGTTGTTGTTACTAATACTGTAAACATTGGCAACAACTAAAAAAGT
65 ATTTCGCAACAACTT-AGTTTTTGTTGTTACGAAAACTGT-AACATTGGCAACAACTAAAAAAGT
*
4683 C
128 G
4684 TTGTGTAAAATACCATCAAAATCACTTAGGCAACCTTTTTATAAAGTTGTTACGAATAGTTTATG
1 TTGTGTAAAATACCATCAAAATCACTTAGGCAACC-TTTTATAAAGTTGTTACGAATAGTTTATG
* * * * *
4749 ATTT--C-ACAAC-GAGTTTTTTTTGTTACGAAAATTGTAAGCATTGGCAACGACTAAAAAGGTG
65 ATTTCGCAACAACTTAGTTTTTGTTGTTACGAAAACTGTAA-CATTGGCAACAACTAAAAAAGTG
* * *
4810 TTGTGTAAAACACCATCAAAATCACTTAGGCAACATTTTTATAAAGTTGTTACGAATAGTTTAGG
1 TTGTGTAAAATACCATCAAAATCACTTAGGCAAC-CTTTTATAAAGTTGTTACGAATAGTTTATG
* * * * * * *
4875 ATTTTGCAACGACTTTGTTTTTGTTGTTACGAGAAGTGTAAGCATTGGCAACGACTAAAAAAGTA
65 ATTTCGCAACAACTTAGTTTTTGTTGTTACGAAAACTGTAA-CATTGGCAACAACTAAAAAAGTG
* ** *
4940 TTGTGT-AAA-ACTATCAAAATCACTTAGCCAACGAGGCAACGAGTTTATAAAATTGTTACGAAT
1 TTGTGTAAAATACCATCAAAATCACTT--------AGGCAAC-CTTTTATAAAGTTGTTACGAAT
* * * * *
5003 AGATTATGATTTCGCAACAACTTTGTTTTTGTTGTTACGAAAACTATAAACATTGGCAATAATTA
57 AGTTTATGATTTCGCAACAACTTAGTTTTTGTTGTTACGAAAACTGT-AACATTGGCAACAACTA
5068 AAAAAGTCG
121 AAAAAGT-G
**
5077 TTGAATAAAATACCATCAAAATCAC-TAGGCAAC
1 TTGTGTAAAATACCATCAAAATCACTTAGGCAAC
5110 TACTTTTAAT
Statistics
Matches: 483, Mismatches: 53, Indels: 42
0.84 0.09 0.07
Matches are distributed among these distances:
125 2 0.00
126 102 0.21
128 20 0.04
129 8 0.02
130 91 0.19
131 149 0.31
132 3 0.01
136 85 0.18
137 6 0.01
138 4 0.01
139 13 0.03
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (128 bp):
TTGTGTAAAATACCATCAAAATCACTTAGGCAACCTTTTATAAAGTTGTTACGAATAGTTTATGA
TTTCGCAACAACTTAGTTTTTGTTGTTACGAAAACTGTAACATTGGCAACAACTAAAAAAGTG
Found at i:4839 original size:257 final size:259
Alignment explanation
Indices: 4422--5117 Score: 728
Period size: 257 Copynumber: 2.7 Consensus size: 259
4412 AACATTGGCA
4422 ATTGTGTAAAATACCATCAAAATCACTTAGGCAA-CTTTTTATAAAGTTGTTACAAATAGTTTAT
1 ATTGTGTAAAATACCATCAAAATCACTTAGGCAACCTTTTTATAAAGTTGTTACAAATAGTTTAT
* *
4486 GATTTCGCAACAACTTAAGAAGCTGTTGTTACGAATACTGTAACTATTGGTAACAACTAAAAAAG
66 GATTTC-CAACAAC-TAAGAAGCTGTTGTTACGAAAACTGTAACTATTGGCAACAACTAAAAAAG
* * *
4551 TGTTGTGTAAAATACCATCAAAATCACTTAGGTAACGCTTTTATAAAGTTGTTACGAATAGATTA
129 TGTTGTGTAAAACACCATCAAAATCACTTAGGCAACACTTTTATAAAGTTGTTACGAATAGATTA
* * *
4616 TGATTTCGCAGCAACTTAAGAAGTTGTTGTTACTA-ATACTGTAAACATTGGCAACAACTAAAAA
194 GGATTTCGCAACAACTT-AGAAGTTGTTGTTACGAGA-ACTGTAAACATTGGCAACAACTAAAAA
4680 AGT
257 AGT
* *
4683 CTTGTGTAAAATACCATCAAAATCACTTAGGCAACCTTTTTATAAAGTTGTTACGAATAGTTTAT
1 ATTGTGTAAAATACCATCAAAATCACTTAGGCAACCTTTTTATAAAGTTGTTACAAATAGTTTAT
* **** * * * *
4748 GATTT-C-ACAAC-GAGTTTTTTTTGTTACGAAAATTGTAAGC-ATTGGCAACGACTAAAAAGGT
66 GATTTCCAACAACTAAGAAGCTGTTGTTACGAAAACTGTAA-CTATTGGCAACAACTAAAAAAGT
* *
4809 GTTGTGTAAAACACCATCAAAATCACTTAGGCAACATTTTTATAAAGTTGTTACGAATAGTTTAG
130 GTTGTGTAAAACACCATCAAAATCACTTAGGCAACACTTTTATAAAGTTGTTACGAATAGATTAG
* * * *** * * *
4874 GATTTTGCAACGACTTTGTTTTTGTTGTTACGAGAAGTGTAAGCATTGGCAACGACTAAAAAAGT
195 GATTTCGCAACAACTTAGAAGTTGTTGTTACGAGAACTGTAAACATTGGCAACAACTAAAAAAGT
* *** * *
4939 ATTGTGT-AAA-ACTATCAAAATCACTTAGCCAACGAGGCAACGAGTTTATAAAATTGTTACGAA
1 ATTGTGTAAAATACCATCAAAATCACTT--------AGGCAACCTTTTTATAAAGTTGTTACAAA
* ** **** * * *
5002 TAGATTATGATTTCGCAACAACTTTGTTTTTGTTGTTACGAAAACTATAAAC-ATTGGCAATAAT
58 TAGTTTATGATTTC-CAACAACTAAGAAGCTGTTGTTACGAAAACTGT-AACTATTGGCAACAAC
** *
5066 TAAAAAAGTCGTTGAATAAAATACCATCAAAATCAC-TAGGCAACTACTTTTA
121 TAAAAAAGT-GTTGTGTAAAACACCATCAAAATCACTTAGGCAAC-ACTTTTA
5118 ATTATTGTTG
Statistics
Matches: 367, Mismatches: 50, Indels: 30
0.82 0.11 0.07
Matches are distributed among these distances:
254 15 0.04
255 3 0.01
256 45 0.12
257 110 0.30
258 1 0.00
259 5 0.01
260 1 0.00
261 33 0.09
262 71 0.19
264 1 0.00
265 5 0.01
266 46 0.13
267 31 0.08
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (259 bp):
ATTGTGTAAAATACCATCAAAATCACTTAGGCAACCTTTTTATAAAGTTGTTACAAATAGTTTAT
GATTTCCAACAACTAAGAAGCTGTTGTTACGAAAACTGTAACTATTGGCAACAACTAAAAAAGTG
TTGTGTAAAACACCATCAAAATCACTTAGGCAACACTTTTATAAAGTTGTTACGAATAGATTAGG
ATTTCGCAACAACTTAGAAGTTGTTGTTACGAGAACTGTAAACATTGGCAACAACTAAAAAAGT
Found at i:7171 original size:15 final size:15
Alignment explanation
Indices: 7151--7184 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
7141 TTCTCATCTA
*
7151 AAATTCCAAAATTCT
1 AAATTCCAAAATTCC
*
7166 AAATTCTAAAATTCC
1 AAATTCCAAAATTCC
7181 AAAT
1 AAAT
7185 ACCCAATTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATTCCAAAATTCC
Found at i:12278 original size:77 final size:77
Alignment explanation
Indices: 12027--12333 Score: 389
Period size: 77 Copynumber: 4.0 Consensus size: 77
12017 TATTTTTTGC
* * * * * *
12027 ACGGGGACACCAGTGTTGGTGTTCGGCCGTTGTGATGAAATGGTCTCAATGGAGACGTTCGGTTC
1 ACGGGGACACCAGTGTTGGTGTTCGACCGTTGCGATGAAACGGCCTCAAGGGAGACGTTCGTTTC
**
12092 ATTTATTGTTAC
66 ATTTATTGTTGT
** * ** * * * * * *
12104 ACGGGGACACCAGCATTGGTGTTCGTCCGTTTTGAAGAGACGGTCTCATGGGGAGACGTTCATCT
1 ACGGGGACACCAGTGTTGGTGTTCGACCGTTGCGATGAAACGGCCTCA-AGGGAGACGTTCGTTT
12169 CATTTATTGTTTGT
65 CATTTATTG-TTGT
*
12183 ACGGGGACACCAGTGTTGGTGTTCGACCGTTGCGATGAAACAGCCTCAAGGGAGACGTTCGTTTC
1 ACGGGGACACCAGTGTTGGTGTTCGACCGTTGCGATGAAACGGCCTCAAGGGAGACGTTCGTTTC
12248 ATTTATTGTTGT
66 ATTTATTGTTGT
* * *
12260 ACGGGGACACCAGTGTTGGTGTTCGACCATTGCGATGAAACGACCTCAAGGAAGACGTTCGTTTC
1 ACGGGGACACCAGTGTTGGTGTTCGACCGTTGCGATGAAACGGCCTCAAGGGAGACGTTCGTTTC
12325 ATTTATTGT
66 ATTTATTGT
12334 CAATTTCGGA
Statistics
Matches: 198, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
77 115 0.58
78 42 0.21
79 41 0.21
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (77 bp):
ACGGGGACACCAGTGTTGGTGTTCGACCGTTGCGATGAAACGGCCTCAAGGGAGACGTTCGTTTC
ATTTATTGTTGT
Found at i:19134 original size:2 final size:2
Alignment explanation
Indices: 19123--19157 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
19113 CCGTTCTACC
19123 AT AT AT -T 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
19158 TACTATTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:26145 original size:18 final size:18
Alignment explanation
Indices: 26122--26156 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
26112 AGAAAAATTG
26122 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
26140 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
26157 TGTAATAATT
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:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:26223 original size:15 final size:14
Alignment explanation
Indices: 26195--26236 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 14
26185 AACGAACAAA
26195 ATAT-TATATAATT
1 ATATATATATAATT
26208 ATATATATATATATT
1 ATATATATATA-ATT
26223 ATATATA-ATAATT
1 ATATATATATAATT
26236 A
1 A
26237 AATTTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 8 0.30
14 9 0.33
15 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATATATATAATT
Found at i:26400 original size:35 final size:35
Alignment explanation
Indices: 26361--26435 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
26351 TTATATAAAC
*
26361 GAACACTTAAATGAACAATAAACGAGTCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
26396 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
26431 GAACA
1 GAACA
26436 TAAACGAACT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (35 bp):
GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
Found at i:32399 original size:3 final size:3
Alignment explanation
Indices: 32391--32530 Score: 145
Period size: 3 Copynumber: 46.7 Consensus size: 3
32381 GGCTCCTTTT
32391 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * * * * * *
32439 CTC TTC TTC TTC TTC TTC GTC TTC CTC TTC TTC ATC ATC ATC ATC ATC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * * * * *
32487 ATC ATC TTC TTC TTC TCC TTC TCC TTC GTA TAC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
32531 GTCTATGATC
Statistics
Matches: 119, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 119 1.00
ACGTcount: A:0.06, C:0.35, G:0.01, T:0.57
Consensus pattern (3 bp):
TTC
Found at i:54037 original size:31 final size:29
Alignment explanation
Indices: 53999--54092 Score: 89
Period size: 29 Copynumber: 3.1 Consensus size: 29
53989 TTAATGCCCT
*
53999 TTTTGCCCCCTAAACTTGTACGGTTTGGACG
1 TTTTGCCCCCTAAACTT-TA-AGTTTGGACG
* *
54030 TTTTGCCCCATAAACTTTAATTTTGGACG
1 TTTTGCCCCCTAAACTTTAAGTTTGGACG
** * * *
54059 TTTTGTTCCCTAAACTCTCAATTTTGGACA
1 TTTTGCCCCCTAAACT-TTAAGTTTGGACG
54089 TTTT
1 TTTT
54093 AGTCCCTCTC
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 21 0.39
30 17 0.31
31 16 0.30
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (29 bp):
TTTTGCCCCCTAAACTTTAAGTTTGGACG
Found at i:54072 original size:29 final size:30
Alignment explanation
Indices: 54022--54092 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
54012 ACTTGTACGG
*
54022 TTTGGACGTTTTGCCCCATAAACT-TTAAT
1 TTTGGACGTTTTGCCCCATAAACTCTCAAT
*
54051 TTTGGACGTTTTGTTCCC-TAAACTCTCAAT
1 TTTGGACGTTTTG-CCCCATAAACTCTCAAT
*
54081 TTTGGACATTTT
1 TTTGGACGTTTT
54093 AGTCCCTCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.51
30 18 0.49
ACGTcount: A:0.21, C:0.20, G:0.14, T:0.45
Consensus pattern (30 bp):
TTTGGACGTTTTGCCCCATAAACTCTCAAT
Found at i:54099 original size:30 final size:28
Alignment explanation
Indices: 54022--54099 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 28
54012 ACTTGTACGG
* *
54022 TTTGGACGTTTTGCCCCATAAACTTTAAT
1 TTTGGACGTTTTGTCCC-TAAACTTCAAT
54051 TTTGGACGTTTTGTTCCCTAAACTCTCAAT
1 TTTGGACGTTTTG-TCCCTAAACT-TCAAT
*
54081 TTTGGACATTTTAGTCCCT
1 TTTGGACGTTTT-GTCCCT
54100 CTCAGACGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 19 0.44
30 23 0.53
31 1 0.02
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.44
Consensus pattern (28 bp):
TTTGGACGTTTTGTCCCTAAACTTCAAT
Found at i:54287 original size:29 final size:30
Alignment explanation
Indices: 54225--54288 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
54215 GAGAGGGACT
* *
54225 AAAACGTCCAAAATTGAGAGTTTAGGGGGC
1 AAAACGTCCAAAATTGAAAGTTTAGGGGGA
54255 AAAACGTCCAAAATT-AAAGTTTAGGGGGA
1 AAAACGTCCAAAATTGAAAGTTTAGGGGGA
54284 AAAAC
1 AAAAC
54289 ATACAAACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 17 0.53
30 15 0.47
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (30 bp):
AAAACGTCCAAAATTGAAAGTTTAGGGGGA
Found at i:54295 original size:29 final size:30
Alignment explanation
Indices: 54233--54295 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
54223 CTAAAACGTC
* * * *
54233 CAAAATTGAGAGTTTAGGGGGCAAAACGTC
1 CAAAATTGAAAGTTTAGGGGGAAAAACATA
54263 CAAAATT-AAAGTTTAGGGGGAAAAACATA
1 CAAAATTGAAAGTTTAGGGGGAAAAACATA
54292 CAAA
1 CAAA
54296 CCATACAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (30 bp):
CAAAATTGAAAGTTTAGGGGGAAAAACATA
Found at i:66528 original size:79 final size:79
Alignment explanation
Indices: 66397--66552 Score: 267
Period size: 79 Copynumber: 2.0 Consensus size: 79
66387 CTGTTGACTA
* *
66397 ATTTCATCATTCCCTCCTCAAGTTGGCGCGTAAAGATTCGCAACACCCAACTTGAACACTAATGG
1 ATTTCATCACTCCCTCCTCAAGTTGGCGCGTAAAGATTCGCAACACCCAACTTGAACACTAATGA
66462 TTCAAATCGATCTG
66 TTCAAATCGATCTG
* * *
66476 ATTTCATCACTCCCTCCTCAAGTTGGCGCGTGAAGATTCGCAACGCCCAACTTGAATACTAATGA
1 ATTTCATCACTCCCTCCTCAAGTTGGCGCGTAAAGATTCGCAACACCCAACTTGAACACTAATGA
66541 TTCAAATCGATC
66 TTCAAATCGATC
66553 CTTGTCCAAG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 72 1.00
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (79 bp):
ATTTCATCACTCCCTCCTCAAGTTGGCGCGTAAAGATTCGCAACACCCAACTTGAACACTAATGA
TTCAAATCGATCTG
Found at i:67349 original size:39 final size:39
Alignment explanation
Indices: 67306--67419 Score: 167
Period size: 39 Copynumber: 2.9 Consensus size: 39
67296 TGACTAGTTG
67306 CCAGAGGATGCAGATTCGCTGCTCTCATTGTCAGATTTA
1 CCAGAGGATGCAGATTCGCTGCTCTCATTGTCAGATTTA
* *
67345 CCAGAGGATGCAGATTCGCTGCTCTCACTATCAGATTTA
1 CCAGAGGATGCAGATTCGCTGCTCTCATTGTCAGATTTA
* **
67384 CCAGAGGATGCAGCTTTACTGCTCTC-TCTGTCAGAT
1 CCAGAGGATGCAGATTCGCTGCTCTCAT-TGTCAGAT
67420 CTGGCCATGA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
39 67 1.00
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (39 bp):
CCAGAGGATGCAGATTCGCTGCTCTCATTGTCAGATTTA
Found at i:68651 original size:3 final size:3
Alignment explanation
Indices: 68645--68739 Score: 181
Period size: 3 Copynumber: 31.3 Consensus size: 3
68635 TTATATATAT
68645 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
68693 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
68739 A
1 A
68740 ATAAAATATA
Statistics
Matches: 91, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 88 0.97
4 3 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:68756 original size:20 final size:20
Alignment explanation
Indices: 68639--68758 Score: 150
Period size: 18 Copynumber: 6.3 Consensus size: 20
68629 ATTTTATTAT
68639 ATATATATAATAATAATAATA
1 ATATATA-AATAATAATAATA
68660 ATA-AT-AATAATAATAATA
1 ATATATAAATAATAATAATA
68678 ATA-AT-AATAATAATAATA
1 ATATATAAATAATAATAATA
68696 ATA-AT-AATAATAATAATA
1 ATATATAAATAATAATAATA
68714 ATA-AT-AATAATAATAATA
1 ATATATAAATAATAATAATA
68732 ATATATAAATAA-AATATATA
1 ATATATAAATAATAATA-ATA
*
68752 TTATATA
1 ATATATA
68759 TATAGTAGTA
Statistics
Matches: 95, Mismatches: 1, Indels: 7
0.92 0.01 0.07
Matches are distributed among these distances:
18 70 0.74
19 6 0.06
20 16 0.17
21 3 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATATATAAATAATAATAATA
Found at i:70390 original size:23 final size:23
Alignment explanation
Indices: 70364--70412 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
70354 CTAAATTTCT
* * *
70364 AAGTTTAAATAGTCATCTCTATA
1 AAGTTTAAACAATCAACTCTATA
70387 AAGTTTAAACAATCAACTCTATA
1 AAGTTTAAACAATCAACTCTATA
70410 AAG
1 AAG
70413 CTAAATTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33
Consensus pattern (23 bp):
AAGTTTAAACAATCAACTCTATA
Done.