Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013878.1 Corchorus olitorius cultivar O-4 contig13911, 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: 37548
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:4187 original size:18 final size:18
Alignment explanation
Indices: 4164--4198 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4154 AAAGGGTAAT
*
4164 TAAAAAAAATTGTTTTTA
1 TAAAAAAAAGTGTTTTTA
*
4182 TAAAAAGAAGTGTTTTT
1 TAAAAAAAAGTGTTTTT
4199 CATGATAGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (18 bp):
TAAAAAAAAGTGTTTTTA
Found at i:8701 original size:32 final size:32
Alignment explanation
Indices: 8660--8736 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
8650 ATATTCTGGG
*
8660 TTAGCGGCGTTTCTCACTAGGA-ACGCCACTAT
1 TTAGCGGCGTTTCTCACCA-GACACGCCACTAT
*
8692 TTAGCGGCGTTTCTCACCAGACACGCCATTAT
1 TTAGCGGCGTTTCTCACCAGACACGCCACTAT
*
8724 TTAGTGGCGTTTC
1 TTAGCGGCGTTTC
8737 GAGTATAAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 2 0.05
32 39 0.95
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.31
Consensus pattern (32 bp):
TTAGCGGCGTTTCTCACCAGACACGCCACTAT
Found at i:9008 original size:162 final size:163
Alignment explanation
Indices: 8714--9029 Score: 528
Period size: 162 Copynumber: 1.9 Consensus size: 163
8704 CTCACCAGAC
* *
8714 ACGCCATTATTTAGTGGCGTTTCGAGTATAAACGCCACTATATATTGAGGGAGAAATTATATTTT
1 ACGCCACTATTTAGTGGCGTTTCGAGTATAAACGCCACTATATATTAAGGGAGAAATTATATTTT
** *
8779 TTTAAGGGAAAAATTCACTCCCGTAATATAATTATAATAATAATAGTATATTTTTTCCTAGAATA
66 TTTAAGGGAAAAATTCACTCCCCCAATATAATTATAATAATAATAGTATATTTTTTCCTAAAATA
8844 TATTGATTATATATAGCGGCGTTTCATATAGAA
131 TATTGATTATATATAGCGGCGTTTCATATAGAA
* ** *
8877 ACGCCACTATTTAGTGGCGTTTCGAGTTTAAACGCTGCTATATTTTAAGGGAGAAATTATATTTT
1 ACGCCACTATTTAGTGGCGTTTCGAGTATAAACGCCACTATATATTAAGGGAGAAATTATATTTT
8942 TTTAA-GGAAAAATTCACTCCCCCAATATAATTATAATAATAATCA-TATATTTTTTCCTAAAAT
66 TTTAAGGGAAAAATTCACTCCCCCAATATAATTATAATAATAAT-AGTATATTTTTTCCTAAAAT
9005 ATATTGATTATATATAGCGGCGTTT
130 ATATTGATTATATATAGCGGCGTTT
9030 AGAAACGCCG
Statistics
Matches: 143, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
162 78 0.55
163 65 0.45
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (163 bp):
ACGCCACTATTTAGTGGCGTTTCGAGTATAAACGCCACTATATATTAAGGGAGAAATTATATTTT
TTTAAGGGAAAAATTCACTCCCCCAATATAATTATAATAATAATAGTATATTTTTTCCTAAAATA
TATTGATTATATATAGCGGCGTTTCATATAGAA
Found at i:9091 original size:2 final size:2
Alignment explanation
Indices: 9078--9114 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
9068 CCACTATTTG
*
9078 TA TA TT TA TA TA 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 TA TA TA TA TA TA T
9115 TCTATGTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:9269 original size:30 final size:30
Alignment explanation
Indices: 9231--9475 Score: 119
Period size: 30 Copynumber: 8.5 Consensus size: 30
9221 TAAATATTAT
9231 TTTCTAATTATAATTTCATTACATATATAA
1 TTTCTAATTATAATTTCATTACATATATAA
* *
9261 TTGCTAATTATTATTT--TCTA-A-ATATAA
1 TTTCTAATTATAATTTCAT-TACATATATAA
* ** * * * *
9288 TTTTTAAAAAT-TTTTAATTTC-TA-ATAT
1 TTTCTAATTATAATTTCATTACATATATAA
* *
9315 TTTTTAATTATAATTTCAATACATATATAA
1 TTTCTAATTATAATTTCATTACATATATAA
*
9345 TTTCTAAATA-ATATTTCATTACATATATAA
1 TTTCTAATTATA-ATTTCATTACATATATAA
* * *
9375 TTTATAA-TATAA-TTC-CTA-AT-TTTAA
1 TTTCTAATTATAATTTCATTACATATATAA
* * *
9400 TTTCTTCACATATATAGTTTC--TAAATAT-TAT
1 TTTC-T-A-AT-TATAATTTCATTACATATATAA
*
9431 TTTCTAAATGAT-ATTTCATTACATATATAA
1 TTTCT-AATTATAATTTCATTACATATATAA
* *
9461 TTTATAAATATAATT
1 TTTCTAATTATAATT
9476 CCTAATTATA
Statistics
Matches: 160, Mismatches: 33, Indels: 44
0.68 0.14 0.19
Matches are distributed among these distances:
25 7 0.04
26 6 0.04
27 33 0.21
28 16 0.10
29 20 0.12
30 66 0.41
31 11 0.07
32 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.51
Consensus pattern (30 bp):
TTTCTAATTATAATTTCATTACATATATAA
Found at i:9306 original size:44 final size:44
Alignment explanation
Indices: 9178--9319 Score: 141
Period size: 44 Copynumber: 3.3 Consensus size: 44
9168 GCAATATTCA
* * *
9178 AATT-TTATTTTCTAAATATAATTTCTAAATATTTTAAAATTTCT
1 AATTATTATTTTCTAAATATAATTTTTAAAAATTTT-TAATTTCT
* * * * * *
9222 AAATATTATTTTCTAATTATAATTTCATT--ACATATATAATTGCT
1 AATTATTATTTTCTAAATATAATTT--TTAAAAATTTTTAATTTCT
9266 AATTATTATTTTCTAAATATAATTTTTAAAAATTTTTAATTTCT
1 AATTATTATTTTCTAAATATAATTTTTAAAAATTTTTAATTTCT
9310 AA-TATT-TTTT
1 AATTATTATTTT
9320 AATTATAATT
Statistics
Matches: 79, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 45 0.57
45 23 0.29
47 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (44 bp):
AATTATTATTTTCTAAATATAATTTTTAAAAATTTTTAATTTCT
Found at i:9307 original size:17 final size:17
Alignment explanation
Indices: 9285--9323 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
9275 TTTCTAAATA
*
9285 TAATTTTTAAAAATTTT
1 TAATTTCTAAAAATTTT
* *
9302 TAATTTCTAATATTTTT
1 TAATTTCTAAAAATTTT
9319 TAATT
1 TAATT
9324 ATAATTTCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TAATTTCTAAAAATTTT
Found at i:9338 original size:84 final size:89
Alignment explanation
Indices: 9178--9360 Score: 261
Period size: 84 Copynumber: 2.1 Consensus size: 89
9168 GCAATATTCA
*
9178 AATT-TTATTTTCTAAATATAATTTCTAAATATTTTAAAATTTCTAAATATTATTTTCTAATTAT
1 AATTATTATTTTCTAAATATAATTTCTAAAAATTTTAAAATTTCTAAATATTATTTTCTAATTAT
*
9242 AATTTCATTACATATATAATTGCT
66 AATTTCAATACATATATAATTGCT
* *
9266 AATTATTATTTTCTAAATATAATTTTTAAAAATTTT-TAATTTCT-AATA-T-TTTT-TAATTAT
1 AATTATTATTTTCTAAATATAATTTCTAAAAATTTTAAAATTTCTAAATATTATTTTCTAATTAT
*
9326 AATTTCAATACATATATAATTTCT
66 AATTTCAATACATATATAATTGCT
* *
9350 AAATAATATTT
1 AATTATTATTT
9361 CATTACATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
84 38 0.44
85 4 0.05
86 1 0.01
87 4 0.05
88 11 0.13
89 29 0.33
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.53
Consensus pattern (89 bp):
AATTATTATTTTCTAAATATAATTTCTAAAAATTTTAAAATTTCTAAATATTATTTTCTAATTAT
AATTTCAATACATATATAATTGCT
Found at i:9345 original size:17 final size:16
Alignment explanation
Indices: 9323--9507 Score: 81
Period size: 17 Copynumber: 12.6 Consensus size: 16
9313 ATTTTTTAAT
9323 TATAATTTCAATACATA
1 TATAATTTC-ATACATA
*
9340 TATAATTTC-TAAATA
1 TATAATTTCATACATA
9355 -AT-ATTTCATTACATA
1 TATAATTTCA-TACATA
9370 TATAATTT-AT--A-A
1 TATAATTTCATACATA
*
9382 TATAA-TTCCTA-AT-
1 TATAATTTCATACATA
* *
9395 TTTAATTTCTTCACATA
1 TATAATTTCAT-ACATA
* *
9412 TATAGTTTC-TAAATA
1 TATAATTTCATACATA
*
9427 T-TATTTTC-TA-A-A
1 TATAATTTCATACATA
9439 TGAT-ATTTCATTACATA
1 T-ATAATTTCA-TACATA
9456 TATAATTT-ATA-A-A
1 TATAATTTCATACATA
*
9469 TATAA-TTCCTA-AT-
1 TATAATTTCATACATA
9482 TATAATTTCATTACATA
1 TATAATTTCA-TACATA
*
9499 TATCATTTC
1 TATAATTTC
9508 TAAATATTAT
Statistics
Matches: 131, Mismatches: 13, Indels: 48
0.68 0.07 0.25
Matches are distributed among these distances:
11 2 0.02
12 11 0.08
13 30 0.23
14 19 0.15
15 23 0.18
16 12 0.09
17 34 0.26
ACGTcount: A:0.40, C:0.11, G:0.01, T:0.48
Consensus pattern (16 bp):
TATAATTTCATACATA
Found at i:9401 original size:156 final size:157
Alignment explanation
Indices: 9234--9519 Score: 366
Period size: 156 Copynumber: 1.8 Consensus size: 157
9224 ATATTATTTT
*
9234 CTAATTATAATTTCATT-ACATATATAATTGCTAATTATTATTTTCTAAAT-ATAATTT-TTAAA
1 CTAATTATAATTTC-TTCACATATATAATTGCTAAATATTATTTTCTAAATGAT-ATTTATT--A
* * * **
9296 AATTTTTAATTTCT-AATAT-TTTTTAATTATAATTTCAATACATATATAATTTCTAAATAATAT
62 AATATATAATTTATAAATATATTCCTAATTATAATTTCAATACATATATAATTTCTAAATAATAT
9359 TTCATTACATATATAATTTATAATATAATTC
127 TTCATTACATATATAATTTATAATATAATTC
* * * *
9390 CTAATTTTAATTTCTTCACATATATAGTTTCTAAATATTATTTTCTAAATGATATTTCATTACAT
1 CTAATTATAATTTCTTCACATATATAATTGCTAAATATTATTTTCTAAATGATATTT-ATTAAAT
* * *
9455 ATATAATTTATAAATATAATTCCTAATTATAATTTCATTACATATATCATTTCTAAATATTATTT
65 ATATAATTTATAAATAT-ATTCCTAATTATAATTTCAATACATATATAATTTCTAAATAATATTT
9520 TCTCATTATA
Statistics
Matches: 110, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
155 2 0.02
156 58 0.53
157 7 0.06
158 2 0.02
159 41 0.37
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.50
Consensus pattern (157 bp):
CTAATTATAATTTCTTCACATATATAATTGCTAAATATTATTTTCTAAATGATATTTATTAAATA
TATAATTTATAAATATATTCCTAATTATAATTTCAATACATATATAATTTCTAAATAATATTTCA
TTACATATATAATTTATAATATAATTC
Found at i:9445 original size:86 final size:87
Alignment explanation
Indices: 9345--9522 Score: 299
Period size: 87 Copynumber: 2.1 Consensus size: 87
9335 ACATATATAA
*
9345 TTTCTAAATAATATTTCATTACATATATAATTTAT-AATATAATTCCTAATTTTAATTTC-TTCA
1 TTTCTAAATAATATTTCATTACATATATAATTTATAAATATAATTCCTAATTATAATTTCATT-A
9408 CATATAT-AGTTTCTAAATATTAT
65 CATATATCA-TTTCTAAATATTAT
*
9431 TTTCTAAATGATATTTCATTACATATATAATTTATAAATATAATTCCTAATTATAATTTCATTAC
1 TTTCTAAATAATATTTCATTACATATATAATTTATAAATATAATTCCTAATTATAATTTCATTAC
9496 ATATATCATTTCTAAATATTAT
66 ATATATCATTTCTAAATATTAT
9518 TTTCT
1 TTTCT
9523 CATTATAATT
Statistics
Matches: 87, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
86 34 0.39
87 50 0.57
88 3 0.03
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.50
Consensus pattern (87 bp):
TTTCTAAATAATATTTCATTACATATATAATTTATAAATATAATTCCTAATTATAATTTCATTAC
ATATATCATTTCTAAATATTAT
Found at i:13542 original size:2 final size:2
Alignment explanation
Indices: 13535--13565 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
13525 TAATACAATG
*
13535 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13566 TCAATTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13745 original size:32 final size:32
Alignment explanation
Indices: 13628--13754 Score: 139
Period size: 32 Copynumber: 4.0 Consensus size: 32
13618 AAAAAAGCCA
* * *
13628 AAATAGCGGCGTTTCT-ATACGTAAACGTCGCT
1 AAATAGTGGCGTTT-TGATACGGAAACGCCGCT
* * * *
13660 AAATAGTGGCATTTTGGTAAGGAAACGCCGTT
1 AAATAGTGGCGTTTTGATACGGAAACGCCGCT
* *
13692 AAATAGTGGCGTTTTGGTACGGAAATGCCGCT
1 AAATAGTGGCGTTTTGATACGGAAACGCCGCT
* *
13724 AAATAGTGGCGTTTTTATACGGAAATGCCGC
1 AAATAGTGGCGTTTTGATACGGAAACGCCGC
13755 GATTCCTAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
31 1 0.01
32 80 0.99
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (32 bp):
AAATAGTGGCGTTTTGATACGGAAACGCCGCT
Found at i:16043 original size:21 final size:22
Alignment explanation
Indices: 16019--16060 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
16009 TAATTGAATG
*
16019 CAATTTGATCCCTG-TTTTATT
1 CAATTTGACCCCTGATTTTATT
16040 CAATTTGACCCCTGATTTTAT
1 CAATTTGACCCCTGATTTTAT
16061 AAATTATGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (22 bp):
CAATTTGACCCCTGATTTTATT
Found at i:16065 original size:21 final size:21
Alignment explanation
Indices: 16020--16065 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
16010 AATTGAATGC
* *
16020 AATTTGATCCCTGTTTTATTC
1 AATTTGACCCCTGTTTTATTA
16041 AATTTGACCCCTGATTTTA-TA
1 AATTTGACCCCTG-TTTTATTA
16062 AATT
1 AATT
16066 ATGCTAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (21 bp):
AATTTGACCCCTGTTTTATTA
Found at i:20139 original size:21 final size:22
Alignment explanation
Indices: 20115--20156 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
20105 TTTGCCTCAT
*
20115 GCATTCATTCAT-CATGCCATG
1 GCATTCATTCATGCATCCCATG
20136 GCATTCATTCATGCATCCCAT
1 GCATTCATTCATGCATCCCAT
20157 CAAACCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.33
Consensus pattern (22 bp):
GCATTCATTCATGCATCCCATG
Found at i:21825 original size:76 final size:76
Alignment explanation
Indices: 21688--21836 Score: 185
Period size: 76 Copynumber: 2.0 Consensus size: 76
21678 TTTATTTGGA
* *
21688 CTGTGAGCAAAGGAATGATGAGTTTTAATCAAAAAAAAATTTCAAAATCAGTTTAAATCAAAACT
1 CTGTGAGCAAAGGAATGATCAGTTTTAATCAAAAAAAAATTTCAAAATCAGTTTAAATCAAAACA
21753 ATGATTTCGAG
66 ATGATTTCGAG
* ** *** *
21764 CTGTGAGCAAAGGAATGA-CAGTGATTTAAT-AAAAAGATGTTTCAAAATCAGTTTTGGTCAAAG
1 CTGTGAGCAAAGGAATGATCAGT--TTTAATCAAAAAAAAATTTCAAAATCAGTTTAAATCAAAA
21827 CAATGATTTC
64 CAATGATTTC
21837 TAGATGACTG
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
75 3 0.05
76 53 0.85
77 6 0.10
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.30
Consensus pattern (76 bp):
CTGTGAGCAAAGGAATGATCAGTTTTAATCAAAAAAAAATTTCAAAATCAGTTTAAATCAAAACA
ATGATTTCGAG
Found at i:24938 original size:27 final size:26
Alignment explanation
Indices: 24908--24968 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
24898 AACCTAAGGA
24908 ACTAACTTTGAATGG-GAAACTGACTT
1 ACTAACTTTGAATGGAG-AACTGACTT
*
24934 GACTAGCTTTGAATGGAGAACTGACTT
1 -ACTAACTTTGAATGGAGAACTGACTT
*
24961 ACTGACTT
1 ACTAACTT
24969 GGACTTATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 6 0.20
27 23 0.77
28 1 0.03
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (26 bp):
ACTAACTTTGAATGGAGAACTGACTT
Found at i:24975 original size:14 final size:14
Alignment explanation
Indices: 24956--24985 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
24946 ATGGAGAACT
24956 GACTTACTGACTTG
1 GACTTACTGACTTG
*
24970 GACTTATTGACTTG
1 GACTTACTGACTTG
24984 GA
1 GA
24986 ATGAGAGACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (14 bp):
GACTTACTGACTTG
Found at i:25351 original size:213 final size:214
Alignment explanation
Indices: 24971--25396 Score: 809
Period size: 213 Copynumber: 2.0 Consensus size: 214
24961 ACTGACTTGG
* *
24971 ACTTATTGACTTGGAATGAGAGACTGACTTGAATGATTCTTAACAGCCTGGACCTCCACCGCCAC
1 ACTTACTGACTTGGAATGAGAGACTGACTTGAATGATCCTTAACAGCCTGGACCTCCACCGCCAC
25036 CGGCTAAAAATCTACGATCAAATAAAAGCAGTCTCCTATGTCCACCCTGGCCACCACCAGGATGA
66 CGGCTAAAAATCTACGATCAAATAAAAGCAGTCTCCTATGTCCACCCTGGCCACCACCAGGATGA
*
25101 GCCGGCTCAGGCTTTGGTTCATTCTGCGGATCATGGCCGATATTAGGAAGATCAACTCTTTTAGC
131 GCCGGCTCAGGCTTTGGTTCATTCTGCGGACCATGGCCGATATTAGGAAGATCAACTCTTTTAGC
25166 GCAAAATAGCATA-TATCA
196 GCAAAATAGCATAGTATCA
25184 ACTTACTGACTTGGAATGAGAGACTGACTTGAATGATCCTTAACAGCCTGGACCTCCACCGCCAC
1 ACTTACTGACTTGGAATGAGAGACTGACTTGAATGATCCTTAACAGCCTGGACCTCCACCGCCAC
25249 CGGCTAAAAATCTACGATCAAATAAAAGCAGTCTCCTATGTCCACCCTGGCCACCACCAGGATGA
66 CGGCTAAAAATCTACGATCAAATAAAAGCAGTCTCCTATGTCCACCCTGGCCACCACCAGGATGA
*
25314 GCCGGCTCAGGCTTTGGTTCATTCTGCGGACCATGGCCGATATTAGGATGATCAACTCTTTTAGC
131 GCCGGCTCAGGCTTTGGTTCATTCTGCGGACCATGGCCGATATTAGGAAGATCAACTCTTTTAGC
25379 GCAAAATAGCATAGTATC
196 GCAAAATAGCATAGTATC
25397 CGCAACCTTT
Statistics
Matches: 208, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
213 204 0.98
214 4 0.02
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (214 bp):
ACTTACTGACTTGGAATGAGAGACTGACTTGAATGATCCTTAACAGCCTGGACCTCCACCGCCAC
CGGCTAAAAATCTACGATCAAATAAAAGCAGTCTCCTATGTCCACCCTGGCCACCACCAGGATGA
GCCGGCTCAGGCTTTGGTTCATTCTGCGGACCATGGCCGATATTAGGAAGATCAACTCTTTTAGC
GCAAAATAGCATAGTATCA
Found at i:26482 original size:26 final size:28
Alignment explanation
Indices: 26452--26504 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 28
26442 AAATTAAATA
26452 AAAATCTATAAGGA-TTAAA-AAAAAAG
1 AAAATCTATAAGGATTTAAATAAAAAAG
26478 AAAATCTATAAGGATTTAAATAAAAAA
1 AAAATCTATAAGGATTTAAATAAAAAA
26505 AAACACAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 14 0.56
27 5 0.20
28 6 0.24
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.23
Consensus pattern (28 bp):
AAAATCTATAAGGATTTAAATAAAAAAG
Found at i:26507 original size:26 final size:25
Alignment explanation
Indices: 26446--26507 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 25
26436 AAAAGGAAAT
*
26446 TAAATAAAAATCTATAAGGATTAAA
1 TAAAAAAAAATCTATAAGGATTAAA
*
26471 AAAAAAGAAAATCTATAAGGATTTAAA
1 TAAAAA-AAAATCTATAAGGA-TTAAA
26498 TAAAAAAAAA
1 TAAAAAAAAA
26508 CACAGGAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.12
26 18 0.56
27 10 0.31
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.23
Consensus pattern (25 bp):
TAAAAAAAAATCTATAAGGATTAAA
Found at i:33449 original size:28 final size:28
Alignment explanation
Indices: 33418--33516 Score: 144
Period size: 28 Copynumber: 3.5 Consensus size: 28
33408 TTAGGATCAA
*
33418 CCAGAGGCATTTTGGTCATTTCGCATGT
1 CCAGGGGCATTTTGGTCATTTCGCATGT
*
33446 CCAGGGGCATTTTGGTCATTTTGCATGT
1 CCAGGGGCATTTTGGTCATTTCGCATGT
** **
33474 CCAGGGGCATTTTGGTCATTTTACACAT
1 CCAGGGGCATTTTGGTCATTTCGCATGT
33502 CCAGGGGCATTTTGG
1 CCAGGGGCATTTTGG
33517 GTCACTTCAA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.35
Consensus pattern (28 bp):
CCAGGGGCATTTTGGTCATTTCGCATGT
Found at i:36665 original size:28 final size:30
Alignment explanation
Indices: 36607--36685 Score: 99
Period size: 28 Copynumber: 2.7 Consensus size: 30
36597 GCTAAATACC
* *
36607 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT-CTTTCGGGA
36638 CAAAATAATCCCTTAT-TTTT-TTTCGGGA
1 CAAAATAATCCCTTATGTTTTCTTTCGGGA
* *
36666 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
36686 CAAAAATGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 21 0.49
29 3 0.07
30 4 0.09
31 15 0.35
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTCGGGA
Found at i:36904 original size:31 final size:31
Alignment explanation
Indices: 36809--36894 Score: 154
Period size: 31 Copynumber: 2.8 Consensus size: 31
36799 AAGGGACTGA
36809 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
36840 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
* *
36871 TTTGTCTCAAAAGAAAAATATAAG
1 TTTGTCCCAAAAGAAAAACATAAG
36895 AGAACTTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATTTT
Done.