Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020652.1 Corchorus olitorius cultivar O-4 contig20685, 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: 27779
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:2972 original size:15 final size:16
Alignment explanation
Indices: 2941--2974 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2931 TTGCTTTGTT
2941 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
2957 TTGTTTTCTA-TTTAA
1 TTGTTTTCTAGTTTAA
2972 TTG
1 TTG
2975 CTCTCTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.18, C:0.06, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:7491 original size:81 final size:81
Alignment explanation
Indices: 7156--7594 Score: 394
Period size: 81 Copynumber: 5.5 Consensus size: 81
7146 TACACTTTTG
** * * * * * *
7156 TTAAACCCAATGTAGCATTTACTGTATATTACTTAATTTACCTTTGCAAGTGGTAGGAAAGCGGG
1 TTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAGGG
7221 TGAGTAAGTCCCTTCA
66 TGAGTAAGTCCCTTCA
* ** * * * *
7237 TTAAA-TCAATGTAAAATTTACTACGCATTACCT-ATTTACCCTTACAAGTGGGAGGAGAGTGTG
1 TTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAGGG
* * **
7300 TGGGTAACTCCCTTTG
66 TGAGTAAGTCCCTTCA
** ** * * * *
7316 TTAAACCCAAT-TCTTCATTTACCGCATATTACCTAATTTACCCTTGC---T---ATGCGAGAGT
1 TTAAACCCAATGT-AGCATTTACTACACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAGG
* * * *
7374 GTCAGTAACTCCTTTCG
65 GTGAGTAAGTCCCTTCA
* * * *
7391 TGAAA-CCAATGTAGGATTTATTACACATTACCTAATTTACCCTTACAAGTGGGAGGAGAGAGGG
1 TTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAGGG
* *
7455 TGAGTAGGTGCCTTCA
66 TGAGTAAGTCCCTTCA
* * * *
7471 TTAAACCTAATGTAGCATTTACTTCACATTACCTAATTTACCTTTGCAAGTGGGAGGAAAGAGGG
1 TTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAGGG
7536 TGAGTAAGTCCCTTCA
66 TGAGTAAGTCCCTTCA
* * * *
7552 TTAAGCCCAATGTATCATTTACTACAAATTACCTGATTTACCC
1 TTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCC
7595 AACCCAATGT
Statistics
Matches: 278, Mismatches: 69, Indels: 22
0.75 0.19 0.06
Matches are distributed among these distances:
74 31 0.11
75 25 0.09
77 1 0.00
78 1 0.00
79 42 0.15
80 60 0.22
81 118 0.42
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (81 bp):
TTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAGGG
TGAGTAAGTCCCTTCA
Found at i:7671 original size:14 final size:15
Alignment explanation
Indices: 7642--7676 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
7632 GTAGAGCTGT
*
7642 GAGATTGGTGATGGG
1 GAGATTGGTAATGGG
7657 GAGATTGG-AATGGG
1 GAGATTGGTAATGGG
7671 GAGATT
1 GAGATT
7677 AGTTACTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.26, C:0.00, G:0.49, T:0.26
Consensus pattern (15 bp):
GAGATTGGTAATGGG
Found at i:8079 original size:2 final size:2
Alignment explanation
Indices: 8072--8104 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
8062 AGGTAACATC
8072 AT AT AT AT AT AT AT AT A- 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
8105 GAGAAAAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8094 original size:15 final size:15
Alignment explanation
Indices: 8074--8103 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
8064 GTAACATCAT
8074 ATATATATATATATA
1 ATATATATATATATA
8089 ATATATATATATATA
1 ATATATATATATATA
8104 TGAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:8094 original size:17 final size:17
Alignment explanation
Indices: 8072--8104 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
8062 AGGTAACATC
8072 ATATATATATATATATA
1 ATATATATATATATATA
8089 ATATATATATATATAT
1 ATATATATATATATAT
8105 GAGAAAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:8690 original size:161 final size:159
Alignment explanation
Indices: 8396--8813 Score: 457
Period size: 161 Copynumber: 2.6 Consensus size: 159
8386 AACAAACAGA
** * *
8396 ACCTAATTTAACCTTGCAAGTGGGAGGAGAGAATGTGAGTAACTCCCTTCGTTGAACTCAATGTA
1 ACCTAATTTAACCTTGCAAGTGGGAGGAGAGAGGGTGAGTAACTCCCTTCGTTAAACCCAATGTA
* * * * * * * *
8461 TGATTTATTTCACATTACCTAATTTACCCTTGCAAGTGGGAGGAAAGTGGATGATTACTCCCTTC
66 -CATTTATTGCACATTACCTAATTTACCCTTGCAAGAGAGAAGAAAGAGGATAAGTACT-CCTTC
* * *
8526 GTTAAACCCAATTTTGCATTTACTTCACATT
129 GTTAAACCCAATGTAGCATTTACTGCACATT
* * *
8557 ACCTGATTTACCCTTGCAAGTGGGAGGAGAGAGGGTGAGTAACTCCCTTCGTTAAACCCAATATA
1 ACCTAATTTAACCTTGCAAGTGGGAGGAGAGAGGGTGAGTAACTCCCTTCGTTAAACCCAATGTA
* *
8622 CATTTATTGCACATTACCTAATTTACCCTTGCAAACGAGAGAAGAGAGAGCGAGTAAGTA-T-TT
66 CATTTATTGCACATTACCTAATTTACCCTTGC-AA-GAGAGAAGAAAGAG-GA-TAAGTACTCCT
*
8685 TCGTTAAGCCCAATGTAGCATTTACTGCACATT
127 TCGTTAAACCCAATGTAGCATTTACTGCACATT
* * * * * *
8718 ACCTAATTTAACCTTGCAAGTGAGAGGTA-AAAGGGTTGA-TAAGTCCCGTCGTTAAATCTAATG
1 ACCTAATTTAACCTTGCAAGTGGGAGG-AGAGAGGG-TGAGTAACTCCCTTCGTTAAACCCAATG
* * *
8781 TAACATTTACTGCACATTTCCTAATTTATCCTT
64 T-ACATTTATTGCACATTACCTAATTTACCCTT
8814 ACACCTTTGT
Statistics
Matches: 217, Mismatches: 33, Indels: 13
0.83 0.13 0.05
Matches are distributed among these distances:
160 30 0.14
161 139 0.64
162 41 0.19
163 3 0.01
164 4 0.02
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (159 bp):
ACCTAATTTAACCTTGCAAGTGGGAGGAGAGAGGGTGAGTAACTCCCTTCGTTAAACCCAATGTA
CATTTATTGCACATTACCTAATTTACCCTTGCAAGAGAGAAGAAAGAGGATAAGTACTCCTTCGT
TAAACCCAATGTAGCATTTACTGCACATT
Found at i:8743 original size:81 final size:81
Alignment explanation
Indices: 8396--8743 Score: 321
Period size: 80 Copynumber: 4.3 Consensus size: 81
8386 AACAAACAGA
* * * * * * * *
8396 ACCTAATTTAACCTTGCAAGTGGGAGGAGAGA-ATGTGAGTAACTCCCTTCGTTGAACTCAATGT
1 ACCTAATTTACCCTTGCAAGTGAGAGAAGAGAGA-GCGAGTAACTACCTTCGTTAAACCCAATAT
* *
8460 ATG-ATTTATTTCACATT
65 A-GCATTTACTGCACATT
* * * * * *
8477 ACCTAATTTACCCTTGCAAGTG-G-GAGGAAAGTG-GATGATTACTCCCTTCGTTAAACCCAATT
1 ACCTAATTTACCCTTGCAAGTGAGAGAAGAGAGAGCGA-G-TAACTACCTTCGTTAAACCCAATA
* *
8539 TTGCATTTACTTCACATT
64 TAGCATTTACTGCACATT
* * * * * *
8557 ACCTGATTTACCCTTGCAAGTGGGAGGAGAGAGGGTGAGTAACTCCCTTCGTTAAACCCAATATA
1 ACCTAATTTACCCTTGCAAGTGAGAGAAGAGAGAGCGAGTAACTACCTTCGTTAAACCCAATATA
*
8622 -CATTTATTGCACATT
66 GCATTTACTGCACATT
** * ** * *
8637 ACCTAATTTACCCTTGCAAACGAGAGAAGAGAGAGCGAGTAAGTATTTTCGTTAAGCCCAATGTA
1 ACCTAATTTACCCTTGCAAGTGAGAGAAGAGAGAGCGAGTAACTACCTTCGTTAAACCCAATATA
8702 GCATTTACTGCACATT
66 GCATTTACTGCACATT
*
8718 ACCTAATTTAACCTTGCAAGTGAGAG
1 ACCTAATTTACCCTTGCAAGTGAGAG
8744 GTAAAAGGGT
Statistics
Matches: 221, Mismatches: 38, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
78 2 0.01
79 7 0.03
80 121 0.55
81 82 0.37
82 7 0.03
83 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (81 bp):
ACCTAATTTACCCTTGCAAGTGAGAGAAGAGAGAGCGAGTAACTACCTTCGTTAAACCCAATATA
GCATTTACTGCACATT
Found at i:8761 original size:81 final size:80
Alignment explanation
Indices: 8396--8813 Score: 391
Period size: 81 Copynumber: 5.2 Consensus size: 80
8386 AACAAACAGA
* * * * *
8396 ACCTAATTTAACCTTGCAAGTGGGAGGAGAGAA-TGTGAGTAACTCCCTTCGTTGAACTCAATGT
1 ACCTAATTTACCCTTGCAAGTGAGAGGA-A-AAGGGTGAGTAACTCCCTTCGTTAAACCCAATGT
* *
8460 ATG-ATTTATTTCACATT
64 A-GCATTTACTGCACATT
* * *
8477 ACCTAATTTACCCTTGCAAGTGGGAGG-AAAGTGGATGA-TTACTCCCTTCGTTAAACCCAATTT
1 ACCTAATTTACCCTTGCAAGTGAGAGGAAAAG-GG-TGAGTAACTCCCTTCGTTAAACCCAATGT
* *
8540 TGCATTTACTTCACATT
64 AGCATTTACTGCACATT
* * * *
8557 ACCTGATTTACCCTTGCAAGTGGGAGGAGAGAGGGTGAGTAACTCCCTTCGTTAAACCCAATATA
1 ACCTAATTTACCCTTGCAAGTGAGAGGA-AAAGGGTGAGTAACTCCCTTCGTTAAACCCAATGTA
*
8622 -CATTTATTGCACATT
65 GCATTTACTGCACATT
** * * * *** *
8637 ACCTAATTTACCCTTGCAAACGAGA-GAAGAGAGAGCGAGTAAGTATTTTCGTTAAGCCCAATGT
1 ACCTAATTTACCCTTGCAAGTGAGAGGAA-A-AGGGTGAGTAACTCCCTTCGTTAAACCCAATGT
8701 AGCATTTACTGCACATT
64 AGCATTTACTGCACATT
* * * * *
8718 ACCTAATTTAACCTTGCAAGTGAGAGGTAAAAGGGTTGA-TAAGTCCCGTCGTTAAATCTAATGT
1 ACCTAATTTACCCTTGCAAGTGAGAGG-AAAAGGG-TGAGTAACTCCCTTCGTTAAACCCAATGT
*
8782 AACATTTACTGCACATT
64 AGCATTTACTGCACATT
* *
8799 TCCTAATTTATCCTT
1 ACCTAATTTACCCTT
8814 ACACCTTTGT
Statistics
Matches: 280, Mismatches: 44, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
78 3 0.01
79 4 0.01
80 124 0.44
81 140 0.50
82 7 0.03
83 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (80 bp):
ACCTAATTTACCCTTGCAAGTGAGAGGAAAAGGGTGAGTAACTCCCTTCGTTAAACCCAATGTAG
CATTTACTGCACATT
Found at i:8932 original size:134 final size:134
Alignment explanation
Indices: 8695--8947 Score: 348
Period size: 134 Copynumber: 1.9 Consensus size: 134
8685 TCGTTAAGCC
*
8695 CAATGTAGCATTTACTGCACATTACCTAATTTAACCTTGCAAGTGAGAGGTAAAAGGGTTGATAA
1 CAATGTAGCATTTACTGCACATTACCTAATTTAACCTTGCAAGTGAGAGGTAAAA-GGATGATAA
* * * *
8760 GTCCCGTCGTTAAATCTAATGTAACATTTACTGCACATTTCCTAATTTATCCTTACACCTTTGTT
65 GTCCCGTCGTTAAACCCAATGTAACATTTACTGCACATTACCTAATTTACCCTTACACCTTTGTT
8825 AAACT
130 AAACT
* * *
8830 CAATGTAGCATTTACTGCACATTA-CTAATTTAACCTTGCAATTGGGAGGATAGAA-GATGAGTA
1 CAATGTAGCATTTACTGCACATTACCTAATTTAACCTTGCAAGTGAGAGG-TAAAAGGATGA-TA
** * * *
8893 AGTCCTTTTGTTAAACCCAATGTAGCATTTACTGTACATTACCTAATTTACCCTT
64 AGTCCCGTCGTTAAACCCAATGTAACATTTACTGCACATTACCTAATTTACCCTT
8948 GCAAGTGGGA
Statistics
Matches: 103, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
133 4 0.04
134 71 0.69
135 28 0.27
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (134 bp):
CAATGTAGCATTTACTGCACATTACCTAATTTAACCTTGCAAGTGAGAGGTAAAAGGATGATAAG
TCCCGTCGTTAAACCCAATGTAACATTTACTGCACATTACCTAATTTACCCTTACACCTTTGTTA
AACT
Found at i:8987 original size:81 final size:81
Alignment explanation
Indices: 8817--9270 Score: 531
Period size: 81 Copynumber: 5.6 Consensus size: 81
8807 TATCCTTACA
* * * * * *
8817 CCTTTGTTAAACTCAATGTAGCATTTACTGCACATTA-CTAATTTAACCTTGCAATTGGGAGGAT
1 CCTTCGTTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTTGCAAGTGGGAGGAG
* *
8881 AGAAGATGAGTAAGTC
66 AGAGGGTGAGTAAGTC
* * **
8897 CTTTTGTTAAACCCAATGTAGCATTTACTGTACATTACCTAATTTACCCTTGCAAGTGGGAGGAG
1 CCTTCGTTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTTGCAAGTGGGAGGAG
* *
8962 AGTGGGTGAGTAAATC
66 AGAGGGTGAGTAAGTC
* ** * *
8978 CCTTCGTTAAACCCAATTTTTCATTTACTGCATATTACCTAATTTACCCTTGCAAGTGGGAGGAG
1 CCTTCGTTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTTGCAAGTGGGAGGAG
*
9043 AGAAGGTGAGTAAGTC
66 AGAGGGTGAGTAAGTC
* * * ** * *
9059 CCTTCGTTAAATCCAATGTAGGATTTACTACACATCAGTTAATTTACCCTTACAAGTGGCAGGAG
1 CCTTCGTTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTTGCAAGTGGGAGGAG
*
9124 AGTGGGTGAGTAAGTC
66 AGAGGGTGAGTAAGTC
* * * * **
9140 CCTTC-TGTAAATCAAATTTTGCATTT-CTACACATTACCTAATTTACCCTTGCAAGTGGGAGCC
1 CCTTCGT-TAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTTGCAAGTGGGAGGA
9203 GAGAGGGTGAGTAA-T-
65 GAGAGGGTGAGTAAGTC
*
9218 CCTAATCGTTAAACCCAATGTAGCATTTATTACACATTACCTAATTTACCCTT
1 CCT--TCGTTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTT
9271 ACACCTGCGT
Statistics
Matches: 317, Mismatches: 51, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
78 3 0.01
79 1 0.00
80 95 0.30
81 218 0.69
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (81 bp):
CCTTCGTTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTTGCAAGTGGGAGGAG
AGAGGGTGAGTAAGTC
Found at i:8987 original size:215 final size:215
Alignment explanation
Indices: 8602--9482 Score: 500
Period size: 215 Copynumber: 4.0 Consensus size: 215
8592 TGAGTAACTC
* * * ** * *
8602 CCTTCGTTAAACCCAATATA-CATTTATTGCACATTACCTAATTTACCCTTGCAAACGAGAGAAG
1 CCTTCGTTAAACCCAATGTAGCATTTACTGCACATTA-CTAATTTAACCTTGCAAGTGGGAGGAG
* * * *
8666 AG-AGAGCGAGTAAGT-ATTTTCGTTAAGCCCAATGTAGCATTTACTGCACATTACCTAATTTAA
65 AGAAGA-TGAGTAAGTCCTTTT-GTTAAACCCAATGTAGCATTTACTGCACATTACCTAATTTAC
* * * * * * *
8729 CCTTGCAAGTGAGAGGTA-AAAGGGTTGA-TAAGTCCCGTCGTTAAATCTAATGTAACATTTACT
128 CCTTGCAAGTGGGAGG-AGAGAGGG-TGAGTAAATCCCTTCGTTAAACCCAATGTAGCATTTACT
* * *
8792 GCACATTTCCTAATTTATCCTTACA
191 ACACATTACCTAATTTACCCTTACA
* * * *
8817 CCTTTGTTAAACTCAATGTAGCATTTACTGCACATTACTAATTTAACCTTGCAATTGGGAGGATA
1 CCTTCGTTAAACCCAATGTAGCATTTACTGCACATTACTAATTTAACCTTGCAAGTGGGAGGAGA
*
8882 GAAGATGAGTAAGTCCTTTTGTTAAACCCAATGTAGCATTTACTGTACATTACCTAATTTACCCT
66 GAAGATGAGTAAGTCCTTTTGTTAAACCCAATGTAGCATTTACTGCACATTACCTAATTTACCCT
* * ** * *
8947 TGCAAGTGGGAGGAGAGTGGGTGAGTAAATCCCTTCGTTAAACCCAATTTTTCATTTACTGCATA
131 TGCAAGTGGGAGGAGAGAGGGTGAGTAAATCCCTTCGTTAAACCCAATGTAGCATTTACTACACA
*
9012 TTACCTAATTTACCCTTGCA
196 TTACCTAATTTACCCTTACA
** ** * *** * * * ** *
9032 -AGT-GGGAGGAGAGAAGGTGAGTAAGTCCCTTCGTTAAATCCA-ATGTA-GGATTTACTACACA
1 CCTTCGTTA-AACCCAA--T--GT-AG---CAT--TT-ACTGCACAT-TACTAATTTA--AC-CT
** ** * * * *** ** * ** *
9093 T-C-AGT-TAATTTACCCTTACAAG-TGGCAGGAGAGTGGGTGAG-TAAGTCCCTTCTGTAAATC
50 TGCAAGTGGGA-GGA----GAGAAGAT-G-AGTA-AGTCCTTTTGTTAA-ACCC-AATGT--AGC
* * **
9153 AAATT-TTGCATTTCTACACATTACCTAATTTACCCTTGCAAGTGGGAGCCGAGAGGGTGAGT-A
103 -ATTTACTGC--------ACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAGGGTGAGTAA
*
9216 AT-CCTAATCGTTAAACCCAATGTAGCATTTATTACACATTACCTAATTTACCCTTACA
159 ATCCCT--TCGTTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTTACA
* *
9274 CCTGCGTTAAACCCAATGTAGCATTTACTGCACATTACTAATTTACCCTTGCAAGTGGGAGGAGA
1 CCTTCGTTAAACCCAATGTAGCATTTACTGCACATTACTAATTTAACCTTGCAAGTGGGAGGAGA
** * * * * * * ** *
9339 GTGGGTGACTAAGTCCCTTCGTTAAACCTAATTTTTCATTTACTGCATATTACCTAATTTACCCT
66 GAAGATGAGTAAGTCCTTTTGTTAAACCCAATGTAGCATTTACTGCACATTACCTAATTTACCCT
* *
9404 TGCAAGTGGGAGGAGAGAAGGTGAGTAAGTCCCTTCGTTAAACCCAATGTAGCATTTACTACACA
131 TGCAAGTGGGAGGAGAGAGGGTGAGTAAATCCCTTCGTTAAACCCAATGTAGCATTTACTACACA
9469 TTACCTAATTTACC
196 TTACCTAATTTACC
9483 ATTGCAAGTG
Statistics
Matches: 493, Mismatches: 117, Indels: 112
0.68 0.16 0.16
Matches are distributed among these distances:
213 2 0.00
214 8 0.02
215 240 0.49
216 25 0.05
217 3 0.01
218 2 0.00
219 2 0.00
222 5 0.01
223 5 0.01
224 10 0.02
225 11 0.02
226 10 0.02
227 7 0.01
228 4 0.01
229 7 0.01
230 8 0.02
231 10 0.02
232 13 0.03
233 10 0.02
234 4 0.01
235 5 0.01
238 2 0.00
239 2 0.00
240 3 0.01
241 4 0.01
242 86 0.17
243 3 0.01
244 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (215 bp):
CCTTCGTTAAACCCAATGTAGCATTTACTGCACATTACTAATTTAACCTTGCAAGTGGGAGGAGA
GAAGATGAGTAAGTCCTTTTGTTAAACCCAATGTAGCATTTACTGCACATTACCTAATTTACCCT
TGCAAGTGGGAGGAGAGAGGGTGAGTAAATCCCTTCGTTAAACCCAATGTAGCATTTACTACACA
TTACCTAATTTACCCTTACA
Found at i:9060 original size:296 final size:296
Alignment explanation
Indices: 8521--9093 Score: 722
Period size: 296 Copynumber: 1.9 Consensus size: 296
8511 ATGATTACTC
* * * * *
8521 CCTTCGTTAAACCCAATTTTGCATTTACTTCACATTACCTGATTTACCCTTGCAAGTGGGAGGAG
1 CCTTCGTTAAACCCAATGTAGCATTTACTGCACATTACCTAATTTAACCTTGCAAGTGGGAGGAG
* * *
8586 AGAGGGTGAGTAACTCCCTTCGTTAAACCCAATATACATTTATTGCACATTACCTAATTTACCCT
66 AGAAGATGAGTAACTCCCTTCGTTAAACCCAATATACATTTACTGCACATTACCTAATTTACCCT
* ** *
8651 TGCAAACGAGAGAAGAGAGAGCGAGTAAGTATTTTCGTTAAGCCCAATGTAGCATTTACTGCACA
131 TGCAAACGAGAGAAGAGAGAGCGAGTAAATACCTTCGTTAAACCCAATGTAGCATTTACTGCACA
*
8716 TTACCTAATTTAACCTTGCAAGTGAGAGGTAAAAGGGTTGATAAGTCCCGTCGTTAAATCTAATG
196 TTACCTAATTTAACCTTGCAAGTGAGAGGTAAAAGGGTTGATAAGTCCCGTCGTTAAATCCAATG
*
8781 TAACATTTACTGCACATTTCCTAATTTATCCTTACA
261 TAACATTTACTACACATTTCCTAATTTATCCTTACA
* * * *
8817 CCTTTGTTAAACTCAATGTAGCATTTACTGCACATTA-CTAATTTAACCTTGCAATTGGGAGGAT
1 CCTTCGTTAAACCCAATGTAGCATTTACTGCACATTACCTAATTTAACCTTGCAAGTGGGAGGAG
* * * * *
8881 AGAAGATGAGTAAGTCCTTTTGTTAAACCCAATGTAGCATTTACTGTACATTACCTAATTTACCC
66 AGAAGATGAGTAACTCCCTTCGTTAAACCCAATATA-CATTTACTGCACATTACCTAATTTACCC
** * * * * * * * ** *
8946 TTGCAAGTGGGAGGAGAGTGGGTGAGTAAATCCCTTCGTTAAACCCAATTTTTCATTTACTGCAT
130 TTGCAAACGAGAGAAGAGAGAGCGAGTAAATACCTTCGTTAAACCCAATGTAGCATTTACTGCAC
* * *
9011 ATTACCTAATTTACCCTTGCAAGTGGGAGG-AGAGAA-GG-TGAGTAAGTCCCTTCGTTAAATCC
195 ATTACCTAATTTAACCTTGCAAGTGAGAGGTA-A-AAGGGTTGA-TAAGTCCCGTCGTTAAATCC
**
9073 AATGTAGGATTTACTACACAT
257 AATGTAACATTTACTACACAT
9094 CAGTTAATTT
Statistics
Matches: 233, Mismatches: 40, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
295 57 0.24
296 174 0.75
297 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (296 bp):
CCTTCGTTAAACCCAATGTAGCATTTACTGCACATTACCTAATTTAACCTTGCAAGTGGGAGGAG
AGAAGATGAGTAACTCCCTTCGTTAAACCCAATATACATTTACTGCACATTACCTAATTTACCCT
TGCAAACGAGAGAAGAGAGAGCGAGTAAATACCTTCGTTAAACCCAATGTAGCATTTACTGCACA
TTACCTAATTTAACCTTGCAAGTGAGAGGTAAAAGGGTTGATAAGTCCCGTCGTTAAATCCAATG
TAACATTTACTACACATTTCCTAATTTATCCTTACA
Found at i:9104 original size:162 final size:162
Alignment explanation
Indices: 8837--9273 Score: 587
Period size: 162 Copynumber: 2.7 Consensus size: 162
8827 ACTCAATGTA
* * * * *
8837 GCATTTACTGCACATTA-CTAATTTAACCTTGCAATTGGGAGGATAGAAGATGAGTAAGTCCTTT
1 GCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAAGGTGAGTAAGTCCCTT
* ** * *
8901 TGTTAAACCCAATGTAGCATTTACTGTACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGTG
66 CGTTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTTACAAGTGGCAGGAGAGTG
*
8966 GGTGAGTAAATCCCTTC-GTTAAACCCAATTTT
131 GGTGAGTAAATCCCTTCTG-TAAACCAAATTTT
* *
8998 TCATTTACTGCATATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAAGGTGAGTAAGTCCCTT
1 GCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAAGGTGAGTAAGTCCCTT
* * * **
9063 CGTTAAATCCAATGTAGGATTTACTACACATCAGTTAATTTACCCTTACAAGTGGCAGGAGAGTG
66 CGTTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTTACAAGTGGCAGGAGAGTG
* *
9128 GGTGAGTAAGTCCCTTCTGTAAATCAAATTTT
131 GGTGAGTAAATCCCTTCTGTAAACCAAATTTT
* ** *
9160 GCATTT-CTACACATTACCTAATTTACCCTTGCAAGTGGGAGCCGAGAGGGTGAGTAA-T-CCTA
1 GCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAAGGTGAGTAAGTCCCT-
*
9222 ATCGTTAAACCCAATGTAGCATTTATTACACATTACCTAATTTACCCTTACA
65 -TCGTTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTTACA
9274 CCTGCGTTAA
Statistics
Matches: 240, Mismatches: 32, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
159 3 0.01
160 1 0.00
161 106 0.44
162 129 0.54
163 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (162 bp):
GCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAAGGTGAGTAAGTCCCTT
CGTTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTTACAAGTGGCAGGAGAGTG
GGTGAGTAAATCCCTTCTGTAAACCAAATTTT
Found at i:9182 original size:376 final size:371
Alignment explanation
Indices: 8441--9566 Score: 1161
Period size: 376 Copynumber: 3.0 Consensus size: 371
8431 TGAGTAACTC
* * * * *
8441 CCTTCGTTGAACTCAATGTATGATTTATTTCACATTACCTAATTTACCCTTGCAAGTGGGAGGAA
1 CCTTTGTTGAACTCAATGTA-GATTTA-TGCACATTA-CTAATTTAACCTTGCAATTGGGAGGAT
** * * *
8506 AGTGGATGATTACTCCCTTCGTTAAACCCAATTTTGCATTTACT-TCACATTACCTGATTTACCC
63 AGAAGATGATTACT-CCTTCGTTAAACCCAATGTAGCATTTACTGT-ACATTACCTAATTTACCC
* * * * * *
8570 TTGCAAGTGGGAGGAGAGAGGGTGAGTAACTCCCTTCGTTAAACCCAA-TATACATTTATTGCAC
126 TTGCAAGTGGGAGGAGAGTGGGTGAGTAAATCCCTTCGTTAAACCCAATTTTTCATTTACTGCAT
** * * * *** *
8634 ATTACCTAATTTACCCTTGCAAACGAGAGAAGAG-AGAGCGAGTAAGTATTTTCGTTAAGCCCAA
191 ATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAAG-GTGAGTAAGTCCCTTCGTTAAACCCAA
* * * *
8698 TGTAGCATTTACTGCACATTACCTAATTTAACCTTGCAAGTGAGAGGTAAAAG-GGTTGA-TAAG
255 TGTAGCATTTACTACACATTACCTAATTTACCCTTGCAAGTG-GAGG--AGAGTGGGTGAGTAAG
* * * * * *
8761 TCCCGTCGTTAAATCTAATGTAACATTTACTGCACATTTCCTAATTTATCCTTACA
317 TCCCTTCG-TAAATCAAATTTTACATTTACTGCACATTACCTAATTTACCCTTACA
*
8817 CCTTTGTTAAACTCAATGTAGCATTTACTGCACATTACTAATTTAACCTTGCAATTGGGAGGATA
1 CCTTTGTTGAACTCAATGTAG-ATTTA-TGCACATTACTAATTTAACCTTGCAATTGGGAGGATA
* * *
8882 GAAGATGAGTAAGTCCTTTTGTTAAACCCAATGTAGCATTTACTGTACATTACCTAATTTACCCT
64 GAAGATGA-TTACTCC-TTCGTTAAACCCAATGTAGCATTTACTGTACATTACCTAATTTACCCT
8947 TGCAAGTGGGAGGAGAGTGGGTGAGTAAATCCCTTCGTTAAACCCAATTTTTCATTTACTGCATA
127 TGCAAGTGGGAGGAGAGTGGGTGAGTAAATCCCTTCGTTAAACCCAATTTTTCATTTACTGCATA
*
9012 TTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAAGGTGAGTAAGTCCCTTCGTTAAATCCAATG
192 TTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAAGGTGAGTAAGTCCCTTCGTTAAACCCAATG
* * ** *
9077 TAGGATTTACTACACATCAGTTAATTTACCCTTACAAGTGGCAGGAGAGTGGGTGAGTAAGTCCC
257 TAGCATTTACTACACATTACCTAATTTACCCTTGCAAGTGG-AGGAGAGTGGGTGAGTAAGTCCC
* * *
9142 TTCTGTAAATCAAATTTTGCATTT-CTACACATTACCTAATTTACCCTTGCA
321 TTC-GTAAATCAAATTTTACATTTACTGCACATTACCTAATTTACCCTTACA
** * * * ** * * * * ***
9193 --AGTG-GGAGC-CGA-G-AGGGTGA-GTA-A-TCCTAATCGTTAAACCCAATGTAGCATTTATT
1 CCTTTGTTGAACTCAATGTAGATTTATGCACATTACTAAT--TT-AA-CC--T-T-GCAATTGGG
** * * * * * *
9249 ACACATTACCTAA-TTTACCCTTACACCTGCGTTAAACCCAATGTAGCATTTACTGCACATTA-C
58 A-GGA-TA--GAAGATGA---TTACTCCTTCGTTAAACCCAATGTAGCATTTACTGTACATTACC
* * *
9312 TAATTTACCCTTGCAAGTGGGAGGAGAGTGGGTGACTAAGTCCCTTCGTTAAACCTAATTTTTCA
116 TAATTTACCCTTGCAAGTGGGAGGAGAGTGGGTGAGTAAATCCCTTCGTTAAACCCAATTTTTCA
9377 TTTACTGCATATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAAGGTGAGTAAGTCCCTTCGT
181 TTTACTGCATATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAAGGTGAGTAAGTCCCTTCGT
*
9442 TAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCATTGCAAGTGGGAGGAGAGTGGGT
246 TAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTTGCAAGT-GGAGGAGAGTGGGT
*
9507 GAGTAAGTCCCTTCGGTAAATTAAATTTTACATTTACTGCACATTACCTAATTTACCCTT
310 GAGTAAGTCCCTTC-GTAAATCAAATTTTACATTTACTGCACATTACCTAATTTACCCTT
9567 GCAAGTGGGA
Statistics
Matches: 634, Mismatches: 90, Indels: 51
0.82 0.12 0.07
Matches are distributed among these distances:
365 6 0.01
366 1 0.00
367 4 0.01
368 2 0.00
369 4 0.01
370 2 0.00
371 2 0.00
372 3 0.00
373 8 0.01
374 3 0.00
375 39 0.06
376 367 0.58
377 186 0.29
378 7 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (371 bp):
CCTTTGTTGAACTCAATGTAGATTTATGCACATTACTAATTTAACCTTGCAATTGGGAGGATAGA
AGATGATTACTCCTTCGTTAAACCCAATGTAGCATTTACTGTACATTACCTAATTTACCCTTGCA
AGTGGGAGGAGAGTGGGTGAGTAAATCCCTTCGTTAAACCCAATTTTTCATTTACTGCATATTAC
CTAATTTACCCTTGCAAGTGGGAGGAGAGAAGGTGAGTAAGTCCCTTCGTTAAACCCAATGTAGC
ATTTACTACACATTACCTAATTTACCCTTGCAAGTGGAGGAGAGTGGGTGAGTAAGTCCCTTCGT
AAATCAAATTTTACATTTACTGCACATTACCTAATTTACCCTTACA
Found at i:9263 original size:457 final size:455
Alignment explanation
Indices: 8398--9645 Score: 1531
Period size: 457 Copynumber: 2.7 Consensus size: 455
8388 CAAACAGAAC
* * *
8398 CTAATTTAACCTTGCAAGTGGGAGGAGAGAATGTGAGTAACTCCCTTCGTTGAACTCAATGTATG
1 CTAATTTAACCTTGCAAGTGGGAGGAGAGAA-GTGAGTAAGTCCCTTCGTTAAACCCAATGTA-G
* * * * *
8463 -ATTTA-TTTCACATTACCTAATTTACCCTTGCAAGTGGGAGGAAAGTGGATGA-TTACTCCCTT
64 CATTTACTGT-ACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGTGGGTGAGTAAATCCCTT
* *
8525 CGTTAAACCCAATTTTGCATTTACTTCACATTACCTGATTTACCCTTGCAAGTGGGAGGAGAGAG
128 CGTTAAACCCAATTTTGCATTTACTACACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAG
* * *
8590 GGTGAGTAACTCCCTTCGTTAAACCCAATATACATTTATTGCACATTACCTAATTTACCCTTGCA
193 GGTGAGTAAGTCCCTTCGTTAAATCCAATATACATTTACTGCACATTACCTAATTTACCCTTGCA
** * * * * * * *
8655 AACGAGAGAAGAGAGAGCGAGTAAGT-ATTTTCGTTAAGCCCAATGTAGCATTTACTGCACATTA
258 AGTG-GAGAAGAGAGGGTGAGTAAGTCCTTCT-GTTAAACCCAATTTAGCATTTACTACACATTA
* ** ** * *
8719 CCTAATTTAACCTTGCAAGTGAGAGGTAAAAGGGTTGATAAGTCCCGTCGTTAAATCTAATGTAA
321 CCTAATTTACCCTTGCAAGTGAGAGCCAAAAGGGTTGATAAGTCCAATCGTTAAACCCAATGTAA
* * * ** *
8784 CATTTACTGCACATTTCCTAATTTATCCTTACACCTTTGTTAAACTCAATGTAGCATTTACTGCA
386 CATTTACTACACATTACCTAATTTACCCTTACACCTGCGTTAAACCCAATGTAGCATTTACTGCA
8849 CATTA
451 CATTA
* * * *
8854 CTAATTTAACCTTGCAATTGGGAGGATAGAAGATGAGTAAGTCCTTTTGTTAAACCCAATGTAGC
1 CTAATTTAACCTTGCAAGTGGGAGGAGAGAAG-TGAGTAAGTCCCTTCGTTAAACCCAATGTAGC
8919 ATTTACTGTACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGTGGGTGAGTAAATCCCTTCG
65 ATTTACTGTACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGTGGGTGAGTAAATCCCTTCG
* * * *
8984 TTAAACCCAATTTTTCATTTACTGCATATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAAGG
130 TTAAACCCAATTTTGCATTTACTACACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAGGG
* * * * ** *
9049 TGAGTAAGTCCCTTCGTTAAATCCAATGTAGGATTTACTACACATCAGTTAATTTACCCTTACAA
195 TGAGTAAGTCCCTTCGTTAAATCCAATATA-CATTTACTGCACATTACCTAATTTACCCTTGCAA
* * * * *
9114 GTGGCAGGAGAGTGGGTGAGTAAGTCCCTTCTG-TAAATCAAATTTTGCATTT-CTACACATTAC
259 GTGG-AGAAGAGAGGGTGAGTAAGT-CCTTCTGTTAAACCCAATTTAGCATTTACTACACATTAC
* * *
9177 CTAATTTACCCTTGCAAGTGGGAGCCGAGAGGG-TGAGTAA-TCCTAATCGTTAAACCCAATGTA
322 CTAATTTACCCTTGCAAGTGAGAGCCAAAAGGGTTGA-TAAGTCC-AATCGTTAAACCCAATGTA
* *
9240 GCATTTATTACACATTACCTAATTTACCCTTACACCTGCGTTAAACCCAATGTAGCATTTACTGC
385 ACATTTACTACACATTACCTAATTTACCCTTACACCTGCGTTAAACCCAATGTAGCATTTACTGC
9305 ACATTA
450 ACATTA
* ** * * * **
9311 CTAATTTACCCTTGCAAGTGGGAGGAGAGTGGGTGACTAAGTCCCTTCGTTAAACCTAATTTTTC
1 CTAATTTAACCTTGCAAGTGGGAGGAGAG-AAGTGAGTAAGTCCCTTCGTTAAACCCAATGTAGC
* * ** *
9376 ATTTACTGCATATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAAGGTGAGTAAGTCCCTTCG
65 ATTTACTGTACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGTGGGTGAGTAAATCCCTTCG
* * * *
9441 TTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCATTGCAAGTGGGAGGAGAGTGGG
130 TTAAACCCAATTTTGCATTTACTACACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAGGG
* ** *
9506 TGAGTAAGTCCCTTCGGTAAATTAAATTTTACATTTACTGCACATTACCTAATTTACCCTTGCAA
195 TGAGTAAGTCCCTTCGTTAAATCCAA-TATACATTTACTGCACATTACCTAATTTACCCTTGCAA
** * * * *
9571 GTGGGAGCCGAAAGGGTGAGTAAGTCCTTTTGTTAAACCCAATTTAGCATTTATTACACATTATC
259 GT-GGAGAAGAGAGGGTGAGTAAGTCCTTCTGTTAAACCCAATTTAGCATTTACTACACATTACC
9636 TAATTTACCC
323 TAATTTACCC
9646 AATTTAGCAT
Statistics
Matches: 673, Mismatches: 104, Indels: 28
0.84 0.13 0.03
Matches are distributed among these distances:
455 2 0.00
456 112 0.17
457 471 0.70
458 84 0.12
459 1 0.00
460 3 0.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Consensus pattern (455 bp):
CTAATTTAACCTTGCAAGTGGGAGGAGAGAAGTGAGTAAGTCCCTTCGTTAAACCCAATGTAGCA
TTTACTGTACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGTGGGTGAGTAAATCCCTTCGT
TAAACCCAATTTTGCATTTACTACACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAGGGT
GAGTAAGTCCCTTCGTTAAATCCAATATACATTTACTGCACATTACCTAATTTACCCTTGCAAGT
GGAGAAGAGAGGGTGAGTAAGTCCTTCTGTTAAACCCAATTTAGCATTTACTACACATTACCTAA
TTTACCCTTGCAAGTGAGAGCCAAAAGGGTTGATAAGTCCAATCGTTAAACCCAATGTAACATTT
ACTACACATTACCTAATTTACCCTTACACCTGCGTTAAACCCAATGTAGCATTTACTGCACATTA
Found at i:9400 original size:134 final size:133
Alignment explanation
Indices: 9160--9404 Score: 332
Period size: 134 Copynumber: 1.8 Consensus size: 133
9150 ATCAAATTTT
* *
9160 GCATTTCTACACATTACCTAATTTACCCTTGCAAGTGGGAGCCGAGAGGGTGAGTAATCCTAATC
1 GCATTTCTACACATTACCTAATTTACCCTTGCAAGTGGGAGCAGAGAGGGTGACTAATCCT-ATC
*
9225 GTTAAACCCAATGTAGCATTTATTACACATTACCTAATTTACCCTTACACCTGCGTTAAACCCAA
65 GTTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTTACACCTGCGTTAAACCCAA
9290 TGTA
130 TGTA
* * *
9294 GCATTTACTGCACATTA-CTAATTTACCCTTGCAAGTGGGAGGAGAGTGGGTGACTAAGTCCCT-
1 GCATTT-CTACACATTACCTAATTTACCCTTGCAAGTGGGAGCAGAGAGGGTGACTAA-T-CCTA
* * ** * *
9357 TCGTTAAACCTAATTTTTCATTTACTGCATATTACCTAATTTACCCTT
63 TCGTTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTT
9405 GCAAGTGGGA
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
134 83 0.86
135 10 0.10
136 3 0.03
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.33
Consensus pattern (133 bp):
GCATTTCTACACATTACCTAATTTACCCTTGCAAGTGGGAGCAGAGAGGGTGACTAATCCTATCG
TTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCCTTACACCTGCGTTAAACCCAAT
GTA
Found at i:9416 original size:81 final size:81
Alignment explanation
Indices: 9278--9645 Score: 497
Period size: 81 Copynumber: 4.6 Consensus size: 81
9268 CTTACACCTG
* *
9278 CGTTAAACCCAATGTAGCATTTACTGCACATTA-CTAATTTACCCTTGCAAGTGGGAGGAGAGTG
1 CGTTAAACCCAATTTAGCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAG
*
9342 GGTGACTAAGTCCCTT
66 GGTGAGTAAGTCCCTT
* ** * *
9358 CGTTAAACCTAATTTTTCATTTACTGCATATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAA
1 CGTTAAACCCAATTTAGCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAG
9423 GGTGAGTAAGTCCCTT
66 GGTGAGTAAGTCCCTT
* * * *
9439 CGTTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCATTGCAAGTGGGAGGAGAGTG
1 CGTTAAACCCAATTTAGCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAG
9504 GGTGAGTAAGTCCCTT
66 GGTGAGTAAGTCCCTT
* *** ** *
9520 CGGTAAATTAAATTTTA-CATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGCCGAAA
1 CGTTAAACCCAA-TTTAGCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGA
*
9584 GGGTGAGTAAGTCCTTT
65 GGGTGAGTAAGTCCCTT
* * * *
9601 TGTTAAACCCAATTTAGCATTTATTACACATTATCTAATTTACCC
1 CGTTAAACCCAATTTAGCATTTACTGCACATTACCTAATTTACCC
9646 AATTTAGCAT
Statistics
Matches: 248, Mismatches: 37, Indels: 5
0.86 0.13 0.02
Matches are distributed among these distances:
80 32 0.13
81 213 0.86
82 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (81 bp):
CGTTAAACCCAATTTAGCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGAG
GGTGAGTAAGTCCCTT
Found at i:9544 original size:162 final size:161
Alignment explanation
Indices: 9278--9644 Score: 567
Period size: 162 Copynumber: 2.3 Consensus size: 161
9268 CTTACACCTG
* *
9278 CGTTAAACCCAATGTAGCATTTACTGCACATTACTAATTTACCCTTGCAAGTGGGAGGAGAGTGG
1 CGTTAAACCCAATGTAGCATTTACTACACATTACTAATTTACCATTGCAAGTGGGAGGAGAGTGG
* * *
9343 GTGACTAAGTCCCTTCGTTAAACCTAATTTTTCATTTACTGCATATTACCTAATTTACCCTTGCA
66 GTGACTAAGTCCCTTCGGTAAACCTAATTTTACATTTACTGCACATTACCTAATTTACCCTTGCA
*
9408 AGTGGGAGGAGAGAA-GGTGAGTAAGTCCCTT
131 AGTGGGAGCAGA-AAGGGTGAGTAAGTCCCTT
9439 CGTTAAACCCAATGTAGCATTTACTACACATTACCTAATTTACCATTGCAAGTGGGAGGAGAGTG
1 CGTTAAACCCAATGTAGCATTTACTACACATTA-CTAATTTACCATTGCAAGTGGGAGGAGAGTG
* *
9504 GGTGAGTAAGTCCCTTCGGTAAA-TTAAATTTTACATTTACTGCACATTACCTAATTTACCCTTG
65 GGTGACTAAGTCCCTTCGGTAAACCT-AATTTTACATTTACTGCACATTACCTAATTTACCCTTG
* *
9568 CAAGTGGGAGCCGAAAGGGTGAGTAAGTCCTTT
129 CAAGTGGGAGCAGAAAGGGTGAGTAAGTCCCTT
* * *
9601 TGTTAAACCCAATTTAGCATTTATTACACATTATCTAATTTACC
1 CGTTAAACCCAATGTAGCATTTACTACACATTA-CTAATTTACC
9645 CAATTTAGCA
Statistics
Matches: 189, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
161 35 0.19
162 154 0.81
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (161 bp):
CGTTAAACCCAATGTAGCATTTACTACACATTACTAATTTACCATTGCAAGTGGGAGGAGAGTGG
GTGACTAAGTCCCTTCGGTAAACCTAATTTTACATTTACTGCACATTACCTAATTTACCCTTGCA
AGTGGGAGCAGAAAGGGTGAGTAAGTCCCTT
Found at i:9923 original size:19 final size:19
Alignment explanation
Indices: 9901--9951 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
9891 GGGCTGAAAT
9901 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
9920 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
9939 TAATT-ATTATTAA
1 TAATTAATTATTAA
9952 AAACTCCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:25470 original size:51 final size:50
Alignment explanation
Indices: 25369--25470 Score: 111
Period size: 51 Copynumber: 2.0 Consensus size: 50
25359 GTTCTTCATA
* **
25369 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
*
25419 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATAA-AAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACA-AACAAACACTCGTACA-GTGT
25470 T
1 T
25471 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
50 7 0.16
51 34 0.77
52 3 0.07
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
Done.