Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022518.1 Corchorus olitorius cultivar O-4 contig22551, 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: 20413
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1697 original size:24 final size:25
Alignment explanation
Indices: 1670--1717 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
1660 AAATTTTCAC
*
1670 TATCCAAAACCGAAA-TCGTTTAAT
1 TATCCAAAACCCAAATTCGTTTAAT
**
1694 TATCCATTACCCAAATTCGTTTAA
1 TATCCAAAACCCAAATTCGTTTAA
1718 AAACCGCTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (25 bp):
TATCCAAAACCCAAATTCGTTTAAT
Found at i:13184 original size:2 final size:2
Alignment explanation
Indices: 13179--13206 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13169 TTGTGTGTAA
13179 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
13207 GAATGAATGA
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:16484 original size:21 final size:21
Alignment explanation
Indices: 16458--16511 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
16448 TCAAGGCTGC
16458 TCAAACCCCAAATATCAATAG
1 TCAAACCCCAAATATCAATAG
16479 TCAAACCCCAAATATCAATAG
1 TCAAACCCCAAATATCAATAG
*
16500 TCAAACCACAAA
1 TCAAACCCCAAA
16512 ACATCATTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.50, C:0.30, G:0.04, T:0.17
Consensus pattern (21 bp):
TCAAACCCCAAATATCAATAG
Found at i:16609 original size:53 final size:53
Alignment explanation
Indices: 16549--16733 Score: 192
Period size: 53 Copynumber: 3.3 Consensus size: 53
16539 CCAAAGGATA
*
16549 ATGGTCAAACCCCAAATTTCAATAGTCAAACCACAAAACATCATTGTACATAC
1 ATGGTCAAACCCCAAATTTCAATAGTCAAACTACAAAACATCATTGTACATAC
* * *
16602 ATGGTCAAACCCCAAAATAT-AATGGTCAAACTACAAAACATCATGGTCAAACCCCATAGGATC
1 ATGGTCAAACCCC-AAATTTCAATAGTCAAACTACAAAACATCATTGT---A---CAT---A-C
* * **
16665 ATGGTTAAACCCCAAATTTCAATAGTCAAACTATAAAACATCATTGTACATGT
1 ATGGTCAAACCCCAAATTTCAATAGTCAAACTACAAAACATCATTGTACATAC
16718 ATGGTCAAACCCCAAA
1 ATGGTCAAACCCCAAA
16734 GGATAATGGT
Statistics
Matches: 108, Mismatches: 12, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
53 52 0.48
54 5 0.05
56 1 0.01
57 3 0.03
59 3 0.03
60 1 0.01
62 6 0.06
63 37 0.34
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.23
Consensus pattern (53 bp):
ATGGTCAAACCCCAAATTTCAATAGTCAAACTACAAAACATCATTGTACATAC
Found at i:16626 original size:21 final size:21
Alignment explanation
Indices: 16596--16680 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
16586 ACATCATTGT
16596 ACATACATGGTCAAACCCCAAA
1 ACAT-CATGGTCAAACCCCAAA
* * **
16618 ATATAATGGTCAAACTACAAA
1 ACATCATGGTCAAACCCCAAA
*
16639 ACATCATGGTCAAACCCCATA
1 ACATCATGGTCAAACCCCAAA
** *
16660 GGATCATGGTTAAACCCCAAA
1 ACATCATGGTCAAACCCCAAA
16681 TTTCAATAGT
Statistics
Matches: 50, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
21 47 0.94
22 3 0.06
ACGTcount: A:0.44, C:0.26, G:0.12, T:0.19
Consensus pattern (21 bp):
ACATCATGGTCAAACCCCAAA
Found at i:16654 original size:74 final size:74
Alignment explanation
Indices: 16458--16632 Score: 280
Period size: 74 Copynumber: 2.4 Consensus size: 74
16448 TCAAGGCTGC
*
16458 TCAAACCCC-AAATATCAATAGTCAAACCCCAAATATCAATAGTCAAACCACAAAACATCATTGT
1 TCAAACCCCAAAATAT-AATGGTCAAACCCCAAATATCAATAGTCAAACCACAAAACATCATTGT
*
16522 ACATGCATGG
65 ACATACATGG
* ** *
16532 TCAAAGCCCAAAGGATAATGGTCAAACCCCAAATTTCAATAGTCAAACCACAAAACATCATTGTA
1 TCAAACCCCAAAATATAATGGTCAAACCCCAAATATCAATAGTCAAACCACAAAACATCATTGTA
16597 CATACATGG
66 CATACATGG
16606 TCAAACCCCAAAATATAATGGTCAAAC
1 TCAAACCCCAAAATATAATGGTCAAAC
16633 TACAAAACAT
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
74 87 0.96
75 4 0.04
ACGTcount: A:0.45, C:0.26, G:0.10, T:0.20
Consensus pattern (74 bp):
TCAAACCCCAAAATATAATGGTCAAACCCCAAATATCAATAGTCAAACCACAAAACATCATTGTA
CATACATGG
Found at i:16666 original size:74 final size:74
Alignment explanation
Indices: 16458--16654 Score: 236
Period size: 74 Copynumber: 2.7 Consensus size: 74
16448 TCAAGGCTGC
* * * * *
16458 TCAAACCCC-AAATATCAATAGTCAAACCCCAAATATCAATAGTCAAACCACAAAACATCATTGT
1 TCAAACCCCAAAAGAT-AATGGTCAAACACAAAACATCAATAGTCAAACCACAAAACATCATTGT
*
16522 ACATGCATGG
65 ACATACATGG
* * * * **
16532 TCAAAGCCCAAAGGATAATGGTCAAACCCCAAATTTCAATAGTCAAACCACAAAACATCATTGTA
1 TCAAACCCCAAAAGATAATGGTCAAACACAAAACATCAATAGTCAAACCACAAAACATCATTGTA
16597 CATACATGG
66 CATACATGG
* *
16606 TCAAACCCCAAAATATAATGGTCAAACTACAAAACATC-ATGGTCAAACC
1 TCAAACCCCAAAAGATAATGGTCAAAC-ACAAAACATCAATAGTCAAACC
16655 CCATAGGATC
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
74 97 0.91
75 10 0.09
ACGTcount: A:0.45, C:0.26, G:0.10, T:0.20
Consensus pattern (74 bp):
TCAAACCCCAAAAGATAATGGTCAAACACAAAACATCAATAGTCAAACCACAAAACATCATTGTA
CATACATGG
Found at i:16690 original size:116 final size:117
Alignment explanation
Indices: 16522--16748 Score: 357
Period size: 116 Copynumber: 1.9 Consensus size: 117
16512 ACATCATTGT
*
16522 ACATGCATGGTCAAAGCCCAAAGGATAATGGTCAAACCCCAAATTTCAATAGTCAAACCACAAAA
1 ACATGCATGGTCAAACCCCAAAGGATAATGGTCAAACCCCAAATTTCAATAGTCAAACCACAAAA
*
16587 CATCATTGTACATACATGGTCAAACCCCAAAATATAATGGTCAAACTACAAA
66 CATCATTGTACATACATGGTCAAACCCCAAAAGATAATGGTCAAACTACAAA
* * * * *
16639 ACAT-CATGGTCAAACCCCATAGGATCATGGTTAAACCCCAAATTTCAATAGTCAAACTATAAAA
1 ACATGCATGGTCAAACCCCAAAGGATAATGGTCAAACCCCAAATTTCAATAGTCAAACCACAAAA
** *
16703 CATCATTGTACATGTATGGTCAAACCCCAAAGGATAATGGTCAAAC
66 CATCATTGTACATACATGGTCAAACCCCAAAAGATAATGGTCAAAC
16749 CCTAAATTTC
Statistics
Matches: 100, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
116 96 0.96
117 4 0.04
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.22
Consensus pattern (117 bp):
ACATGCATGGTCAAACCCCAAAGGATAATGGTCAAACCCCAAATTTCAATAGTCAAACCACAAAA
CATCATTGTACATACATGGTCAAACCCCAAAAGATAATGGTCAAACTACAAA
Found at i:16705 original size:190 final size:191
Alignment explanation
Indices: 16481--16834 Score: 539
Period size: 190 Copynumber: 1.9 Consensus size: 191
16471 ATCAATAGTC
*
16481 AAACCCCAAATATCAATAGTCAAACCACAAAACATCATTGTACATGCATGGTCAAAGCCCAAAGG
1 AAACCCCAAATATCAATAGTCAAACCACAAAACATCATTGTACATGCATGGTCAAACCCCAAAGG
* * *
16546 ATAATGGTCAAACCCCAAATTTCAATAGTCAAACCACAAAACA-TCATTGTACATACATGGTCAA
66 ATAATGGTCAAACCCCAAATTTCAATAGTCAAACAAAAAAACATTCATTGTACATACATAGTCAA
* *
16610 ACCCCAAAATATAATGGTCAAACTACAAAACATCATGGTCAAACCCCATAGGATCATGGTT
131 ACCCCAAAATATAATAGTCAAACCACAAAACATCATGGTCAAACCCCATAGGATCATGGTT
* * * *
16671 AAACCCCAAATTTCAATAGTCAAACTATAAAACATCATTGTACATGTATGGTCAAACCCCAAAGG
1 AAACCCCAAATATCAATAGTCAAACCACAAAACATCATTGTACATGCATGGTCAAACCCCAAAGG
* * * *
16736 ATAATGGTCAAACCCTAAATTTCAATAGTCAAACAAAAAAATATTTCATTGTATATGCATAGTCA
66 ATAATGGTCAAACCCCAAATTTCAATAGTCAAACAAAAAAACA-TTCATTGTACATACATAGTCA
* * *
16801 AACCCCAAAGTTTGATAGTCAAACCACAAAACAT
130 AACCCCAAAATATAATAGTCAAACCACAAAACAT
16835 TTTATTGTAT
Statistics
Matches: 145, Mismatches: 17, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
190 99 0.68
192 46 0.32
ACGTcount: A:0.44, C:0.23, G:0.11, T:0.23
Consensus pattern (191 bp):
AAACCCCAAATATCAATAGTCAAACCACAAAACATCATTGTACATGCATGGTCAAACCCCAAAGG
ATAATGGTCAAACCCCAAATTTCAATAGTCAAACAAAAAAACATTCATTGTACATACATAGTCAA
ACCCCAAAATATAATAGTCAAACCACAAAACATCATGGTCAAACCCCATAGGATCATGGTT
Found at i:16725 original size:74 final size:75
Alignment explanation
Indices: 16639--16810 Score: 231
Period size: 74 Copynumber: 2.3 Consensus size: 75
16629 AAACTACAAA
* * * * *
16639 ACAT-CATGGTCAAACCCCATAGGATCATGGTTAAACCCCAAATTTCAATAGTCAAACTATAAAA
1 ACATGCATGGTCAAACCCCAAAGGATAATGGTCAAACCCCAAATTTCAATAGTCAAACAAAAAAA
16703 CA-TCATTGT
66 CATTCATTGT
* *
16712 ACATGTATGGTCAAACCCCAAAGGATAATGGTCAAACCCTAAATTTCAATAGTCAAACAAAAAAA
1 ACATGCATGGTCAAACCCCAAAGGATAATGGTCAAACCCCAAATTTCAATAGTCAAACAAAAAAA
*
16777 TATTTCATTGT
66 CA-TTCATTGT
* *
16788 ATATGCATAGTCAAACCCCAAAG
1 ACATGCATGGTCAAACCCCAAAG
16811 TTTGATAGTC
Statistics
Matches: 85, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
73 4 0.05
74 54 0.64
76 27 0.32
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.25
Consensus pattern (75 bp):
ACATGCATGGTCAAACCCCAAAGGATAATGGTCAAACCCCAAATTTCAATAGTCAAACAAAAAAA
CATTCATTGT
Found at i:16822 original size:76 final size:74
Alignment explanation
Indices: 16639--16830 Score: 206
Period size: 74 Copynumber: 2.6 Consensus size: 74
16629 AAACTACAAA
* * * * * * *
16639 ACAT-CATGGTCAAACCCCATAGGATCATGGTTAAACCCCAAATTTCAATAGTCAAACTATAAAA
1 ACATGCATAGTCAAACCCCAAAGGATAATAGTCAAACCCCAAATTTCAATAGTCAAACAAAAAAA
16703 CATCATTGT
66 CATCATTGT
* * * *
16712 ACATGTATGGTCAAACCCCAAAGGATAATGGTCAAACCCTAAATTTCAATAGTCAAACAAAAAAA
1 ACATGCATAGTCAAACCCCAAAGGATAATAGTCAAACCCCAAATTTCAATAGTCAAACAAAAAAA
*
16777 TATTTCATTGT
66 CA--TCATTGT
* ** * *
16788 ATATGCATAGTCAAACCCCAAAGTTTGATAGTCAAACCACAAA
1 ACATGCATAGTCAAACCCCAAAGGATAATAGTCAAACCCCAAA
16831 ACATTTTATT
Statistics
Matches: 99, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
73 4 0.04
74 54 0.55
76 41 0.41
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.25
Consensus pattern (74 bp):
ACATGCATAGTCAAACCCCAAAGGATAATAGTCAAACCCCAAATTTCAATAGTCAAACAAAAAAA
CATCATTGT
Found at i:16936 original size:111 final size:111
Alignment explanation
Indices: 16739--16977 Score: 358
Period size: 111 Copynumber: 2.2 Consensus size: 111
16729 CCAAAGGATA
*
16739 ATGGTCAAACCCTAAATTTCAATAGTCAAACAAAAAAATATTTCATTGTATATGCATAGTCAAAC
1 ATGGTCAAACCCTAAATTTCAATAGTCAAACAAAAAAACATTTCATTGTATATGCATAGTCAAAC
*
16804 CCCAAAGTTTGATAGTCAAACCAC-AAAACATTTTATTGTATATGC
66 CCCAAAGTTTGATAGTCAAACCACAAAAACATTTTATTATATATGC
* * * * *
16849 ATTGTCAAACCCTAAAGTTT-GATAGTCAAACCACAAAAACATTTTATTGTATATGCATGGTCAA
1 ATGGTCAAACCCTAAA-TTTCAATAGTCAAA-CAAAAAAACATTTCATTGTATATGCATAGTCAA
*
16913 ACCCCAAAGTTTGATAGTTAAACCACAAAAACATTTTATTATATATGC
64 ACCCCAAAGTTTGATAGTCAAACCACAAAAACATTTTATTATATATGC
16961 ATGGTCAAATCCC-AAAT
1 ATGGTCAAA-CCCTAAAT
16978 GATAATGGTC
Statistics
Matches: 116, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
110 24 0.21
111 58 0.50
112 31 0.27
113 3 0.03
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.30
Consensus pattern (111 bp):
ATGGTCAAACCCTAAATTTCAATAGTCAAACAAAAAAACATTTCATTGTATATGCATAGTCAAAC
CCCAAAGTTTGATAGTCAAACCACAAAAACATTTTATTATATATGC
Found at i:16992 original size:56 final size:56
Alignment explanation
Indices: 16739--16976 Score: 347
Period size: 56 Copynumber: 4.3 Consensus size: 56
16729 CCAAAGGATA
* * * * *
16739 ATGGTCAAACCCTAAA-TTTCAATAGTCAAA-CAAAAAAATATTTCATTGTATATGC
1 ATGGTCAAACCCCAAAGTTT-GATAGTCAAACCACAAAAACATTTTATTGTATATGC
*
16794 ATAGTCAAACCCCAAAGTTTGATAGTCAAACCAC-AAAACATTTTATTGTATATGC
1 ATGGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAACATTTTATTGTATATGC
* *
16849 ATTGTCAAACCCTAAAGTTTGATAGTCAAACCACAAAAACATTTTATTGTATATGC
1 ATGGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAACATTTTATTGTATATGC
* *
16905 ATGGTCAAACCCCAAAGTTTGATAGTTAAACCACAAAAACATTTTATTATATATGC
1 ATGGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAACATTTTATTGTATATGC
*
16961 ATGGTCAAATCCCAAA
1 ATGGTCAAACCCCAAA
16977 TGATAATGGT
Statistics
Matches: 167, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
55 74 0.44
56 93 0.56
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (56 bp):
ATGGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAACATTTTATTGTATATGC
Found at i:17044 original size:130 final size:132
Alignment explanation
Indices: 16894--17233 Score: 412
Period size: 130 Copynumber: 2.6 Consensus size: 132
16884 AAAACATTTT
* *
16894 ATTGTATATGCATGGTCAAACCCCAAAGTTTGATAGTTAAACCACAAAAACATTTTATTATATAT
1 ATTGTATATGCATGGTCAAACCCCAAAGTTTGATAGTCAAACCAC-AAAACATTTTATTGTATAT
* * ** *
16959 GCATGGTCAAATCCCAAATGATAATGGTCAAACCCCA-AATATCAATAG-CAAA-ACCACAAA-A
65 GCATGGTCAAACCCCAAAGGATAATGGTCAAA-CCCATAATATCAATAGTCAAACAAAAAAAATA
17020 CGTA
129 CGTA
* * * *
17024 ATTGTACATGCATGGTCAAACCCCAAA-TTTCAATAGTCAAACCACAAAACA--TCATTGTACAT
1 ATTGTATATGCATGGTCAAACCCCAAAGTTT-GATAGTCAAACCACAAAACATTTTATTGTATAT
* *
17086 GCATGGTCAAACCCCAAAGGATAATGGTCAAACCCATAATTTCAATAGTCAAACAAAAAAAATAT
65 GCATGGTCAAACCCCAAAGGATAATGGTCAAACCCATAATATCAATAGTCAAACAAAAAAAATAC
* *
17151 TTT
130 GTA
*
17154 ATTGTATATGCATGGTCAAA-CCCAAAGTTTGATAGTCAAACTAC--AACATTTTATTGTATATG
1 ATTGTATATGCATGGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAACATTTTATTGTATATG
* * *
17216 CATTGTAAAACCCTAAAG
66 CATGGTCAAACCCCAAAG
17234 TTTGATAGTC
Statistics
Matches: 179, Mismatches: 23, Indels: 17
0.82 0.11 0.08
Matches are distributed among these distances:
126 4 0.02
127 52 0.29
128 4 0.02
129 57 0.32
130 62 0.35
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.27
Consensus pattern (132 bp):
ATTGTATATGCATGGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAACATTTTATTGTATATG
CATGGTCAAACCCCAAAGGATAATGGTCAAACCCATAATATCAATAGTCAAACAAAAAAAATACG
TA
Found at i:17075 original size:370 final size:368
Alignment explanation
Indices: 16664--17344 Score: 1150
Period size: 368 Copynumber: 1.8 Consensus size: 368
16654 CCCATAGGAT
* * * *
16664 CATGGTTAAACCCCAAATTTCAATAGTCAAACTATAAAACATCATTGTACATGTATGGTCAAACC
1 CATGGTCAAACCCCAAATTTCAATAGTCAAACCACAAAACATCATTGTACATGCATGGTCAAACC
16729 CCAAAGGATAATGGTCAAACCC-TAAATTTCAATAGTCAAAC-AAAAAAATATTTCATTGTATAT
66 CCAAAGGATAATGGTCAAACCCAT-AATTTCAATAGTCAAACAAAAAAAATATTTCATTGTATAT
*
16792 GCATAGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAACATTTTATTGTATATGCATTGTCAA
130 GCATAGTCAAA-CCCAAAGTTTGATAGTCAAACCAC--AACATTTTATTGTATATGCATTGTAAA
*
16857 ACCCTAAAGTTTGATAGTCAAACCACAAAAACATTTTATTGTATATGCATGGTCAAACCCCAAAG
192 ACCCTAAAGTTTGATAGTCAAACCACAAAAACATTTTATTGAATATGCATGGTCAAACCCCAAAG
* * * * *
16922 TTTGATAGTTAAACCACAAAAACATTTTATTATATATGCATGGTCAAATCCCAAATGATAATGGT
257 ATTAATAGTCAAACCACAAAAACATTTTATTATATATGCATGGTAAAACCCCAAATGATAATGGT
16987 CAAACCCCAAATATCAATAGCAAAACCACAAAACGTAATTGTACATG
322 CAAACCCCAAATATCAATAGCAAAACCACAAAACGTAATTGTACATG
17034 CATGGTCAAACCCCAAATTTCAATAGTCAAACCACAAAACATCATTGTACATGCATGGTCAAACC
1 CATGGTCAAACCCCAAATTTCAATAGTCAAACCACAAAACATCATTGTACATGCATGGTCAAACC
*
17099 CCAAAGGATAATGGTCAAACCCATAATTTCAATAGTCAAACAAAAAAAATATTTTATTGTATATG
66 CCAAAGGATAATGGTCAAACCCATAATTTCAATAGTCAAACAAAAAAAATATTTCATTGTATATG
* *
17164 CATGGTCAAACCCAAAGTTTGATAGTCAAACTACAACATTTTATTGTATATGCATTGTAAAACCC
131 CATAGTCAAACCCAAAGTTTGATAGTCAAACCACAACATTTTATTGTATATGCATTGTAAAACCC
* *
17229 TAAAGTTTGATAGTCAAACCACAAAATCATTTTATTGAATATGCATTGTCAAACCCCAAAGATTA
196 TAAAGTTTGATAGTCAAACCACAAAAACATTTTATTGAATATGCATGGTCAAACCCCAAAGATTA
* *
17294 ATAGTCAAATCATAAAAACATTTTATTATATATGCATGGTAAAACCCCAAA
261 ATAGTCAAACCACAAAAACATTTTATTATATATGCATGGTAAAACCCCAAA
17345 GTTTGATTGT
Statistics
Matches: 291, Mismatches: 18, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
368 136 0.47
370 123 0.42
371 32 0.11
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (368 bp):
CATGGTCAAACCCCAAATTTCAATAGTCAAACCACAAAACATCATTGTACATGCATGGTCAAACC
CCAAAGGATAATGGTCAAACCCATAATTTCAATAGTCAAACAAAAAAAATATTTCATTGTATATG
CATAGTCAAACCCAAAGTTTGATAGTCAAACCACAACATTTTATTGTATATGCATTGTAAAACCC
TAAAGTTTGATAGTCAAACCACAAAAACATTTTATTGAATATGCATGGTCAAACCCCAAAGATTA
ATAGTCAAACCACAAAAACATTTTATTATATATGCATGGTAAAACCCCAAATGATAATGGTCAAA
CCCCAAATATCAATAGCAAAACCACAAAACGTAATTGTACATG
Found at i:17113 original size:74 final size:75
Alignment explanation
Indices: 17035--17180 Score: 199
Period size: 74 Copynumber: 1.9 Consensus size: 75
17025 TTGTACATGC
* *
17035 ATGGTCAAACCCCA-AATTTCAATAGTCAAAC-CACAAAACA-TCATTGTACATGCATGGTCAAA
1 ATGGTCAAA-CCCATAATTTCAATAGTCAAACAAAAAAAACATTCATTGTACATGCATGGTCAAA
17097 CCCCAAAGGATA
65 -CCCAAAGGATA
* * *
17109 ATGGTCAAACCCATAATTTCAATAGTCAAACAAAAAAAATATTTTATTGTATATGCATGGTCAAA
1 ATGGTCAAACCCATAATTTCAATAGTCAAACAAAAAAAACA-TTCATTGTACATGCATGGTCAAA
17174 CCCAAAG
65 CCCAAAG
17181 TTTGATAGTC
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
73 4 0.06
74 26 0.41
75 6 0.10
76 7 0.11
77 20 0.32
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (75 bp):
ATGGTCAAACCCATAATTTCAATAGTCAAACAAAAAAAACATTCATTGTACATGCATGGTCAAAC
CCAAAGGATA
Found at i:17119 original size:53 final size:53
Alignment explanation
Indices: 16982--17103 Score: 201
Period size: 53 Copynumber: 2.3 Consensus size: 53
16972 CCAAATGATA
*
16982 ATGGTCAAACCCCAAATATCAATAG-CAAAACCACAAAACGTAATTGTACATGC
1 ATGGTCAAACCCCAAATATCAATAGTC-AAACCACAAAACATAATTGTACATGC
* *
17035 ATGGTCAAACCCCAAATTTCAATAGTCAAACCACAAAACATCATTGTACATGC
1 ATGGTCAAACCCCAAATATCAATAGTCAAACCACAAAACATAATTGTACATGC
17088 ATGGTCAAACCCCAAA
1 ATGGTCAAACCCCAAA
17104 GGATAATGGT
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
53 64 0.98
54 1 0.02
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.20
Consensus pattern (53 bp):
ATGGTCAAACCCCAAATATCAATAGTCAAACCACAAAACATAATTGTACATGC
Found at i:17274 original size:56 final size:56
Alignment explanation
Indices: 17130--17405 Score: 273
Period size: 56 Copynumber: 5.1 Consensus size: 56
17120 CATAATTTCA
* * * *
17130 ATAGTCAAACAAAAAAAAT-ATTTTATTGTATATGCATGGTCAAA-CCCAAAGTTTG
1 ATAGTCAAAC-CACAAAATCATTTTATTGAATATGCATGGTAAAACCCCAAAGTTTG
* * * *
17185 ATAGTCAAACTAC--AA-CATTTTATTGTATATGCATTGTAAAACCCTAAAGTTTG
1 ATAGTCAAACCACAAAATCATTTTATTGAATATGCATGGTAAAACCCCAAAGTTTG
* * * *
17238 ATAGTCAAACCACAAAATCATTTTATTGAATATGCATTGTCAAACCCCAAAGATTA
1 ATAGTCAAACCACAAAATCATTTTATTGAATATGCATGGTAAAACCCCAAAGTTTG
* * *
17294 ATAGTCAAATCATAAAAACATTTTATT-ATATATGCATGGTAAAACCCCAAAGTTTG
1 ATAGTCAAACCACAAAATCATTTTATTGA-ATATGCATGGTAAAACCCCAAAGTTTG
* * * * * * *
17350 ATTGTTAAACCACAAAA--A-ATCATTGTACATGCATGGTTAAACCCCAAAGTTTG
1 ATAGTCAAACCACAAAATCATTTTATTGAATATGCATGGTAAAACCCCAAAGTTTG
17403 ATA
1 ATA
17406 ATAAAAAATG
Statistics
Matches: 186, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
52 25 0.13
53 53 0.28
54 2 0.01
55 13 0.07
56 93 0.50
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (56 bp):
ATAGTCAAACCACAAAATCATTTTATTGAATATGCATGGTAAAACCCCAAAGTTTG
Found at i:17348 original size:112 final size:107
Alignment explanation
Indices: 17130--17366 Score: 312
Period size: 112 Copynumber: 2.2 Consensus size: 107
17120 CATAATTTCA
* * * * *
17130 ATAGTCAAACAAAAAAAATATTTTATTGTATATGCATGGTCAAACCCAAAGTTTGATAGTCAAAC
1 ATAGTCAAAC-CACAAAATATTTTATTGAATATGCATGGTCAAACCCAAAGATTAATAGTCAAAC
* * * *
17195 TACAACATTTTATTGTATATGCATTGTAAAACCCTAAAGTTTG
65 TAAAACATTTTATTATATATGCATGGTAAAACCCCAAAGTTTG
*
17238 ATAGTCAAACCACAAAATCATTTTATTGAATATGCATTGTCAAACCCCAAAGATTAATAGTCAAA
1 ATAGTCAAACCACAAAAT-ATTTTATTGAATATGCATGGTCAAA-CCCAAAGATTAATAGTCAAA
17303 TCATAAAAACATTTTATTATATATGCATGGTAAAACCCCAAAGTTTG
64 -C-T-AAAACATTTTATTATATATGCATGGTAAAACCCCAAAGTTTG
* *
17350 ATTGTTAAACCACAAAA
1 ATAGTCAAACCACAAAA
17367 AATCATTGTA
Statistics
Matches: 112, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
107 6 0.05
108 33 0.29
109 18 0.16
110 1 0.01
111 1 0.01
112 53 0.47
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.31
Consensus pattern (107 bp):
ATAGTCAAACCACAAAATATTTTATTGAATATGCATGGTCAAACCCAAAGATTAATAGTCAAACT
AAAACATTTTATTATATATGCATGGTAAAACCCCAAAGTTTG
Found at i:19101 original size:19 final size:21
Alignment explanation
Indices: 19073--19114 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
19063 GAATTAAAGA
19073 ATTTAATTTTT-T-AAAATTT
1 ATTTAATTTTTCTGAAAATTT
*
19092 ATTTACTTTTTCTGAAAATTT
1 ATTTAATTTTTCTGAAAATTT
19113 AT
1 AT
19115 ATGGCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
20 1 0.05
21 9 0.45
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTTAATTTTTCTGAAAATTT
Found at i:19258 original size:35 final size:35
Alignment explanation
Indices: 19212--19282 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
19202 TGACCCAATC
19212 ATTTGTTATGCGATTTCGATGGCTAGGAGATTAAA
1 ATTTGTTATGCGATTTCGATGGCTAGGAGATTAAA
19247 ATTTGTTATGCGATTTCGATGGCTAGGAGATTAAA
1 ATTTGTTATGCGATTTCGATGGCTAGGAGATTAAA
19282 A
1 A
19283 GCCACAATCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.30, C:0.08, G:0.25, T:0.37
Consensus pattern (35 bp):
ATTTGTTATGCGATTTCGATGGCTAGGAGATTAAA
Found at i:20076 original size:10 final size:10
Alignment explanation
Indices: 20061--20085 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
20051 TTCAATTTAA
20061 TTTAATCGGT
1 TTTAATCGGT
20071 TTTAATCGGT
1 TTTAATCGGT
20081 TTTAA
1 TTTAA
20086 AATAGGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (10 bp):
TTTAATCGGT
Found at i:20217 original size:11 final size:11
Alignment explanation
Indices: 20201--20263 Score: 58
Period size: 11 Copynumber: 5.9 Consensus size: 11
20191 AAAAAATTTG
20201 TTATATATATT
1 TTATATATATT
*
20212 TTATATATATC
1 TTATATATATT
* * *
20223 ATAAATATA-A
1 TTATATATATT
20233 TT-TATATATT
1 TTATATATATT
* *
20243 TTACATGTATT
1 TTATATATATT
20254 TTATATATAT
1 TTATATATAT
20264 CATAAATAAT
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
9 5 0.13
10 3 0.08
11 31 0.79
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (11 bp):
TTATATATATT
Done.