Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014605.1 Corchorus olitorius cultivar O-4 contig14638, 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: 22211
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:590 original size:121 final size:117
Alignment explanation
Indices: 359--579 Score: 320
Period size: 119 Copynumber: 1.9 Consensus size: 117
349 ATTAAGCTAG
*
359 TATATTAATCCATTTGTATTAAAAAAAGATATTATGAAACTATTTATATATACACAAGGAAAATG
1 TATATTAATCCATTTGTATTAAAAAAAGACATTATGAAACTA-TTATATATACACAAGGAAAATG
* *
424 AATTTTTGTGATTCAGTACCCATAGAATTAAGCTAGTAGTATTTTATTTAGTTT
65 AATTTTTGTGATTCAGTACCCATAGAA-TAACCTAATAGTATTTTATTTAGTTT
*
478 TATATTAATCCATTTGTATTAAATAAAAAGACATTATGAAACTA-TATATATACACAAGGAAATT
1 TATATTAATCCATTTGTATT-AA-AAAAAGACATTATGAAACTATTATATATACACAAGGAAAAT
* *
542 GAATTATTTGTGTGTTCAGTACCCATAGAA-ACCCTAAT
64 GAATT-TTTGTG-ATTCAGTACCCATAGAATAACCTAAT
580 CATCCATTTT
Statistics
Matches: 92, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
119 49 0.53
120 8 0.09
121 35 0.38
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (117 bp):
TATATTAATCCATTTGTATTAAAAAAAGACATTATGAAACTATTATATATACACAAGGAAAATGA
ATTTTTGTGATTCAGTACCCATAGAATAACCTAATAGTATTTTATTTAGTTT
Found at i:2531 original size:134 final size:134
Alignment explanation
Indices: 2291--2561 Score: 533
Period size: 134 Copynumber: 2.0 Consensus size: 134
2281 CCATTCAACA
2291 TATATATTCTACATATTATTTGAAACACTCAATGAAATTACTAAACGCCCCTTTTGAGAATCGAT
1 TATATATTCTACATATTATTTGAAACACTCAATGAAATTACTAAACGCCCCTTTTGAGAATCGAT
*
2356 GAGGAGGCTTGGTTTAAACTTTTTTGTCATTTTCTGTCTTTTCTCACCTGGTTAATTACCAAAAA
66 GAGGAGGCTTGGTTTAAACTTTTTTATCATTTTCTGTCTTTTCTCACCTGGTTAATTACCAAAAA
2421 ATAC
131 ATAC
2425 TATATATTCTACATATTATTTGAAACACTCAATGAAATTACTAAACGCCCCTTTTGAGAATCGAT
1 TATATATTCTACATATTATTTGAAACACTCAATGAAATTACTAAACGCCCCTTTTGAGAATCGAT
2490 GAGGAGGCTTGGTTTAAACTTTTTTATCATTTTCTGTCTTTTCTCACCTGGTTAATTACCAAAAA
66 GAGGAGGCTTGGTTTAAACTTTTTTATCATTTTCTGTCTTTTCTCACCTGGTTAATTACCAAAAA
2555 ATAC
131 ATAC
2559 TAT
1 TAT
2562 TAATGTTAAT
Statistics
Matches: 136, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 136 1.00
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (134 bp):
TATATATTCTACATATTATTTGAAACACTCAATGAAATTACTAAACGCCCCTTTTGAGAATCGAT
GAGGAGGCTTGGTTTAAACTTTTTTATCATTTTCTGTCTTTTCTCACCTGGTTAATTACCAAAAA
ATAC
Found at i:3115 original size:28 final size:27
Alignment explanation
Indices: 3073--3127 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
3063 TTTTTATTTG
*
3073 AGTTTGTTTTTGAGTCGGTTT-GAGTC
1 AGTTTGTTTTTGAGTCAGTTTCGAGTC
3099 AGTTTGTTTTTTCGAGTCAGTTTCGAGTC
1 AGTTTG-TTTTT-GAGTCAGTTTCGAGTC
3128 TAGTCTCAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 6 0.24
27 5 0.20
28 9 0.36
29 5 0.20
ACGTcount: A:0.13, C:0.11, G:0.27, T:0.49
Consensus pattern (27 bp):
AGTTTGTTTTTGAGTCAGTTTCGAGTC
Found at i:4026 original size:16 final size:16
Alignment explanation
Indices: 4005--4061 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
3995 ATTATTATTT
4005 ATTATAGCAATCCCTA
1 ATTATAGCAATCCCTA
**
4021 ATTATAGCAA-CTTGTA
1 ATTATAGCAATC-CCTA
4037 TTTATTATAGCAATCCCTA
1 ---ATTATAGCAATCCCTA
4056 ATTATA
1 ATTATA
4062 TTTGTTTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 1 0.03
16 18 0.56
19 12 0.38
20 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.39
Consensus pattern (16 bp):
ATTATAGCAATCCCTA
Found at i:4060 original size:19 final size:19
Alignment explanation
Indices: 4003--4060 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
3993 AAATTATTAT
4003 TTATTATAGCAATCCCT-A
1 TTATTATAGCAATCCCTAA
** *
4021 --ATTATAGCAA-CTTGTAT
1 TTATTATAGCAATC-CCTAA
4038 TTATTATAGCAATCCCTAA
1 TTATTATAGCAATCCCTAA
4057 TTAT
1 TTAT
4061 ATTTGTTTCT
Statistics
Matches: 29, Mismatches: 6, Indels: 9
0.66 0.14 0.20
Matches are distributed among these distances:
15 1 0.03
16 11 0.38
19 16 0.55
20 1 0.03
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (19 bp):
TTATTATAGCAATCCCTAA
Found at i:10421 original size:26 final size:26
Alignment explanation
Indices: 10392--10445 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
10382 TTGCCTAGAT
10392 CATCATTTTCAATCTTGTATCAAATG
1 CATCATTTTCAATCTTGTATCAAATG
10418 CATCATTTTCAATCTTGTATCAAATG
1 CATCATTTTCAATCTTGTATCAAATG
10444 CA
1 CA
10446 AACGAGGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.41
Consensus pattern (26 bp):
CATCATTTTCAATCTTGTATCAAATG
Found at i:10737 original size:24 final size:24
Alignment explanation
Indices: 10705--10750 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
10695 TGGGTGATTC
*
10705 TCTCACAACAACCTAAAGCTATTA
1 TCTCACAACAACCTAAAACTATTA
*
10729 TCTCACAACAATCTAAAACTAT
1 TCTCACAACAACCTAAAACTAT
10751 CTTAGATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.28, G:0.02, T:0.26
Consensus pattern (24 bp):
TCTCACAACAACCTAAAACTATTA
Found at i:13082 original size:21 final size:21
Alignment explanation
Indices: 13053--13094 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
13043 TCGCTCGGTC
*
13053 TCTACAAACCAATC-ATCACA
1 TCTACAAACCAAACAATCACA
13073 TCTACCAAACCAAACAATCACA
1 TCTA-CAAACCAAACAATCACA
13095 CACACACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.17
Consensus pattern (21 bp):
TCTACAAACCAAACAATCACA
Found at i:14770 original size:2 final size:2
Alignment explanation
Indices: 14763--14800 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
14753 TTCTTATTAC
14763 AT AT AT AT AT 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 AT
14801 CTTAATAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15300 original size:81 final size:81
Alignment explanation
Indices: 15186--15420 Score: 245
Period size: 74 Copynumber: 3.0 Consensus size: 81
15176 ACAGAAAAAC
* * * * ** *
15186 ATCATTGTACATGCATGGTCAAAACTCAAAGGATAATGTTCAAA-CTCCGAAATTTGATATTCAA
1 ATCAATGTACATGCATGGTCAAAACCCAAAGGATAATGGTCAAATC-CCAAAATTCAATAGTCAA
15250 ACCACAAAAAATATTAA
65 ACCACAAAAAATATTAA
* *
15267 ATCAATGTATATGCATGGTCAAAACCCAAAGGATGATGGTCAAATCCCAAAATTCAATAGTCAAA
1 ATCAATGTACATGCATGGTCAAAACCCAAAGGATAATGGTCAAATCCCAAAATTCAATAGTCAAA
*
15332 CCAC----AA-A--AC
66 CCACAAAAAATATTAA
* * * *
15341 ATCATTGTACATGCATGGTCAAACCCCAAAGGATTATGGTCAAA-CCTCAAGATTCAATAGTCAA
1 ATCAATGTACATGCATGGTCAAAACCCAAAGGATAATGGTCAAATCC-CAAAATTCAATAGTCAA
*
15405 ACTACAAAAAAATATT
65 ACCAC-AAAAAATATT
15421 TCATTGTATA
Statistics
Matches: 128, Mismatches: 16, Indels: 19
0.79 0.10 0.12
Matches are distributed among these distances:
73 2 0.02
74 61 0.48
76 1 0.01
77 2 0.02
79 2 0.02
80 1 0.01
81 58 0.45
82 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (81 bp):
ATCAATGTACATGCATGGTCAAAACCCAAAGGATAATGGTCAAATCCCAAAATTCAATAGTCAAA
CCACAAAAAATATTAA
Found at i:15405 original size:155 final size:154
Alignment explanation
Indices: 15165--15450 Score: 373
Period size: 155 Copynumber: 1.8 Consensus size: 154
15155 TTGTACATGC
* *
15165 ATAGTCAAACCACAGAAAAACATCATTGTACATGCATGGTCAAAACTCAAAGGATAATGTTCAAA
1 ATAGTCAAACCAC--AAAAACATCATTGTACATGCATGGTCAAAACCCAAAGGATAATGGTCAAA
** * * *
15230 CTCCGAAATTTGATATTCAAACCAC-AAAAAATATTAAATCAATGTATATGCATGGTCAAAACCC
64 CTCCGAAATTCAATAGTCAAACCACAAAAAAATATT---TCAATGTATATGCACGGCCAAAACCC
15294 AAAGGATGATGGTCAAATCCCAAAATTCA
126 AAAGGATGATGGTCAAATCCCAAAATTCA
* *
15323 ATAGTCAAACCAC-AAAACATCATTGTACATGCATGGTCAAACCCCAAAGGATTATGGTCAAAC-
1 ATAGTCAAACCACAAAAACATCATTGTACATGCATGGTCAAAACCCAAAGGATAATGGTCAAACT
* * *
15386 CTC-AAGATTCAATAGTCAAACTACAAAAAAATATTTCATTGTATATGCACGGCCAAACCCCAAA
66 C-CGAA-ATTCAATAGTCAAACCACAAAAAAATATTTCAATGTATATGCACGGCCAAAACCCAAA
15450 G
129 G
15451 TTTGATAGTC
Statistics
Matches: 113, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
153 26 0.23
154 3 0.03
155 61 0.54
156 10 0.09
158 13 0.12
ACGTcount: A:0.44, C:0.21, G:0.13, T:0.23
Consensus pattern (154 bp):
ATAGTCAAACCACAAAAACATCATTGTACATGCATGGTCAAAACCCAAAGGATAATGGTCAAACT
CCGAAATTCAATAGTCAAACCACAAAAAAATATTTCAATGTATATGCACGGCCAAAACCCAAAGG
ATGATGGTCAAATCCCAAAATTCA
Found at i:15471 original size:58 final size:59
Alignment explanation
Indices: 15397--15508 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
15387 TCAAGATTCA
* ** *
15397 ATAGTCAAACTACAAAAA-AATATTTCATTGTATATGCACGGCCAAACCCCAAAGTTTG
1 ATAGTCAAACCACAAAAACAATAAATCATTGTACATGCACGGCCAAACCCCAAAGTTTG
* * *
15455 ATAGTCAAACCACAAAAACATTAAATCATTGTACATGCATGGTCAAACCCCAAA
1 ATAGTCAAACCACAAAAACAATAAATCATTGTACATGCACGGCCAAACCCCAAA
15509 ATTCAACAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
58 17 0.37
59 29 0.63
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.23
Consensus pattern (59 bp):
ATAGTCAAACCACAAAAACAATAAATCATTGTACATGCACGGCCAAACCCCAAAGTTTG
Found at i:15649 original size:53 final size:55
Alignment explanation
Indices: 15566--15805 Score: 238
Period size: 53 Copynumber: 4.3 Consensus size: 55
15556 TCAAAGGAAG
*
15566 ATGGTCAAACCCCCAAA-TTCAATAGTCAAACCAC-AAA-ATAGCATTGTACATGC
1 ATGGTCAAA-CCCCAAAGTTCAATAGTCAAACCACAAAACATATCATTGTACATGC
* * *
15619 ATAGTCAAACCCCAAAGTTCAATAGTCAAACCACAAAAAACATTTCATTGTATATGC
1 ATGGTCAAACCCCAAAGTTCAATAGTCAAACCAC--AAAACATATCATTGTACATGC
* * ** * * *
15676 ACGGTCAAACCCCAAATTTTGATAGTTAAACCACAAAAAACATTAAATCATTATATATGC
1 ATGGTCAAACCCCAAAGTTCAATAGTCAAACCAC--AAAACA-T--ATCATTGTACATGC
* * **
15736 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAAC--ATCATTGTACTTAA
1 ATGGTCAAACCCCAAAGTTCAATAGTCAAACCACAAAACATATCATTGTACATGC
15789 ATGGTCAAACCCCAAAG
1 ATGGTCAAACCCCAAAG
15806 AAAGATGGTC
Statistics
Matches: 156, Mismatches: 23, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
52 7 0.04
53 50 0.32
56 3 0.02
57 49 0.31
58 6 0.04
60 41 0.26
ACGTcount: A:0.44, C:0.24, G:0.10, T:0.23
Consensus pattern (55 bp):
ATGGTCAAACCCCAAAGTTCAATAGTCAAACCACAAAACATATCATTGTACATGC
Found at i:15687 original size:57 final size:56
Alignment explanation
Indices: 15566--15804 Score: 244
Period size: 57 Copynumber: 4.3 Consensus size: 56
15556 TCAAAGGAAG
** *
15566 ATGGTCAAACCCCCAAATTCAATAGTCAAACCAC---AAA-ATAGCATTGTACATGC
1 ATGGTCAAA-CCCCAAATTCAATAGTCAAACCACAAAAAACATTTCATTGTATATGC
*
15619 ATAGTCAAACCCCAAAGTTCAATAGTCAAACCACAAAAAACATTTCATTGTATATGC
1 ATGGTCAAACCCCAAA-TTCAATAGTCAAACCACAAAAAACATTTCATTGTATATGC
* ** * *
15676 ACGGTCAAACCCCAAATTTTGATAGTTAAACCACAAAAAACATTAAATCATTATATATGC
1 ATGGTCAAACCCCAAA-TTCAATAGTCAAACCACAAAAAACATT---TCATTGTATATGC
**
15736 ATGGTCAAACCCCAAAATTCAATAGTCAAACCAC--AAAACA--TCATTGTACT-TAA
1 ATGGTCAAACCCC-AAATTCAATAGTCAAACCACAAAAAACATTTCATTGTA-TATGC
15789 ATGGTCAAACCCCAAA
1 ATGGTCAAACCCCAAA
15805 GAAAGATGGT
Statistics
Matches: 158, Mismatches: 18, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
52 10 0.06
53 46 0.29
54 1 0.01
56 3 0.02
57 51 0.32
58 6 0.04
60 38 0.24
61 3 0.02
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.23
Consensus pattern (56 bp):
ATGGTCAAACCCCAAATTCAATAGTCAAACCACAAAAAACATTTCATTGTATATGC
Found at i:15754 original size:243 final size:244
Alignment explanation
Indices: 15379--15821 Score: 694
Period size: 243 Copynumber: 1.8 Consensus size: 244
15369 AAGGATTATG
* * *
15379 GTCAAACCTCAAGATTCAATAGTCAAACTACAAAAAAATATTTCATTGTATATGCACGGCCAAAC
1 GTCAAACCCCAAGATTCAATAGTCAAACCACAAAAAAACATTTCATTGTATATGCACGGCCAAAC
*
15444 CCCAAAGTTTGATAGTCAAACCACAAAAACATTAAATCATTGTACATGCATGGTCAAACCCCAAA
66 CCCAAAGTTTGATAGTCAAACCACAAAAACATTAAATCATTATACATGCATGGTCAAACCCCAAA
** * * *
15509 ATTCAACAATCAAACCACAAAACATCATTGTACATGCATTAT-AAACCTCAAAGGAAGATGGTCA
131 ATTCAACAATCAAACCACAAAACATCATTGTACATAAATGATCAAACCCCAAAGAAAGATGGTCA
15573 AACCCCCAAATTCAATAGTCAAACCACAAAATAGCATTGTACATGCATA
196 AACCCCCAAATTCAATAGTCAAACCACAAAATAGCATTGTACATGCATA
*
15622 GTCAAACCCCAA-AGTTCAATAGTCAAACCAC-AAAAAACATTTCATTGTATATGCACGGTCAAA
1 GTCAAACCCCAAGA-TTCAATAGTCAAACCACAAAAAAACATTTCATTGTATATGCACGGCCAAA
* * *
15685 CCCCAAATTTTGATAGTTAAACCACAAAAAACATTAAATCATTATATATGCATGGTCAAACCCCA
65 CCCCAAAGTTTGATAGTCAAACCAC-AAAAACATTAAATCATTATACATGCATGGTCAAACCCCA
* * * *
15750 AAATTCAATAGTCAAACCACAAAACATCATTGTACTTAAATGGTCAAACCCCAAAGAAAGATGGT
129 AAATTCAACAATCAAACCACAAAACATCATTGTACATAAATGATCAAACCCCAAAGAAAGATGGT
15815 CAAACCC
194 CAAACCC
15822 GAAAGGAAGA
Statistics
Matches: 180, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
242 54 0.30
243 101 0.56
244 25 0.14
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.22
Consensus pattern (244 bp):
GTCAAACCCCAAGATTCAATAGTCAAACCACAAAAAAACATTTCATTGTATATGCACGGCCAAAC
CCCAAAGTTTGATAGTCAAACCACAAAAACATTAAATCATTATACATGCATGGTCAAACCCCAAA
ATTCAACAATCAAACCACAAAACATCATTGTACATAAATGATCAAACCCCAAAGAAAGATGGTCA
AACCCCCAAATTCAATAGTCAAACCACAAAATAGCATTGTACATGCATA
Found at i:15767 original size:117 final size:117
Alignment explanation
Indices: 15376--15773 Score: 403
Period size: 117 Copynumber: 3.3 Consensus size: 117
15366 CCAAAGGATT
* * * * *
15376 ATGGTCAAACCTCAAGATTCAATAGTCAAACTACAAAAAAATATTTCATTGTATATGCACGGCCA
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCAC-AAAAAACATTTCATTGTATATGCACGGTCA
15441 AACCCCAAAGTTTGATAGTCAAACCAC-AAAAACATTAAATCATTGTACATGC
65 AACCCCAAAGTTTGATAGTCAAACCACAAAAAACATTAAATCATTGTACATGC
* * * ***
15493 ATGGTCAAACCCCAAAATTCAACAATCAAACCAC--AAAACA--TCATTGTACATGCATTAT-AA
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAAAACATTTCATTGTATATGCACGGTCAA
* *** * **
15553 ACCTCAAAGGAAGATGGTCAAACCCCCAAATTCAATAGTCAAACCACAAAATAGCATTGTACATG
66 ACCCCAAAGTTTGATAGTCAAA---CC--A--CAA-A---AAA-CATTAAAT--CATTGTACATG
15618 C
117 C
* *
15619 ATAGTCAAACCCCAAAGTTCAATAGTCAAACCACAAAAAACATTTCATTGTATATGCACGGTCAA
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAAAACATTTCATTGTATATGCACGGTCAA
* * * *
15684 ACCCCAAATTTTGATAGTTAAACCACAAAAAACATTAAATCATTATATATGC
66 ACCCCAAAGTTTGATAGTCAAACCACAAAAAACATTAAATCATTGTACATGC
15736 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAA
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAA
15774 CATCATTGTA
Statistics
Matches: 222, Mismatches: 39, Indels: 40
0.74 0.13 0.13
Matches are distributed among these distances:
111 19 0.09
112 13 0.06
114 7 0.03
116 1 0.00
117 75 0.34
118 1 0.00
119 7 0.03
120 4 0.02
123 4 0.02
124 9 0.04
126 43 0.19
128 8 0.04
130 14 0.06
131 17 0.08
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.23
Consensus pattern (117 bp):
ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAAAACATTTCATTGTATATGCACGGTCAA
ACCCCAAAGTTTGATAGTCAAACCACAAAAAACATTAAATCATTGTACATGC
Found at i:15813 original size:21 final size:21
Alignment explanation
Indices: 15789--15847 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
15779 TTGTACTTAA
15789 ATGGTCAAACCCCAAAGAAAG
1 ATGGTCAAACCCCAAAGAAAG
* *
15810 ATGGTCAAACCCGAAAGGAAG
1 ATGGTCAAACCCCAAAGAAAG
15831 ATGGTCAAACCCTCAAA
1 ATGGTCAAACCC-CAAA
15848 TTCAATAGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 31 0.91
22 3 0.09
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.12
Consensus pattern (21 bp):
ATGGTCAAACCCCAAAGAAAG
Found at i:15892 original size:74 final size:73
Alignment explanation
Indices: 15813--16163 Score: 508
Period size: 74 Copynumber: 4.8 Consensus size: 73
15803 AAGAAAGATG
* * ** *
15813 GTCAAAC-CCGAAAGGAAGATGGTCAAACCCTCAAATTCAATAGTCAAACCACAAAATAGTATTT
1 GTCAAACTCC-AAAAGATGATGGTCAAACCC-CAAATTCAATAGTCAAACCACAAAATAACATTG
*
15877 TACATGAATA
64 TACATGCATA
*
15887 GTCAAACTCCAAAAGATGATGGTCAAA-CCCAAAGTTCGATAGTCAAACCACAAAATAACATTGT
1 GTCAAACTCCAAAAGATGATGGTCAAACCCCAAA-TTCAATAGTCAAACCACAAAATAACATTGT
15951 ACATGCATA
65 ACATGCATA
* *
15960 GTCAAACTCCAAATGATGATAGTCAAACCCCCAAATTCAATAGTCAAACCACAAAATAACATTGT
1 GTCAAACTCCAAAAGATGATGGTCAAA-CCCCAAATTCAATAGTCAAACCACAAAATAACATTGT
*
16025 ACATGCACA
65 ACATGCATA
* *
16034 GTCAAACTCCAAAAGATGATGGTCAAACCCCCAAATTCAATAGGCAAACCACAAAATAGCATTGT
1 GTCAAACTCCAAAAGATGATGGTCAAA-CCCCAAATTCAATAGTCAAACCACAAAATAACATTGT
16099 ACATGCATA
65 ACATGCATA
* *
16108 GTCAAACTCCAAAAGATAATGGTCAAACCCCAAAGTTCGATAGTCAAACCACAAAA
1 GTCAAACTCCAAAAGATGATGGTCAAACCCCAAA-TTCAATAGTCAAACCACAAAA
16164 AGCATTAAAT
Statistics
Matches: 253, Mismatches: 19, Indels: 10
0.90 0.07 0.04
Matches are distributed among these distances:
72 4 0.02
73 68 0.27
74 173 0.68
75 8 0.03
ACGTcount: A:0.44, C:0.23, G:0.13, T:0.20
Consensus pattern (73 bp):
GTCAAACTCCAAAAGATGATGGTCAAACCCCAAATTCAATAGTCAAACCACAAAATAACATTGTA
CATGCATA
Found at i:15899 original size:95 final size:94
Alignment explanation
Indices: 15736--15920 Score: 250
Period size: 95 Copynumber: 2.0 Consensus size: 94
15726 TTATATATGC
* *
15736 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTGTACTTAAATGGTCAAACCC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATAAATAGTCAAACCC
15801 C-AAAGAAAGATGGTCAAACCCGAAAGGAAG
66 CAAAAG-AAGATGGTCAAACCC-AAAGGAAG
* * *
15831 ATGGTCAAACCCTC-AAATTCAATAGTCAAACCACAAAATAGT-ATTTTACATGAATAGTCAAAC
1 ATGGTCAAACCC-CAAAATTCAATAGTCAAACCACAAAACA-TCATTGTACATAAATAGTCAAAC
* *
15894 TCCAAAAGATGATGGTCAAACCCAAAG
64 CCCAAAAGAAGATGGTCAAACCCAAAG
15921 TTCGATAGTC
Statistics
Matches: 80, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
94 4 0.05
95 70 0.88
96 6 0.08
ACGTcount: A:0.45, C:0.22, G:0.14, T:0.19
Consensus pattern (94 bp):
ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATAAATAGTCAAACCC
CAAAAGAAGATGGTCAAACCCAAAGGAAG
Found at i:15931 original size:20 final size:19
Alignment explanation
Indices: 15884--15940 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
15874 TTTTACATGA
15884 ATAGTCAAACTCCAAAAGATG
1 ATAGTCAAAC-CC-AAAGATG
* *
15905 ATGGTCAAACCCAAAGTTCG
1 ATAGTCAAACCCAAAGAT-G
15925 ATAGTCAAACCACAAA
1 ATAGTCAAACC-CAAA
15941 ATAACATTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 5 0.16
20 13 0.42
21 13 0.42
ACGTcount: A:0.46, C:0.23, G:0.14, T:0.18
Consensus pattern (19 bp):
ATAGTCAAACCCAAAGATG
Found at i:16223 original size:60 final size:54
Alignment explanation
Indices: 16126--16474 Score: 219
Period size: 53 Copynumber: 6.5 Consensus size: 54
16116 CCAAAAGATA
* *
16126 ATGGTCAAACCCCAAAGTTCGATAGTCAAACCACAAAAAGCATTAAATCATTGTACATGC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAAA-C-----ATCATTGTACATGC
* * *
16186 ATGTTCAAACCCCAAAATTCAATAATCAAACCAC-AAAACATCATTGTGCATGC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAAACATCATTGTACATGC
*
16239 ATGGTCAAACCCCAAAATTCAATAGTCAAACCAC-AAAATATCATTGTACATGC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAAACATCATTGTACATGC
** * * * * *
16292 ATATTCAAACTCCAAAAGAT-GAT-GATCAAACC-C-----CA--A-AGTTC--G-
1 ATGGTCAAACCCCAAAA-TTCAATAG-TCAAACCACAAAAACATCATTGTACATGC
* * * * * * * *
16334 ATAGTCAAACCACAAATTTTAATGGTCAAGCTACAAAAAACATAATTGTACATGC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCAC-AAAAACATCATTGTACATGC
* * * *
16389 ATAGTCAAACCCCAAAGTTCAATAGTCAAACCACAAAAAGTATTTCATTGTATATGC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAAA-CA--TCATTGTACATGC
* *
16446 TTGGTCAAACCCCAAATATT-GATAGTCAA
1 ATGGTCAAACCCCAAA-ATTCAATAGTCAA
16475 CCTTAAAGTT
Statistics
Matches: 228, Mismatches: 40, Indels: 45
0.73 0.13 0.14
Matches are distributed among these distances:
41 1 0.00
42 20 0.09
43 3 0.01
45 3 0.01
46 1 0.00
48 1 0.00
49 2 0.01
51 1 0.00
52 5 0.02
53 85 0.37
54 7 0.03
55 29 0.13
57 33 0.14
58 3 0.01
59 4 0.02
60 30 0.13
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.24
Consensus pattern (54 bp):
ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAAACATCATTGTACATGC
Found at i:16252 original size:53 final size:53
Alignment explanation
Indices: 16172--16308 Score: 220
Period size: 53 Copynumber: 2.6 Consensus size: 53
16162 AAAGCATTAA
16172 ATCATTGTACATGCATGTTCAAACCCCAAAATTCAATAATCAAACCACAAAAC
1 ATCATTGTACATGCATGTTCAAACCCCAAAATTCAATAATCAAACCACAAAAC
* * * *
16225 ATCATTGTGCATGCATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAAT
1 ATCATTGTACATGCATGTTCAAACCCCAAAATTCAATAATCAAACCACAAAAC
* *
16278 ATCATTGTACATGCATATTCAAACTCCAAAA
1 ATCATTGTACATGCATGTTCAAACCCCAAAA
16309 GATGATGATC
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 76 1.00
ACGTcount: A:0.43, C:0.25, G:0.08, T:0.24
Consensus pattern (53 bp):
ATCATTGTACATGCATGTTCAAACCCCAAAATTCAATAATCAAACCACAAAAC
Found at i:16751 original size:35 final size:35
Alignment explanation
Indices: 16705--16775 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
16695 TTTTAAATTG
*
16705 TAATTGTCTACTAGTATTCTCATGTTTAGTTGTTT
1 TAATTGTCTACTAGTATTATCATGTTTAGTTGTTT
16740 TAATTGTCTACTAGTATTATCATGTTTAGTTGTTT
1 TAATTGTCTACTAGTATTATCATGTTTAGTTGTTT
16775 T
1 T
16776 TGTAATTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.21, C:0.10, G:0.14, T:0.55
Consensus pattern (35 bp):
TAATTGTCTACTAGTATTATCATGTTTAGTTGTTT
Found at i:17203 original size:5 final size:5
Alignment explanation
Indices: 17189--17219 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
17179 TCCTTTGTAA
*
17189 CCTTT ACTTT CCTTT CCTTT CCTTT CCTTT C
1 CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT C
17220 TTCCACAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.03, C:0.39, G:0.00, T:0.58
Consensus pattern (5 bp):
CCTTT
Done.