Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013187.1 Corchorus olitorius cultivar O-4 contig13220, 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: 55835
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:1096 original size:30 final size:29
Alignment explanation
Indices: 1053--1109 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
1043 TTAGGATTAG
1053 TTATTTATGCTTTAATTTTCAA-TTTCCT
1 TTATTTATGCTTTAATTTTCAAGTTTCCT
1081 TTATCTTATGTCTTTAATTTTCAAGTTTC
1 TTAT-TTATG-CTTTAATTTTCAAGTTTC
1110 ATTAATAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.15
29 5 0.19
30 13 0.50
31 4 0.15
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (29 bp):
TTATTTATGCTTTAATTTTCAAGTTTCCT
Found at i:1775 original size:19 final size:18
Alignment explanation
Indices: 1753--1788 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1743 AGGGTAATTA
*
1753 AAAAAAAATTGTTTTCAT
1 AAAAAAAAGTGTTTTCAT
*
1771 AAAAAGAAGTGTTTTCAT
1 AAAAAAAAGTGTTTTCAT
1789 GATAGAGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (18 bp):
AAAAAAAAGTGTTTTCAT
Found at i:1914 original size:80 final size:79
Alignment explanation
Indices: 1823--1985 Score: 308
Period size: 80 Copynumber: 2.1 Consensus size: 79
1813 TAAATAAAAA
1823 AAATTCATTGTTGTCACTCTTTTCTTGAACAAAAGGAGTTAGTAACCCTTGGAAAGAGGATAAGA
1 AAATTCATTGTTGTCACTCTTTTCTTGAACAAAAGGAGTTAG-AACCCTTGGAAAGAGGATAAGA
*
1888 GGCATGGAATTATAG
65 GGCATGGAATTACAG
1903 AAATTCATTGTTGTCACTCTTTTCTTGAACAAAAGGAGTTAGAACCCTTGGAAAGAGGATAAGAG
1 AAATTCATTGTTGTCACTCTTTTCTTGAACAAAAGGAGTTAGAACCCTTGGAAAGAGGATAAGAG
1968 GCATGGAATTACAG
66 GCATGGAATTACAG
1982 AAAT
1 AAAT
1986 ATTGTCCCTC
Statistics
Matches: 82, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
79 40 0.49
80 42 0.51
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (79 bp):
AAATTCATTGTTGTCACTCTTTTCTTGAACAAAAGGAGTTAGAACCCTTGGAAAGAGGATAAGAG
GCATGGAATTACAG
Found at i:2722 original size:22 final size:21
Alignment explanation
Indices: 2697--2750 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
2687 GAAGTTCGTG
2697 TTTGAAGACTTATTGAAGACAA
1 TTTGAAGA-TTATTGAAGACAA
*
2719 TTTGAAGA-T-TTGAAGACGA
1 TTTGAAGATTATTGAAGACAA
2738 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
2751 TTCAAGAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGACAA
Found at i:5050 original size:31 final size:30
Alignment explanation
Indices: 5012--5179 Score: 134
Period size: 31 Copynumber: 5.6 Consensus size: 30
5002 TATGGCTAAT
5012 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTG-CAAAA
* * *
5043 TGCTCAAATAAGGGCCCAATC-TTT-TAATTA
1 TGCTCAAATAAGGGCCTAA-CGTTTGCAA-AA
* *
5073 GGC-CAAATAAGGGCCTAATGTTATTG-AAAA
1 TGCTCAAATAAGGGCCTAACG-T-TTGCAAAA
* * **
5103 TGCTCAAATAAGGGCCTGATC-TTT-TAATT
1 TGCTCAAATAAGGGCCT-AACGTTTGCAAAA
5132 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTG-CAAAA
5163 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
5180 GACATCAGTT
Statistics
Matches: 107, Mismatches: 16, Indels: 28
0.71 0.11 0.19
Matches are distributed among these distances:
28 2 0.02
29 37 0.35
30 12 0.11
31 54 0.50
32 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACGTTTGCAAAA
Found at i:5148 original size:29 final size:29
Alignment explanation
Indices: 5047--5150 Score: 120
Period size: 29 Copynumber: 3.5 Consensus size: 29
5037 CCAAAATGCT
* *
5047 CAAATAAGGGCCCAATCTTTTAATTAGGC
1 CAAATAAGGGCCTAATCTTTTAATTTGGC
* **
5076 CAAATAAGGGCCTAATGTTATTGAAAAT-GC
1 CAAATAAGGGCCTAATCTT-TT-AATTTGGC
*
5106 TCAAATAAGGGCCTGATCTTTTAATTTGGC
1 -CAAATAAGGGCCTAATCTTTTAATTTGGC
5136 CAAATAAGGGCCTAA
1 CAAATAAGGGCCTAA
5151 CGTTTGCCAA
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
29 34 0.56
30 8 0.13
31 19 0.31
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (29 bp):
CAAATAAGGGCCTAATCTTTTAATTTGGC
Found at i:5179 original size:60 final size:60
Alignment explanation
Indices: 5016--5181 Score: 264
Period size: 60 Copynumber: 2.8 Consensus size: 60
5006 GCTAATTGCT
**
5016 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTAGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTAGGC
* *
5076 CAAATAAGGGCCTAATGTTATTG--AAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACG-T-TTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTAGGC
5136 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGA
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGA
5182 CATCAGTTTG
Statistics
Matches: 97, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
58 3 0.03
59 1 0.01
60 89 0.92
61 1 0.01
62 3 0.03
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTAGGC
Found at i:5256 original size:31 final size:31
Alignment explanation
Indices: 5221--5385 Score: 123
Period size: 31 Copynumber: 5.5 Consensus size: 31
5211 CGATGCCAGG
5221 CCCTTATTTGAGCATTTTGGCAAACGTTAGA
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGA
** **
5252 CCCTTATTTG-GCCAAATT-AAAAGACCG--AG-
1 CCCTTATTTGAG-CATTTTGGCAA-A-CGTTAGA
5281 CCCTTATTTGAGCATTTTGGCAAACGTTAGA
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGA
** * ** *
5312 CCCTTATTTG-GCCAAATT---AAAAGATCGGG
1 CCCTTATTTGAG-CATTTTGGCAAACG-TTAGA
*
5341 CCCTTATTTGAGCATTTTGGCAAACGTTAGG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGA
5372 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
5386 GTTAGCCAGC
Statistics
Matches: 101, Mismatches: 19, Indels: 28
0.68 0.13 0.19
Matches are distributed among these distances:
28 6 0.06
29 31 0.31
30 12 0.12
31 46 0.46
32 6 0.06
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTGGCAAACGTTAGA
Found at i:5290 original size:29 final size:28
Alignment explanation
Indices: 5252--5350 Score: 76
Period size: 29 Copynumber: 3.4 Consensus size: 28
5242 AAACGTTAGA
5252 CCCTTATTTGGCCAAATTAAAAGACCGAG
1 CCCTTATTTGGCCAAATTAAAAGA-CGAG
** **
5281 CCCTTATTTGAG-CATTTTGGCAA-ACGTTAG
1 CCCTTATTTG-GCCAAATT-AAAAGACG--AG
*
5311 ACCCTTATTTGGCCAAATTAAAAGATCGGG
1 -CCCTTATTTGGCCAAATTAAAAGA-CGAG
5341 CCCTTATTTG
1 CCCTTATTTG
5351 AGCATTTTGG
Statistics
Matches: 53, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
28 2 0.04
29 25 0.47
30 9 0.17
31 15 0.28
32 2 0.04
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (28 bp):
CCCTTATTTGGCCAAATTAAAAGACGAG
Found at i:5313 original size:60 final size:60
Alignment explanation
Indices: 5220--5381 Score: 297
Period size: 60 Copynumber: 2.7 Consensus size: 60
5210 TCGATGCCAG
5220 GCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGGCCAAATTAAAAGACCGA
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGGCCAAATTAAAAGACCGA
* *
5280 GCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGGCCAAATTAAAAGACCGA
*
5340 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTG
5382 AGCAGTTAGC
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 99 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (60 bp):
GCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGGCCAAATTAAAAGACCGA
Found at i:10705 original size:2 final size:2
Alignment explanation
Indices: 10698--10726 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10688 ATACAATGTT
10698 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 T
10727 TCAATTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12632 original size:160 final size:160
Alignment explanation
Indices: 12304--12652 Score: 393
Period size: 159 Copynumber: 2.2 Consensus size: 160
12294 GCCGCCATAT
** *
12304 TAATATATGGAGGGAGAGATTTTTTTTCTGTTTTTTTGGAGGGAAAAATTCCCTCCCCCTAAAAC
1 TAATATATGGAGGGAGAGATTTTTTTTCCCTTTTTTTAGAGGGAAAAATTCCCTCCCCCTAAAAC
* *
12369 AAAGAAAGTTTCCAACTTTACGCCTATAATACATGGCGGCGTTTAAACATCAGACGCCGCTAAGT
66 AAAGAAAGTTTCCAACTCTACGCCTATAATACATAGCGGCGTTTAAACA-CAGACGCCGCTAAGT
* * * * *
12434 AAAATTCCTTGAAAATGAAATGCCACTATTT
130 AAAATGCCTTGAAAAGGAAACGCCACAATTG
**
12465 TAATATATTTAGGGAGAGA-TTTTTTTCCCTTTTTTTAGAGGGAAAAATTCCCT-CCCCTAAAAC
1 TAATATATGGAGGGAGAGATTTTTTTTCCCTTTTTTTAGAGGGAAAAATTCCCTCCCCCTAAAAC
* * *
12528 AAAGAAATTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTTCTAAC-CAGACGCCGCTAA-
66 AAAGAAAGTTTCCAACTCTACGCCTATAATACATAGCGGCG-TTT-AAACACAGACGCCGCTAAG
* * * * * *
12591 T-TAGTGGCGTTTAGGAAGGAAAACGCCGCAATTG
129 TAAAAT-GCCTTGA-AAAGG-AAACGCCACAATTG
* *
12625 TAATATATGGAGTGAGATAATTTTTTTT
1 TAATATATGGAGGGAGA-GATTTTTTTT
12653 GGAGGTAAAA
Statistics
Matches: 156, Mismatches: 25, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
157 2 0.01
158 5 0.03
159 63 0.40
160 58 0.37
161 21 0.13
162 7 0.04
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (160 bp):
TAATATATGGAGGGAGAGATTTTTTTTCCCTTTTTTTAGAGGGAAAAATTCCCTCCCCCTAAAAC
AAAGAAAGTTTCCAACTCTACGCCTATAATACATAGCGGCGTTTAAACACAGACGCCGCTAAGTA
AAATGCCTTGAAAAGGAAACGCCACAATTG
Found at i:15373 original size:19 final size:19
Alignment explanation
Indices: 15349--15385 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
15339 CTGTTTAGCA
15349 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
15368 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
15386 TTAGAGCAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.27
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:23204 original size:27 final size:27
Alignment explanation
Indices: 23168--23296 Score: 213
Period size: 27 Copynumber: 4.8 Consensus size: 27
23158 GACTGTTGCC
*
23168 GCAGTGGATCCTTCCACTTCGACCCCA
1 GCAGTGGATCCTCCCACTTCGACCCCA
* *
23195 GTAGTGGATCCTCCCGCTTCGACCCCA
1 GCAGTGGATCCTCCCACTTCGACCCCA
*
23222 GCAGTGGATCCTCCCACTTCGACCCTA
1 GCAGTGGATCCTCCCACTTCGACCCCA
*
23249 GCAGTGGATCCTCGCACTTCGACCCCA
1 GCAGTGGATCCTCCCACTTCGACCCCA
23276 GCAGTGGATCCTCCCACTTCG
1 GCAGTGGATCCTCCCACTTCG
23297 CCTCGGGTCG
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 93 1.00
ACGTcount: A:0.17, C:0.40, G:0.21, T:0.22
Consensus pattern (27 bp):
GCAGTGGATCCTCCCACTTCGACCCCA
Found at i:24134 original size:17 final size:17
Alignment explanation
Indices: 24112--24146 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
24102 GAAAAAGTGC
24112 ATTCTTGTTGGTACATT
1 ATTCTTGTTGGTACATT
*
24129 ATTCTTGTTGGTATATT
1 ATTCTTGTTGGTACATT
24146 A
1 A
24147 ACATTATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.09, G:0.17, T:0.54
Consensus pattern (17 bp):
ATTCTTGTTGGTACATT
Found at i:25711 original size:32 final size:32
Alignment explanation
Indices: 25669--25900 Score: 349
Period size: 32 Copynumber: 7.2 Consensus size: 32
25659 GTGTGAAAAG
25669 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
*
25701 AAAAAGCCCTTATTTAGCGGCGTCTAAAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
25733 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
25765 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
* * * *
25797 AAAACGCACTTATTTTGTGGCGTCTAAAAAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
**
25829 AAAACAACCTTATTTAGCGGCGTCTGAAAGAA-
1 AAAACGCCCTTATTTAGCGGCGTCT-AAAGAAC
* **
25861 AAAACGCCCTTAATTAGCGGCGTCTTCAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
*
25893 AAAGCGCC
1 AAAACGCC
25901 GCTAAATTTA
Statistics
Matches: 180, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
31 4 0.02
32 171 0.95
33 5 0.03
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.22
Consensus pattern (32 bp):
AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
Found at i:26069 original size:24 final size:24
Alignment explanation
Indices: 26042--26102 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
26032 CAGATAGCGA
26042 CGTCTAGACGCCGTTAAATAGTGG
1 CGTCTAGACGCCGTTAAATAGTGG
26066 CGTCTAGACGCCGTTAAATAGTGG
1 CGTCTAGACGCCGTTAAATAGTGG
26090 CGTCTAGACGCCG
1 CGTCTAGACGCCG
26103 CTATATATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.23
Consensus pattern (24 bp):
CGTCTAGACGCCGTTAAATAGTGG
Found at i:29101 original size:2 final size:2
Alignment explanation
Indices: 29094--29128 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
29084 TAAGCAGGAC
29094 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29129 CATACATAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29813 original size:54 final size:53
Alignment explanation
Indices: 29755--30466 Score: 547
Period size: 47 Copynumber: 14.1 Consensus size: 53
29745 AGTTTAATTG
* *
29755 CTAATTACTGCTTACTCTTTCTTTTACTCTTTAGTTTACTTACCCAGAATTAAA
1 CTAA-TACTGCTTACTCTTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAA
* * *
29809 CTAATTACCG-TT-CATTTCTTCTTTTACTATTTAGTTTAATTAACCAGAATTAAA
1 CTAA-TACTGCTTAC-TCT-TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAA
* * * ** * *
29863 CTGACCT-CTGTTTACT-TCTTCTTTTATTCCTAAGTTTAATT-----TAATTAAA
1 CT-A-ATACTGCTTACTCT-TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAA
* *
29912 CTAACCT-CTGTTTACT-TCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAA
1 CTAA--TACTGCTTACTCT-TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAA
* ** ** * * *
29966 CTAATTACTGTTTACTCCATGATTTACTCTTTAGTTTAATTACCCATAGTTAAA
1 CTAA-TACTGCTTACTCTTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAA
* * *
30020 CTAATTACTGTTTACTCCTTCTTTTACTATTTAGCTTAATTACCCAGAATTAAA
1 CTAA-TACTGCTTACTCTTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAA
* *
30074 CTAATTACTGTTTACT-TCTTCTTTTACTCTTTAGTTTAATTA-CCAGAATTAAA
1 CTAA-TACTGCTTACTCT-TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAA
* *
30127 CTAAT-CTTTGTTTACT-TCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAA
1 CTAATAC--TGCTTACTCT-TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAA
* *
30181 CTAA-CCT-CTT-C-C--TCTTTTACTATTTAGTTTAATTACCCAAAATTAAA
1 CTAATACTGCTTACTCTTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAA
*
30228 CTAA-CCT-C-T--TC-TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAA
1 CTAATACTGCTTACTCTTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAA
* *
30275 CTAA-CCT-C-T--TC-TTCTTTTACTATTTAATTTAATTACCCAGAATTAAA
1 CTAATACTGCTTACTCTTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAA
*
30322 CTAAT-CT-C-TAC-C-TT-TTTTACTATTTAGTTTAATTACCCATAATTAAA
1 CTAATACTGCTTACTCTTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAA
* *
30369 CTAA-CCT-CTT-CT-TCTT-TTTTA--ATTTACTTTAATTACCCAGAATTAAA
1 CTAATACTGCTTACTCT-TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAA
* *
30416 CT-A-ACTTC-T--TC-TTCTTTTACTATTTAGTTTAATTACCCAGAATTTAA
1 CTAATACTGCTTACTCTTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAA
30463 CTAA
1 CTAA
30467 CCTCTTCTAC
Statistics
Matches: 575, Mismatches: 46, Indels: 80
0.82 0.07 0.11
Matches are distributed among these distances:
44 2 0.00
45 6 0.01
46 6 0.01
47 221 0.38
48 6 0.01
49 48 0.08
50 1 0.00
51 3 0.01
52 3 0.01
53 54 0.09
54 219 0.38
55 5 0.01
56 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.46
Consensus pattern (53 bp):
CTAATACTGCTTACTCTTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAA
Found at i:29925 original size:49 final size:49
Alignment explanation
Indices: 29856--29952 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 49
29846 AATTAACCAG
* *
29856 AATTAAACTGACCTCTGTTTACTTCTTCTTTTATTCCTAAGTTTAATTT
1 AATTAAACTAACCTCTGTTTACTTCTTCTTTTACTCCTAAGTTTAATTT
* *
29905 AATTAAACTAACCTCTGTTTACTTCTTCTTTTACTCTTTAGTTTAATT
1 AATTAAACTAACCTCTGTTTACTTCTTCTTTTACTCCTAAGTTTAATT
29953 ACCCAGAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.25, C:0.19, G:0.05, T:0.52
Consensus pattern (49 bp):
AATTAAACTAACCTCTGTTTACTTCTTCTTTTACTCCTAAGTTTAATTT
Found at i:30082 original size:47 final size:47
Alignment explanation
Indices: 30037--30496 Score: 577
Period size: 47 Copynumber: 9.5 Consensus size: 47
30027 CTGTTTACTC
*
30037 CTTCTTTTACTATTTAGCTTAATTACCCAGAATTAAACTAATTACTGTTTACTT
1 CTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACT-A--AC---TT-CTT
*
30091 CTTCTTTTACTCTTTAGTTTAATTA-CCAGAATTAAACTAATCTTTGTTTACTT
1 CTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAA-C-----TT-CTT
* *
30144 CTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACCTCTT
1 CTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACTTCTT
* * *
30191 CCTCTTTTACTATTTAGTTTAATTACCCAAAATTAAACTAACCTCTT
1 CTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACTTCTT
*
30238 CTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTT
1 CTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACTTCTT
* *
30285 CTTCTTTTACTATTTAATTTAATTACCCAGAATTAAACTAA-TCTCTAC
1 CTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACT-TCT-T
* *
30333 CTT-TTTTACTATTTAGTTTAATTACCCATAATTAAACTAACCTCTT
1 CTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACTTCTT
* *
30379 CTTCTTTT-TTAATTTACTTTAATTACCCAGAATTAAACTAACTTCTT
1 CTTCTTTTACT-ATTTAGTTTAATTACCCAGAATTAAACTAACTTCTT
* *
30426 CTTCTTTTACTATTTAGTTTAATTACCCAGAATTTAACTAACCTCTT
1 CTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACTTCTT
* *
30473 CTACTTTTACTGTTTAGTTTAATT
1 CTTCTTTTACTATTTAGTTTAATT
30497 GCTCTGATTT
Statistics
Matches: 371, Mismatches: 25, Indels: 27
0.88 0.06 0.06
Matches are distributed among these distances:
46 4 0.01
47 273 0.74
48 5 0.01
50 1 0.00
51 1 0.00
52 1 0.00
53 48 0.13
54 38 0.10
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (47 bp):
CTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACTTCTT
Found at i:30324 original size:141 final size:143
Alignment explanation
Indices: 29773--30496 Score: 637
Period size: 141 Copynumber: 4.8 Consensus size: 143
29763 TGCTTACTCT
* * *
29773 TTCTTTTACTCTTTAGTTTACTTACCCAGAATTAAACTAATTACCGTTCATTTCTTCTTTTACTA
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAA-T-CC--T-ACTTCTTCTTTTACTA
* * * *
29838 TTTAGTTTAATTAACCAGAATTAAACTGACCTCTGTTTACTTCTTCTT-TTATTCCTAAGTTTAA
61 TTTAGTTTAATTACCCAGAATTAAACTAACCTC---TT-CCTCTT-TTACTATT--T-AGTTTAA
*
29902 TT-----TAATTAAACTAACCTCTGTTTACTTC
118 TTACCCAAAATTAAACTAA-C-C----T-CTTC
* * ** * *
29930 TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACTGTTTACTCCATGATTTACTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAA-TCCTACTT-CTTC-T--TTTACTA
* * * * *
29995 TTTAGTTTAATTACCCATAGTTAAACTAATTACTGTTTACTCCTTCTTTTACTATTTAGCTTAAT
61 TTTAGTTTAATTACCCAGAATTAAACT-A--AC-CTCT--TCC-TCTTTTACTATTTAGTTTAAT
* *
30060 TACCCAGAATTAAACTAATTACTGTTTACTTC
119 TACCCAAAATTAAACT-A--AC---CT-CTTC
* * *
30092 TTCTTTTACTCTTTAGTTTAATTA-CCAGAATTAAACTAATCTTTGTTTACTTCTTCTTTTACTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATC-----CTACTTCTTCTTTTACTA
30156 TTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCCTCTTTTACTATTTAGTTTAATTACCCAA
61 TTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCCTCTTTTACTATTTAGTTTAATTACCCAA
30221 AATTAAACTAACCTCTTC
126 AATTAAACTAACCTCTTC
*
30239 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAA-CCT-CTTCTTCTTTTACTATTTAA
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATCCTACTTCTTCTTTTACTATTTAG
* * * *
30302 TTTAATTACCCAGAATTAAACTAATCTCTACCTTTTTTACTATTTAGTTTAATTACCCATAATTA
66 TTTAATTACCCAGAATTAAACTAACCTCTTCCTCTTTTACTATTTAGTTTAATTACCCAAAATTA
30367 AACTAACCTCTTC
131 AACTAACCTCTTC
* * *
30380 TTCTTTT-TTAATTTACTTTAATTACCCAGAATTAAACTAA--CTTCTTCTTCTTTTACTATTTA
1 TTCTTTTACT-ATTTAGTTTAATTACCCAGAATTAAACTAATCCTACTTCTTCTTTTACTATTTA
* *
30442 GTTTAATTACCCAGAATTTAACTAACCTCTT-CTACTTTTACTGTTTAGTTTAATT
65 GTTTAATTACCCAGAATTAAACTAACCTCTTCCT-CTTTTACTATTTAGTTTAATT
30497 GCTCTGATTT
Statistics
Matches: 492, Mismatches: 44, Indels: 78
0.80 0.07 0.13
Matches are distributed among these distances:
140 5 0.01
141 193 0.39
142 1 0.00
147 28 0.06
148 16 0.03
151 2 0.00
153 4 0.01
154 39 0.08
155 4 0.01
156 1 0.00
157 81 0.16
158 4 0.01
159 3 0.01
160 13 0.03
161 48 0.10
162 39 0.08
163 2 0.00
164 4 0.01
165 4 0.01
166 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.47
Consensus pattern (143 bp):
TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATCCTACTTCTTCTTTTACTATTTAG
TTTAATTACCCAGAATTAAACTAACCTCTTCCTCTTTTACTATTTAGTTTAATTACCCAAAATTA
AACTAACCTCTTC
Found at i:30511 original size:94 final size:94
Alignment explanation
Indices: 29773--30496 Score: 641
Period size: 94 Copynumber: 7.2 Consensus size: 94
29763 TGCTTACTCT
* *
29773 TTCTTTTACTCTTTAGTTTACTTACCCAGAATTAAACTAATTACCGTTCATTTCTTCTTTTACTA
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACT-A--A-C-TTC--TTCTTCTTTTACTA
* *
29838 TTTAGTTTAATTAACCAGAATTAAACTGACCTCTGTTTAC
59 TTTAGTTTAATTACCCAGAATTAAACTAACCTC---TT-C
* *** * * *** *
29878 TTCTTCTT-TTATTCCTAAGTTTAATTTAATTA-AACTAACCTCTGTTTACTTCTTCTTTTACTC
1 TTCTT-TTACTATT--T-AGTTTAA-TTACCCAGAATTAAACT-AACTT-CTTCTTCTTTTACTA
* *
29941 TTTAGTTTAATTACCCAGAATTAAACTAATTACTGTTTAC
59 TTTAGTTTAATTACCCAGAATTAAACTAA--CCT-CTT-C
* * * * *
29981 TCCATGATTTACTCTTTAGTTTAATTACCCATAGTTAAACTAATTACTGTTTACTCCTTCTTTTA
1 TTC-T--TTTACTATTTAGTTTAATTACCCAGAATTAAACT-A--AC---TT-CTTCTTCTTTTA
* *
30046 CTATTTAGCTTAATTACCCAGAATTAAACTAATTACTGTTTACTTC
56 CTATTTAGTTTAATTACCCAGAATTAAACT-A--AC---CT-CTTC
* *
30092 TTCTTTTACTCTTTAGTTTAATTA-CCAGAATTAAACTAATCTTTGTTTACTTCTTCTTTTACTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAA-C-----TT-CTTCTTCTTTTACTA
30156 TTTAGTTTAATTACCCAGAATTAAACTAACCTCTTC
59 TTTAGTTTAATTACCCAGAATTAAACTAACCTCTTC
* * *
30192 CTCTTTTACTATTTAGTTTAATTACCCAAAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTT
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACTTCTTCTTCTTTTACTATTTAGTT
30257 TAATTACCCAGAATTAAACTAACCTCTTC
66 TAATTACCCAGAATTAAACTAACCTCTTC
* *
30286 TTCTTTTACTATTTAATTTAATTACCCAGAATTAAACTAA-TCTCTACCTT-TTTTACTATTTAG
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACT-TCT-TCTTCTTTTACTATTTAG
*
30349 TTTAATTACCCATAATTAAACTAACCTCTTC
64 TTTAATTACCCAGAATTAAACTAACCTCTTC
* *
30380 TTCTTTT-TTAATTTACTTTAATTACCCAGAATTAAACTAACTTCTTCTTCTTTTACTATTTAGT
1 TTCTTTTACT-ATTTAGTTTAATTACCCAGAATTAAACTAACTTCTTCTTCTTTTACTATTTAGT
*
30444 TTAATTACCCAGAATTTAACTAACCTCTTC
65 TTAATTACCCAGAATTAAACTAACCTCTTC
* *
30474 TACTTTTACTGTTTAGTTTAATT
1 TTCTTTTACTATTTAGTTTAATT
30497 GCTCTGATTT
Statistics
Matches: 520, Mismatches: 64, Indels: 81
0.78 0.10 0.12
Matches are distributed among these distances:
93 4 0.01
94 231 0.44
95 6 0.01
100 27 0.05
101 15 0.03
102 4 0.01
103 59 0.11
104 7 0.01
105 14 0.03
106 8 0.02
107 57 0.11
108 75 0.14
109 5 0.01
110 1 0.00
111 4 0.01
112 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.47
Consensus pattern (94 bp):
TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACTTCTTCTTCTTTTACTATTTAGTT
TAATTACCCAGAATTAAACTAACCTCTTC
Found at i:38856 original size:15 final size:16
Alignment explanation
Indices: 38836--38865 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
38826 TTGAAAATAA
38836 CAATTAAA-AAGAAAG
1 CAATTAAACAAGAAAG
38851 CAATTAAACAAGAAA
1 CAATTAAACAAGAAA
38866 ACAAAGCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.13
Consensus pattern (16 bp):
CAATTAAACAAGAAAG
Found at i:50148 original size:15 final size:16
Alignment explanation
Indices: 50124--50163 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
50114 AGAGGTTGAA
*
50124 AGAAAGCAATTA-AAT
1 AGAAAACAATTATAAT
*
50139 AGAAAACAATTATACT
1 AGAAAACAATTATAAT
50155 AGAAAACAA
1 AGAAAACAA
50164 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.17
Consensus pattern (16 bp):
AGAAAACAATTATAAT
Found at i:50981 original size:9 final size:10
Alignment explanation
Indices: 50950--50983 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
50940 TAAAGAGAAT
50950 TATGTGAAGG
1 TATGTGAAGG
50960 TATGTGAAGG
1 TATGTGAAGG
50970 TATGTG-AGG
1 TATGTGAAGG
50979 TATGT
1 TATGT
50984 TACAGGAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.35
Consensus pattern (10 bp):
TATGTGAAGG
Done.