Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015160.1 Corchorus olitorius cultivar O-4 contig15193, 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: 137324
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:211 original size:28 final size:29
Alignment explanation
Indices: 169--242 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
159 CCGTGTATTC
169 ACAAAGGC-AGAGAATTTTTTTGGTGAAA
1 ACAAAGGCTAGAGAATTTTTTTGGTGAAA
* *
197 ATAAAGGCTA-AGAATGTTTTTTTGTTGAAA
1 ACAAAGGCTAGAGAA--TTTTTTTGGTGAAA
227 ACAAAGG-TAGAGAATT
1 ACAAAGGCTAGAGAATT
243 AGAGTGAGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
28 13 0.33
29 3 0.08
30 23 0.59
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (29 bp):
ACAAAGGCTAGAGAATTTTTTTGGTGAAA
Found at i:2928 original size:6 final size:6
Alignment explanation
Indices: 2910--2939 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
2900 GTTTAGACTT
2910 ATATAG TATATAG ATATAG ATATAG ATATA
1 ATATAG -ATATAG ATATAG ATATAG ATATA
2940 TAATAATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (6 bp):
ATATAG
Found at i:7348 original size:46 final size:47
Alignment explanation
Indices: 7277--7747 Score: 166
Period size: 48 Copynumber: 10.0 Consensus size: 47
7267 TTAATTACCA
* * *
7277 AATTTTGGTCTTCGAGGGTCATGATGATTAACCTTTGACATTTT-GCC
1 AATTTTGGCCATCGAGGGTCGTGATG-TTAACCTTTGACATTTTGGCC
*
7324 -ATTTTGGCCATCGAGGGTTGTGATGGGTTAACCTTT-ACATTTTGGCC
1 AATTTTGGCCATCGAGGGTCGTGAT--GTTAACCTTTGACATTTTGGCC
* * * * * *
7371 AATTTTTGCCACCGAGTGTCGTGATGTTAACCCTTGGACATTTAGGCA
1 AATTTTGGCCATCGAGGGTCGTGATGTTAA-CCTTTGACATTTTGGCC
* * * * * * * *
7419 AATTCTAGCCACCGAGGGTCGGGAAGGTTAGCCTTT-TCTATTTTGACC
1 AATTTTGGCCATCGAGGGTCGTG-ATGTTAACCTTTGAC-ATTTTGGCC
* * ** * * * * **
7467 AGTTTTGGCCAACGAATGT-TTGGATAGTTAGCTTTTGGCATTTTGGAT
1 AATTTTGGCCATCGAGGGTCGT-GAT-GTTAACCTTTGACATTTTGGCC
* ** * * * ** *
7515 GATTTTGATCAGC-ATTGGTCGTGGTGGTTAACCTTT-AGTGTTTTGCCC
1 AATTTTGGCCATCGA-GGGTCGTGAT-GTTAACCTTTGA-CATTTTGGCC
* * * * * * *
7563 AA-TTTGACCATCAAGGGCCGTGATGGTTAGCCCTTG-CA-CTTCGCC
1 AATTTTGGCCATCGAGGGTCGTGAT-GTTAACCTTTGACATTTTGGCC
* * * * *
7608 TAATTTTGGCCACCGAGGGTCGTGATTGTT-AGC--TGTCATTTTGACA
1 -AATTTTGGCCATCGAGGGTCGTGA-TGTTAACCTTTGACATTTTGGCC
* * * * *
7654 AATTTTGG-CACCGATGGTCGTGATGGTTAGCCTTTGTCATTTTGACC
1 AATTTTGGCCATCGAGGGTCGTGAT-GTTAACCTTTGACATTTTGGCC
* *
7701 AATTTTGG-CATCAAGGGTCGTGATGGTTAA-CTTGGTA-ATTTTGGCC
1 AATTTTGGCCATCGAGGGTCGTGAT-GTTAACCTTTG-ACATTTTGGCC
7747 A
1 A
7748 TCGAGGATTG
Statistics
Matches: 310, Mismatches: 88, Indels: 53
0.69 0.20 0.12
Matches are distributed among these distances:
43 1 0.00
44 19 0.06
45 15 0.05
46 51 0.16
47 101 0.33
48 116 0.37
49 7 0.02
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (47 bp):
AATTTTGGCCATCGAGGGTCGTGATGTTAACCTTTGACATTTTGGCC
Found at i:7709 original size:47 final size:46
Alignment explanation
Indices: 7576--7729 Score: 172
Period size: 47 Copynumber: 3.3 Consensus size: 46
7566 TTGACCATCA
* * *
7576 AGGGCCGTGATGGTTAGCCCTTG-CACTTCG-CCTAATTTTGGCCACCG
1 AGGGTCGTGATGGTTAG-CCTTGTCATTTTGACC-AATTTTGG-CACCG
* *
7623 AGGGTCGTGATTGTTAG-C-TGTCATTTTGACAAATTTTGGCACCG
1 AGGGTCGTGATGGTTAGCCTTGTCATTTTGACCAATTTTGGCACCG
* * *
7667 ATGGTCGTGATGGTTAGCCTTTGTCATTTTGACCAATTTTGGCATCA
1 AGGGTCGTGATGGTTAGCC-TTGTCATTTTGACCAATTTTGGCACCG
7714 AGGGTCGTGATGGTTA
1 AGGGTCGTGATGGTTA
7730 ACTTGGTAAT
Statistics
Matches: 91, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
44 22 0.24
45 15 0.16
46 1 0.01
47 53 0.58
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.34
Consensus pattern (46 bp):
AGGGTCGTGATGGTTAGCCTTGTCATTTTGACCAATTTTGGCACCG
Found at i:8070 original size:47 final size:47
Alignment explanation
Indices: 7969--8071 Score: 116
Period size: 47 Copynumber: 2.2 Consensus size: 47
7959 AATTTAAGCC
* * * *
7969 CAAAGGAGTCGTGATGGTTAGGCTTGGCCATTATGGCTAATTTTGCCA
1 CAAAGG-GTCGTGATGGTTAGGCTTGGACATTATGACCAATTTGGCCA
* * * * *
8017 CCAAGGGTCGTGATGGTTAGTCTTTGACATTTTGACCAATTTGGCGA
1 CAAAGGGTCGTGATGGTTAGGCTTGGACATTATGACCAATTTGGCCA
8064 CAAAGGGT
1 CAAAGGGT
8072 TGAGATGATT
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
47 40 0.89
48 5 0.11
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (47 bp):
CAAAGGGTCGTGATGGTTAGGCTTGGACATTATGACCAATTTGGCCA
Found at i:12132 original size:40 final size:40
Alignment explanation
Indices: 12066--12184 Score: 177
Period size: 40 Copynumber: 3.0 Consensus size: 40
12056 AAATTGAATC
*
12066 TTTGATTGCCTCTTTGATTGACATAAAAAAGGGAAAAAGTA
1 TTTGATTGCCTCTTTGATTGACAT-AAAAAGGGAAAAAATA
*
12107 TTTGATTGCCTC-TTGATTGACATAAAAAGGGAAAAAAATC
1 TTTGATTGCCTCTTTGATTGACATAAAAAGGG-AAAAAATA
* *
12147 TTTGTTTGCCTCTTTGATTGACATAAAAAGGAAAAAAA
1 TTTGATTGCCTCTTTGATTGACATAAAAAGGGAAAAAA
12185 AATACGTTTC
Statistics
Matches: 72, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
39 8 0.11
40 34 0.47
41 30 0.42
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (40 bp):
TTTGATTGCCTCTTTGATTGACATAAAAAGGGAAAAAATA
Found at i:12144 original size:41 final size:41
Alignment explanation
Indices: 12066--12185 Score: 181
Period size: 41 Copynumber: 3.0 Consensus size: 41
12056 AAATTGAATC
*
12066 TTTGATTGCCTCTTTGATTGACATAAAAAAGGG-AAAAAGTA
1 TTTGATTGCCTCTTTGATTGACAT-AAAAAGGGAAAAAAATA
*
12107 TTTGATTGCCTC-TTGATTGACATAAAAAGGGAAAAAAATC
1 TTTGATTGCCTCTTTGATTGACATAAAAAGGGAAAAAAATA
* *
12147 TTTGTTTGCCTCTTTGATTGACATAAAAAGGAAAAAAAA
1 TTTGATTGCCTCTTTGATTGACATAAAAAGGGAAAAAAA
12186 ATACGTTTCC
Statistics
Matches: 73, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
39 8 0.11
40 28 0.38
41 37 0.51
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (41 bp):
TTTGATTGCCTCTTTGATTGACATAAAAAGGGAAAAAAATA
Found at i:13146 original size:5 final size:5
Alignment explanation
Indices: 13136--13170 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
13126 ACTTCCATCC
* *
13136 CCTTT CCTTT CCTTT CATTT CCCTT CCTTT CCTTT
1 CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT
13171 AAAAACTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.03, C:0.40, G:0.00, T:0.57
Consensus pattern (5 bp):
CCTTT
Found at i:16149 original size:38 final size:38
Alignment explanation
Indices: 16087--16191 Score: 117
Period size: 38 Copynumber: 2.8 Consensus size: 38
16077 GTGGCCAAAA
*
16087 TTGACCAAAATGCTTAAGGCTAACCATCACGAA-CCAAG
1 TTGACCAAAATGCTCAAGGCTAACCATCA-GAACCCAAG
* *
16125 TTTG-CCAAAATGCTCAAGGTTAACCATCATAACCCAAG
1 -TTGACCAAAATGCTCAAGGCTAACCATCAGAACCCAAG
* *
16163 TTGACCAAAATGGC-AAAGACTAACCATCA
1 TTGACCAAAAT-GCTCAAGGCTAACCATCA
16192 ATATATAAGG
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
37 5 0.09
38 47 0.82
39 5 0.09
ACGTcount: A:0.40, C:0.26, G:0.14, T:0.20
Consensus pattern (38 bp):
TTGACCAAAATGCTCAAGGCTAACCATCAGAACCCAAG
Found at i:16798 original size:48 final size:48
Alignment explanation
Indices: 16746--16873 Score: 159
Period size: 48 Copynumber: 2.7 Consensus size: 48
16736 CGTTGGTAGT
16746 CAAAATTGAACAACATGGCCAAGGCTAACTATAACGACCCTCAGTGGC
1 CAAAATTGAACAACATGGCCAAGGCTAACTATAACGACCCTCAGTGGC
* * * * *
16794 CAAAATTGGATAACATGGCCAAGACTAACTATCACGACCCTCAGTGGT
1 CAAAATTGAACAACATGGCCAAGGCTAACTATAACGACCCTCAGTGGC
* * * *
16842 CAAAATCGACCAAAAT-GCCAAATGCTAACTAT
1 CAAAATTGAACAACATGGCC-AAGGCTAACTAT
16874 CCAAACATTT
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
47 3 0.04
48 64 0.96
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (48 bp):
CAAAATTGAACAACATGGCCAAGGCTAACTATAACGACCCTCAGTGGC
Found at i:17018 original size:47 final size:48
Alignment explanation
Indices: 16962--17066 Score: 115
Period size: 47 Copynumber: 2.2 Consensus size: 48
16952 ATGTTCAAGG
* * *
16962 GCTAA-CATCACAACATTTGATGGCAAAAATTGGCCAAAATGT-AAAA
1 GCTAACCATCACAACACTCGATGGCAAAAATTGGACAAAATGTCAAAA
* * * * *
17008 GCTAACCATCACGACCCTCGATGGCCAAAATTGTACAAAATGTCAAAG
1 GCTAACCATCACAACACTCGATGGCAAAAATTGGACAAAATGTCAAAA
*
17056 GTTAACCATCA
1 GCTAACCATCA
17067 TGACCCTCAA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
46 5 0.10
47 30 0.62
48 13 0.27
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (48 bp):
GCTAACCATCACAACACTCGATGGCAAAAATTGGACAAAATGTCAAAA
Found at i:17066 original size:48 final size:48
Alignment explanation
Indices: 16980--17190 Score: 140
Period size: 48 Copynumber: 4.3 Consensus size: 48
16970 CACAACATTT
* ** *
16980 GATGGCAAAAATTGGCCAAAATGT-AAAAGCTAACCATCACGACCCTC
1 GATGGCCAAAATTGTACAAAATGTCAAAGGCTAACCATCACGACCCTC
* *
17027 GATGGCCAAAATTGTACAAAATGTCAAAGGTTAACCATCATGACCCTC
1 GATGGCCAAAATTGTACAAAATGTCAAAGGCTAACCATCACGACCCTC
* * * ** * * * * * *
17075 AATGACCAAAATT-TACCCAAATAACCAAGGCTGACAATTACGACCATTGGGTTT
1 GATGGCCAAAATTGTA-CAAAATGTCAAAGGCTAACCATCACGACC------CTC
* * *
17129 GGTGGCCAAAATTGTGCAAAATGTCAAAGG-TCAACCATCACGACACTC
1 GATGGCCAAAATTGTACAAAATGTCAAAGGCT-AACCATCACGACCCTC
*
17177 GGTGGCCAAAATTG
1 GATGGCCAAAATTG
17191 GCAAAAATGG
Statistics
Matches: 121, Mismatches: 33, Indels: 19
0.70 0.19 0.11
Matches are distributed among these distances:
47 23 0.19
48 66 0.55
53 1 0.01
54 30 0.25
55 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (48 bp):
GATGGCCAAAATTGTACAAAATGTCAAAGGCTAACCATCACGACCCTC
Found at i:22379 original size:7 final size:7
Alignment explanation
Indices: 22367--22393 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
22357 TAGGGACAGG
22367 TCATAAC
1 TCATAAC
22374 TCATAAC
1 TCATAAC
22381 TCATAAC
1 TCATAAC
22388 TCATAA
1 TCATAA
22394 GTGGTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (7 bp):
TCATAAC
Found at i:35447 original size:12 final size:12
Alignment explanation
Indices: 35430--35457 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
35420 CCCAAAAAAA
35430 TAAATTTTGGAT
1 TAAATTTTGGAT
35442 TAAATTTTGGAT
1 TAAATTTTGGAT
35454 TAAA
1 TAAA
35458 CTTTCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.46
Consensus pattern (12 bp):
TAAATTTTGGAT
Found at i:35516 original size:35 final size:34
Alignment explanation
Indices: 35464--35531 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 34
35454 TAAACTTTCA
35464 TTTTTGAGATAGGTTTATATAATATAA-TAAATTT
1 TTTTTGAGATAGGTTTATATAATA-AATTAAATTT
*
35498 TTTTTGAGGTAAGGTTTATATAATAAATTAAATT
1 TTTTTGAGAT-AGGTTTATATAATAAATTAAATT
35532 AACTGAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
34 11 0.35
35 20 0.65
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (34 bp):
TTTTTGAGATAGGTTTATATAATAAATTAAATTT
Found at i:36356 original size:13 final size:13
Alignment explanation
Indices: 36338--36365 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
36328 TCACCGTACG
36338 TACTCTTCAATTT
1 TACTCTTCAATTT
36351 TACTCTTCAATTT
1 TACTCTTCAATTT
36364 TA
1 TA
36366 AAGTCCTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.21, G:0.00, T:0.54
Consensus pattern (13 bp):
TACTCTTCAATTT
Found at i:39898 original size:32 final size:37
Alignment explanation
Indices: 39857--39926 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 37
39847 GTGGATATAT
39857 ACAAGGTATATATT-G-CC-TT-TCAAAA-AAAAAAA
1 ACAAGGTATATATTAGCCCTTTATCAAAAGAAAAAAA
*
39889 ACAAGGTATATCTTAGCCCTTTATCAAAAGAAAAAAA
1 ACAAGGTATATATTAGCCCTTTATCAAAAGAAAAAAA
39926 A
1 A
39927 AAAAAGTGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
32 13 0.41
33 1 0.03
34 2 0.06
35 2 0.06
36 6 0.19
37 8 0.25
ACGTcount: A:0.51, C:0.14, G:0.10, T:0.24
Consensus pattern (37 bp):
ACAAGGTATATATTAGCCCTTTATCAAAAGAAAAAAA
Found at i:52250 original size:6 final size:6
Alignment explanation
Indices: 52239--52267 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
52229 CCTCTTTCAT
52239 TGCCAA TGCCAA TGCCAA TGCCAA TGCCA
1 TGCCAA TGCCAA TGCCAA TGCCAA TGCCA
52268 TTCCTGTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.34, G:0.17, T:0.17
Consensus pattern (6 bp):
TGCCAA
Found at i:73086 original size:27 final size:27
Alignment explanation
Indices: 73031--73088 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
73021 TGTTTAAGTG
* * *
73031 AGATCATACTTATAATTATTATCTGTA
1 AGATCATACTTATAATGATCATATGTA
* *
73058 AGATCATAGTTATAATGATCATATTTA
1 AGATCATACTTATAATGATCATATGTA
73085 AGAT
1 AGAT
73089 TATAACTAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (27 bp):
AGATCATACTTATAATGATCATATGTA
Found at i:84510 original size:20 final size:20
Alignment explanation
Indices: 84485--84524 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
84475 AGAATATTTT
*
84485 CTAATTTGTATTGGGTATTA
1 CTAATTTGTATTGGATATTA
84505 CTAATTTGTATTGGATATTA
1 CTAATTTGTATTGGATATTA
84525 TTAAATACCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.17, T:0.50
Consensus pattern (20 bp):
CTAATTTGTATTGGATATTA
Found at i:87383 original size:45 final size:45
Alignment explanation
Indices: 87319--87408 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
87309 TTTGACTAAC
*
87319 GTGATTATATGATTCAGTATTCTCATTGTATATTTCATCTTTACT
1 GTGATTATATGATTCAGTATTCTCATTGTACATTTCATCTTTACT
87364 GTGATTATATGATTCAGTATTCTCATTGTACATTTCATCTTTACT
1 GTGATTATATGATTCAGTATTCTCATTGTACATTTCATCTTTACT
87409 TTGCTTGTCG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.50
Consensus pattern (45 bp):
GTGATTATATGATTCAGTATTCTCATTGTACATTTCATCTTTACT
Found at i:94836 original size:21 final size:21
Alignment explanation
Indices: 94812--94872 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
94802 GCCCATGGCG
94812 GCTTTCTTTGCAACCTTGCCT
1 GCTTTCTTTGCAACCTTGCCT
*
94833 GCTTTCTTTGCACCCTTGCCT
1 GCTTTCTTTGCAACCTTGCCT
*
94854 GCTTTCTTTGCAGCCTTGC
1 GCTTTCTTTGCAACCTTGC
94873 TGTCTCCGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.07, C:0.34, G:0.16, T:0.43
Consensus pattern (21 bp):
GCTTTCTTTGCAACCTTGCCT
Found at i:96089 original size:76 final size:77
Alignment explanation
Indices: 95961--96107 Score: 260
Period size: 76 Copynumber: 1.9 Consensus size: 77
95951 AATTTCTCCG
* *
95961 ACGTGAGTGTGCAAGTGGGGAGGAGAAATAATCTGGTGGATTTTGGCGCACGTTAAATTGGTGAG
1 ACGTGAGTGTGCAAGTGGGGAAGAGAAATAATCTGGTGGATTTTGGCACACGTTAAATTGGTGAG
96026 CTGGCAATGCAT
66 CTGGCAATGCAT
*
96038 ACGTGAGTGTGGAAGTGGGGAAGAG-AATAATCTGGTGGATTTTGGCACACGTTAAATTGGTGAG
1 ACGTGAGTGTGCAAGTGGGGAAGAGAAATAATCTGGTGGATTTTGGCACACGTTAAATTGGTGAG
96102 CTGGCA
66 CTGGCA
96108 CTGGCATCAT
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
76 44 0.66
77 23 0.34
ACGTcount: A:0.27, C:0.11, G:0.37, T:0.26
Consensus pattern (77 bp):
ACGTGAGTGTGCAAGTGGGGAAGAGAAATAATCTGGTGGATTTTGGCACACGTTAAATTGGTGAG
CTGGCAATGCAT
Found at i:96858 original size:185 final size:185
Alignment explanation
Indices: 96546--96910 Score: 604
Period size: 185 Copynumber: 2.0 Consensus size: 185
96536 TATCAGTTGT
* *
96546 TTTTGTTGGTCCCCTTTTATCTTTCACTTTAGGACATAATTCATCTTGATATCCAAAATATCCTT
1 TTTTGTTGGTCCCCTTTTATCTTTCACTTTAGGACATAATTCATCTTGATACCCAAAATATCCTC
* ** * * *
96611 GTTAAATACAAAACCTCATATAGTTTAAGTTTCCAATTACTCTATCTTTTTACCTAATTCAAGTT
66 ATTAAATACAAAACCTCATATAGTCAAAGTTTCCAATTACTCCATCCTTTTACCTAATTCAAGCT
* * *
96676 TCATCGTCATTGGAATTGTATCAAACATTAGATACATGACTTGTATCAAATGTCG
131 TCATCATCATTGGAATTGTATCAAAAATTAGATACATGAATTGTATCAAATGTCG
* *
96731 TTTTGTTGGTCCCTTTTTATCTTTCACTTTTGGACATAATTCATCTTGATACCCAAAATATCCTC
1 TTTTGTTGGTCCCCTTTTATCTTTCACTTTAGGACATAATTCATCTTGATACCCAAAATATCCTC
*
96796 ATTAAATACAAAACCTCCTATAGTCAAAGTTTCCAATTACTCCATCCTTTTACCTAATTCAAGCT
66 ATTAAATACAAAACCTCATATAGTCAAAGTTTCCAATTACTCCATCCTTTTACCTAATTCAAGCT
96861 TCATCATCATTGGAATTGTATCAAAAATTAGATACATGAATTGTATCAAA
131 TCATCATCATTGGAATTGTATCAAAAATTAGATACATGAATTGTATCAAA
96911 CATTAAATAC
Statistics
Matches: 166, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
185 166 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (185 bp):
TTTTGTTGGTCCCCTTTTATCTTTCACTTTAGGACATAATTCATCTTGATACCCAAAATATCCTC
ATTAAATACAAAACCTCATATAGTCAAAGTTTCCAATTACTCCATCCTTTTACCTAATTCAAGCT
TCATCATCATTGGAATTGTATCAAAAATTAGATACATGAATTGTATCAAATGTCG
Found at i:96901 original size:25 final size:25
Alignment explanation
Indices: 96873--96922 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
96863 ATCATCATTG
*
96873 GAATTGTATCAAAAATTAGATACAT
1 GAATTGTATCAAAAATTAAATACAT
*
96898 GAATTGTATCAAACATTAAATACAT
1 GAATTGTATCAAAAATTAAATACAT
96923 TACTAAGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.32
Consensus pattern (25 bp):
GAATTGTATCAAAAATTAAATACAT
Found at i:102144 original size:19 final size:19
Alignment explanation
Indices: 102109--102145 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
102099 TGTTTAGATG
* *
102109 CAAAAGAAATAACCAAAAC
1 CAAAAGAAAGAAACAAAAC
102128 CAAAAGAAAGAAACAAAA
1 CAAAAGAAAGAAACAAAA
102146 AATAGAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.73, C:0.16, G:0.08, T:0.03
Consensus pattern (19 bp):
CAAAAGAAAGAAACAAAAC
Found at i:109159 original size:14 final size:14
Alignment explanation
Indices: 109135--109181 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
109125 AATAATTCTC
109135 AAATTAAAACAAAA
1 AAATTAAAACAAAA
**
109149 AAATTTGAACAAAAA
1 AAATTAAAAC-AAAA
109164 AAATTAAAACAAAA
1 AAATTAAAACAAAA
109178 AAAT
1 AAAT
109182 AAATGAAGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.17
Consensus pattern (14 bp):
AAATTAAAACAAAA
Found at i:109165 original size:15 final size:15
Alignment explanation
Indices: 109135--109180 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
109125 AATAATTCTC
109135 AAATTAAAAC-AAAA
1 AAATTAAAACAAAAA
**
109149 AAATTTGAACAAAAA
1 AAATTAAAACAAAAA
109164 AAATTAAAACAAAAA
1 AAATTAAAACAAAAA
109179 AA
1 AA
109181 TAAATGAAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 8 0.30
15 19 0.70
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.15
Consensus pattern (15 bp):
AAATTAAAACAAAAA
Found at i:121083 original size:39 final size:39
Alignment explanation
Indices: 121039--121167 Score: 204
Period size: 39 Copynumber: 3.3 Consensus size: 39
121029 TTTTGTCGTG
* *
121039 TCAGGATGACGAAGAGGAAGATGTTGGTCAACTTGAGGA
1 TCAGGAAGACGAAGAGGAAGATGTTGGACAACTTGAGGA
*
121078 TCAGGAAGACGAAGAGGAAGACGTTGGACAACTTGAGGA
1 TCAGGAAGACGAAGAGGAAGATGTTGGACAACTTGAGGA
* **
121117 TCAGGAAGATGAAGAGGAAGATGTTGGACATTTTGAGGA
1 TCAGGAAGACGAAGAGGAAGATGTTGGACAACTTGAGGA
121156 TCAGGAAGACGA
1 TCAGGAAGACGA
121168 TGGTGGTCCA
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 82 1.00
ACGTcount: A:0.36, C:0.10, G:0.36, T:0.18
Consensus pattern (39 bp):
TCAGGAAGACGAAGAGGAAGATGTTGGACAACTTGAGGA
Found at i:131882 original size:16 final size:16
Alignment explanation
Indices: 131830--131889 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
131820 GTGGAAAATA
131830 ACAAAATGATCATGTTC
1 ACAAAAT-ATCATGTTC
* *
131847 ACAATATATTCCA--TTG
1 ACAAAATA-T-CATGTTC
131863 ACAAAATATCATGTTC
1 ACAAAATATCATGTTC
131879 ACAATAATATC
1 ACAA-AATATC
131890 GTTATTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 2 0.06
15 1 0.03
16 16 0.47
17 13 0.38
18 2 0.06
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (16 bp):
ACAAAATATCATGTTC
Found at i:131917 original size:40 final size:40
Alignment explanation
Indices: 131863--131969 Score: 135
Period size: 45 Copynumber: 2.6 Consensus size: 40
131853 TATTCCATTG
131863 ACAAAAT-ATCATGTTCACAATAATATCGTTATTAAAATA
1 ACAAAATGATCATGTTCACAATAATATCGTTATTAAAATA
* *
131902 ACAAAATGATCATGTTCAATTGGACATAGTATCGTTATTAAAATA
1 ACAAAATGATCATGTTC-A---CA-ATAATATCGTTATTAAAATA
*
131947 ACAAAATGATCAAGTTCACAATA
1 ACAAAATGATCATGTTCACAATA
131970 TAGTCAAATC
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
39 7 0.12
40 12 0.21
41 2 0.03
44 2 0.03
45 35 0.60
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.31
Consensus pattern (40 bp):
ACAAAATGATCATGTTCACAATAATATCGTTATTAAAATA
Found at i:132053 original size:24 final size:24
Alignment explanation
Indices: 132021--132067 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
132011 ATTAGATTAG
132021 TGGAAAGGAAAGATGGAATCATAC
1 TGGAAAGGAAAGATGGAATCATAC
132045 TGGAAAGGAAAGATGGAATCATA
1 TGGAAAGGAAAGATGGAATCATA
132068 TTTGAGTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.06, G:0.30, T:0.17
Consensus pattern (24 bp):
TGGAAAGGAAAGATGGAATCATAC
Found at i:134690 original size:19 final size:20
Alignment explanation
Indices: 134666--134710 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
134656 TTTTACATCT
*
134666 ATAAAAGGAA-CAACAAAAA
1 ATAAAAGAAATCAACAAAAA
134685 ATAAAAAGAAATCAACAAAAA
1 AT-AAAAGAAATCAACAAAAA
*
134706 TTAAA
1 ATAAA
134711 CCCTAGCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 2 0.09
20 10 0.45
21 10 0.45
ACGTcount: A:0.73, C:0.09, G:0.07, T:0.11
Consensus pattern (20 bp):
ATAAAAGAAATCAACAAAAA
Found at i:134702 original size:21 final size:20
Alignment explanation
Indices: 134668--134710 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
134658 TTACATCTAT
*
134668 AAAAGGAACAACAAAAAATA
1 AAAAGAAACAACAAAAAATA
*
134688 AAAAGAAATCAACAAAAATTA
1 AAAAGAAA-CAACAAAAAATA
134709 AA
1 AA
134711 CCCTAGCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.74, C:0.09, G:0.07, T:0.09
Consensus pattern (20 bp):
AAAAGAAACAACAAAAAATA
Done.