Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023653.1 Corchorus olitorius cultivar O-4 contig23686, 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: 28124
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:1070 original size:12 final size:13
Alignment explanation
Indices: 1048--1077 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1038 ACTAACAATT
1048 AAAATCAATCAAG
1 AAAATCAATCAAG
1061 AAAA-CAATCAAG
1 AAAATCAATCAAG
1073 AAAAT
1 AAAAT
1078 TAAAGAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAATCAATCAAG
Found at i:2688 original size:32 final size:32
Alignment explanation
Indices: 2647--2732 Score: 129
Period size: 32 Copynumber: 2.7 Consensus size: 32
2637 GACTCAATCA
2647 GGCGTCTATAGAACAAAACGCCCTTATTTAGC
1 GGCGTCTATAGAACAAAACGCCCTTATTTAGC
*
2679 GGCGTCTATAGAACAAAACGCCCTTATTTAGT
1 GGCGTCTATAGAACAAAACGCCCTTATTTAGC
* *
2711 AGCGTCTACA-ATACAAAACGCC
1 GGCGTCTATAGA-ACAAAACGCC
2733 GCTATAGTGT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
31 1 0.02
32 49 0.98
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (32 bp):
GGCGTCTATAGAACAAAACGCCCTTATTTAGC
Found at i:7651 original size:32 final size:32
Alignment explanation
Indices: 7602--7670 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
7592 CGTGATTGAA
* * *
7602 ATTAACTCATAATACAATAATCCTACACCGGG
1 ATTAACTCATAATACAATAATCCCAAACCAGG
* *
7634 ATTAACTGATGAA-ACAATGATCCCAAACCAGG
1 ATTAACTCAT-AATACAATAATCCCAAACCAGG
7666 ATTAA
1 ATTAA
7671 AATAAAGCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 29 0.94
33 2 0.06
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.23
Consensus pattern (32 bp):
ATTAACTCATAATACAATAATCCCAAACCAGG
Found at i:7738 original size:31 final size:30
Alignment explanation
Indices: 7648--8208 Score: 719
Period size: 30 Copynumber: 18.1 Consensus size: 30
7638 ACTGATGAAA
*
7648 CAATGATCCCAAACCAGGATTAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
* * *
7678 CAATGATCTTAAATCAGGATTGAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
7708 CAATGATCCTAAACCAGGATTAAAAATAAAG
1 CAATGATCCTAAACCAGGATT-AAAATAAAG
*
7739 CAGTGATCCTAAACCAGGATTAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
* * *
7769 CAATGATCCTCAACCAAGATTAAAATAAAA
1 CAATGATCCTAAACCAGGATTAAAATAAAG
*
7799 CAATAATCCTAAACCAGGATTAAAATGAAA-
1 CAATGATCCTAAACCAGGATTAAAAT-AAAG
* *
7829 CAATGATCCTCAACCAGGATTAAAATGAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
* *
7859 CAATGATCCTAAACCAAGATAAAAAATAACCGATAAAG
1 CAATGATCCTAAACCAGGAT------TAA--AATAAAG
*
7897 CATTGATCCTAAACCAGGATTAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
*
7927 CAATGATCCTAAACCATGATTAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
* *
7957 AAATAATCCTAAACCAGGATTAAAAATAAAG
1 CAATGATCCTAAACCAGGATT-AAAATAAAG
* *
7988 CAATGATCCTCAACCAAGATTAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
8018 CAATGATCCTAAACCAGGATTAAAAATAAAG
1 CAATGATCCTAAACCAGGATT-AAAATAAAG
*
8049 CAATGATCCTCAACCAGGATTAAAAATAAAG
1 CAATGATCCTAAACCAGGATT-AAAATAAAG
*
8080 CAATGATCCTCAACCAGGATTAAAAATAAAG
1 CAATGATCCTAAACCAGGATT-AAAATAAAG
* *
8111 CAATATATCCTCAACCAGGATTAAAAATAAAG
1 CAAT-GATCCTAAACCAGGATT-AAAATAAAG
*
8143 CAATGATCCTCAACCAGGATTAAAAATAAAG
1 CAATGATCCTAAACCAGGATT-AAAATAAAG
* *
8174 CAATATATCCTCAACCAGGATTAAAATAAAG
1 CAAT-GATCCTAAACCAGGATTAAAATAAAG
8205 CAAT
1 CAAT
8209 AAAGCAATGA
Statistics
Matches: 476, Mismatches: 40, Indels: 29
0.87 0.07 0.05
Matches are distributed among these distances:
29 2 0.00
30 225 0.47
31 174 0.37
32 49 0.10
36 3 0.01
38 23 0.05
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.20
Consensus pattern (30 bp):
CAATGATCCTAAACCAGGATTAAAATAAAG
Found at i:7765 original size:61 final size:61
Alignment explanation
Indices: 7648--8208 Score: 736
Period size: 61 Copynumber: 9.1 Consensus size: 61
7638 ACTGATGAAA
* * * *
7648 CAATGATCCCAAACCAGGATT-AAAATAAAGCAATGATCTTAAATCAGGATTGAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAAATAAAGCAATGATCCTAAACCAGGATTAAAATAAAG
*
7708 CAATGATCCTAAACCAGGATTAAAAATAAAGCAGTGATCCTAAACCAGGATTAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAAATAAAGCAATGATCCTAAACCAGGATTAAAATAAAG
* * * *
7769 CAATGATCCTCAACCAAGATT-AAAATAAAACAATAATCCTAAACCAGGATTAAAATGAAA-
1 CAATGATCCTAAACCAGGATTAAAAATAAAGCAATGATCCTAAACCAGGATTAAAAT-AAAG
* * * *
7829 CAATGATCCTCAACCAGGATT-AAAATGAAGCAATGATCCTAAACCAAGATAAAAAATAACCGAT
1 CAATGATCCTAAACCAGGATTAAAAATAAAGCAATGATCCTAAACCAGGAT------TAA--AAT
7893 AAAG
58 AAAG
* *
7897 CATTGATCCTAAACCAGGATT-AAAATAAAGCAATGATCCTAAACCATGATTAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAAATAAAGCAATGATCCTAAACCAGGATTAAAATAAAG
* * * *
7957 AAATAATCCTAAACCAGGATTAAAAATAAAGCAATGATCCTCAACCAAGATTAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAAATAAAGCAATGATCCTAAACCAGGATTAAAATAAAG
*
8018 CAATGATCCTAAACCAGGATTAAAAATAAAGCAATGATCCTCAACCAGGATTAAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAAATAAAGCAATGATCCTAAACCAGGATT-AAAATAAAG
* * *
8080 CAATGATCCTCAACCAGGATTAAAAATAAAGCAATATATCCTCAACCAGGATTAAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAAATAAAGCAAT-GATCCTAAACCAGGATT-AAAATAAAG
* * *
8143 CAATGATCCTCAACCAGGATTAAAAATAAAGCAATATATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAAATAAAGCAAT-GATCCTAAACCAGGATTAAAATAAAG
8205 CAAT
1 CAAT
8209 AAAGCAATGA
Statistics
Matches: 456, Mismatches: 31, Indels: 26
0.89 0.06 0.05
Matches are distributed among these distances:
60 121 0.27
61 143 0.31
62 59 0.13
63 79 0.17
66 3 0.01
67 3 0.01
68 48 0.11
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.20
Consensus pattern (61 bp):
CAATGATCCTAAACCAGGATTAAAAATAAAGCAATGATCCTAAACCAGGATTAAAATAAAG
Found at i:8229 original size:38 final size:40
Alignment explanation
Indices: 8167--8250 Score: 111
Period size: 39 Copynumber: 2.1 Consensus size: 40
8157 CAGGATTAAA
* * *
8167 AATAAAGCAATATATCCTCAACCAGGAT-TAAAATAAAGC-
1 AATAAAGCAATAGATCCTAAACCAGGATCGAAAATAAA-CT
8206 AATAAAGCAAT-GATCCTAAACCAGGATCGAAAATAAACT
1 AATAAAGCAATAGATCCTAAACCAGGATCGAAAATAAACT
8245 AATAAA
1 AATAAA
8251 ATAGAATAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
38 15 0.38
39 25 0.62
ACGTcount: A:0.54, C:0.17, G:0.11, T:0.19
Consensus pattern (40 bp):
AATAAAGCAATAGATCCTAAACCAGGATCGAAAATAAACT
Found at i:8317 original size:20 final size:20
Alignment explanation
Indices: 8277--8317 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
8267 AAAAAACATG
*
8277 AAATGCCCAGAGGTCTCATC
1 AAATGCCCAGAGGACTCATC
* *
8297 AAATGCCCGGAGGACTTATC
1 AAATGCCCAGAGGACTCATC
8317 A
1 A
8318 GAATTTGTGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.20
Consensus pattern (20 bp):
AAATGCCCAGAGGACTCATC
Found at i:8916 original size:35 final size:35
Alignment explanation
Indices: 8805--9277 Score: 534
Period size: 36 Copynumber: 13.5 Consensus size: 35
8795 GATATTTAAA
* *
8805 CTGGGTCAACTGAAACAAACTGAAGAAAAGATCGCC
1 CTGGATCAACTGAAATAAACTGAAG-AAAGATCGCC
* * *
8841 CTGGATGAACTGAAATAGACTGCAGAAAAGATCGCC
1 CTGGATCAACTGAAATAAACTGAAG-AAAGATCGCC
* * *
8877 CTGGATCAATTGAAATAAACTGAATAAGGATCGCC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
*
8912 CTGGATCAAACTGAAATAAACTGAAGAAAGATCTCC
1 CTGGATC-AACTGAAATAAACTGAAGAAAGATCGCC
*
8948 CTGGATCAACTGAAATAAATTGAAGAAAGGATCGCC
1 CTGGATCAACTGAAATAAACTGAAGAAA-GATCGCC
* *
8984 TTGGATCAACTGAAATAAATTGAAGGAAAGATCGCC
1 CTGGATCAACTGAAATAAACTGAA-GAAAGATCGCC
*
9020 TTGGATCAACTGAAATAAACTGAAGGAAAGATCGCC
1 CTGGATCAACTGAAATAAACTGAA-GAAAGATCGCC
* *
9056 CTGGATCAACTGAAATAAACTCAAGAGAGATCGCC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
* * * *
9091 CTGGATCAACTGAAATAAACTAAAGAAACACCACC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
* * * *
9126 CTGGGTCAACTGAAATAAATTGAAGAAAGACCACC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
*
9161 CTGGGTCAACTG-----AA--G-A-AAAGATCGCC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
* * *
9187 CTGGATCAACTGAAATAAAATGAAGAAAGACCACC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
*
9222 CTAGG-TCAACTTGAAATAAACTAAAGCAAAGATCGCC
1 CT-GGATCAAC-TGAAATAAACTGAAG-AAAGATCGCC
*
9259 CTGGATCAACTAAAATAAA
1 CTGGATCAACTGAAATAAA
9278 TTGAGTAAGG
Statistics
Matches: 380, Mismatches: 41, Indels: 32
0.84 0.09 0.07
Matches are distributed among these distances:
26 19 0.05
27 1 0.00
28 1 0.00
30 2 0.01
31 2 0.01
33 1 0.00
34 1 0.00
35 134 0.35
36 200 0.53
37 19 0.05
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.18
Consensus pattern (35 bp):
CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
Found at i:9188 original size:26 final size:25
Alignment explanation
Indices: 9146--9200 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
9136 TGAAATAAAT
*
9146 TGAAGAAAGACCACCCTGGGTCAAC
1 TGAAGAAAGACCACCCTGGATCAAC
* *
9171 TGAAGAAAAGATCGCCCTGGATCAAC
1 TGAAG-AAAGACCACCCTGGATCAAC
9197 TGAA
1 TGAA
9201 ATAAAATGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (25 bp):
TGAAGAAAGACCACCCTGGATCAAC
Found at i:9203 original size:96 final size:98
Alignment explanation
Indices: 9083--9269 Score: 279
Period size: 96 Copynumber: 1.9 Consensus size: 98
9073 AACTCAAGAG
* * *
9083 AGATCGCCCTGGATCAACTGAAATAAACTAAAGAAACACCACCCTGGGTCAAC-TGAAATAAATT
1 AGATCGCCCTGGATCAACTGAAATAAAATAAAGAAACACCACCCTAGGTCAACTTGAAATAAACT
* *
9147 GAAG-AAAGACCACCCTGGGTCAACTGAAGAAA
66 AAAGCAAAGACCACCCTGGATCAACTGAAGAAA
* *
9179 AGATCGCCCTGGATCAACTGAAATAAAATGAAGAAAGACCACCCTAGGTCAACTTGAAATAAACT
1 AGATCGCCCTGGATCAACTGAAATAAAATAAAGAAACACCACCCTAGGTCAACTTGAAATAAACT
* *
9244 AAAGCAAAGATCGCCCTGGATCAACT
66 AAAGCAAAGACCACCCTGGATCAACT
9270 AAAATAAATT
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
96 49 0.61
97 13 0.16
98 18 0.22
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.17
Consensus pattern (98 bp):
AGATCGCCCTGGATCAACTGAAATAAAATAAAGAAACACCACCCTAGGTCAACTTGAAATAAACT
AAAGCAAAGACCACCCTGGATCAACTGAAGAAA
Found at i:9297 original size:35 final size:34
Alignment explanation
Indices: 9185--9301 Score: 110
Period size: 35 Copynumber: 3.3 Consensus size: 34
9175 GAAAAGATCG
*
9185 CCCTGGATCAACTGAAATAAAATGAAGAAAGACCA
1 CCCTGGATCAACTGAAATAAATTG-AGAAAGACCA
** * *
9220 CCCTAGG-TCAACTTGAAATAAACTAAAGCAAAGATCG
1 CCCT-GGATCAAC-TGAAATAAA-TTGAG-AAAGACCA
* *
9257 CCCTGGATCAACTAAAATAAATTGAGTAAGGACCA
1 CCCTGGATCAACTGAAATAAATTGAG-AAAGACCA
9292 CCCTGGATCA
1 CCCTGGATCA
9302 GTCGAAATTA
Statistics
Matches: 65, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
35 27 0.42
36 23 0.35
37 15 0.23
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.18
Consensus pattern (34 bp):
CCCTGGATCAACTGAAATAAATTGAGAAAGACCA
Found at i:11277 original size:2 final size:2
Alignment explanation
Indices: 11270--11298 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11260 AAGAATAGAA
11270 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 A
11299 CACACACACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18332 original size:28 final size:28
Alignment explanation
Indices: 18287--18359 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
18277 GTCATTCAGG
**
18287 GGGCATTTTGGTCA-TTTGCATGT-TCAA
1 GGGCATTTTGGTCATTTTGCACATCT-AA
*
18314 GGGCATTTTTGTCATTTTGCACATCTAA
1 GGGCATTTTGGTCATTTTGCACATCTAA
18342 GGGCATTTTGGTCATTTT
1 GGGCATTTTGGTCATTTT
18360 AGGTTCGCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 13 0.32
28 26 0.65
29 1 0.03
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.44
Consensus pattern (28 bp):
GGGCATTTTGGTCATTTTGCACATCTAA
Found at i:24002 original size:14 final size:13
Alignment explanation
Indices: 23973--24021 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
23963 AGAGTCACAT
23973 ATTTTC-AAAA-G
1 ATTTTCAAAAATG
23984 ATTTTCCAAAAATG
1 ATTTT-CAAAAATG
23998 ATTTTTCAAAAATG
1 A-TTTTCAAAAATG
*
24012 GTTTTCAAAA
1 ATTTTCAAAA
24022 TTCGTTTTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 5 0.15
12 1 0.03
13 13 0.39
14 10 0.30
15 4 0.12
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:24008 original size:13 final size:14
Alignment explanation
Indices: 23974--24021 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
23964 GAGTCACATA
23974 TTTTC-AAAA-GAT
1 TTTTCAAAAATGAT
*
23986 TTTCCAAAAATGAT
1 TTTTCAAAAATGAT
*
24000 TTTTCAAAAATG-G
1 TTTTCAAAAATGAT
24013 TTTTCAAAA
1 TTTTCAAAA
24022 TTCGTTTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 4 0.13
13 13 0.42
14 14 0.45
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (14 bp):
TTTTCAAAAATGAT
Found at i:25649 original size:70 final size:70
Alignment explanation
Indices: 25531--25667 Score: 211
Period size: 70 Copynumber: 2.0 Consensus size: 70
25521 ATTTCAGATG
* * * * *
25531 CTTCAGTTCATTTCAGTTGACCCAGGGCGATCTTTATTCAGTTTATTTCAGCTGACCCAGGGTGG
1 CTTCAATTCACTTCAGTTGACCCAGGGCGATCCTTATTCAATTCATTTCAGCTGACCCAGGGTGG
25596 TCTTT
66 TCTTT
* *
25601 CTTCAATTCACTTCAGTTGATCCAGGGCGATCCTTATTCAATTCATTTCAGTTGACCCAGGGTGG
1 CTTCAATTCACTTCAGTTGACCCAGGGCGATCCTTATTCAATTCATTTCAGCTGACCCAGGGTGG
25666 TC
66 TC
25668 CTATTTCAGT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.36
Consensus pattern (70 bp):
CTTCAATTCACTTCAGTTGACCCAGGGCGATCCTTATTCAATTCATTTCAGCTGACCCAGGGTGG
TCTTT
Found at i:25728 original size:36 final size:36
Alignment explanation
Indices: 25531--25916 Score: 314
Period size: 36 Copynumber: 11.1 Consensus size: 36
25521 ATTTCAGATG
* *
25531 CTTCAGTTCATTTCAGTTGACCCAGGGCGATC-TTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * * *
25566 ATTCAGTTTATTTCAGCTGACCCAGGGTGGTC-TTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * *
25601 CTTCAATTCACTTCAGTTGATCCAGGGCGATC-CTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * * * * * *
25636 ATTCAATTCATTTCAGTTGACCCAGGGTGGTCCTAT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* *
25672 -TTCAGTTTATTTCATTTTGATCCAGGGCAATCTTTT
1 CTTCAGTTTATTTCA-GTTGATCCAGGGCGATCTTTT
* *
25708 CTTCAGTTTATTTCAATTGATCCAGAGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * ** **
25744 CTTCAGTTGATTTCAATTGATCTGGGGTAATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* *
25780 CTTCAGTTTATTTCAATTGATCCAGGGTGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* *
25816 CTTCAG------T---TT-ATCCAAGGCGATCATTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* ** *
25842 CTTCAGTTTATTTCAATTGATCTGGGGCAATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* *
25878 CTTCAGTTTATTTTAGTTGATCGAGGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
25914 CTT
1 CTT
25917 TAATTGATCT
Statistics
Matches: 282, Mismatches: 56, Indels: 25
0.78 0.15 0.07
Matches are distributed among these distances:
26 20 0.07
27 2 0.01
30 1 0.00
32 1 0.00
35 97 0.34
36 147 0.52
37 14 0.05
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.43
Consensus pattern (36 bp):
CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
Found at i:25863 original size:26 final size:26
Alignment explanation
Indices: 25799--25852 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
25789 ATTTCAATTG
* *
25799 ATCCAGGGTGATCTTTTCTTCAGTTT
1 ATCCAAGGTGATCATTTCTTCAGTTT
*
25825 ATCCAAGGCGATCATTTCTTCAGTTT
1 ATCCAAGGTGATCATTTCTTCAGTTT
25851 AT
1 AT
25853 TTCAATTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (26 bp):
ATCCAAGGTGATCATTTCTTCAGTTT
Found at i:25933 original size:98 final size:98
Alignment explanation
Indices: 25719--25935 Score: 317
Period size: 98 Copynumber: 2.2 Consensus size: 98
25709 TTCAGTTTAT
* * *
25719 TTCAATTGATCCAGAGCGATCTTTTCTTCAGTTGATTTCAATTGATCTGGGGTAATCTTTTCTTC
1 TTCAATTGATCCAGGGCGATCATTTCTTCAGTTGATTTCAATTGATCTGGGGCAATCTTTTCTTC
*
25784 AGTTTATTTCAATTGATCCAGGGTGATCTTTTC
66 AGTTTATTTCAATTGATCCAGGGCGATCTTTTC
* * * *
25817 TTCAGTTTATCCAAGGCGATCATTTCTTCAGTTTATTTCAATTGATCTGGGGCAATCTTTTCTTC
1 TTCAATTGATCCAGGGCGATCATTTCTTCAGTTGATTTCAATTGATCTGGGGCAATCTTTTCTTC
* * *
25882 AGTTTATTTTAGTTGATCGAGGGCGATCTTTTC
66 AGTTTATTTCAATTGATCCAGGGCGATCTTTTC
* *
25915 TTTAATTGATCTAGGGCGATC
1 TTCAATTGATCCAGGGCGATC
25936 TTCTCTGTAG
Statistics
Matches: 103, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
98 103 1.00
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.44
Consensus pattern (98 bp):
TTCAATTGATCCAGGGCGATCATTTCTTCAGTTGATTTCAATTGATCTGGGGCAATCTTTTCTTC
AGTTTATTTCAATTGATCCAGGGCGATCTTTTC
Found at i:26257 original size:30 final size:30
Alignment explanation
Indices: 26221--27274 Score: 1556
Period size: 30 Copynumber: 35.1 Consensus size: 30
26211 TGCTTTATCA
* *
26221 GCTTTATTTTAATCCTATTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
26251 GCTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
* * *
26281 GCTTTATGTTAATCCTGGTCGAGGATCGTT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
* *
26311 GCTTTATTTTAATCGTGTTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
* *
26341 GCTCTATGTTAATCCTGTTTAAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
* *
26371 GCTTTATGATAATCCTGGTTT-AGGATCGTT
1 GCTTTATGTTAATCCT-GTTTGAGGATCATT
* *
26401 GCATTATTTTAATCCTGTTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
26431 GCTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
26461 GCTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
* *
26491 GCTTTATGTTAATCCTGGTTGAGGATCGTT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
*
26521 GCTTTATTTTAATCCTGTTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
26551 GCTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
* * *
26581 GCTATATTTTAATCCTGTTTGAGGGTCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
26611 GCTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
26641 GCTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
26671 GCTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
* *
26701 GCTTTATGTTAATCCTGGTTGAGGATCGTT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
*
26731 GCTTTATTTTAATCCTGTTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
26761 GCTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
* * *
26791 GCTATATTTTAATCCTGTTTGAGGGTCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
26821 GCTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
26851 GCTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
26881 GCTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
* * * *
26911 GCTTTATGTTATTCCTGGTTGAGAATCGTT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
* *
26941 GCTTTATTTTAATCCTATTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
* * * *
26971 GCTTTATGTTATTCCTGGTTGAGAATCGTT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
* *
27001 GCTTTATTTTAATCCTTTTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
*
27031 GCTTTATGTTAATCTTGTTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
** * *
27061 GCTTTATGTTAATCCTGGATGACGATCGTT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
*
27091 GCTTTATTTTAATCCTGTTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
* * *
27121 GCTATATTTTAATCCTGGTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
* * *
27151 GCTTCATTTTAATCCTGGTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
* * *
27181 GCTATATTTTAATCCTGGTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
* * *
27211 GCTTCATTTTAATCCTGGTTGAGGATCATT
1 GCTTTATGTTAATCCTGTTTGAGGATCATT
*
27241 GCTTTATTTTAATCCTGGTTT-AGGGA-CATT
1 GCTTTATGTTAATCCT-GTTTGA-GGATCATT
27271 GCTT
1 GCTT
27275 CATTAGATAA
Statistics
Matches: 928, Mismatches: 92, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
29 4 0.00
30 914 0.98
31 10 0.01
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (30 bp):
GCTTTATGTTAATCCTGTTTGAGGATCATT
Found at i:27823 original size:27 final size:27
Alignment explanation
Indices: 27793--27865 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 27
27783 GGTCATTAAG
**
27793 GGGGCATTTTGGTCATTTGCATGT-TCA
1 GGGGCATTTTGGTCATTTGCACATCT-A
*
27820 GGGGCATTTTTGTCATTTTGCACATCTA
1 GGGGCATTTTGGTCA-TTTGCACATCTA
*
27848 AGGGCATTTTGGTCATTT
1 GGGGCATTTTGGTCATTT
27866 TAGGTTCGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
27 17 0.44
28 21 0.54
29 1 0.03
ACGTcount: A:0.16, C:0.15, G:0.26, T:0.42
Consensus pattern (27 bp):
GGGGCATTTTGGTCATTTGCACATCTA
Done.