Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012753.1 Corchorus capsularis cultivar CVL-1 contig12774, 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: 54769
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:949 original size:37 final size:37
Alignment explanation
Indices: 898--972 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
888 AAAAATTGTC
*
898 TCCAATTATGTCAATAGTACAAAGTAGAATTATTGAT
1 TCCAATTATATCAATAGTACAAAGTAGAATTATTGAT
935 TCCAATTATATCAATAGTACAAAGTAGAATTATTGAT
1 TCCAATTATATCAATAGTACAAAGTAGAATTATTGAT
972 T
1 T
973 GCATTGAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (37 bp):
TCCAATTATATCAATAGTACAAAGTAGAATTATTGAT
Found at i:2801 original size:32 final size:33
Alignment explanation
Indices: 2734--2802 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
2724 CTTGCTCAAC
* *
2734 TTGTAAAGGCGTGATGAAGCCCCGTGAACTTCA
1 TTGTAAAGGCGTGATGAAGCCACGTCAACTTCA
* *
2767 TTGTAACGGCGTGATGAAGGCACG-CAACTTCA
1 TTGTAAAGGCGTGATGAAGCCACGTCAACTTCA
2799 TTGT
1 TTGT
2803 TTGTAAGAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 11 0.34
33 21 0.66
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (33 bp):
TTGTAAAGGCGTGATGAAGCCACGTCAACTTCA
Found at i:13058 original size:15 final size:15
Alignment explanation
Indices: 13031--13071 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
13021 TAGGGTGAAT
*
13031 GGTGCAAACAACAAC
1 GGTGCAAATAACAAC
* *
13046 GGTGCGAATAACAAT
1 GGTGCAAATAACAAC
13061 GGTGCAAATAA
1 GGTGCAAATAA
13072 TCATGTTGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (15 bp):
GGTGCAAATAACAAC
Found at i:13148 original size:15 final size:15
Alignment explanation
Indices: 13114--13148 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
13104 ATGGCAATGG
13114 TGCACATCACCAGGT
1 TGCACATCACCAGGT
* *
13129 CGCACATCACCATGT
1 TGCACATCACCAGGT
13144 TGCAC
1 TGCAC
13149 CTCCACCACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.37, G:0.17, T:0.20
Consensus pattern (15 bp):
TGCACATCACCAGGT
Found at i:14536 original size:19 final size:20
Alignment explanation
Indices: 14507--14545 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
14497 ATAAAAAAAT
14507 CAAGATATTACAAAGTTAAC
1 CAAGATATTACAAAGTTAAC
14527 CAAG-TATTACAAAGTTAAC
1 CAAGATATTACAAAGTTAAC
14546 TGGAATTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26
Consensus pattern (20 bp):
CAAGATATTACAAAGTTAAC
Found at i:18275 original size:21 final size:22
Alignment explanation
Indices: 18249--18299 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
18239 TGGTGTCTCC
18249 TTTCTTTACTCTTCCTTCCA-G
1 TTTCTTTACTCTTCCTTCCATG
* * * *
18270 TTTCTTTTCTTTTTCTTCCATT
1 TTTCTTTACTCTTCCTTCCATG
18292 TTTCTTTA
1 TTTCTTTA
18300 TTTTCCTCTC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.08, C:0.25, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTCTTTACTCTTCCTTCCATG
Found at i:20900 original size:26 final size:26
Alignment explanation
Indices: 20854--20904 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
20844 CATATCACAT
*
20854 CATATCCTATTAATTCGCATTAGAAC
1 CATATCCTATTAATTCACATTAGAAC
* *
20880 CATATCCTATTAGTTTACATTAGAA
1 CATATCCTATTAATTCACATTAGAA
20905 TCATGTTGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (26 bp):
CATATCCTATTAATTCACATTAGAAC
Found at i:25067 original size:21 final size:21
Alignment explanation
Indices: 25043--25082 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
25033 AATTCGGTGC
25043 AATTAAGTAAATTGGTAATTA
1 AATTAAGTAAATTGGTAATTA
*
25064 AATTAAGTAATTTGGTAAT
1 AATTAAGTAAATTGGTAAT
25083 CAACTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (21 bp):
AATTAAGTAAATTGGTAATTA
Found at i:25079 original size:56 final size:56
Alignment explanation
Indices: 25012--25117 Score: 194
Period size: 56 Copynumber: 1.9 Consensus size: 56
25002 AAGATTCAAG
25012 AAGTAATTTGGTAATCAACTTAATTCGGTGCAATTAAGTAAATTGGTAATTAAATT
1 AAGTAATTTGGTAATCAACTTAATTCGGTGCAATTAAGTAAATTGGTAATTAAATT
* *
25068 AAGTAATTTGGTAATCAACTTAATTCGGTGTAATTAAGTAATTTGGTAAT
1 AAGTAATTTGGTAATCAACTTAATTCGGTGCAATTAAGTAAATTGGTAAT
25118 CAACTTAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.39
Consensus pattern (56 bp):
AAGTAATTTGGTAATCAACTTAATTCGGTGCAATTAAGTAAATTGGTAATTAAATT
Found at i:25103 original size:35 final size:35
Alignment explanation
Indices: 25064--25187 Score: 230
Period size: 35 Copynumber: 3.5 Consensus size: 35
25054 TTGGTAATTA
25064 AATTAAGTAATTTGGTAATCAACTTAATTCGGTGT
1 AATTAAGTAATTTGGTAATCAACTTAATTCGGTGT
25099 AATTAAGTAATTTGGTAATCAACTTAATTCGGTGT
1 AATTAAGTAATTTGGTAATCAACTTAATTCGGTGT
*
25134 AATTAAGTAATTTGGTAATCAACTTAATTCGGTGC
1 AATTAAGTAATTTGGTAATCAACTTAATTCGGTGT
*
25169 AATTAAGTAAATTGGTAAT
1 AATTAAGTAATTTGGTAAT
25188 TAAATTAAGT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 87 1.00
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (35 bp):
AATTAAGTAATTTGGTAATCAACTTAATTCGGTGT
Found at i:25193 original size:21 final size:21
Alignment explanation
Indices: 25169--25210 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
25159 AATTCGGTGC
**
25169 AATTAAGTAAATTGGTAATTA
1 AATTAAGTAAATCAGTAATTA
25190 AATTAAGTAAATCAGTAATTA
1 AATTAAGTAAATCAGTAATTA
25211 GCTAAATTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (21 bp):
AATTAAGTAAATCAGTAATTA
Found at i:25194 original size:91 final size:89
Alignment explanation
Indices: 25012--25236 Score: 231
Period size: 91 Copynumber: 2.5 Consensus size: 89
25002 AAGATTCAAG
* * *
25012 AAGTAATTTGGTAATCAACTTAATTCGGTGCAATTAAGTAAATTGGTAATTAAATTAAGTAATTT
1 AAGTAATTTGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTAAACT-A-TAATTC
*
25077 GGTAATCAACTTAATTCGGTGTAATT
64 GGTAATCAACTAAATTCGGTGTAATT
* *
25103 AAGTAATTTGGTAATCAACTTAATTCGGTGTAATTAAGTAATTTGGTAA-TCAACT-TAATTCGG
1 AAGTAATTTGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTAAACTATAATTCGG
* * *
25166 TGCAATTAAGTAAATT-GGTAATTAAATT
66 T--AATCAACTAAATTCGGT--GT-AATT
* ** * * *
25194 AAGTAAATCAGTAATTAGCTAAATTCGGTGTAATTAAGTAAAT
1 AAGTAATTTGGTAATCAACTTAATTCGGTGTAATTAAGTAAAT
25237 AAATGGCTCA
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
87 8 0.07
88 3 0.03
89 10 0.09
90 5 0.04
91 87 0.77
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (89 bp):
AAGTAATTTGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTAAACTATAATTCGG
TAATCAACTAAATTCGGTGTAATT
Found at i:26238 original size:25 final size:25
Alignment explanation
Indices: 26204--26253 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
26194 TTCATATGAA
*
26204 GATAAATGACTAAAAGTTCTAATGT
1 GATAAATGACTAAAAGTGCTAATGT
*
26229 GATAAATGACTAAAGGTGCTAATGT
1 GATAAATGACTAAAAGTGCTAATGT
26254 CAAATTACTA
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:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (25 bp):
GATAAATGACTAAAAGTGCTAATGT
Found at i:26472 original size:24 final size:26
Alignment explanation
Indices: 26440--26487 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
26430 AAAACGGTTC
26440 TAATGCAAA-T-ATAGGATATGATTA
1 TAATGCAAATTAATAGGATATGATTA
26464 TAATGCAAATTAATAGGATATGAT
1 TAATGCAAATTAATAGGATATGAT
26488 GTGATATGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 9 0.41
25 1 0.05
26 12 0.55
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (26 bp):
TAATGCAAATTAATAGGATATGATTA
Found at i:26917 original size:50 final size:50
Alignment explanation
Indices: 26830--26924 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
26820 CTTTCATGAG
* * *
26830 CTGTCTTCTAATTCATTCTTAAGAAAACTGTCTTCCGATCATCTTTTGAA
1 CTGTCTTCCAATTCATTCTTAAGAAAACCGTCCTCCGATCATCTTTTGAA
*
26880 CTGTCTTCCAATTCATTCTTAA-AAGGACCGTCCTCCGATCATCTT
1 CTGTCTTCCAATTCATTCTTAAGAA-AACCGTCCTCCGATCATCTT
26925 CCTTTTATCT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
49 2 0.05
50 38 0.95
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (50 bp):
CTGTCTTCCAATTCATTCTTAAGAAAACCGTCCTCCGATCATCTTTTGAA
Found at i:27017 original size:50 final size:50
Alignment explanation
Indices: 26954--27292 Score: 363
Period size: 50 Copynumber: 6.7 Consensus size: 50
26944 CCTCGAAATC
*
26954 GTCTTCCAATTCATTCTTAAAAGGACCGTCTTCCGCTTATCCTTCGAACT
1 GTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTCGAACT
* * * * * * *
27004 GTCTTCCAATTCATTCTTAGAAGGATCGTCATCCGATCAACTTCTTCGAACT
1 GTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCT-TA-TCCTTCGAACT
* * * * *
27056 GTCTTCCAATTCAATATTAAAAGGACCATCTTCCGATCAACTTCTTCGAACT
1 GTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCT-TA-TCCTTCGAACT
* * **
27108 GTCTTCCAATTCAATCTTAAAAGGACTGTCTTCCGCTTATCCTTTGAAAA
1 GTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTCGAACT
* * * * * * * * * *
27158 ATCTTTCAATTCAATCTTAGAGGGATCATCTTCTGGTTATCCTTTGAATT
1 GTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTCGAACT
* * *
27208 GTCTTCTAATTCAAACTTAAAAGGACCGTCTTCCGCTTATCCTTCGAATT
1 GTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTCGAACT
*
27258 ATCTTCCAATTCAATCTTAAAAGGACCGTCTTCCG
1 GTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCG
27293 ATCAACTTTA
Statistics
Matches: 241, Mismatches: 46, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
50 150 0.62
51 2 0.01
52 89 0.37
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (50 bp):
GTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTCGAACT
Found at i:27137 original size:27 final size:27
Alignment explanation
Indices: 27053--27141 Score: 83
Period size: 27 Copynumber: 3.4 Consensus size: 27
27043 ACTTCTTCGA
*
27053 ACTGTCTTCCAATTCAATATTAAAAGG
1 ACTGTCTTCCAATTCAATCTTAAAAGG
** * **** *
27080 ACCATCTTCCGA-TCAA-CTTCTTCGA
1 ACTGTCTTCCAATTCAATCTTAAAAGG
27105 ACTGTCTTCCAATTCAATCTTAAAAGG
1 ACTGTCTTCCAATTCAATCTTAAAAGG
27132 ACTGTCTTCC
1 ACTGTCTTCC
27142 GCTTATCCTT
Statistics
Matches: 43, Mismatches: 17, Indels: 4
0.67 0.27 0.06
Matches are distributed among these distances:
25 12 0.28
26 8 0.19
27 23 0.53
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (27 bp):
ACTGTCTTCCAATTCAATCTTAAAAGG
Found at i:27537 original size:59 final size:60
Alignment explanation
Indices: 27406--27614 Score: 221
Period size: 59 Copynumber: 3.5 Consensus size: 60
27396 TCATAACTTG
* * * * *
27406 TCTTCAGATTCAT-TCGTGAGCTGTCTTCAGTCTCA-ATCTTAAAAGC-ATTAAGGAACTT
1 TCTTCAGATCCATCTCGTGAGCTGTCTTCAGTCTCATTTCTTAAAATCTTTTAA-GAACTA
* *
27464 TCTTCAGATCCATCT-GTGAGCTGTCTTCAGTCTCATTTGTTAATATCTTTTAAGAACTA
1 TCTTCAGATCCATCTCGTGAGCTGTCTTCAGTCTCATTTCTTAAAATCTTTTAAGAACTA
* * * * * *
27523 TCTTCAGATCCATCT-ATGAGCTGTCTTTAGTTTCATTTCTTAAAAATCTTTGAGGAACTG
1 TCTTCAGATCCATCTCGTGAGCTGTCTTCAGTCTCATTTCTT-AAAATCTTTTAAGAACTA
* *
27583 TCTTCATATCCATCTTCGTGAACTGTCTTCAG
1 TCTTCAGATCCATC-TCGTGAGCTGTCTTCAG
27615 ATTTACCCTT
Statistics
Matches: 126, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
58 32 0.25
59 50 0.40
60 31 0.25
61 1 0.01
62 12 0.10
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.40
Consensus pattern (60 bp):
TCTTCAGATCCATCTCGTGAGCTGTCTTCAGTCTCATTTCTTAAAATCTTTTAAGAACTA
Found at i:28800 original size:8 final size:8
Alignment explanation
Indices: 28789--28820 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
28779 GTCTTAATGT
28789 ATGTATGC
1 ATGTATGC
28797 ATGTATGC
1 ATGTATGC
28805 ATGTATGC
1 ATGTATGC
*
28813 ATCTATGC
1 ATGTATGC
28821 CTACGTATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.38
Consensus pattern (8 bp):
ATGTATGC
Found at i:29580 original size:3 final size:3
Alignment explanation
Indices: 29572--29605 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
29562 CACCCTAGAG
29572 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT -TT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
29606 CTTTTTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:34843 original size:40 final size:40
Alignment explanation
Indices: 34762--34872 Score: 179
Period size: 40 Copynumber: 2.8 Consensus size: 40
34752 AAGCTGGCGA
*
34762 GATCTTTGCCTAAATTGAAAACTTTG-AAAAACTTGATGG
1 GATCTTTCCCTAAATTGAAAACTTTGAAAAAACTTGATGG
*
34801 GATCTTTCCCCAAATTGAAAACTTTGAAAAAACTTGATGG
1 GATCTTTCCCTAAATTGAAAACTTTGAAAAAACTTGATGG
* *
34841 GATCTTTCCCTAAATTGAAATCTGTGAAAAAA
1 GATCTTTCCCTAAATTGAAAACTTTGAAAAAA
34873 AATTTCTTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 24 0.36
40 42 0.64
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (40 bp):
GATCTTTCCCTAAATTGAAAACTTTGAAAAAACTTGATGG
Found at i:35769 original size:23 final size:20
Alignment explanation
Indices: 35729--35772 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 20
35719 AGTATAAACA
35729 TTTTCTTTTCCTCCTCTTCT
1 TTTTCTTTTCCTCCTCTTCT
35749 TTTTCTTCTTCCTTCCGTCTTCT
1 TTTTCTT-TTCC-TCC-TCTTCT
35772 T
1 T
35773 CAACTCGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 4 0.19
22 3 0.14
23 7 0.33
ACGTcount: A:0.00, C:0.34, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTCTTTTCCTCCTCTTCT
Found at i:37134 original size:21 final size:20
Alignment explanation
Indices: 37110--37149 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
37100 AAAATAGACT
37110 TTCTATCTTATAAATAAAAAA
1 TTCTATCTTAT-AATAAAAAA
* *
37131 TTCTTTCTTCTAATAAAAA
1 TTCTATCTTATAATAAAAA
37150 TCTTAAACTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (20 bp):
TTCTATCTTATAATAAAAAA
Found at i:38573 original size:14 final size:14
Alignment explanation
Indices: 38538--38582 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
38528 ATAAAAAATG
**
38538 AATATTTTTATTTT
1 AATATTTTTATTAA
38552 AATATTTTTATTAA
1 AATATTTTTATTAA
*
38566 AATTTTTTTAATTAA
1 AATATTTTT-ATTAA
38581 AA
1 AA
38583 AAATCTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 20 0.74
15 7 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
AATATTTTTATTAA
Found at i:38848 original size:112 final size:112
Alignment explanation
Indices: 38642--38877 Score: 440
Period size: 112 Copynumber: 2.1 Consensus size: 112
38632 TCTCCTCGAT
38642 TAAA-AAGATCAAACAGCCCTATTTATGTTTTTTCTGTTACAATACGTTTGAGTTTCCTGATAAA
1 TAAACAAGATCAAACAGCCCTATTTATGTTTTTTCTGTTACAATACGTTTGAGTTTCCTGATAAA
*
38706 TGTTTTTTGATCTTCAATCTAGGAGAGAGTAATGTTTAATTGAGGAG
66 TGCTTTTTGATCTTCAATCTAGGAGAGAGTAATGTTTAATTGAGGAG
38753 TAAACAAGATCAAACAGCCCTATTTATGTTTTTTCTGTTACAATACGTTTGAGTTTCCTGATAAA
1 TAAACAAGATCAAACAGCCCTATTTATGTTTTTTCTGTTACAATACGTTTGAGTTTCCTGATAAA
*
38818 TGCTTTTTGATCTTCAATCTAGGAGGGAGTAATGTTTAATTGAGGAG
66 TGCTTTTTGATCTTCAATCTAGGAGAGAGTAATGTTTAATTGAGGAG
38865 TAAACAA-ATCAAA
1 TAAACAAGATCAAA
38878 ATTTATGACG
Statistics
Matches: 122, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
111 10 0.08
112 112 0.92
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (112 bp):
TAAACAAGATCAAACAGCCCTATTTATGTTTTTTCTGTTACAATACGTTTGAGTTTCCTGATAAA
TGCTTTTTGATCTTCAATCTAGGAGAGAGTAATGTTTAATTGAGGAG
Found at i:40282 original size:78 final size:78
Alignment explanation
Indices: 40145--40302 Score: 219
Period size: 78 Copynumber: 2.0 Consensus size: 78
40135 CTTTATCATA
* * * *
40145 GATAGGATTTCTACGAACATGTTCAGGTCTTTCAATAGGGCCACCACGAGCTATTTCCACCCCTG
1 GATAGGATTTCTACAAACATGTACAGGTCTTTCAATAGGGCCACCACGAGCCATCTCCACCCCTG
40210 GCTTTCTATTGTC
66 GCTTTCTATTGTC
* * * * *
40223 GATAGGATTTCTGCAAACA-GATACAGGTTTTTCAATAGGGTCACCATGAGCCATCTCCACCCTT
1 GATAGGATTTCTACAAACATG-TACAGGTCTTTCAATAGGGCCACCACGAGCCATCTCCACCCCT
40287 GGCTTTCTATTGTC
65 GGCTTTCTATTGTC
40301 GA
1 GA
40303 CTTGCCTCTC
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
77 1 0.01
78 69 0.99
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (78 bp):
GATAGGATTTCTACAAACATGTACAGGTCTTTCAATAGGGCCACCACGAGCCATCTCCACCCCTG
GCTTTCTATTGTC
Found at i:41051 original size:291 final size:290
Alignment explanation
Indices: 40521--41099 Score: 1104
Period size: 291 Copynumber: 2.0 Consensus size: 290
40511 CTGATTACCA
40521 ACTGACGCAGCGTGTAGCGTGAAATCAAACTCACCAAGAATCCACTTGGATGAAAGTTGATAAAA
1 ACTGACGCAGCGTGTAGCGTGAAATCAAACTCACCAAGAATCCACTTGGATGAAAGTTGATAAAA
40586 ATTCCATACAGGAAAATAAACTGAGATAAACTTGAGAAAATAATTGATTCTACATAAACTAGGGT
66 ATTCCATACAGGAAAATAAACTGAGATAAACTTGAGAAAATAATTGATTCTACATAAACTAGGGT
40651 TTTCTAAACCTTAAATACCCTGTCAAAACTAATTAAAGTACTAAATAAAATAAAATACTAAAGCC
131 TTTCTAAACCTTAAATACCCTGTCAAAACTAATTAAAGTACTAAATAAAATAAAATACTAAAGCC
* *
40716 CGATAATAAAATAGAGTCCAAAATGTAATTATAAAATCCAACCAATTCAGCCAGCTCAAAAGCCC
196 CAATAATAAAATAGAGTCCAAAATGTAATTATAAAATCCAACCAATTCAGCCAACTCAAAAGCCC
40781 AATTAATTTCTTCTTGTCCCCCGCGTCATT
261 AATTAATTTCTTCTTGTCCCCCGCGTCATT
40811 ACTGACGCAGCGTGTAGCGTGAAATCAAACTCACCAAGAATCCACTTGGATGAAAGTTGATAAAA
1 ACTGACGCAGCGTGTAGCGTGAAATCAAACTCACCAAGAATCCACTTGGATGAAAGTTGATAAAA
*
40876 ATTCCATACCAGGAAAATAAACTGAGATAAACTTGAGAAAATAATTGATTCTACATAAATTAGGG
66 ATTCCATA-CAGGAAAATAAACTGAGATAAACTTGAGAAAATAATTGATTCTACATAAACTAGGG
*
40941 TTTTCTAAATCTTAAATACCCTGTCAAAACTAATTAAAGTACTAAATAAAATAAAATACTAAAGC
130 TTTTCTAAACCTTAAATACCCTGTCAAAACTAATTAAAGTACTAAATAAAATAAAATACTAAAGC
*
41006 CCAATAATAAAATAGAGTCCAAAATGTAATTATAAAATTCAACCAATTCAGCCAACTCAAAAGCC
195 CCAATAATAAAATAGAGTCCAAAATGTAATTATAAAATCCAACCAATTCAGCCAACTCAAAAGCC
41071 CAATTAATTTCTTCTTGTCCCCCGCGTCA
260 CAATTAATTTCTTCTTGTCCCCCGCGTCA
41100 ATTTGGCAGC
Statistics
Matches: 283, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
290 73 0.26
291 210 0.74
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.26
Consensus pattern (290 bp):
ACTGACGCAGCGTGTAGCGTGAAATCAAACTCACCAAGAATCCACTTGGATGAAAGTTGATAAAA
ATTCCATACAGGAAAATAAACTGAGATAAACTTGAGAAAATAATTGATTCTACATAAACTAGGGT
TTTCTAAACCTTAAATACCCTGTCAAAACTAATTAAAGTACTAAATAAAATAAAATACTAAAGCC
CAATAATAAAATAGAGTCCAAAATGTAATTATAAAATCCAACCAATTCAGCCAACTCAAAAGCCC
AATTAATTTCTTCTTGTCCCCCGCGTCATT
Found at i:42029 original size:15 final size:15
Alignment explanation
Indices: 41989--42021 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
41979 TTTTTTAATT
41989 AAAAAAATT-AAATA
1 AAAAAAATTAAAATA
42003 AAAAAAATTAAAATA
1 AAAAAAATTAAAATA
42018 AAAA
1 AAAA
42022 TATTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAAAAATTAAAATA
Found at i:42265 original size:15 final size:15
Alignment explanation
Indices: 42225--42257 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
42215 CTTTTTAATT
42225 AAAAAAATT-AAATA
1 AAAAAAATTAAAATA
42239 AAAAAAATTAAAATA
1 AAAAAAATTAAAATA
42254 AAAA
1 AAAA
42258 TATTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAAAAATTAAAATA
Found at i:42623 original size:76 final size:76
Alignment explanation
Indices: 42497--42643 Score: 258
Period size: 76 Copynumber: 1.9 Consensus size: 76
42487 ATTTGCTAGC
*
42497 ACAAAACGGTCGGAGAAGCTTCACAACTGATACTCATCTCAGTGAACGGTTGATTGTGAGGATAC
1 ACAAAACGGTCGGAGAAGCTTCACAACTGATACTCATCTCAGTGAACGGTTGATTGTGAGAATAC
42562 CATAGAAGAAT
66 CATAGAAGAAT
* * *
42573 ACAAAACGGTCGGAGAAGTTTCACAACTGGTACTCATCTCGGTGAACGGTTGATTGTGAGAATAC
1 ACAAAACGGTCGGAGAAGCTTCACAACTGATACTCATCTCAGTGAACGGTTGATTGTGAGAATAC
42638 CATAGA
66 CATAGA
42644 GGAAGGGATT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 67 1.00
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.23
Consensus pattern (76 bp):
ACAAAACGGTCGGAGAAGCTTCACAACTGATACTCATCTCAGTGAACGGTTGATTGTGAGAATAC
CATAGAAGAAT
Found at i:45837 original size:28 final size:29
Alignment explanation
Indices: 45774--45842 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
45764 ATCCATGGGC
45774 ATTTTGGTCATTTTCACATCTAGGGGGGT
1 ATTTTGGTCATTTTCACATCTAGGGGGGT
** *
45803 ATTTTGGTCATTTTTGCATTTA-GGGGGT
1 ATTTTGGTCATTTTCACATCTAGGGGGGT
45831 ATTTTGGTCATT
1 ATTTTGGTCATT
45843 CTTAATCTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
28 18 0.49
29 19 0.51
ACGTcount: A:0.16, C:0.10, G:0.26, T:0.48
Consensus pattern (29 bp):
ATTTTGGTCATTTTCACATCTAGGGGGGT
Found at i:50093 original size:30 final size:31
Alignment explanation
Indices: 50057--50128 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 31
50047 AGTAAAAAGG
50057 GCAATCAGTAATTAAGTTCAATAAGGAAA-A-
1 GCAATCAGTAATTAAGTTCAATAA-GAAAGAT
* *
50087 GTAATCAGTGATTAAGTTCAATAAGAAAGAT
1 GCAATCAGTAATTAAGTTCAATAAGAAAGAT
50118 GCAATCAGTAA
1 GCAATCAGTAA
50129 AAGGTAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 4 0.11
30 23 0.64
31 9 0.25
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (31 bp):
GCAATCAGTAATTAAGTTCAATAAGAAAGAT
Found at i:50148 original size:22 final size:23
Alignment explanation
Indices: 50120--50179 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
50110 AGAAAGATGC
*
50120 AATCAGTAAAAG-GTAAAATGGT
1 AATCAGTAAAAGAGTAAAATGAT
*
50142 AATCAGT-AAAGAGTAAAGTGAT
1 AATCAGTAAAAGAGTAAAATGAT
50164 AATCAGT-AAAGAGTAA
1 AATCAGTAAAAGAGTAA
50180 TAGAGATCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.11
22 31 0.89
ACGTcount: A:0.52, C:0.05, G:0.22, T:0.22
Consensus pattern (23 bp):
AATCAGTAAAAGAGTAAAATGAT
Found at i:50244 original size:55 final size:55
Alignment explanation
Indices: 50176--50320 Score: 200
Period size: 55 Copynumber: 2.6 Consensus size: 55
50166 TCAGTAAAGA
* * *
50176 GTAATAGAGATCAGTAAATCAGTAATTAAGTGAAAAGAAATTAATCAGGGTCAAG
1 GTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTCAAG
* *
50231 GTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAG
1 GTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTCAAG
* * * * *
50286 GTAGTAGTAATTAGTAAATCAGTAATCAGGTAAAA
1 GTAATAGAAATCAGTAAATCAGTAATTAAGTAAAA
50321 GATAGTAATC
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 80 1.00
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (55 bp):
GTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTCAAG
Found at i:50431 original size:22 final size:24
Alignment explanation
Indices: 50396--50439 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
50386 AATGGTAATC
50396 AGTGAATCGATAATTAAGAGTTAA
1 AGTGAATCGATAATTAAGAGTTAA
50420 AGTG-ATC-ATAATTAAGAGTT
1 AGTGAATCGATAATTAAGAGTT
50440 GAGTGGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.65
23 3 0.15
24 4 0.20
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (24 bp):
AGTGAATCGATAATTAAGAGTTAA
Found at i:50694 original size:22 final size:20
Alignment explanation
Indices: 50597--50824 Score: 79
Period size: 21 Copynumber: 11.4 Consensus size: 20
50587 AATAGCATGC
* *
50597 AATCAGTAAAAAGTAAAAAGT
1 AATCAGT-AAGAGTAAAAGGT
* * *
50618 -ATCTGAAAGGGTAAAATGGT
1 AATCAGTAAGAGTAAAA-GGT
*
50638 AATTAGTAAGAGTAAAAGGT
1 AATCAGTAAGAGTAAAAGGT
* *
50658 AATCATTAAAAAGTAAGAAGGT
1 AATCAGT-AAGAGTAA-AAGGT
50680 AATCAGTAAGGAGT--AA---
1 AATCAGTAA-GAGTAAAAGGT
50696 AATCAGTAAAGAGT--AA---
1 AATCAGT-AAGAGTAAAAGGT
* *
50712 AAT-AGTAATCAGTAAAAGAT
1 AATCAGTAA-GAGTAAAAGGT
* *
50732 AATCAGTAAGAGTAAAACAGC
1 AATCAGTAAGAGTAAAA-GGT
* **
50753 AACCAGTAAG-GGCAAAGTGAT
1 AATCAGTAAGAGTAAAAG-G-T
*
50774 AATTAGTAAGAGTCAAATA-GT
1 AATCAGTAAGAGT-AAA-AGGT
*
50795 AATCAGTAAAGAGTAAAGGGT
1 AATCAGT-AAGAGTAAAAGGT
*
50816 GATCAGTAA
1 AATCAGTAA
50825 TTCAAAGAGT
Statistics
Matches: 155, Mismatches: 31, Indels: 43
0.68 0.14 0.19
Matches are distributed among these distances:
14 2 0.01
15 6 0.04
16 16 0.10
17 4 0.03
19 10 0.06
20 31 0.20
21 61 0.39
22 22 0.14
23 2 0.01
24 1 0.01
ACGTcount: A:0.50, C:0.07, G:0.22, T:0.21
Consensus pattern (20 bp):
AATCAGTAAGAGTAAAAGGT
Found at i:50701 original size:16 final size:16
Alignment explanation
Indices: 50680--50719 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
50670 GTAAGAAGGT
*
50680 AATCAGTAAGGAGTAA
1 AATCAGTAAAGAGTAA
50696 AATCAGTAAAGAGTAA
1 AATCAGTAAAGAGTAA
50712 AAT-AGTAA
1 AATCAGTAA
50720 TCAGTAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (16 bp):
AATCAGTAAAGAGTAA
Found at i:50711 original size:38 final size:36
Alignment explanation
Indices: 50678--50748 Score: 99
Period size: 38 Copynumber: 1.9 Consensus size: 36
50668 AAGTAAGAAG
*
50678 GTAATCAGTAAGGAGTAAAATCAGTAAAGAGTAAAATA
1 GTAATCAGTAA-AAG-AAAATCAGTAAAGAGTAAAATA
*
50716 GTAATCAGTAAAAGATAATCAGT-AAGAGTAAAA
1 GTAATCAGTAAAAGAAAATCAGTAAAGAGTAAAA
50749 CAGCAACCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
35 10 0.32
36 8 0.26
37 2 0.06
38 11 0.35
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.21
Consensus pattern (36 bp):
GTAATCAGTAAAAGAAAATCAGTAAAGAGTAAAATA
Found at i:50725 original size:15 final size:15
Alignment explanation
Indices: 50691--50740 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
50681 ATCAGTAAGG
**
50691 AGTAAAATCAGTAAAG
1 AGTAAAAT-AGTAATC
50707 AGTAAAATAGTAATC
1 AGTAAAATAGTAATC
*
50722 AGTAAAAGA-TAATC
1 AGTAAAATAGTAATC
50736 AGTAA
1 AGTAA
50741 GAGTAAAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 10 0.32
15 13 0.42
16 8 0.26
ACGTcount: A:0.56, C:0.06, G:0.16, T:0.22
Consensus pattern (15 bp):
AGTAAAATAGTAATC
Found at i:50736 original size:14 final size:15
Alignment explanation
Indices: 50707--50740 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
50697 ATCAGTAAAG
*
50707 AGTAAAATAGTAATC
1 AGTAAAAGAGTAATC
50722 AGTAAAAGA-TAATC
1 AGTAAAAGAGTAATC
50736 AGTAA
1 AGTAA
50741 GAGTAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:50901 original size:29 final size:27
Alignment explanation
Indices: 50876--50952 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 27
50866 GTAAAAAGTG
50876 GTAATAAATAAAAGAGAGCAAGAAAAGA
1 GTAATAAATAAAA-AGAGCAAGAAAAGA
* * *
50904 GTAATTAGTAAAAAGAGTAAGAAAAGA
1 GTAATAAATAAAAAGAGCAAGAAAAGA
50931 GTAA-AAATGATAAAAGTAGCAA
1 GTAATAAAT-A-AAAAG-AGCAA
50953 AAGTAATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 2 0.05
27 18 0.45
28 16 0.40
29 4 0.10
ACGTcount: A:0.61, C:0.03, G:0.21, T:0.16
Consensus pattern (27 bp):
GTAATAAATAAAAAGAGCAAGAAAAGA
Done.