Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007075.1 Corchorus capsularis cultivar CVL-1 contig07096, 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: 34734
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:10344 original size:37 final size:37
Alignment explanation
Indices: 10303--10382 Score: 90
Period size: 37 Copynumber: 2.1 Consensus size: 37
10293 GAAACCTTCC
** * *
10303 TCAAAGTGTGATCTTTTCAAA-AGGAAAAATGTTTTCT
1 TCAAAGTGAAATCTTTTCAAACAGAAAAAATGATTT-T
*
10340 TCAAAGTGAAATCTTTTGAAACGAGAAAAAATGATTTT
1 TCAAAGTGAAATCTTTTCAAAC-AGAAAAAATGATTTT
10378 TCAAA
1 TCAAA
10383 AAGATTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
37 18 0.50
38 6 0.17
39 12 0.33
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (37 bp):
TCAAAGTGAAATCTTTTCAAACAGAAAAAATGATTTT
Found at i:11578 original size:35 final size:36
Alignment explanation
Indices: 11538--12219 Score: 646
Period size: 35 Copynumber: 18.9 Consensus size: 36
11528 GCGATCTTTT
* * * *
11538 GAAGTTTTCAGAGGTTTA-AGTTGATCTCAATCCAA
1 GAAGTTTTCAGAGGATCAGAGTTGATCTCATTTCAA
* *
11573 GAAGTTTTC-GAAGATCAGAGTTGATCTCATTCCAA
1 GAAGTTTTCAGAGGATCAGAGTTGATCTCATTTCAA
* * *
11608 GAAGTTTCCA-ATGATCAGAGTTGATCTCATTCCAA
1 GAAGTTTTCAGAGGATCAGAGTTGATCTCATTTCAA
*
11643 GAAGTTTTC-GAAGATCAGAGTTGATCTCATTTCAA
1 GAAGTTTTCAGAGGATCAGAGTTGATCTCATTTCAA
* * * *
11678 GAAGTTTTTA-ACGATCGGAGTTGATTTCATTTCAA
1 GAAGTTTTCAGAGGATCAGAGTTGATCTCATTTCAA
* *
11713 GAAGTTTTC-GAAGATCAGAGTTGATCTCATTCCAA
1 GAAGTTTTCAGAGGATCAGAGTTGATCTCATTTCAA
* * *
11748 GAAGTTTCCA-ATGATCAGAGTTGATCTCTTTTCAA
1 GAAGTTTTCAGAGGATCAGAGTTGATCTCATTTCAA
* *
11783 GAAGTTTTC-GAAGATTAGAGTTGATCTCATTTCAA
1 GAAGTTTTCAGAGGATCAGAGTTGATCTCATTTCAA
* *
11818 GAAGTTTTTA-ACGATCAGAGTTGATCTCATTTCAA
1 GAAGTTTTCAGAGGATCAGAGTTGATCTCATTTCAA
* * * * *
11853 AAAGTTTTTA-ACGATCAGAGTTGATTTTATTTCAA
1 GAAGTTTTCAGAGGATCAGAGTTGATCTCATTTCAA
11888 GAAGTTTTCA-AGGATCAGAGTTGATCTCATTTCAA
1 GAAGTTTTCAGAGGATCAGAGTTGATCTCATTTCAA
* *
11923 GAAGTTTTTAGA-GATTTA-AGTTGATCTCATTTCAA
1 GAAGTTTTCAGAGGA-TCAGAGTTGATCTCATTTCAA
* *
11958 GAAGTTTTTAGA-GATTTA-AGTTGATCTCATTTCAA
1 GAAGTTTTCAGAGGA-TCAGAGTTGATCTCATTTCAA
* * *
11993 GAAGTTTTC-CATGATCAGAGTTGATCTTATTTCAA
1 GAAGTTTTCAGAGGATCAGAGTTGATCTCATTTCAA
* *
12028 GAAGTTTTC-CATGATCAGAGTTGATCTCATTTCAA
1 GAAGTTTTCAGAGGATCAGAGTTGATCTCATTTCAA
12063 GAAGTTTTCCACGATCAGAGTTGATCAGAGTTGATCTCATTTCAA
1 GAAG-TTT------TCAGAG--GATCAGAGTTGATCTCATTTCAA
*
12108 GAAGTTTTCCACGATCAGAGTTGATCAGAGTTGATCTCAATTCAA
1 GAAG-TTT------TCAGAG--GATCAGAGTTGATCTCATTTCAA
*** *
12153 GAAGTTTTC-CTTGACCAGAGTTGATCTCATTTCAA
1 GAAGTTTTCAGAGGATCAGAGTTGATCTCATTTCAA
* * *
12188 GAAGTTTTC-CATGATCAGAGTTGATATCATTT
1 GAAGTTTTCAGAGGATCAGAGTTGATCTCATTT
12220 GATCTCATTT
Statistics
Matches: 570, Mismatches: 55, Indels: 44
0.85 0.08 0.07
Matches are distributed among these distances:
34 8 0.01
35 477 0.84
36 6 0.01
38 2 0.00
42 2 0.00
43 1 0.00
44 3 0.01
45 71 0.12
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (36 bp):
GAAGTTTTCAGAGGATCAGAGTTGATCTCATTTCAA
Found at i:11630 original size:70 final size:70
Alignment explanation
Indices: 11556--12219 Score: 721
Period size: 70 Copynumber: 9.2 Consensus size: 70
11546 CAGAGGTTTA
* * *
11556 AGTTGATCTCAATCCAAGAAGTTTTCGAAGATCAGAGTTGATCTCATTCCAAGAAGTTTCCAATG
1 AGTTGATCTCATTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTCAAGAAGTTTCCAATG
11621 ATCAG
66 ATCAG
* ** *
11626 AGTTGATCTCATTCCAAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTCAAGAAGTTTTTAACG
1 AGTTGATCTCATTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTCAAGAAGTTTCCAATG
*
11691 ATCGG
66 ATCAG
* *
11696 AGTTGATTTCATTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTCATTCCAAGAAGTTTCCAATG
1 AGTTGATCTCATTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTCAAGAAGTTTCCAATG
11761 ATCAG
66 ATCAG
* * ** *
11766 AGTTGATCTCTTTTCAAGAAGTTTTCGAAGATTAGAGTTGATCTCATTTCAAGAAGTTTTTAACG
1 AGTTGATCTCATTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTCAAGAAGTTTCCAATG
11831 ATCAG
66 ATCAG
* * * * * *
11836 AGTTGATCTCATTTCAAAAAGTTTT-TAACGATCAGAGTTGATTTTATTTCAAGAAGTTTTCAAG
1 AGTTGATCTCATTTCAAGAAGTTTTCGAA-GATCAGAGTTGATCTCATTTCAAGAAGTTTCCAAT
11900 GATCAG
65 GATCAG
* * **
11906 AGTTGATCTCATTTCAAGAAGTTTT-TAGAGATTTA-AGTTGATCTCATTTCAAGAAGTTTTTAG
1 AGTTGATCTCATTTCAAGAAGTTTTCGA-AGA-TCAGAGTTGATCTCATTTCAAGAAGTTTCCA-
*
11969 A-GATTTA-
63 ATGA-TCAG
* * *
11976 AGTTGATCTCATTTCAAGAAGTTTTCCATGATCAGAGTTGATCTTATTTCAAGAAGTTTTCC-AT
1 AGTTGATCTCATTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTCAAGAAG-TTTCCAAT
12040 GATCAG
65 GATCAG
12046 AGTTGATCTCATTTCAAGAAGTTTTCCACGATCAGAGTTGATCAGAGTTGATCTCATTTCAAGAA
1 AGTTGATCTCATTTCAAGAAGTTTT---CG---A-A---GATCAGAGTTGATCTCATTTCAAGAA
12111 GTTTTCCACGATCAGAGTTGATCAG
56 G-TTT---C---CA-A--TGATCAG
* *** *
12136 AGTTGATCTCAATTCAAGAAGTTTTCCTTGACCAGAGTTGATCTCATTTCAAGAAGTTTTCC-AT
1 AGTTGATCTCATTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTCAAGAAG-TTTCCAAT
12200 GATCAG
65 GATCAG
*
12206 AGTTGATATCATTT
1 AGTTGATCTCATTT
12220 GATCTCATTT
Statistics
Matches: 513, Mismatches: 51, Indels: 60
0.82 0.08 0.10
Matches are distributed among these distances:
69 7 0.01
70 396 0.77
71 10 0.02
72 1 0.00
73 1 0.00
74 1 0.00
76 1 0.00
77 1 0.00
80 60 0.12
83 1 0.00
86 1 0.00
87 1 0.00
88 1 0.00
90 31 0.06
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (70 bp):
AGTTGATCTCATTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTCAAGAAGTTTCCAATG
ATCAG
Found at i:12090 original size:45 final size:45
Alignment explanation
Indices: 12039--12241 Score: 275
Period size: 45 Copynumber: 4.7 Consensus size: 45
12029 AAGTTTTCCA
12039 TGATCAGAGTTGATCTCATTTCAAGAAGTTTTCCACGATCAGAGT
1 TGATCAGAGTTGATCTCATTTCAAGAAGTTTTCCACGATCAGAGT
12084 TGATCAGAGTTGATCTCATTTCAAGAAGTTTTCCACGATCAGAGT
1 TGATCAGAGTTGATCTCATTTCAAGAAGTTTTCCACGATCAGAGT
*
12129 TGATCAGAGTTGATCTCAATTCAAGAAGTTTT---C---C----T
1 TGATCAGAGTTGATCTCATTTCAAGAAGTTTTCCACGATCAGAGT
* *
12164 TGACCAGAGTTGATCTCATTTCAAGAAGTTTTCCATGATCAGAGT
1 TGATCAGAGTTGATCTCATTTCAAGAAGTTTTCCACGATCAGAGT
* *
12209 TGAT-ATCATTTGATCTCATTTCAAGAAGTTTTC
1 TGATCA-GAGTTGATCTCATTTCAAGAAGTTTTC
12242 GATAATCAGG
Statistics
Matches: 140, Mismatches: 7, Indels: 22
0.83 0.04 0.13
Matches are distributed among these distances:
35 31 0.22
39 1 0.01
41 1 0.01
42 1 0.01
44 1 0.01
45 105 0.75
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (45 bp):
TGATCAGAGTTGATCTCATTTCAAGAAGTTTTCCACGATCAGAGT
Found at i:12256 original size:80 final size:80
Alignment explanation
Indices: 11978--12261 Score: 308
Period size: 80 Copynumber: 3.5 Consensus size: 80
11968 GAGATTTAAG
*
11978 TTGATCTCATTTCAAGAAGTTTTCCATGATCAGAGTTGATCTTATTTCAAGAAGTTTTCCATGAT
1 TTGATCTCATTTCAAGAAGTTTTCCATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCCATGAT
*
12043 CAGAGTTGATCTCAT
66 CAGAGTTGATATCAT
** * ******
12058 TTCAAGAAGT--TTTCCACG-A-TCAGAGTTGATCAGAGTTGATCTCATTTCAAGAAGTTTTCCA
1 TT---GATCTCATTT-CAAGAAGTTTTCCATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCCA
* * *
12119 CGATCAGAGTTGATCA-GAG
62 TGATCAGAGTTGAT-ATCAT
* * *
12138 TTGATCTCAATTCAAGAAGTTTTCCTTGACCAGAGTTGATCTCATTTCAAGAAGTTTTCCATGAT
1 TTGATCTCATTTCAAGAAGTTTTCCATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCCATGAT
12203 CAGAGTTGATATCAT
66 CAGAGTTGATATCAT
* * *
12218 TTGATCTCATTTCAAGAAGTTTTCGATAATCAGGGTTGATCTCA
1 TTGATCTCATTTCAAGAAGTTTTCCATGATCAGAGTTGATCTCA
12262 AATTGATCCA
Statistics
Matches: 161, Mismatches: 33, Indels: 20
0.75 0.15 0.09
Matches are distributed among these distances:
77 3 0.02
78 3 0.02
79 4 0.02
80 141 0.88
81 4 0.02
82 3 0.02
83 3 0.02
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.37
Consensus pattern (80 bp):
TTGATCTCATTTCAAGAAGTTTTCCATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCCATGAT
CAGAGTTGATATCAT
Found at i:14589 original size:12 final size:12
Alignment explanation
Indices: 14538--14687 Score: 117
Period size: 12 Copynumber: 12.5 Consensus size: 12
14528 TCTGCAGCCA
*
14538 CAGATTGTTGTC
1 CAGATTGCTGTC
* *
14550 CTGATCGCTGTC
1 CAGATTGCTGTC
14562 CAGAATT-CTGAT-
1 CAG-ATTGCTG-TC
14574 CAGATTGCTGTC
1 CAGATTGCTGTC
* *
14586 CAGAGTGTTGTC
1 CAGATTGCTGTC
* *
14598 CAGATGGCTGCC
1 CAGATTGCTGTC
*
14610 CAAATTGCTGTC
1 CAGATTGCTGTC
*
14622 CAGATGGCTGTC
1 CAGATTGCTGTC
14634 CA-ATTGGCTGTC
1 CAGATT-GCTGTC
* *
14646 CAGATTGCTCTT
1 CAGATTGCTGTC
*
14658 GAGATTGCTGTC
1 CAGATTGCTGTC
* * *
14670 GAGATGGCTGTT
1 CAGATTGCTGTC
14682 CAGATT
1 CAGATT
14688 CAGAAACAGT
Statistics
Matches: 106, Mismatches: 26, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
11 6 0.06
12 94 0.89
13 6 0.06
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.33
Consensus pattern (12 bp):
CAGATTGCTGTC
Found at i:20554 original size:2 final size:2
Alignment explanation
Indices: 20549--20599 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
20539 TCTCTCTCTC
* *
20549 TA TA TA TA TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
20591 TA TC TA TA T
1 TA TA TA TA T
20600 GATTAAAAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21282 original size:17 final size:17
Alignment explanation
Indices: 21260--21292 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
21250 GTCTACAATA
*
21260 ATGTTTTAGCTGAGATC
1 ATGTTTTAGATGAGATC
21277 ATGTTTTAGATGAGAT
1 ATGTTTTAGATGAGAT
21293 TTGTTTAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.42
Consensus pattern (17 bp):
ATGTTTTAGATGAGATC
Found at i:22953 original size:58 final size:59
Alignment explanation
Indices: 22860--23009 Score: 259
Period size: 58 Copynumber: 2.6 Consensus size: 59
22850 CTTTTTATTT
22860 TTAACTGACTCAATTACCCTGAATTAAGCTC-TTATTACTGATTATC-TTTCCTTGATTC
1 TTAACTGACTCAATTACCCTGAATTAAGC-CATTATTACTGATTATCTTTTCCTTGATTC
*
22918 TTAACTGACTCAATTACCCTGAATTAAGCCATTATTACTGATTATCTTTTCTTTGATTC
1 TTAACTGACTCAATTACCCTGAATTAAGCCATTATTACTGATTATCTTTTCCTTGATTC
*
22977 TTAACTGACTCAATTACCCTGAATTGAGCCATT
1 TTAACTGACTCAATTACCCTGAATTAAGCCATT
23010 TTATTTTCCC
Statistics
Matches: 88, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
57 1 0.01
58 44 0.50
59 43 0.49
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.41
Consensus pattern (59 bp):
TTAACTGACTCAATTACCCTGAATTAAGCCATTATTACTGATTATCTTTTCCTTGATTC
Found at i:23086 original size:35 final size:36
Alignment explanation
Indices: 23040--23345 Score: 413
Period size: 35 Copynumber: 8.8 Consensus size: 36
23030 TTCTTACTAA
*
23040 ACTTAATTACCCTGAATTAAATTACTTATTGAACT-
1 ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
*
23075 ACTTAATTACCCTGAATTAAGTTACTTA-TAAACTC
1 ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
*
23110 ACTTAATCACCCTGAATTAAGTTACTTATTGAACT-
1 ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
23145 ACTTAATTACCCTGAATTAAGTTACTTATT-AACTC
1 ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
23180 ACTTAATTACCCTGAATTAAGTTACTTATTGAACT-
1 ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
23215 ACTTAATTACCCTGAATTAAGTTACTTATT-AACTC
1 ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
*
23250 GCTTAATTACCCTGAATTAAGTTAC----TG-ACTC
1 ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
* ** *
23281 ACTTAATTGCCCTGAATTAAGTTGA-TTACCG-ACTT
1 ACTTAATTACCCTGAATTAAGTT-ACTTATTGAACTC
* * *
23316 GCTTAATTACCCTGAATTAAATTGCTTATT
1 ACTTAATTACCCTGAATTAAGTTACTTATT
23346 ACTGATTCAC
Statistics
Matches: 243, Mismatches: 16, Indels: 24
0.86 0.06 0.08
Matches are distributed among these distances:
31 26 0.11
32 1 0.00
34 13 0.05
35 194 0.80
36 9 0.04
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.39
Consensus pattern (36 bp):
ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
Found at i:27146 original size:71 final size:70
Alignment explanation
Indices: 27013--27433 Score: 434
Period size: 71 Copynumber: 5.9 Consensus size: 70
27003 TAAAATAAGT
* * * * * *
27013 AACTAAAGAAAGACCACCCTGGATC-ATTGCAAACTGAAA-TGAAAAATGACCACCATCGATCAT
1 AACTGAAGAAAGACCACCCTGGGTCAACTG-AAA-T-AAACTGAAGAACGACCACCCTCGATCAT
*
27076 TCCGACGTA
63 TCTGAC-TA
** * * *
27085 CCCTGACGAAAGACCACCCTGGGTCAACTAAAATAAACTGAAGGACGACCACCCTCGATCATTCC
1 AACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT-C
*
27150 GGACTA
65 TGACTA
* * * * *
27156 AACTGATGAAAGACCACCTTGGGTCAACTGAAATAAACTAAAGAAACGACCACCCTCGATCACTA
1 AACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAG-AACGACCACCCTCGATCATTC
27221 TGACTCAA
65 TGACT--A
* * * * *
27229 AACTGAAGAAAGACCACCCTTGGTTTAACTTAAATACACTGAAGAACGACCACCCTCGATCATTT
1 AACTGAAGAAAGACCACCC-TGGGTCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATTC
*
27294 TGACACA
65 TGAC-TA
* *
27301 AACTGAAGAAAGACCACCCTGGGTCAATTGAAATAAACTGAAGAACGACCATCCTCGATCA-TCT
1 AACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATTC-
*
27365 TGAAATA
65 TG-ACTA
* * * *
27372 AATTGATGGAAGACCACCCTGGGTCAACTGAAATAAATTGAAGAACGACCACCCTCGATCAT
1 AACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAACGACCACCCTCGATCAT
27434 CTTGAAATAA
Statistics
Matches: 291, Mismatches: 47, Indels: 22
0.81 0.13 0.06
Matches are distributed among these distances:
70 4 0.01
71 159 0.55
72 66 0.23
73 43 0.15
74 19 0.07
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (70 bp):
AACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATTCT
GACTA
Found at i:27286 original size:145 final size:142
Alignment explanation
Indices: 27087--27433 Score: 439
Period size: 145 Copynumber: 2.4 Consensus size: 142
27077 CCGACGTACC
* *
27087 CTGACGAAAGACCACCCTGGGTCAACTAAAATAAACTGAAGGACGACCACCCTCGATCATTCCGG
1 CTGAAGAAAGACCACCCTGGGTCAACTAAAATAAACTGAAGAACGACCACCCTCGATCATT-CGG
* * *
27152 AC-TAAACTGATGAAAGACCACCTTGGGTCAACTGAAATAAACTAAAGAAACGACCACCCTCGAT
65 ACACAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTAAAG-AACGACCACCCTCGAT
*
27216 CA-CTATG-ACTCAAAA
129 CATCT-TGAAAT--AAA
* * * * **
27231 CTGAAGAAAGACCACCCTTGGTTTAACTTAAATACACTGAAGAACGACCACCCTCGATCATTTTG
1 CTGAAGAAAGACCACCC-TGGGTCAACTAAAATAAACTGAAGAACGACCACCCTCGATCATTCGG
* * *
27296 ACACAAACTGAAGAAAGACCACCCTGGGTCAATTGAAATAAACTGAAGAACGACCATCCTCGATC
65 ACACAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTAAAGAACGACCACCCTCGATC
27361 ATCTTGAAATAAA
130 ATCTTGAAATAAA
* * * * *
27374 TTGATGGAAGACCACCCTGGGTCAACTGAAATAAATTGAAGAACGACCACCCTCGATCAT
1 CTGAAGAAAGACCACCCTGGGTCAACTAAAATAAACTGAAGAACGACCACCCTCGATCAT
27434 CTTGAAATAA
Statistics
Matches: 176, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
142 38 0.22
143 17 0.10
144 38 0.22
145 83 0.47
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (142 bp):
CTGAAGAAAGACCACCCTGGGTCAACTAAAATAAACTGAAGAACGACCACCCTCGATCATTCGGA
CACAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTAAAGAACGACCACCCTCGATCA
TCTTGAAATAAA
Found at i:27434 original size:71 final size:71
Alignment explanation
Indices: 27087--27450 Score: 437
Period size: 71 Copynumber: 5.1 Consensus size: 71
27077 CCGACGTACC
* * * *
27087 CTGACGAAAGACCACCCTGGGTCAACTAAAATAAACTGAAGGACGACCACCCTCGATCAT-TCCG
1 CTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATCT-TG
* *
27151 GACTAAA
65 AAATAAA
* * *
27158 CTGATGAAAGACCACCTTGGGTCAACTGAAATAAACTAAAGAAACGACCACCCTCGATCA-CTAT
1 CTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAG-AACGACCACCCTCGATCATCT-T
*
27222 G-ACTCAAAA
64 GAAAT--AAA
* * * * *
27231 CTGAAGAAAGACCACCCTTGGTTTAACTTAAATACACTGAAGAACGACCACCCTCGATCATTTTG
1 CTGAAGAAAGACCACCC-TGGGTCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATCTTG
* *
27296 ACACAAA
65 AAATAAA
* *
27303 CTGAAGAAAGACCACCCTGGGTCAATTGAAATAAACTGAAGAACGACCATCCTCGATCATCTTGA
1 CTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATCTTGA
27368 AATAAA
66 AATAAA
* * * *
27374 TTGATGGAAGACCACCCTGGGTCAACTGAAATAAATTGAAGAACGACCACCCTCGATCATCTTGA
1 CTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATCTTGA
27439 AATAAA
66 AATAAA
*
27445 TTGAAG
1 CTGAAG
27451 CATTGAAGAA
Statistics
Matches: 252, Mismatches: 34, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
71 155 0.62
72 39 0.15
73 38 0.15
74 20 0.08
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.20
Consensus pattern (71 bp):
CTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATCTTGA
AATAAA
Found at i:27447 original size:36 final size:36
Alignment explanation
Indices: 27115--27450 Score: 256
Period size: 36 Copynumber: 9.4 Consensus size: 36
27105 GGGTCAACTA
* *
27115 AAATAAACTGAAGGACGACCACCCTCGATCAT-TCCG
1 AAATAAACTGAAGAACGACCACCCTCGATCATCT-TG
* * * * * * * *
27151 GACTAAACTGATGAAAGACCACCTTGGGTCAAC-TG
1 AAATAAACTGAAGAACGACCACCCTCGATCATCTTG
*
27186 AAATAAACTAAAGAAACGACCACCCTCGATCA-CTATG
1 AAATAAACTGAAG-AACGACCACCCTCGATCATCT-TG
* * * * * *
27223 -ACTCAAAACTGAAGAAAGACCACCCTTGGTTTAACTT-
1 AAAT--AAACTGAAGAACGACCACCC-TCGATCATCTTG
* *
27260 AAATACACTGAAGAACGACCACCCTCGATCATTTTG
1 AAATAAACTGAAGAACGACCACCCTCGATCATCTTG
* * * * * *
27296 ACACAAACTGAAGAAAGACCACCCTGGGTCA-ATTG
1 AAATAAACTGAAGAACGACCACCCTCGATCATCTTG
*
27331 AAATAAACTGAAGAACGACCATCCTCGATCATCTTG
1 AAATAAACTGAAGAACGACCACCCTCGATCATCTTG
* * * * *
27367 AAATAAATTGATGGAA-GACCACCCTGGGTCAAC-TG
1 AAATAAACTGA-AGAACGACCACCCTCGATCATCTTG
*
27402 AAATAAATTGAAGAACGACCACCCTCGATCATCTTG
1 AAATAAACTGAAGAACGACCACCCTCGATCATCTTG
*
27438 AAATAAATTGAAG
1 AAATAAACTGAAG
27451 CATTGAAGAA
Statistics
Matches: 230, Mismatches: 56, Indels: 28
0.73 0.18 0.09
Matches are distributed among these distances:
34 3 0.01
35 72 0.31
36 123 0.53
37 15 0.07
38 15 0.07
39 2 0.01
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.20
Consensus pattern (36 bp):
AAATAAACTGAAGAACGACCACCCTCGATCATCTTG
Found at i:27457 original size:8 final size:8
Alignment explanation
Indices: 27443--27497 Score: 65
Period size: 8 Copynumber: 6.9 Consensus size: 8
27433 TCTTGAAATA
27443 AATTGAAG
1 AATTGAAG
*
27451 CATTGAAG
1 AATTGAAG
*
27459 AATCGAAG
1 AATTGAAG
27467 AATTGAAG
1 AATTGAAG
* *
27475 AATTAAAT
1 AATTGAAG
*
27483 AATTGAAA
1 AATTGAAG
27491 AATTGAA
1 AATTGAA
27498 ACAAGACCAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 39 1.00
ACGTcount: A:0.53, C:0.04, G:0.18, T:0.25
Consensus pattern (8 bp):
AATTGAAG
Found at i:28628 original size:16 final size:17
Alignment explanation
Indices: 28607--28638 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28597 CACCCTAGAG
28607 CTTC-TTTTTCTTTTTC
1 CTTCTTTTTTCTTTTTC
28623 CTTCTTTTTTCTTTTT
1 CTTCTTTTTTCTTTTT
28639 TACTCTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (17 bp):
CTTCTTTTTTCTTTTTC
Found at i:28647 original size:19 final size:17
Alignment explanation
Indices: 28607--28651 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
28597 CACCCTAGAG
*
28607 CTTC-TTTTTCTTTTTC
1 CTTCTTTTTTCTTTTTA
28623 CTTCTTTTTTCTTTTTTA
1 CTTCTTTTTTC-TTTTTA
28641 CTCTCTTTTTT
1 CT-TCTTTTTT
28652 TCATGCACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 4 0.16
17 6 0.24
18 7 0.28
19 8 0.32
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (17 bp):
CTTCTTTTTTCTTTTTA
Found at i:28973 original size:25 final size:26
Alignment explanation
Indices: 28945--29000 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
28935 TATACCTTCG
* *
28945 TTTTTCCTTTTC-CTTTCTTTTTCAA
1 TTTTTCATTTTCACTTTCATTTTCAA
*
28970 -TTTTCATTTTCACTTTCATTTTCAT
1 TTTTTCATTTTCACTTTCATTTTCAA
28995 TTTTTC
1 TTTTTC
29001 GCTCTTTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 10 0.38
25 11 0.42
26 5 0.19
ACGTcount: A:0.11, C:0.21, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTTTCATTTTCACTTTCATTTTCAA
Found at i:28978 original size:6 final size:6
Alignment explanation
Indices: 28958--28997 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
28948 TTCCTTTTCC
* *
28958 TTTCTT TTTCAAT TTTCAT TTTCAC TTTCAT TTTCAT TTT
1 TTTCAT TTTC-AT TTTCAT TTTCAT TTTCAT TTTCAT TTT
28998 TTCGCTCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTCAT
Found at i:28988 original size:12 final size:12
Alignment explanation
Indices: 28947--28993 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
28937 TACCTTCGTT
*
28947 TTTCCTTTTC-C
1 TTTCATTTTCAC
* *
28958 TTTCTTTTTCAAT
1 TTTCATTTTC-AC
28971 TTTCATTTTCAC
1 TTTCATTTTCAC
28983 TTTCATTTTCA
1 TTTCATTTTCA
28994 TTTTTTCGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 9 0.30
12 12 0.40
13 9 0.30
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTCATTTTCAC
Found at i:29707 original size:2 final size:2
Alignment explanation
Indices: 29700--29728 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29690 ATGAACAGCA
29700 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
29729 CACAAAAAGC
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:34397 original size:7 final size:7
Alignment explanation
Indices: 34361--34385 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
34351 TGAAATTTTG
34361 TTTTGAA
1 TTTTGAA
34368 TTTTGAA
1 TTTTGAA
34375 TTTTGAA
1 TTTTGAA
34382 TTTT
1 TTTT
34386 TTTTTGGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (7 bp):
TTTTGAA
Done.