Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008063.1 Corchorus capsularis cultivar CVL-1 contig08084, 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: 136635
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:424 original size:70 final size:70
Alignment explanation
Indices: 341--495 Score: 231
Period size: 70 Copynumber: 2.2 Consensus size: 70
331 TAATTAAAAT
* * * * * *
341 AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
406 AGTTG
66 AGTTG
*
411 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
476 AGTTG
66 AGTTG
481 AGTAAAACTA-TAAAA
1 AGTAAAA-TAGTAAAA
496 ACCTAAACAA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
70 75 0.97
71 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.37
Consensus pattern (70 bp):
AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
AGTTG
Found at i:3245 original size:2 final size:2
Alignment explanation
Indices: 3226--3264 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
3216 AGGTATATTA
* *
3226 AT AT AT TT AT -T AT TT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3265 CTAGATATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:5987 original size:9 final size:9
Alignment explanation
Indices: 5975--6000 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5965 AGTTAAGTTT
5975 GGCATCTTC
1 GGCATCTTC
5984 GGCATCTTC
1 GGCATCTTC
5993 GGCATCTT
1 GGCATCTT
6001 TGGGATGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.31, G:0.23, T:0.35
Consensus pattern (9 bp):
GGCATCTTC
Found at i:11765 original size:15 final size:15
Alignment explanation
Indices: 11745--11791 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
11735 GTTTGATGTA
11745 ACTCGATTAATTAGG
1 ACTCGATTAATTAGG
*
11760 ACTCGA-T--GT--G
1 ACTCGATTAATTAGG
11770 ACTCGATTAATTAGG
1 ACTCGATTAATTAGG
11785 ACTCGAT
1 ACTCGAT
11792 GTGGTTGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
10 7 0.28
11 1 0.04
12 1 0.04
13 1 0.04
14 1 0.04
15 14 0.56
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (15 bp):
ACTCGATTAATTAGG
Found at i:11794 original size:25 final size:25
Alignment explanation
Indices: 11739--11794 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
11729 CATAGGGTTT
*
11739 GATGTAACTCGATTAATTAGGACTC
1 GATGTGACTCGATTAATTAGGACTC
11764 GATGTGACTCGATTAATTAGGACTC
1 GATGTGACTCGATTAATTAGGACTC
11789 GATGTG
1 GATGTG
11795 GTTGTTAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (25 bp):
GATGTGACTCGATTAATTAGGACTC
Found at i:11914 original size:51 final size:51
Alignment explanation
Indices: 11854--11963 Score: 159
Period size: 51 Copynumber: 2.2 Consensus size: 51
11844 TCGATGAGAT
* * * *
11854 TATAAGATCGAAGCGGCTCGACTCCGAACATGA-CCTGATGTTATTATTGTA
1 TATAGGATCGAAGCGACTCGACTCCGAACATGATCC-GATATTATTATCGTA
11905 TATAGGATCGAAGCGACTCGACTCCGAACATGATCCGATATTATTATCGTA
1 TATAGGATCGAAGCGACTCGACTCCGAACATGATCCGATATTATTATCGTA
*
11956 TATCGGAT
1 TATAGGAT
11964 AATTGACTCG
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
51 51 0.96
52 2 0.04
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (51 bp):
TATAGGATCGAAGCGACTCGACTCCGAACATGATCCGATATTATTATCGTA
Found at i:14350 original size:18 final size:18
Alignment explanation
Indices: 14316--14353 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
14306 TCTTTTATGG
*
14316 AACTAAAATATACTCATA
1 AACTAAAAAATACTCATA
14334 AACTAAAAAAATA-TCATA
1 AACT-AAAAAATACTCATA
14352 AA
1 AA
14354 AAGCAAAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.63, C:0.13, G:0.00, T:0.24
Consensus pattern (18 bp):
AACTAAAAAATACTCATA
Found at i:33601 original size:83 final size:83
Alignment explanation
Indices: 33508--33677 Score: 322
Period size: 83 Copynumber: 2.0 Consensus size: 83
33498 TTGCATGTAT
33508 CTTTTTTACTTGAAAGCAGAGTTGAGGATGCTCTAATCCAAGTTAGTATCCGTTGAGTGCATTAA
1 CTTTTTTACTTGAAAGCAGAGTTGAGGATGCTCTAATCCAAGTTAGTATCCGTTGAGTGCATTAA
33573 ATATACGATGTTAAATAC
66 ATATACGATGTTAAATAC
*
33591 CTTTTTTACTTGAAAGCAGAGTTGAGGATGCTCTGATCCAAGTTAGTATCCGTTGAGTGCATTAA
1 CTTTTTTACTTGAAAGCAGAGTTGAGGATGCTCTAATCCAAGTTAGTATCCGTTGAGTGCATTAA
*
33656 ATATACGATGTTAAATTC
66 ATATACGATGTTAAATAC
33674 CTTT
1 CTTT
33678 CAGATCATAA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 85 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.36
Consensus pattern (83 bp):
CTTTTTTACTTGAAAGCAGAGTTGAGGATGCTCTAATCCAAGTTAGTATCCGTTGAGTGCATTAA
ATATACGATGTTAAATAC
Found at i:42690 original size:27 final size:27
Alignment explanation
Indices: 42660--42713 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
42650 AAAAAAAAAT
42660 CTACAAAGTAATTGATGGATTGATTGA
1 CTACAAAGTAATTGATGGATTGATTGA
42687 CTACAAAGTAATTGATGGATTGATTGA
1 CTACAAAGTAATTGATGGATTGATTGA
42714 TTAAGACTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.33
Consensus pattern (27 bp):
CTACAAAGTAATTGATGGATTGATTGA
Found at i:45535 original size:23 final size:22
Alignment explanation
Indices: 45491--45535 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
45481 GTATATGAAC
* *
45491 GTAATAAAAAAAAATGTCATTT
1 GTAATAAAAAAAAACGTAATTT
45513 GTAATAGAAAAAAAACGTAATTT
1 GTAATA-AAAAAAAACGTAATTT
45536 ATTTCATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.56, C:0.04, G:0.11, T:0.29
Consensus pattern (22 bp):
GTAATAAAAAAAAACGTAATTT
Found at i:45998 original size:19 final size:18
Alignment explanation
Indices: 45974--46009 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
45964 CTGAACTCTA
45974 TTGATGAATATATTGATTT
1 TTGATGAATATA-TGATTT
*
45993 TTGATGCATATATGATT
1 TTGATGAATATATGATT
46010 CTGGAATTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.50
Consensus pattern (18 bp):
TTGATGAATATATGATTT
Found at i:48657 original size:2 final size:2
Alignment explanation
Indices: 48650--48679 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
48640 CCATAACAAG
48650 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48680 TGTTCCACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50907 original size:2 final size:2
Alignment explanation
Indices: 50902--50928 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
50892 AAAAAAAGGG
50902 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
50929 GATCAATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51683 original size:14 final size:15
Alignment explanation
Indices: 51664--51692 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
51654 CAATTACGAG
51664 TTATAGTAT-AAATT
1 TTATAGTATCAAATT
51678 TTATAGTATCAAATT
1 TTATAGTATCAAATT
51693 ATATGTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (15 bp):
TTATAGTATCAAATT
Found at i:71990 original size:322 final size:321
Alignment explanation
Indices: 71405--72165 Score: 1380
Period size: 322 Copynumber: 2.4 Consensus size: 321
71395 AAGATCCGAG
*
71405 GATCTATTGTGGTTTATATAATAGAGATCTAACCTAAATCTTGTGAGGCGCCTTTTGGGAAGGGC
1 GATCTATTGTGGTTTATATAATAGAGATCTAACCCAAA-CTTGTGAGGCGCCTTTTGGGAAGGGC
* *
71470 AAAGCCGTGAGGCCTTTGGGCCAAAGCGGGCAATACCTCGCAAGTTGGGCCGGGTCTCTACAGTT
65 AAAGCCGTGAGGCCTTTGGGCCAAAGCGGACAATACCTCGCAGGTTGGGCCGGGTCTCTACAGTT
*
71535 GGTAATCAGAGCTTTAATCGGGCGTGTAGCGGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGG
130 GGTAATCAGAGCTTTAACCGGGCGTGTAGCGGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGG
*
71600 AGCCACCTCTAGAATCCCGACGCCCGGTGGGTCCTGGTGATTGTGATTATGTGGGCTTGCCGGGG
195 AGCCACCTCTAGAATCCCGACGCCCGGTGGGTCCTGGTGAATGTGATTATGTGGGCTTGCCGGGG
*
71665 ACGACAAACCTATAAGGGGGTAGATTGTGACGCCCCAAGATCCCACATCAGGAGGATGTGGT
260 ACGACAAACCTATAAGGGGGTAGATTGTGACGCCCCAAGATCACACATCAGGAGGATGTGGT
71727 GATCTATTGTGGTTTATATAATAGAGATCTAACCCAAACCTTGTGAGGCGCCTTTTGGGAAGGGC
1 GATCTATTGTGGTTTATATAATAGAGATCTAACCCAAA-CTTGTGAGGCGCCTTTTGGGAAGGGC
*
71792 AAATCCGTGAGGCCTTTGGGCCAAAGCGGACAATACCTCGCAGGTTGGGCCGGGTCTCTACAGTT
65 AAAGCCGTGAGGCCTTTGGGCCAAAGCGGACAATACCTCGCAGGTTGGGCCGGGTCTCTACAGTT
*
71857 GGTAATCAGAGCTTTCACCGGGCGTGTAGCGGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGG
130 GGTAATCAGAGCTTTAACCGGGCGTGTAGCGGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGG
* * *
71922 AGCCACCTCTAGAATCCCGGCGCCCGGTGGGTCCTGGTGAATGTGATTGTGTGGGCTTGTCGGGG
195 AGCCACCTCTAGAATCCCGACGCCCGGTGGGTCCTGGTGAATGTGATTATGTGGGCTTGCCGGGG
*
71987 ACGACAAGCCTATAAGGGGGTAGATTGTGACGCCCCAAGATCACACATCAGGAGGATGTGGT
260 ACGACAAACCTATAAGGGGGTAGATTGTGACGCCCCAAGATCACACATCAGGAGGATGTGGT
72049 GATCTATTGTGGTTTATATAATAGAGATGC-AACCCAAACTTGTGAGGCGCCTTTTGGGAAGGGC
1 GATCTATTGTGGTTTATATAATAGAGAT-CTAACCCAAACTTGTGAGGCGCCTTTTGGGAAGGGC
72113 AAAGCCGTGAGGCCTTTGGGCCAAAGCGGACAATACCTCGCAGGTTGGGCCGG
65 AAAGCCGTGAGGCCTTTGGGCCAAAGCGGACAATACCTCGCAGGTTGGGCCGG
72166 ACTGTAGAGA
Statistics
Matches: 424, Mismatches: 14, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
321 78 0.18
322 345 0.81
323 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.23
Consensus pattern (321 bp):
GATCTATTGTGGTTTATATAATAGAGATCTAACCCAAACTTGTGAGGCGCCTTTTGGGAAGGGCA
AAGCCGTGAGGCCTTTGGGCCAAAGCGGACAATACCTCGCAGGTTGGGCCGGGTCTCTACAGTTG
GTAATCAGAGCTTTAACCGGGCGTGTAGCGGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGGA
GCCACCTCTAGAATCCCGACGCCCGGTGGGTCCTGGTGAATGTGATTATGTGGGCTTGCCGGGGA
CGACAAACCTATAAGGGGGTAGATTGTGACGCCCCAAGATCACACATCAGGAGGATGTGGT
Found at i:75449 original size:64 final size:64
Alignment explanation
Indices: 75348--75476 Score: 249
Period size: 64 Copynumber: 2.0 Consensus size: 64
75338 TAATAGTTTT
*
75348 TTAAAAAGGAAAAAAAAACAAAGTAGTGAACACATAAGTTTTTGCTATGGTAAATATTGGCATG
1 TTAAAAAGAAAAAAAAAACAAAGTAGTGAACACATAAGTTTTTGCTATGGTAAATATTGGCATG
75412 TTAAAAAGAAAAAAAAAACAAAGTAGTGAACACATAAGTTTTTGCTATGGTAAATATTGGCATG
1 TTAAAAAGAAAAAAAAAACAAAGTAGTGAACACATAAGTTTTTGCTATGGTAAATATTGGCATG
75476 T
1 T
75477 ATATTCTTCA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.27
Consensus pattern (64 bp):
TTAAAAAGAAAAAAAAAACAAAGTAGTGAACACATAAGTTTTTGCTATGGTAAATATTGGCATG
Found at i:95041 original size:27 final size:27
Alignment explanation
Indices: 95003--95056 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
94993 TCAGGAACTT
95003 ACATCGCTGCTTACAGTTGATGCCTTC
1 ACATCGCTGCTTACAGTTGATGCCTTC
95030 ACATCGCTGCTTACAGTTGATGCCTTC
1 ACATCGCTGCTTACAGTTGATGCCTTC
95057 GAAGTAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.33
Consensus pattern (27 bp):
ACATCGCTGCTTACAGTTGATGCCTTC
Found at i:110448 original size:16 final size:15
Alignment explanation
Indices: 110418--110478 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 15
110408 TGATAAAAAG
*
110418 CCACTT-ACCAGTTA
1 CCACTTGACCAATTA
110432 CCACCTTGACCAATTA
1 CCA-CTTGACCAATTA
*
110448 CTCA-TT-ACCAGTTA
1 C-CACTTGACCAATTA
110462 CCACTTTGACCAATTA
1 CCAC-TTGACCAATTA
110478 C
1 C
110479 TCATTGATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
13 2 0.05
14 11 0.29
15 7 0.18
16 16 0.42
17 2 0.05
ACGTcount: A:0.30, C:0.34, G:0.07, T:0.30
Consensus pattern (15 bp):
CCACTTGACCAATTA
Found at i:110458 original size:30 final size:30
Alignment explanation
Indices: 110422--110483 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
110412 AAAAAGCCAC
110422 TTACCAGTTACCACCTTGACCAATTACTCA
1 TTACCAGTTACCACCTTGACCAATTACTCA
*
110452 TTACCAGTTACCACTTTGACCAATTACTCA
1 TTACCAGTTACCACCTTGACCAATTACTCA
110482 TT
1 TT
110484 GATATTCACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.34
Consensus pattern (30 bp):
TTACCAGTTACCACCTTGACCAATTACTCA
Found at i:112869 original size:11 final size:10
Alignment explanation
Indices: 112852--112876 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
112842 ATCAGATAGG
112852 ATTTTTTTTT
1 ATTTTTTTTT
112862 ATTTTTTTTT
1 ATTTTTTTTT
112872 ATTTT
1 ATTTT
112877 GCCAAACCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:116103 original size:21 final size:21
Alignment explanation
Indices: 116077--116116 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
116067 CATCAAGAAC
116077 TTTACTACAACAATAGTAAAG
1 TTTACTACAACAATAGTAAAG
116098 TTTACTACAACAATAGTAA
1 TTTACTACAACAATAGTAA
116117 GAGGGAGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTACTACAACAATAGTAAAG
Found at i:116551 original size:57 final size:57
Alignment explanation
Indices: 116488--116601 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
116478 TAAAAAAACT
116488 ATAACAACAATAATATATTAACATAAAATAACAACTGGAGTACCCTTAAGTAGAGTG
1 ATAACAACAATAATATATTAACATAAAATAACAACTGGAGTACCCTTAAGTAGAGTG
116545 ATAACAACAATAATATATTAACATAAAATAACAACTGGAGTACCCTTAAGTAGAGTG
1 ATAACAACAATAATATATTAACATAAAATAACAACTGGAGTACCCTTAAGTAGAGTG
116602 TTATCTGCGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (57 bp):
ATAACAACAATAATATATTAACATAAAATAACAACTGGAGTACCCTTAAGTAGAGTG
Found at i:116779 original size:12 final size:12
Alignment explanation
Indices: 116762--116787 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
116752 ACCAATTAGC
116762 AACCTAAAGCAA
1 AACCTAAAGCAA
116774 AACCTAAAGCAA
1 AACCTAAAGCAA
116786 AA
1 AA
116788 GGTATTCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.23, G:0.08, T:0.08
Consensus pattern (12 bp):
AACCTAAAGCAA
Found at i:127176 original size:16 final size:16
Alignment explanation
Indices: 127155--127189 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
127145 AAGTTTAAGT
127155 AAGAAGTCCCGAATTA
1 AAGAAGTCCCGAATTA
127171 AAGAAGTCCCGAATTA
1 AAGAAGTCCCGAATTA
127187 AAG
1 AAG
127190 TTTAGGAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (16 bp):
AAGAAGTCCCGAATTA
Found at i:136158 original size:2 final size:2
Alignment explanation
Indices: 136151--136180 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
136141 TCATTTCATA
136151 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
136181 TCATATTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.