Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020749.1 Corchorus olitorius cultivar O-4 contig20782, 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: 107125
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3213 original size:19 final size:20
Alignment explanation
Indices: 3183--3246 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
3173 TTGACATTGT
3183 TTAGCAACTGTACAGATAAGA
1 TTAGC-ACTGTACAGATAAGA
* *
3204 TTA-CACTGTACAAATTAGA
1 TTAGCACTGTACAGATAAGA
* *
3223 TTAGGTACTGTACAGATGAGA
1 TTA-GCACTGTACAGATAAGA
3244 TTA
1 TTA
3247 TTAGAGCGGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 16 0.44
20 1 0.03
21 19 0.53
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (20 bp):
TTAGCACTGTACAGATAAGA
Found at i:11788 original size:60 final size:60
Alignment explanation
Indices: 11717--11853 Score: 186
Period size: 60 Copynumber: 2.3 Consensus size: 60
11707 AACATTCGCT
* * * *
11717 AAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGCCAAATAAG-GACCTAATGTTATCA
1 AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAGAG-CCTAACGTTATAA
* * * *
11777 AACATGTTCAAATAAGAGCCCGATCTTTTAATTTGTCCAAATAAGAGCCTAACGTTATAA
1 AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAGAGCCTAACGTTATAA
11837 AAAATGCTCAAATAAGG
1 AAAATGCTCAAATAAGG
11854 ACCTGGCGTC
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 64 0.98
61 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.29
Consensus pattern (60 bp):
AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAGAGCCTAACGTTATAA
Found at i:11995 original size:60 final size:60
Alignment explanation
Indices: 11925--12059 Score: 150
Period size: 60 Copynumber: 2.2 Consensus size: 60
11915 TTCGATAGTG
* * *** *
11925 TTAGGTCCTTATTTGGTCAAATTAAAAG-TTTGGACCCTTATTTGAGCATTTAT-G-ATAACA
1 TTAGGCCCTTATTTGGCCAAATTAAAAGACCAGG-CCCTTATTAGAGCATTT-TGGCA-AACA
* *
11985 TTAGGCCCTTATTTGGCCAAATTAGAAGACCAGGCCCTTATTAGAGCATTTTGGCAAATA
1 TTAGGCCCTTATTTGGCCAAATTAAAAGACCAGGCCCTTATTAGAGCATTTTGGCAAACA
12045 TTAGGCCCTTATTTG
1 TTAGGCCCTTATTTG
12060 AGCAATTAAC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
59 1 0.02
60 60 0.94
61 3 0.05
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (60 bp):
TTAGGCCCTTATTTGGCCAAATTAAAAGACCAGGCCCTTATTAGAGCATTTTGGCAAACA
Found at i:12074 original size:31 final size:31
Alignment explanation
Indices: 12016--12077 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
12006 TTAGAAGACC
* ***
12016 AGGCCCTTATTAGAGCATTTTGGCAAATATT
1 AGGCCCTTATTAGAGCAATTAACCAAATATT
*
12047 AGGCCCTTATTTGAGCAATTAACCAAATATT
1 AGGCCCTTATTAGAGCAATTAACCAAATATT
12078 GTGGATTCGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (31 bp):
AGGCCCTTATTAGAGCAATTAACCAAATATT
Found at i:23768 original size:60 final size:60
Alignment explanation
Indices: 23675--23800 Score: 207
Period size: 60 Copynumber: 2.1 Consensus size: 60
23665 ACTTGATGGA
* * * * *
23675 TTTTCACGAGAGGGATCCAATTGCTCCGTTAACTCCGCTTCCGGGACCGAATTGCTCATT
1 TTTTCAAGAGAGGGACCCAATTGCTCCATTAACTCCACTTCAGGGACCGAATTGCTCATT
23735 TTTTCAAGAGAGGGACCCAATTGCTCCATTAACTCCACTTCAGGGACCGAATTGCTCATT
1 TTTTCAAGAGAGGGACCCAATTGCTCCATTAACTCCACTTCAGGGACCGAATTGCTCATT
23795 TTTTCA
1 TTTTCA
23801 CTTGAGAGAT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (60 bp):
TTTTCAAGAGAGGGACCCAATTGCTCCATTAACTCCACTTCAGGGACCGAATTGCTCATT
Found at i:23788 original size:31 final size:31
Alignment explanation
Indices: 23685--23791 Score: 85
Period size: 31 Copynumber: 3.5 Consensus size: 31
23675 TTTTCACGAG
* *
23685 AGGGATCC-AATTGCTCCGTTAACTCCGCTTC
1 AGGGA-CCGAATTGCTCCATTAACTCCACTTC
* ** * ****
23716 CGGGACCGAATTGCT-CATT-TTTTCAAGAG
1 AGGGACCGAATTGCTCCATTAACTCCACTTC
*
23745 AGGGACCCAATTGCTCCATTAACTCCACTTC
1 AGGGACCGAATTGCTCCATTAACTCCACTTC
23776 AGGGACCGAATTGCTC
1 AGGGACCGAATTGCTC
23792 ATTTTTTCAC
Statistics
Matches: 53, Mismatches: 20, Indels: 6
0.67 0.25 0.08
Matches are distributed among these distances:
29 15 0.28
30 9 0.17
31 29 0.55
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (31 bp):
AGGGACCGAATTGCTCCATTAACTCCACTTC
Found at i:27847 original size:4 final size:4
Alignment explanation
Indices: 27840--27875 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
27830 GAAGAAGAAG
27840 AAGA AAGA AAGA AAG- AAG- AAG- AAGA AAGA AAGA AAG
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAG
27876 CACTAAGAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 9 0.29
4 22 0.71
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:27857 original size:21 final size:21
Alignment explanation
Indices: 27827--27875 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
27817 AAAAAAAAAA
27827 AAAG-AAGAAGAAGAAGAAAG
1 AAAGAAAGAAGAAGAAGAAAG
27847 AAAGAAAGAAGAAGAAGAAAG
1 AAAGAAAGAAGAAGAAGAAAG
27868 AAAGAAAG
1 AAAGAAAG
27876 CACTAAGAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (21 bp):
AAAGAAAGAAGAAGAAGAAAG
Found at i:39095 original size:1 final size:1
Alignment explanation
Indices: 39089--39113 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
39079 TCAAGGATTA
39089 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
39114 CTGTCTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:40872 original size:23 final size:23
Alignment explanation
Indices: 40829--40879 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
40819 CCCTTCCTCT
**
40829 TTTTTTTTTTATTATTTATTT-A
1 TTTTTTTTTTACGATTTATTTCA
*
40851 TTTTTTTTTTACGCTTTCATTTCA
1 TTTTTTTTTTACGATTT-ATTTCA
40875 TTTTT
1 TTTTT
40880 CATTCAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 14 0.58
23 4 0.17
24 6 0.25
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (23 bp):
TTTTTTTTTTACGATTTATTTCA
Found at i:57088 original size:28 final size:28
Alignment explanation
Indices: 57054--57107 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
57044 TCATGAATTT
* * *
57054 ATAAGACTATAATCATTTTTTTTGAAAA
1 ATAAGACTACAATCATTCTATTTGAAAA
57082 ATAAGACTACAATCATTCTATTTGAA
1 ATAAGACTACAATCATTCTATTTGAA
57108 CATGAAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (28 bp):
ATAAGACTACAATCATTCTATTTGAAAA
Found at i:61491 original size:48 final size:48
Alignment explanation
Indices: 61420--61515 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
61410 ATTACTCTTC
*
61420 CTGTTTTTAATAAATGCTTCCAGCTATCTAGCAACAATTGCATGGGGG
1 CTGTTTTTAATAAATGCTTCCAGCTATCTAGCAACAACTGCATGGGGG
**
61468 CTGTTTTTGGTAAATGCTTCCAGCTATCTAGCAACAACTGCATGGGGG
1 CTGTTTTTAATAAATGCTTCCAGCTATCTAGCAACAACTGCATGGGGG
61516 GAAAGTTAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (48 bp):
CTGTTTTTAATAAATGCTTCCAGCTATCTAGCAACAACTGCATGGGGG
Found at i:62782 original size:6 final size:6
Alignment explanation
Indices: 62759--62809 Score: 81
Period size: 6 Copynumber: 9.0 Consensus size: 6
62749 GTGAAATCTG
62759 AAAA-A AAAAG- AAAA-A AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
62804 AAAAGA
1 AAAAGA
62810 GAGAGTAGGC
Statistics
Matches: 43, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
5 12 0.28
6 31 0.72
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:70077 original size:15 final size:15
Alignment explanation
Indices: 70057--70087 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
70047 ATACTGTAAA
70057 TTAATGGGAGATATG
1 TTAATGGGAGATATG
70072 TTAATGGGAGATATG
1 TTAATGGGAGATATG
70087 T
1 T
70088 AGTCAACGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (15 bp):
TTAATGGGAGATATG
Found at i:70459 original size:16 final size:16
Alignment explanation
Indices: 70438--70472 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
70428 AAAGGAGGGG
70438 TTTGTTTT-TGTTTTGT
1 TTTGTTTTGT-TTTTGT
70454 TTTGTTTTGTTTTTGT
1 TTTGTTTTGTTTTTGT
70470 TTT
1 TTT
70473 TTATATTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 17 0.94
17 1 0.06
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (16 bp):
TTTGTTTTGTTTTTGT
Found at i:70473 original size:6 final size:5
Alignment explanation
Indices: 70438--70472 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
70428 AAAGGAGGGG
70438 TTTGTT TTTGT TTTGT TTTGT TTTGTT TTTGT TTT
1 TTTG-T TTTGT TTTGT TTTGT TTTG-T TTTGT TTT
70473 TTATATTTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 19 0.68
6 9 0.32
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
TTTGT
Found at i:71594 original size:39 final size:40
Alignment explanation
Indices: 71540--71626 Score: 167
Period size: 40 Copynumber: 2.2 Consensus size: 40
71530 TGTATTATAT
71540 ATGACGTGT-AAAAAAAAAAAGAAAACTTATATATGACTA
1 ATGACGTGTAAAAAAAAAAAAGAAAACTTATATATGACTA
71579 ATGACGTGTAAAAAAAAAAAAGAAAACTTATATATGACTA
1 ATGACGTGTAAAAAAAAAAAAGAAAACTTATATATGACTA
71619 ATGACGTG
1 ATGACGTG
71627 AGTGGAACGC
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 9 0.19
40 38 0.81
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (40 bp):
ATGACGTGTAAAAAAAAAAAAGAAAACTTATATATGACTA
Found at i:72062 original size:17 final size:18
Alignment explanation
Indices: 72022--72066 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
72012 TCATTTGGCA
72022 TCGTTTTTGTTTTTCTAT
1 TCGTTTTTGTTTTTCTAT
* *
72040 T-TTTTTTGTTTTTGT-T
1 TCGTTTTTGTTTTTCTAT
72056 TCGTTTTTGTT
1 TCGTTTTTGTT
72067 GTGCTTTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 2 0.09
17 20 0.87
18 1 0.04
ACGTcount: A:0.02, C:0.07, G:0.13, T:0.78
Consensus pattern (18 bp):
TCGTTTTTGTTTTTCTAT
Found at i:81000 original size:317 final size:319
Alignment explanation
Indices: 80424--81059 Score: 1089
Period size: 318 Copynumber: 2.0 Consensus size: 319
80414 TTAACTTACC
80424 CAAGTTACCCTTGCTAGTGGAAAAAATTTATGAAGAGAGATAGTGAATGGGAGGAGAAGAGAGAT
1 CAAGTTACCCTTGCTAGTGGAAAAAATTTATGAAGAGAGATAGTGAATGGGAGGAGAAGAGAGAT
80489 TAAGTGGGGGAGAGAGAAAAAATGGCAAACTTGGAAGAAGAAGATAAAAGATTACAAAATTTAGA
66 TAAGTGGGGGAGAGAGAAAAAATGGCAAACTTGGAAGAAGAAGATAAAAGATTACAAAATTTAGA
* **
80554 GCTTTAACTGTATTTCTTAATATTTGCAATACAACTAAAGGGACTTATAAAAAGGGACAAAGGGA
131 GCTTTAACTGTATTTCTTAATATATGCAATACAACTAAAGGGACTTATAAAAAAAGACAAAGGGA
* *
80619 GTATCTATACTAATTATAATGTGAAGTCCTGAGTTTGTGTCACGAGTTGACTCGGTAACAAACTC
196 GTATCTATACTAATTATAATGTGAAGACCTGAGTTTATGTCACGAGTTGACTCGGTAACAAACTC
*
80684 AG-TTTTAAAAACAATCAAAACAAAATAAAAACTATCCATTTTAAATAAAACTACCCAT
261 AGTTTTTAAAAAAAATCAAAACAAAATAAAAACTATCCATTTTAAATAAAACTACCCAT
* *
80742 CAAGTTACCCTTGCTAGTGGAAAAAATTTATGAAGAGAGATAGTGAGTGGGAGGAGGAGAGAGAT
1 CAAGTTACCCTTGCTAGTGGAAAAAATTTATGAAGAGAGATAGTGAATGGGAGGAGAAGAGAGAT
* *
80807 TAAGT-GGGGAGAGAG-AAAAATTGCAAACTTGGAAGAAGAAGATAAAAGATTACAGAATTTAGA
66 TAAGTGGGGGAGAGAGAAAAAATGGCAAACTTGGAAGAAGAAGATAAAAGATTACAAAATTTAGA
* ** * *
80870 GTTTTAACTGTATTTCTTAATATATGCAATACAGTTGAAAGGGACTTATAAAAAAAGATAGAGGG
131 GCTTTAACTGTATTTCTTAATATATGCAATACAACT-AAAGGGACTTATAAAAAAAGACAAAGGG
* *
80935 AGTATCTATACTAATTATAATGTGACGACCTGAGTTTATGTCACGAGTTGATTCGGTAACAAACT
195 AGTATCTATACTAATTATAATGTGAAGACCTGAGTTTATGTCACGAGTTGACTCGGTAACAAACT
81000 CAGTTTTTAAAAAAAATCAAAACAAAATAAAAACTATCCATTTTAAATAAAACTACCCAT
260 CAGTTTTTAAAAAAAATCAAAACAAAATAAAAACTATCCATTTTAAATAAAACTACCCAT
81060 TGGCGGATAA
Statistics
Matches: 299, Mismatches: 17, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
316 78 0.26
317 98 0.33
318 123 0.41
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (319 bp):
CAAGTTACCCTTGCTAGTGGAAAAAATTTATGAAGAGAGATAGTGAATGGGAGGAGAAGAGAGAT
TAAGTGGGGGAGAGAGAAAAAATGGCAAACTTGGAAGAAGAAGATAAAAGATTACAAAATTTAGA
GCTTTAACTGTATTTCTTAATATATGCAATACAACTAAAGGGACTTATAAAAAAAGACAAAGGGA
GTATCTATACTAATTATAATGTGAAGACCTGAGTTTATGTCACGAGTTGACTCGGTAACAAACTC
AGTTTTTAAAAAAAATCAAAACAAAATAAAAACTATCCATTTTAAATAAAACTACCCAT
Found at i:82339 original size:21 final size:21
Alignment explanation
Indices: 82315--82358 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
82305 TTCAATACAT
82315 TGTTAGTGGAATTTAGCAGAC
1 TGTTAGTGGAATTTAGCAGAC
* *
82336 TGTTTGTGGAGTTTAGCAGAC
1 TGTTAGTGGAATTTAGCAGAC
82357 TG
1 TG
82359 CACGTATGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.09, G:0.32, T:0.36
Consensus pattern (21 bp):
TGTTAGTGGAATTTAGCAGAC
Found at i:82520 original size:6 final size:6
Alignment explanation
Indices: 82509--82542 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
82499 ATAATTACTT
* *
82509 TATTAC TATTAC TATTAT TATTAC TACTAC TATT
1 TATTAC TATTAC TATTAC TATTAC TATTAC TATT
82543 TAACTTCACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (6 bp):
TATTAC
Found at i:85847 original size:2 final size:2
Alignment explanation
Indices: 85840--85972 Score: 103
Period size: 2 Copynumber: 72.0 Consensus size: 2
85830 AGTTTTCTTT
85840 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA GT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
*
85881 GA TA TA TA TA TA TA T- TA TA T- TA TA T- TA TA TA TA -A TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
85918 TGA -A T- TA TA AA TG TA AA TA TA TA TA TA -A TA TA -A T- TA AA
1 T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
85956 AA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
85973 GTCGGTTTTT
Statistics
Matches: 106, Mismatches: 10, Indels: 30
0.73 0.07 0.21
Matches are distributed among these distances:
1 13 0.12
2 91 0.86
3 2 0.02
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:85950 original size:23 final size:20
Alignment explanation
Indices: 85923--85968 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 20
85913 AATAATGAAT
85923 TATAAATGTAAATATATATATAA
1 TATAAAT-TAAA-A-ATATATAA
85946 TAT-AATTAAAAATATATAA
1 TATAAATTAAAAATATATAA
85965 TATA
1 TATA
85969 TATAGTCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
19 11 0.50
20 1 0.05
21 4 0.18
22 3 0.14
23 3 0.14
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
TATAAATTAAAAATATATAA
Found at i:86594 original size:21 final size:21
Alignment explanation
Indices: 86536--86596 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
86526 TGCAACAGCG
* * *
86536 CAGCGATGGGTAATATCAGCG
1 CAGCCATGGGTAATATGAGCA
*
86557 CAGACATGGGTAATATGAGCA
1 CAGCCATGGGTAATATGAGCA
*
86578 CAGCCATGGATAATATGAG
1 CAGCCATGGGTAATATGAG
86597 ATTAGACCCT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (21 bp):
CAGCCATGGGTAATATGAGCA
Found at i:89141 original size:65 final size:65
Alignment explanation
Indices: 89037--89166 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
89027 ATTCCTGTTA
89037 TTGCATATTGTATGTAGAAGCAGCTGATATCCCACAGTTAAGACTAATGAAGCCTGAAAAAGACC
1 TTGCATATTGTATGTAGAAGCAGCTGATATCCCACAGTTAAGACTAATGAAGCCTGAAAAAGACC
89102 TTGCATATTGTATGTAGAAGCAGCTGATATCCCACAGTTAAGACTAATGAAGCCTGAAAAAGACC
1 TTGCATATTGTATGTAGAAGCAGCTGATATCCCACAGTTAAGACTAATGAAGCCTGAAAAAGACC
89167 AAAAACACCC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (65 bp):
TTGCATATTGTATGTAGAAGCAGCTGATATCCCACAGTTAAGACTAATGAAGCCTGAAAAAGACC
Found at i:89179 original size:42 final size:42
Alignment explanation
Indices: 89132--89215 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
89122 CAGCTGATAT
89132 CCCACAGTTAAGACTAATGAAGCCTGAAAAAGACCAAAAACA
1 CCCACAGTTAAGACTAATGAAGCCTGAAAAAGACCAAAAACA
89174 CCCACAGTTAAGACTAATGAAGCCTGAAAAAGACCAAAAACA
1 CCCACAGTTAAGACTAATGAAGCCTGAAAAAGACCAAAAACA
89216 AAATTATCAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.50, C:0.24, G:0.14, T:0.12
Consensus pattern (42 bp):
CCCACAGTTAAGACTAATGAAGCCTGAAAAAGACCAAAAACA
Found at i:90230 original size:32 final size:32
Alignment explanation
Indices: 90194--90257 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
90184 GTAAGACTCT
90194 TTGTGTATTTGGTAGGTAGATAGTTTGCCTCA
1 TTGTGTATTTGGTAGGTAGATAGTTTGCCTCA
*
90226 TTGTGTATTTGGTAGGTAGATAGTTTGGCTCA
1 TTGTGTATTTGGTAGGTAGATAGTTTGCCTCA
90258 GGCGACTTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.19, C:0.08, G:0.30, T:0.44
Consensus pattern (32 bp):
TTGTGTATTTGGTAGGTAGATAGTTTGCCTCA
Found at i:100418 original size:73 final size:73
Alignment explanation
Indices: 100299--100509 Score: 404
Period size: 73 Copynumber: 2.9 Consensus size: 73
100289 AACATGCCAG
100299 TACTAACACTAATTTTCCACATTTCTTCCGGAAGAAATAGACACTCTTATATGATTCTTTTTTCC
1 TACTAACACTAATTTTCCACATTTCTTCCGGAAGAAATAGACACTCTTATATGATTCTTTTTTCC
100364 ACTCTTAT
66 ACTCTTAT
100372 TACTAACACTAATTTTCCACATTTCTTCCGGAAGAAATAGACACTCTTATATGATTCTTTTTTCC
1 TACTAACACTAATTTTCCACATTTCTTCCGGAAGAAATAGACACTCTTATATGATTCTTTTTTCC
100437 ACTCTTAT
66 ACTCTTAT
*
100445 TACTAACACTAATTTTCCACATTTCTTCCGGAAGAAATAGACACTCTTATTATGATTTTTTTTTC
1 TACTAACACTAATTTTCCACATTTCTTCCGGAAGAAATAGACACTCTTA-TATGATTCTTTTTTC
100510 GCATTTGAGG
Statistics
Matches: 136, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
73 122 0.90
74 14 0.10
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (73 bp):
TACTAACACTAATTTTCCACATTTCTTCCGGAAGAAATAGACACTCTTATATGATTCTTTTTTCC
ACTCTTAT
Found at i:102710 original size:19 final size:19
Alignment explanation
Indices: 102683--102721 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
102673 CCACATTGCA
*
102683 TTTTGGTCCAACGTGGCAT
1 TTTTGGTCCAACATGGCAT
* *
102702 TTTTTGTCCGACATGGCAT
1 TTTTGGTCCAACATGGCAT
102721 T
1 T
102722 GCCACATCAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.41
Consensus pattern (19 bp):
TTTTGGTCCAACATGGCAT
Done.