Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017814.1 Corchorus olitorius cultivar O-4 contig17847, 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: 105056
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1851 original size:438 final size:436
Alignment explanation
Indices: 1111--2314 Score: 1648
Period size: 437 Copynumber: 2.8 Consensus size: 436
1101 TCAAAAGTAC
* * * * * *
1111 TTTTTAGAATTGAAACATGAAAATTAGCTTTTGAGTCTTTCATAAAAGTTGTAGATCATAAAATT
1 TTTTTAGAATTAAAACATAAAAATTTGCTTTTGAGTC-CTCATGAAAGTTGTAGATCATGAAATT
* * * * *
1176 ACCTTTTAATAGACACCTGATTTACCTTAATTGGACAAATAGAACAAAGAA-AAAAAAAGATGAA
65 ACCTTTTAATAGACACATGAATCACCTTAATCGGACAAATAGAACAAAGAATAAAAAAA-ATAAA
* * * * * * * *
1240 GCGTT-AAA--TCGAATAAGATAAAATTTGTAAATGACTAAGTAGCATAAAATAGAAAAGTATGA
129 TC-TTAAAAGTTAGATTAAGATAAAATATGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGA
* * * * * *
1302 GGGTCATTTGATAACTACTAATTCAAATAAGAAAATATTTCTTAATAGATATCTTGAAACATAAA
193 GGGTCATTTGATAA--A-TAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAGCATAAA
* * *
1367 AATTTCCTTTTGAACCCTTCATGAAACTCGTAGATCAAA-TTAGCTTTCAGGTTCTTCATGAAAG
255 AATTCCCTTTTGAACCCTTTATGAAACTCGTAGATCAAATTTAGCTTT-AGGTCCTTCATGAAAG
* * * * * * *
1431 TCGTAGATCATACAGTAACCTTTTAACCGACACTTGAATAACTTTAATCGGACATGTGTATCGAA
319 TCATAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTGAATCGGACATGTGGA-CAAA
* * * * *
1496 AATTATATGGTATTAAATAGACCAATAATCGAAACGACAAAATTTAGGAAGCAT
383 AATTAGACGATATTAAATAGACCAATAATCAAAACCACAAAATTTAGGAAGCAT
*
1550 TTTTTTGAATTAAAACATAAAAATTTGCTTTTGAGTCCTCATGAAAGTTGTAGATCATGAAATTA
1 TTTTTAGAATTAAAACATAAAAATTTGCTTTTGAGTCCTCATGAAAGTTGTAGATCATGAAATTA
*
1615 CCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAACAAAGAATAAAAAAAATAAATC
66 CCTTTTAATAGACACATGAATCACCTTAATCGGACAAATAGAACAAAGAATAAAAAAAATAAATC
* *
1680 TTAAAAGTTAGATTAAGATAGAATCTGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAGGG
131 TTAAAAGTTAGATTAAGATAAAATATGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAGGG
1745 TCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAGCATAAAAATTCC
196 TCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAGCATAAAAATTCC
* * * *
1810 CTTTTGGACCTTTTATGAAACTCATAGATCAAATTTAGCTTTTGGGTCCTTCATGAAAGTCATAA
261 CTTTTGAACCCTTTATGAAACTCGTAGATCAAATTTAGC-TTTAGGTCCTTCATGAAAGTCATAA
* *
1875 ATCATACAATAACCTTTTAACTGACACTTCAATAACTTGAATCTGACATGTGGACAAAAATTAGA
325 ATCATACAATAACCTTTTAACCGACACTTCAATAACTTGAATCGGACATGTGGACAAAAATTAGA
* *** * *
1940 CGATATTAAATTGACTGGTAATCAAAACCACAAAATTTTGGAAGTAT
390 CGATATTAAATAGACCAATAATCAAAACCACAAAATTTAGGAAGCAT
** * * *
1987 TTTTTAGAACCAAAACATTAAAA-TTGATTTTTGAGTTCCTCATGAAAATTGTAGATCATGAAAT
1 TTTTTAGAATTAAAACATAAAAATTTG-CTTTTGAG-TCCTCATGAAAGTTGTAGATCATGAAAT
* *
2051 TACCTTTTAATAGACACTTGAATCACCTTAATCGGACAAATAGAACAAAGAAT-AAAAAAACAAA
64 TACCTTTTAATAGACACATGAATCACCTTAATCGGACAAATAGAACAAAGAATAAAAAAAATAAA
* *
2115 TCTTAAACGTTAGATTAAGATATAATATGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAG
129 TCTTAAAAGTTAGATTAAGATAAAATATGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAG
2180 GGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAGCATAAAAATT
194 GGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAGCATAAAAATT
* *
2245 CCCTTTTGAACCCTTTATGAAACTCGTAGATCAAATTTAGCTTTTGGATCCTTCATGAAAGTCAA
259 CCCTTTTGAACCCTTTATGAAACTCGTAGATCAAATTTAGCTTTAGG-TCCTTCATGAAAGTCAT
2310 AAATC
323 AAATC
2315 TTAGTGGAGG
Statistics
Matches: 684, Mismatches: 72, Indels: 20
0.88 0.09 0.03
Matches are distributed among these distances:
436 8 0.01
437 345 0.50
438 228 0.33
439 43 0.06
440 60 0.09
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (436 bp):
TTTTTAGAATTAAAACATAAAAATTTGCTTTTGAGTCCTCATGAAAGTTGTAGATCATGAAATTA
CCTTTTAATAGACACATGAATCACCTTAATCGGACAAATAGAACAAAGAATAAAAAAAATAAATC
TTAAAAGTTAGATTAAGATAAAATATGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAGGG
TCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAGCATAAAAATTCC
CTTTTGAACCCTTTATGAAACTCGTAGATCAAATTTAGCTTTAGGTCCTTCATGAAAGTCATAAA
TCATACAATAACCTTTTAACCGACACTTCAATAACTTGAATCGGACATGTGGACAAAAATTAGAC
GATATTAAATAGACCAATAATCAAAACCACAAAATTTAGGAAGCAT
Found at i:38417 original size:2 final size:2
Alignment explanation
Indices: 38412--38439 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38402 TCTCTTCAAT
38412 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38440 AACTAATACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39223 original size:7 final size:7
Alignment explanation
Indices: 39211--39240 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
39201 ACGAAACCTC
39211 TGCAAAG
1 TGCAAAG
39218 TGCAAAG
1 TGCAAAG
39225 TGCAAAG
1 TGCAAAG
39232 TGCAAAG
1 TGCAAAG
39239 TG
1 TG
39241 TTGTGATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.40, C:0.13, G:0.30, T:0.17
Consensus pattern (7 bp):
TGCAAAG
Found at i:46217 original size:20 final size:21
Alignment explanation
Indices: 46194--46243 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
46184 ATAATTAAAG
*
46194 TATGGAGAGAGACAATA-GAA
1 TATGGAGAGAGAAAATATGAA
46214 TATGGAGA-AGAAAATATGAA
1 TATGGAGAGAGAAAATATGAA
* *
46234 GAAGGAGAGA
1 TATGGAGAGA
46244 AATTGTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 7 0.28
20 17 0.68
21 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.32, T:0.14
Consensus pattern (21 bp):
TATGGAGAGAGAAAATATGAA
Found at i:46446 original size:11 final size:11
Alignment explanation
Indices: 46432--46469 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
46422 ATTCATAACA
46432 AATTTATAATT
1 AATTTATAATT
46443 AATTTATAATT
1 AATTTATAATT
46454 -ATTTGATAATT
1 AATTT-ATAATT
*
46465 TATTT
1 AATTT
46470 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:51501 original size:18 final size:18
Alignment explanation
Indices: 51478--51518 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
51468 ATCAATATAA
51478 ATGATGATG-ATGATAATG
1 ATGATGA-GAATGATAATG
*
51496 ATGATGAGAATGTTAATG
1 ATGATGAGAATGATAATG
51514 ATGAT
1 ATGAT
51519 AGCTTCAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (18 bp):
ATGATGAGAATGATAATG
Found at i:56858 original size:14 final size:14
Alignment explanation
Indices: 56839--56865 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
56829 GAAAAATGGG
56839 GAAAAAGAAAAAAA
1 GAAAAAGAAAAAAA
56853 GAAAAAGAAAAAA
1 GAAAAAGAAAAAA
56866 GGAGGCAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
GAAAAAGAAAAAAA
Found at i:57894 original size:23 final size:21
Alignment explanation
Indices: 57868--57910 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
57858 TATTAAAAGA
57868 TAAAAAGAAATTAAAAGAAAATC
1 TAAAAAG-AATTAAAA-AAAATC
*
57891 TAAAAAGATTTAAAAAAAAT
1 TAAAAAGAATTAAAAAAAAT
57911 GCAGATTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (21 bp):
TAAAAAGAATTAAAAAAAATC
Found at i:62715 original size:31 final size:31
Alignment explanation
Indices: 62674--62790 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 31
62664 GCTAAATAAT
*
62674 CAATTTAGGATATAAGGTTTGATGAAAAACG
1 CAATTCAGGATATAAGGTTTGATGAAAAACG
* ** **
62705 CAATTCAGGATATAACGTTACAAATCTCGAACTAAATAAT
1 CAATTCAGGATATAAGGTT--TGA--T-G-A--AAA-ACG
*
62745 CAATTCAGGATATAAGGTTTGACGAAAAACG
1 CAATTCAGGATATAAGGTTTGATGAAAAACG
62776 CAATTCAGGATATAA
1 CAATTCAGGATATAA
62791 TGTTACAAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
31 33 0.51
32 3 0.05
33 1 0.02
34 1 0.02
35 2 0.03
36 1 0.02
37 1 0.02
38 1 0.02
39 3 0.05
40 19 0.29
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (31 bp):
CAATTCAGGATATAAGGTTTGATGAAAAACG
Found at i:62781 original size:71 final size:71
Alignment explanation
Indices: 62665--62799 Score: 243
Period size: 71 Copynumber: 1.9 Consensus size: 71
62655 TTCGAGAGGG
* *
62665 CTAAATAATCAATTTAGGATATAAGGTTTGATGAAAAACGCAATTCAGGATATAACGTTACAAAT
1 CTAAATAATCAATTCAGGATATAAGGTTTGACGAAAAACGCAATTCAGGATATAACGTTACAAAT
62730 CTCGAA
66 CTCGAA
*
62736 CTAAATAATCAATTCAGGATATAAGGTTTGACGAAAAACGCAATTCAGGATATAATGTTACAAA
1 CTAAATAATCAATTCAGGATATAAGGTTTGACGAAAAACGCAATTCAGGATATAACGTTACAAA
62800 AAAGTTAATT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (71 bp):
CTAAATAATCAATTCAGGATATAAGGTTTGACGAAAAACGCAATTCAGGATATAACGTTACAAAT
CTCGAA
Found at i:62811 original size:29 final size:29
Alignment explanation
Indices: 62745--62825 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 29
62735 ACTAAATAAT
* *
62745 CAATTCAGGATATAAGGTTTGACGAAAAACG
1 CAATTCAGGATATAACG-TT-ACGAAAAAAG
*
62776 CAATTCAGGATATAATGTTAC-AAAAAAG
1 CAATTCAGGATATAACGTTACGAAAAAAG
*
62804 TTAATTCAGGATATAACGTTAC
1 -CAATTCAGGATATAACGTTAC
62826 CTAATCCGAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
28 6 0.13
29 21 0.47
30 2 0.04
31 16 0.36
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.27
Consensus pattern (29 bp):
CAATTCAGGATATAACGTTACGAAAAAAG
Found at i:71740 original size:33 final size:33
Alignment explanation
Indices: 71703--71774 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
71693 CCTCCGAAGG
71703 CGGCACTCCCATGGTCATGCCGCCCTAGGAGGA
1 CGGCACTCCCATGGTCATGCCGCCCTAGGAGGA
71736 CGGCACTCCCATGGTCATGCCGCCCTAGGAGGA
1 CGGCACTCCCATGGTCATGCCGCCCTAGGAGGA
71769 CGGCAC
1 CGGCAC
71775 CGCGTCTAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.18, C:0.38, G:0.31, T:0.14
Consensus pattern (33 bp):
CGGCACTCCCATGGTCATGCCGCCCTAGGAGGA
Found at i:72380 original size:30 final size:32
Alignment explanation
Indices: 72344--72402 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
72334 ATGAATTAAC
*
72344 TTTTTTGT-AACG-TTATATCCTGAATTGCAT
1 TTTTTTGTAAAAGCTTATATCCTGAATTGCAT
72374 TTTTTTGTAAAAGCTTATATCCTGAATTG
1 TTTTTTGTAAAAGCTTATATCCTGAATTG
72403 ATTATTTAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 8 0.31
31 3 0.12
32 15 0.58
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (32 bp):
TTTTTTGTAAAAGCTTATATCCTGAATTGCAT
Found at i:83384 original size:93 final size:93
Alignment explanation
Indices: 83203--83385 Score: 312
Period size: 94 Copynumber: 2.0 Consensus size: 93
83193 TAAAATAATC
* * *
83203 ACCCATCTGCAACAATTTAACTACTATTAATCCCAAATACTATTCAAAGTCACATGCCAAATTAG
1 ACCCATCTGCAACAATTAAACTACTATTAAGCCCAAATACAATTCAAAGTCACATGCCAAATTAG
83268 TTTAAGAATTTAAAAGTAAAAAAATACA
66 TTTAAGAATTTAAAAGTAAAAAAATACA
83296 ACCCATCTGCAACAATTAAACTACTATTAAAGCCCAAATACAATTCAAAGTCACATGCCAAATTA
1 ACCCATCTGCAACAATTAAACTACTATT-AAGCCCAAATACAATTCAAAGTCACATGCCAAATTA
* *
83361 GTTTACGTATTTAAAAGTAAAAAAA
65 GTTTAAGAATTTAAAAGTAAAAAAA
83386 AATACAACAC
Statistics
Matches: 84, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
93 27 0.32
94 57 0.68
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.27
Consensus pattern (93 bp):
ACCCATCTGCAACAATTAAACTACTATTAAGCCCAAATACAATTCAAAGTCACATGCCAAATTAG
TTTAAGAATTTAAAAGTAAAAAAATACA
Found at i:85776 original size:19 final size:19
Alignment explanation
Indices: 85749--85787 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
85739 ATGAACCCTC
*
85749 TGGCTAGAGTTTCAGAGAT
1 TGGCCAGAGTTTCAGAGAT
85768 TGGCCAGAGTTTCAGAGAT
1 TGGCCAGAGTTTCAGAGAT
85787 T
1 T
85788 CCAATCTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.31
Consensus pattern (19 bp):
TGGCCAGAGTTTCAGAGAT
Found at i:86019 original size:47 final size:47
Alignment explanation
Indices: 85950--86043 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
85940 ATTGTAAAAG
*
85950 ACTGCGTCGAACATGTTAATAACTGATATTAAATGT-AGTAGTTTGCC
1 ACTGCGTCGAACATGCTAATAACTGATATTAAATGTGA-TAGTTTGCC
*
85997 ACTGCGTGGAACATGCTAATAACTGATATTAAATGTGATAGTTTGCC
1 ACTGCGTCGAACATGCTAATAACTGATATTAAATGTGATAGTTTGCC
86044 GGAATGGGGG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 43 0.98
48 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (47 bp):
ACTGCGTCGAACATGCTAATAACTGATATTAAATGTGATAGTTTGCC
Found at i:86153 original size:27 final size:27
Alignment explanation
Indices: 86123--86175 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
86113 ATTATGTGGA
86123 TACAAATGGTAGTTTTATTGCTCCCAT
1 TACAAATGGTAGTTTTATTGCTCCCAT
*
86150 TACAAATGTTAGTTTTATTGCTCCCA
1 TACAAATGGTAGTTTTATTGCTCCCA
86176 ATCTGCTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (27 bp):
TACAAATGGTAGTTTTATTGCTCCCAT
Found at i:92821 original size:99 final size:98
Alignment explanation
Indices: 92637--92833 Score: 342
Period size: 99 Copynumber: 2.0 Consensus size: 98
92627 TTTAATAAAA
* * *
92637 TTACATATTAAACCTTAAAAGTTAAATATAATATTTAAAGTTAAAAATGGTATTTTAGATATTTC
1 TTACATATTAAACCTTAAAAGTTAAATATAATATTAAAAATTAAAAAGGGTATTTTAGATATTTC
92702 AGATCAAGGTTTTTGAAGTTTAGGATTATAGAG
66 AGATCAAGGTTTTTGAAGTTTAGGATTATAGAG
92735 TTACATATTAAACCTTAAAAGTTAAATATAATACTTAAAAAATT-AAAAGGGTATTTTAGATATT
1 TTACATATTAAACCTTAAAAGTTAAATATAATA-TT-AAAAATTAAAAAGGGTATTTTAGATATT
92799 TCAGATCAAGGTTTTTGAAGTTTAGGATTATAGAG
64 TCAGATCAAGGTTTTTGAAGTTTAGGATTATAGAG
92834 AGTTTTTTCA
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
98 33 0.35
99 56 0.60
100 5 0.05
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.39
Consensus pattern (98 bp):
TTACATATTAAACCTTAAAAGTTAAATATAATATTAAAAATTAAAAAGGGTATTTTAGATATTTC
AGATCAAGGTTTTTGAAGTTTAGGATTATAGAG
Found at i:92889 original size:137 final size:137
Alignment explanation
Indices: 92735--93108 Score: 660
Period size: 138 Copynumber: 2.7 Consensus size: 137
92725 GATTATAGAG
*
92735 TTACATATTAAACCTTAAAAGTTAAATATAATACTTAAAAAATTAAAAGGGTATTTTAGATATTT
1 TTACATATTAAACCTTAAAAGTTAAATATAATATTTAAAAAATTAAAAGGGTATTTTAGATATTT
*
92800 CAGATCAAGGTTTTTGAAGTTTAGGATTATAGAGAGTTTTTTCAATATTTAAGAAATATATTTGA
66 CAGATCAAGGTTTTTGAAGTTTAGGATTATAGAGAGTTTTTTCAATATTTAAGAAATATATTCGA
92865 AATAAAA
131 AATAAAA
*
92872 TTACATATTAAACCTTAAAAGTCAAATATAATATTTAAAAAATTATAAAGGGTATTTTAGATATT
1 TTACATATTAAACCTTAAAAGTTAAATATAATATTTAAAAAATTA-AAAGGGTATTTTAGATATT
** *
92937 TTTGATCAAGGTTTTTGAAGTTTAGGATTATACAGAGTTTTTTCAATATTTAAGAAATATATTCG
65 TCAGATCAAGGTTTTTGAAGTTTAGGATTATAGAGAGTTTTTTCAATATTTAAGAAATATATTCG
*
93002 AAATATAA
130 AAATAAAA
93010 TTACATATTAAACCTTAAAAGTTAAATATAATATTTAAAAAATTAAAAAGGGTATTTTAGATATT
1 TTACATATTAAACCTTAAAAGTTAAATATAATATTTAAAAAATT-AAAAGGGTATTTTAGATATT
93075 TCAGATCAA-GTTTTTGAAGTTTAGGATTATAGAG
65 TCAGATCAAGGTTTTTGAAGTTTAGGATTATAGAG
93109 TTACATATTA
Statistics
Matches: 224, Mismatches: 11, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
137 67 0.30
138 156 0.70
139 1 0.00
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.39
Consensus pattern (137 bp):
TTACATATTAAACCTTAAAAGTTAAATATAATATTTAAAAAATTAAAAGGGTATTTTAGATATTT
CAGATCAAGGTTTTTGAAGTTTAGGATTATAGAGAGTTTTTTCAATATTTAAGAAATATATTCGA
AATAAAA
Found at i:94681 original size:22 final size:22
Alignment explanation
Indices: 94636--94681 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
94626 ATTGTTTTAA
* * *
94636 TATTAAATTTTTATTTATATAT
1 TATTAAATTTTTACTTAAAAAT
*
94658 TATTATATTTTTACTTAAAAAT
1 TATTAAATTTTTACTTAAAAAT
94680 TA
1 TA
94682 CTCATAATCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTAAATTTTTACTTAAAAAT
Found at i:105026 original size:2 final size:2
Alignment explanation
Indices: 105019--105056 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
105009 TCACTATTGT
105019 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.