Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011668.1 Corchorus capsularis cultivar CVL-1 contig11689, 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: 30275
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:786 original size:48 final size:48
Alignment explanation
Indices: 581--928 Score: 332
Period size: 49 Copynumber: 7.2 Consensus size: 48
571 GGGTGTCTAC
* * * *
581 ACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAG-GACTTTCCG
1 ACCGGGAAGGGGCATTTTTGG-AA-TAATAAAGAAAACTGTGACCTTCCG
* * * * * *
630 ACTGGGAAGGGGCATTTTTCGAATAAACAAAGAAAACAGGGACCTTTCG
1 ACCGGGAAGGGGCATTTTTGGAAT-AATAAAGAAAACTGTGACCTTCCG
* * * *
679 ACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCTTCCG
1 ACCGGGAAGGGGCATTTTTGG-AA-TAATAAAGAAAACTGTGACCTTCCG
*
729 ACCGAGAAGGGGCATTTTTGGAATGAATAAAG-AAACTGTGACCTTCCG
1 ACCGGGAAGGGGCATTTTTGGAAT-AATAAAGAAAACTGTGACCTTCCG
* * *
777 ACCAGGAAGGGGCTTTTTTGG---AAT-AAGAAAACTGTGACCTTGCG
1 ACCGGGAAGGGGCATTTTTGGAATAATAAAGAAAACTGTGACCTTCCG
* * * *
821 ATC-GGAAAGGGCATTTTTGAAATAAGAGAAGAAAACTGTGACCTTCCG
1 ACCGGGAAGGGGCATTTTTGGAATAATA-AAGAAAACTGTGACCTTCCG
* * * * *
869 ACTGGGAAAGGGCATTTTTGAAATAAGAGAAGAAAACTGTGAGCTTCCG
1 ACCGGGAAGGGGCATTTTTGGAATAATA-AAGAAAACTGTGACCTTCCG
918 ACCGGGAAGGG
1 ACCGGGAAGGG
929 CAAACTGGGA
Statistics
Matches: 254, Mismatches: 33, Indels: 24
0.82 0.11 0.08
Matches are distributed among these distances:
43 17 0.07
44 20 0.08
46 2 0.01
48 67 0.26
49 105 0.41
50 43 0.17
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.20
Consensus pattern (48 bp):
ACCGGGAAGGGGCATTTTTGGAATAATAAAGAAAACTGTGACCTTCCG
Found at i:857 original size:92 final size:92
Alignment explanation
Indices: 606--896 Score: 239
Period size: 92 Copynumber: 3.1 Consensus size: 92
596 TTTGGGAAAC
* * * * * * *
606 AAATAAAGAAAACA-GGACTTTCCGACTGGGAAGGGGCATTTTTCG-AATAAACAAAGAAAACAG
1 AAAT-AAGAAAACAGGGACCTTCCGACCGAGAAAGGGCATTTTT-GAAATGAAGAAAG-AAACTG
* * * * *
669 GGACCTTTCGACCGGGAAGGGGCATTTTGGG
63 TGACCTTCCGACCAGGAAAGGGCATTTT-TG
* * *
700 AAACAAATAAAGAAAACAGGGACCTTCCGACCGAGAAGGGGCATTTTTGGAATGAATAAAGAAAC
1 ----AAAT-AAGAAAACAGGGACCTTCCGACCGAGAAAGGGCATTTTTGAAATGAAGAAAGAAAC
* *
765 TGTGACCTTCCGACCAGGAAGGGGCTTTTTTG
61 TGTGACCTTCCGACCAGGAAAGGGCATTTTTG
* * * * *
797 GAATAAGAAAACTGTGACCTTGCGATCG-GAAAGGGCATTTTTGAAAT-AAGAGAAGAAAACTGT
1 AAATAAGAAAACAGGGACCTTCCGACCGAGAAAGGGCATTTTTGAAATGAAGA-AAG-AAACTGT
**
860 GACCTTCCGACTGGGAAAGGGCATTTTTG
64 GACCTTCCGACCAGGAAAGGGCATTTTTG
889 AAATAAGA
1 AAATAAGA
897 GAAGAAAACT
Statistics
Matches: 165, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
90 3 0.02
91 20 0.12
92 59 0.36
93 3 0.02
97 1 0.01
98 44 0.27
99 35 0.21
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.21
Consensus pattern (92 bp):
AAATAAGAAAACAGGGACCTTCCGACCGAGAAAGGGCATTTTTGAAATGAAGAAAGAAACTGTGA
CCTTCCGACCAGGAAAGGGCATTTTTG
Found at i:1008 original size:41 final size:40
Alignment explanation
Indices: 922--1033 Score: 127
Period size: 41 Copynumber: 2.8 Consensus size: 40
912 CTTCCGACCG
* * *
922 GGAAGGGC-AAACTGGGAAACTAAACAGCACCATCCTGTGG
1 GGAAGGGCAAAAC-GGGAAACTAAACAACACCATCCGGTGA
*
962 GGAAGGGCAAAACGGGAAATCTAAACAACACCTTCCGGTGA
1 GGAAGGGCAAAACGGGAAA-CTAAACAACACCATCCGGTGA
* * *
1003 TGAAGGGTAAAACAGGAAAACTAAACAACAC
1 GGAAGGGCAAAAC-GGGAAACTAAACAACAC
1034 ACAAACTGAG
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
40 14 0.23
41 43 0.69
42 5 0.08
ACGTcount: A:0.42, C:0.21, G:0.26, T:0.12
Consensus pattern (40 bp):
GGAAGGGCAAAACGGGAAACTAAACAACACCATCCGGTGA
Found at i:1168 original size:13 final size:13
Alignment explanation
Indices: 1150--1174 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1140 CAAGACTGAT
1150 CTTTTCAATTTTA
1 CTTTTCAATTTTA
1163 CTTTTCAATTTT
1 CTTTTCAATTTT
1175 TGACATGAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (13 bp):
CTTTTCAATTTTA
Found at i:1715 original size:51 final size:51
Alignment explanation
Indices: 1610--1928 Score: 269
Period size: 51 Copynumber: 6.3 Consensus size: 51
1600 GTCTCAATTT
* * * * *
1610 TTTATTTACAAATTAAT-CAAAATTCAATCTTTTAGTTCATAGATTTCACC
1 TTTATTTACAAATTAATCCAAAGTTTAATCATTTAGTTCAAAGATTTCATC
* * *
1660 TTTATTTACAAATTGATCCAGAGTTTAATCATTTAGTTCAAAGATCTT-ATT
1 TTTATTTACAAATTAATCCAAAGTTTAATCATTTAGTTCAAAGAT-TTCATC
* * *
1711 TTTATTTACAAATTAAT-CACAAGTTCAATCATTTAATTCAAAGATCTCATC
1 TTTATTTACAAATTAATCCA-AAGTTTAATCATTTAGTTCAAAGATTTCATC
* * *
1762 TTTATTTACAAATTAATCAAAAGTTTAATTA-TTAGCTT-AAAGATTTCACC
1 TTTATTTACAAATTAATCCAAAGTTTAATCATTTAG-TTCAAAGATTTCATC
* * * * *
1812 TTTA-TCACCAAATTAATCCAAAGTTTCATCTTTTAATTCAAA-AGTTTCATT
1 TTTATTTA-CAAATTAATCCAAAGTTTAATCATTTAGTTCAAAGA-TTTCATC
** ** * * * *
1863 TTTATTTACAAATTTCTTAAAAGATTCAATC-TTTCACTT-AAACATTTAATC
1 TTTATTTACAAATTAATCCAAAG-TTTAATCATTT-AGTTCAAAGATTTCATC
1914 TTTATTTACAAATTA
1 TTTATTTACAAATTA
1929 CTTAAAAATC
Statistics
Matches: 216, Mismatches: 39, Indels: 27
0.77 0.14 0.10
Matches are distributed among these distances:
49 2 0.01
50 58 0.27
51 142 0.66
52 14 0.06
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.44
Consensus pattern (51 bp):
TTTATTTACAAATTAATCCAAAGTTTAATCATTTAGTTCAAAGATTTCATC
Found at i:1837 original size:152 final size:152
Alignment explanation
Indices: 1610--1928 Score: 373
Period size: 152 Copynumber: 2.1 Consensus size: 152
1600 GTCTCAATTT
* * * *
1610 TTTATTTACAAATTAATCAAAATTCAATCTTTTAGTTCATAGATTTCACCTTTATTTACAAATTG
1 TTTATTTACAAATTAATCAAAATTCAATCTATTAGTTCAAAGATTTCACCTTTATTCACAAATTA
* * *
1675 ATCCAGAGTTTAATCATTTAGTTC-AAAGATCTT-ATTTTTATTTACAAATTAATCACAAG-TTC
66 ATCCAAAGTTTAATCATTTAATTCAAAAG-T-TTCATTTTTATTTACAAATTAATCAAAAGATTC
* *
1737 AATCATTT-AATTCAAAGATCTCATC
129 AATC-TTTCAATT-AAACATCTAATC
*
1762 TTTATTTACAAATTAATCAAAAGTTTAAT-TATTAGCTT-AAAGATTTCACCTTTA-TCACCAAA
1 TTTATTTACAAATTAATCAAAA-TTCAATCTATTAG-TTCAAAGATTTCACCTTTATTCA-CAAA
* * ** *
1824 TTAATCCAAAGTTTCATCTTTTAATTCAAAAGTTTCATTTTTATTTACAAATTTCTTAAAAGATT
63 TTAATCCAAAGTTTAATCATTTAATTCAAAAGTTTCATTTTTATTTACAAATTAATCAAAAGATT
* *
1889 CAATCTTTCACTTAAACATTTAATC
128 CAATCTTTCAATTAAACATCTAATC
1914 TTTATTTACAAATTA
1 TTTATTTACAAATTA
1929 CTTAAAAATC
Statistics
Matches: 143, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
151 4 0.03
152 118 0.83
153 21 0.15
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.44
Consensus pattern (152 bp):
TTTATTTACAAATTAATCAAAATTCAATCTATTAGTTCAAAGATTTCACCTTTATTCACAAATTA
ATCCAAAGTTTAATCATTTAATTCAAAAGTTTCATTTTTATTTACAAATTAATCAAAAGATTCAA
TCTTTCAATTAAACATCTAATC
Found at i:1853 original size:20 final size:20
Alignment explanation
Indices: 1824--1866 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1814 TATCACCAAA
1824 TTAATCC-AAAGTTTCATCTT
1 TTAATCCAAAAGTTTCAT-TT
*
1844 TTAATTCAAAAGTTTCATTT
1 TTAATCCAAAAGTTTCATTT
1864 TTA
1 TTA
1867 TTTACAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.49
Consensus pattern (20 bp):
TTAATCCAAAAGTTTCATTT
Found at i:8409 original size:19 final size:20
Alignment explanation
Indices: 8374--8411 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
8364 TTCTAATTCA
8374 TTTGGGTTTACTTTATTTGT
1 TTTGGGTTTACTTTATTTGT
*
8394 TTTGGGTTT-GTTTATTTG
1 TTTGGGTTTACTTTATTTG
8412 GACTTGTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.08, C:0.03, G:0.24, T:0.66
Consensus pattern (20 bp):
TTTGGGTTTACTTTATTTGT
Found at i:16353 original size:16 final size:16
Alignment explanation
Indices: 16328--16369 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
16318 TTTTTTTATA
*
16328 ATATTCATTAAGTAAT
1 ATATTAATTAAGTAAT
* *
16344 ATATTAATTAATTATT
1 ATATTAATTAAGTAAT
16360 ATA-TAATTAA
1 ATATTAATTAA
16370 ACTTTACTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
ATATTAATTAAGTAAT
Found at i:17247 original size:65 final size:65
Alignment explanation
Indices: 17171--17301 Score: 210
Period size: 65 Copynumber: 2.0 Consensus size: 65
17161 ACCTCCTTTT
* *
17171 TCTTGTGAAACTTGTATAGTTGAGGAAGATCAAAACAGAGCTGAACAAAATACA-GGAAAGTGGG
1 TCTTGTGAAACTTGTATAGTTAAGGAACATCAAAACAGAGCTGAACAAAATACACGG-AAGTGGG
17235 G
65 G
* *
17236 TCTTGTGAAACTTGTATAGTTAAGGAACATCAAAACGGAGCTGGACAAAATACACGGAAGTGGGG
1 TCTTGTGAAACTTGTATAGTTAAGGAACATCAAAACAGAGCTGAACAAAATACACGGAAGTGGGG
17301 T
1 T
17302 GAGGAAAAGA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
65 59 0.97
66 2 0.03
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.22
Consensus pattern (65 bp):
TCTTGTGAAACTTGTATAGTTAAGGAACATCAAAACAGAGCTGAACAAAATACACGGAAGTGGGG
Found at i:18114 original size:21 final size:21
Alignment explanation
Indices: 18089--18132 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
18079 CAAATCTGGA
18089 TTGCTAAAT-ACCGCCCCATTT
1 TTGCT-AATCACCGCCCCATTT
* *
18110 TTGCTATTCATCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
18131 TT
1 TT
18133 TACGCTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:18535 original size:33 final size:31
Alignment explanation
Indices: 18431--18543 Score: 136
Period size: 32 Copynumber: 3.5 Consensus size: 31
18421 ATTTTGGTCT
* *
18431 AGCCGCCCCACCGGGGCGGCCTGCCGTGGCAA
1 AGCCGCCCCA-TGGGGCGGCCTGCCGTGGCGA
*
18463 AGCCGCCCCATGAGGGTGGCCTGCCGTGGCGA
1 AGCCGCCCCATG-GGGCGGCCTGCCGTGGCGA
* *
18495 AGCCGCCCCAGTGGGGCGGCCTGTCCATGGTGA
1 AGCCGCCCCA-TGGGGCGGCCTG-CCGTGGCGA
18528 AGCCGCCCCAATGGGG
1 AGCCGCCCC-ATGGGG
18544 AGGTTCCGCC
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
31 1 0.01
32 46 0.65
33 23 0.32
34 1 0.01
ACGTcount: A:0.13, C:0.37, G:0.39, T:0.11
Consensus pattern (31 bp):
AGCCGCCCCATGGGGCGGCCTGCCGTGGCGA
Found at i:18574 original size:66 final size:64
Alignment explanation
Indices: 18431--18563 Score: 153
Period size: 64 Copynumber: 2.0 Consensus size: 64
18421 ATTTTGGTCT
** * *
18431 AGCCGCCCCACCGGGGCGGCCTGCCGTGGCAAAGCCGCCCCATGAGGGTGGCCTGCCGTGGCGA
1 AGCCGCCCCAGTGGGGCGGCCTGCCATGGCAAAGCCGCCCCATGAGGGAGGCCTGCCGTGGCGA
**
18495 AGCCGCCCCAGTGGGGCGGCCTGTCCATGGTGAAGCCGCCCCAATG-GGGAGGTTCC-GCCGTGG
1 AGCCGCCCCAGTGGGGCGGCCTG-CCATGGCAAAGCCGCCCC-ATGAGGGAGG--CCTGCCGTGG
*
18558 CTA
62 CGA
18561 AGC
1 AGC
18564 TGTCCTAGTG
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
64 21 0.36
65 20 0.34
66 15 0.26
67 2 0.03
ACGTcount: A:0.14, C:0.36, G:0.38, T:0.12
Consensus pattern (64 bp):
AGCCGCCCCAGTGGGGCGGCCTGCCATGGCAAAGCCGCCCCATGAGGGAGGCCTGCCGTGGCGA
Found at i:18827 original size:31 final size:32
Alignment explanation
Indices: 18767--18827 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
18757 AATGTTAAAC
* *
18767 ATAAGGATATAATATAGTATTTTAAAAGTTAA
1 ATAAGGATACAATATAGCATTTTAAAAGTTAA
* *
18799 ATAAGGATACGATATA-CATTTTATAAGTT
1 ATAAGGATACAATATAGCATTTTAAAAGTT
18828 TTACAAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 11 0.44
32 14 0.56
ACGTcount: A:0.46, C:0.03, G:0.13, T:0.38
Consensus pattern (32 bp):
ATAAGGATACAATATAGCATTTTAAAAGTTAA
Found at i:18882 original size:17 final size:16
Alignment explanation
Indices: 18854--18891 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
18844 TACAGTACCG
*
18854 ATATAGATAGATGTAT
1 ATATAGATAGATATAT
18870 ATATAGTATAGATATAT
1 ATATAG-ATAGATATAT
18887 ATATA
1 ATATA
18892 CTCACAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (16 bp):
ATATAGATAGATATAT
Found at i:20827 original size:30 final size:30
Alignment explanation
Indices: 20793--20853 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
20783 GAGATGAGCG
20793 AATAAGGGCAAAACATTTTCGAATTTTACA
1 AATAAGGGCAAAACATTTTCGAATTTTACA
** **
20823 AATAAGGGCAAAAGGTTTTCGGGTTTTACA
1 AATAAGGGCAAAACATTTTCGAATTTTACA
20853 A
1 A
20854 CACTTTTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (30 bp):
AATAAGGGCAAAACATTTTCGAATTTTACA
Found at i:22751 original size:15 final size:16
Alignment explanation
Indices: 22717--22791 Score: 98
Period size: 16 Copynumber: 4.8 Consensus size: 16
22707 ATTTTTGGGT
*
22717 ACCCGAACCCAAAATT
1 ACCCGAACCCAAAATG
**
22733 ACCCGAATTC-AAATG
1 ACCCGAACCCAAAATG
*
22748 ACCCGAACCCGAAATG
1 ACCCGAACCCAAAATG
*
22764 ACCCAAACCCAAAATG
1 ACCCGAACCCAAAATG
22780 ACCCGAACCCAA
1 ACCCGAACCCAA
22792 TCAACCCAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
15 12 0.24
16 38 0.76
ACGTcount: A:0.43, C:0.37, G:0.11, T:0.09
Consensus pattern (16 bp):
ACCCGAACCCAAAATG
Found at i:22755 original size:31 final size:32
Alignment explanation
Indices: 22717--22791 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 32
22707 ATTTTTGGGT
* * **
22717 ACCCGAACCCAAAATTACCCGAATTC-AAATG
1 ACCCGAACCCAAAATGACCCAAACCCAAAATG
*
22748 ACCCGAACCCGAAATGACCCAAACCCAAAATG
1 ACCCGAACCCAAAATGACCCAAACCCAAAATG
22780 ACCCGAACCCAA
1 ACCCGAACCCAA
22792 TCAACCCAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 21 0.57
32 16 0.43
ACGTcount: A:0.43, C:0.37, G:0.11, T:0.09
Consensus pattern (32 bp):
ACCCGAACCCAAAATGACCCAAACCCAAAATG
Found at i:23815 original size:2 final size:2
Alignment explanation
Indices: 23808--23888 Score: 58
Period size: 2 Copynumber: 39.5 Consensus size: 2
23798 TATTATATTT
* * *
23808 TA TA TA TA TA TA TA TA TA GTA TA TA TA TA GTA TA AA TCA GA GA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA T-A TA TA
* **
23851 CA TA TGA CC TA -A TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23889 TTGTACTGAT
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
1 2 0.03
2 56 0.88
3 6 0.09
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (2 bp):
TA
Found at i:23830 original size:11 final size:11
Alignment explanation
Indices: 23808--23841 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
23798 TATTATATTT
23808 TATATATA-TA
1 TATATATAGTA
23818 TATATATAGTA
1 TATATATAGTA
23829 TATATATAGTA
1 TATATATAGTA
23840 TA
1 TA
23842 AATCAGAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (11 bp):
TATATATAGTA
Found at i:24244 original size:15 final size:15
Alignment explanation
Indices: 24190--24246 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
24180 TCCGAACCGT
*
24190 ATGACCCGAAACCGAAA
1 ATGACCCG-AACC-CAA
*
24207 ACGACCC-AACCCAGA
1 ATGACCCGAACCCA-A
24222 ATTGACCCGAACCCAA
1 A-TGACCCGAACCCAA
24238 ATGACCCGA
1 ATGACCCGA
24247 CATTTGATCG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 1 0.03
15 14 0.41
16 7 0.21
17 12 0.35
ACGTcount: A:0.40, C:0.37, G:0.16, T:0.07
Consensus pattern (15 bp):
ATGACCCGAACCCAA
Found at i:26629 original size:16 final size:16
Alignment explanation
Indices: 26588--26632 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
26578 TCGGATTTTG
**
26588 TCGGTTTCGGGTTATC
1 TCGGTTTCGGGTTAAA
*
26604 TC-GATTCGGGTTAAA
1 TCGGTTTCGGGTTAAA
26619 TCGGTTTCGGGTTA
1 TCGGTTTCGGGTTA
26633 TAGTACTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.13, C:0.16, G:0.31, T:0.40
Consensus pattern (16 bp):
TCGGTTTCGGGTTAAA
Found at i:30057 original size:10 final size:10
Alignment explanation
Indices: 30044--30108 Score: 60
Period size: 10 Copynumber: 6.2 Consensus size: 10
30034 TTAAATTTAT
30044 TATTATATAA
1 TATTATATAA
30054 TATTAT-TAA
1 TATTATATAA
*
30063 TTAATATATATA
1 -TATTATATA-A
30075 TATATATATATA
1 TAT-TATATA-A
*
30087 TAATATATAA
1 TATTATATAA
*
30097 TATAATATAA
1 TATTATATAA
30107 TA
1 TA
30109 AAACGAAAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
9 3 0.07
10 22 0.48
11 10 0.22
12 11 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TATTATATAA
Found at i:30071 original size:2 final size:2
Alignment explanation
Indices: 30066--30105 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
30056 TTATTAATTA
30066 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30105 A
1 A
30106 ATAAAACGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Done.