Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024660.1 Corchorus olitorius cultivar O-4 contig24693, 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: 36188
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Found at i:2954 original size:18 final size:19
Alignment explanation
Indices: 2927--2968 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
2917 AATCAATCAC
2927 AACAAAAAAA-CACAGT-TA
1 AACAAAAAAAGCA-AGTATA
*
2945 AACAATAAAAGCAAGTATA
1 AACAAAAAAAGCAAGTATA
2964 AACAA
1 AACAA
2969 CAAACATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (19 bp):
AACAAAAAAAGCAAGTATA
Found at i:3653 original size:30 final size:30
Alignment explanation
Indices: 3619--3701 Score: 94
Period size: 32 Copynumber: 2.7 Consensus size: 30
3609 ATTTTACTAA
** * *
3619 TTTCCAAAATCTTCTTTTGGATTTCTTTAT
1 TTTCCAAAATCTTCTTTTGGATAACCTTAC
*
3649 TTTCCAAAATCTCCTTTTGGGGATAACCTTAC
1 TTTCCAAAATCTTCTTTT--GGATAACCTTAC
*
3681 ATTCCAAAATCTTCTTTTGGA
1 TTTCCAAAATCTTCTTTTGGA
3702 GTTTACTTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
30 20 0.45
32 24 0.55
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (30 bp):
TTTCCAAAATCTTCTTTTGGATAACCTTAC
Found at i:7981 original size:27 final size:27
Alignment explanation
Indices: 7951--8091 Score: 142
Period size: 28 Copynumber: 5.1 Consensus size: 27
7941 AGTAGACTTT
*
7951 AAATGACTAAAACT-CCCCTGAACATGC
1 AAATGACCAAAA-TGCCCCTGAACATGC
*
7978 AAATGACCAAAATGCCCCT-AGACTTGC
1 AAATGACCAAAATGCCCCTGA-ACATGC
* * *
8005 AAAATGAACAAAATGCCCCTAAACTTGC
1 -AAATGACCAAAATGCCCCTGAACATGC
* *
8033 AAAATGACCAAAATGCCCCTGGACATGAA
1 -AAATGACCAAAATGCCCCTGAACATG-C
* *
8062 AAATGACCAAAATGCCCCTGGATATGC
1 AAATGACCAAAATGCCCCTGAACATGC
8089 AAA
1 AAA
8092 AATGATCAAT
Statistics
Matches: 99, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
26 2 0.02
27 24 0.24
28 72 0.73
29 1 0.01
ACGTcount: A:0.43, C:0.26, G:0.14, T:0.17
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAACATGC
Found at i:8105 original size:29 final size:29
Alignment explanation
Indices: 7978--8223 Score: 254
Period size: 29 Copynumber: 8.7 Consensus size: 29
7968 CTGAACATGC
7978 AAATGACCAAAATGCCCCTAGACT-TGC-A
1 AAATGACCAAAATGCCCCTAGA-TATGCAA
* *
8006 AAATGAACAAAATGCCCCTAAACT-TGC-A
1 AAATGACCAAAATGCCCCTAGA-TATGCAA
* *
8034 AAATGACCAAAATGCCCCTGGACATG-AA
1 AAATGACCAAAATGCCCCTAGATATGCAA
*
8062 AAATGACCAAAATGCCCCTGGATATGCAA
1 AAATGACCAAAATGCCCCTAGATATGCAA
* * * *
8091 AAATGATCAATATGCTCTTAGATATGCAA
1 AAATGACCAAAATGCCCCTAGATATGCAA
* * * *
8120 AAATGATCAAGATGCTCTTAGATATGCAA
1 AAATGACCAAAATGCCCCTAGATATGCAA
* * *
8149 AAATGACCAAGATGCTCTTAGATATGCAA
1 AAATGACCAAAATGCCCCTAGATATGCAA
* * *
8178 AAATGACCAAAATG-CCCTTG-GAGGCAA
1 AAATGACCAAAATGCCCCTAGATATGCAA
8205 AAATGACCAAAATGCCCCT
1 AAATGACCAAAATGCCCCT
8224 GGGCGAGCAA
Statistics
Matches: 194, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
27 19 0.10
28 80 0.41
29 95 0.49
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (29 bp):
AAATGACCAAAATGCCCCTAGATATGCAA
Found at i:14805 original size:15 final size:15
Alignment explanation
Indices: 14775--14816 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
14765 TTACTCTGCT
14775 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
14791 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
14806 TTGCTTTCTGT
1 TTGTTTTCTGT
14817 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:15347 original size:23 final size:23
Alignment explanation
Indices: 15290--15368 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 23
15280 AAAAATATGT
*
15290 TTGTTTTTGCGTCGA-AAAAAATA
1 TTGTTTTTGCGTC-ATAAAAAAAA
*
15313 TATATTTTTGCGTCATAAAAAAAA
1 T-TGTTTTTGCGTCATAAAAAAAA
*
15337 TTGTTTCTGCGTCATAAAAAAAA
1 TTGTTTTTGCGTCATAAAAAAAA
15360 --GTTTTTGCG
1 TTGTTTTTGCG
15369 ATTTTCTTCC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
21 8 0.16
23 22 0.45
24 19 0.39
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.39
Consensus pattern (23 bp):
TTGTTTTTGCGTCATAAAAAAAA
Found at i:15356 original size:24 final size:24
Alignment explanation
Indices: 15290--15359 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
15280 AAAAATATGT
* *
15290 TTGTTTTTGCGTC-GAAAAAAATA
1 TTGTTTTTGCGTCATAAAAAAAAA
*
15313 TATATTTTTGCGTCAT-AAAAAAAA
1 T-TGTTTTTGCGTCATAAAAAAAAA
*
15337 TTGTTTCTGCGTCATAAAAAAAA
1 TTGTTTTTGCGTCATAAAAAAAA
15360 GTTTTTGCGA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
23 13 0.33
24 26 0.67
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (24 bp):
TTGTTTTTGCGTCATAAAAAAAAA
Found at i:15406 original size:24 final size:24
Alignment explanation
Indices: 15292--15412 Score: 74
Period size: 23 Copynumber: 4.9 Consensus size: 24
15282 AAATATGTTT
*
15292 GTTTTTGCGTCGA-AAAAAATATATA
1 GTTTTTGCGTC-ATAAAAAA-AAATA
*
15317 -TTTTTGCGTCAT-AAAAAAAATT
1 GTTTTTGCGTCATAAAAAAAAATA
*
15339 GTTTCTGCGTCAT--AAAAAAA-A
1 GTTTTTGCGTCATAAAAAAAAATA
* *
15360 GTTTTTGCGATTTTCTTCCAAAAAAAAAGA
1 GTTTTTGCG----TCAT--AAAAAAAAATA
15390 GTTTTTGCGTCATAAAAAGAAAA
1 GTTTTTGCGTCATAAAAA-AAAA
15413 AAAAATTTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 24
0.71 0.06 0.22
Matches are distributed among these distances:
21 8 0.10
22 10 0.13
23 17 0.22
24 15 0.19
25 7 0.09
26 3 0.04
29 7 0.09
30 10 0.13
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (24 bp):
GTTTTTGCGTCATAAAAAAAAATA
Found at i:18608 original size:21 final size:21
Alignment explanation
Indices: 18582--18634 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
18572 GCCATTCACT
**
18582 GTGCCACCACCGGTTAAGCCC
1 GTGCCACCACCGGCCAAGCCC
*
18603 GTGCCACCACCGGCCATGCCC
1 GTGCCACCACCGGCCAAGCCC
*
18624 GTGCCATCACC
1 GTGCCACCACC
18635 ATTCCAAGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (21 bp):
GTGCCACCACCGGCCAAGCCC
Found at i:21543 original size:15 final size:15
Alignment explanation
Indices: 21513--21554 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
21503 TTACTCTGCT
21513 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
21529 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
21544 TTGCTTTCTGT
1 TTGTTTTCTGT
21555 CAATCTCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:24904 original size:5 final size:5
Alignment explanation
Indices: 24890--24932 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
24880 CAAATAACAC
* * *
24890 CAAAA C-AAA CAAAA CAAAA CAAAA CAGAC CAAAA CAACA CAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAA
24933 GCAACCATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.72, C:0.26, G:0.02, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:24937 original size:10 final size:10
Alignment explanation
Indices: 24885--24937 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
24875 AAGAGCAAAT
24885 AACACCAAAAC
1 AACA-CAAAAC
24896 AA-ACAAAAC
1 AACACAAAAC
*
24905 AAAACAAAAC
1 AACACAAAAC
24915 AGAC-CAAAAC
1 A-ACACAAAAC
*
24925 AACACAAAGC
1 AACACAAAAC
24935 AAC
1 AAC
24938 CATTTTATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
9 10 0.27
10 24 0.65
11 3 0.08
ACGTcount: A:0.68, C:0.28, G:0.04, T:0.00
Consensus pattern (10 bp):
AACACAAAAC
Found at i:25493 original size:48 final size:48
Alignment explanation
Indices: 25415--25938 Score: 308
Period size: 48 Copynumber: 11.8 Consensus size: 48
25405 AGGGAATAGG
* * * *
25415 AACAACTCCTTCCGA-TGGAGAAGGGCAAAACGGGAACAAAACATTGAA
1 AACAACACCTTCCGACCGG-GAAGGGCAAAACAGGAATAAAACATTGAA
* *
25463 AATAACACCTTCCGACCGGGAAGGGCAAAAC----AT--GA-A-T-AA
1 AACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAACATTGAA
* * * *
25502 AACAACATCTTTCG-CTGGGGAAAGGCAAAACAGGAATAAAACATTGAA
1 AACAACACCTTCCGAC-CGGGAAGGGCAAAACAGGAATAAAACATTGAA
* * ** *
25550 CACAACACCTTCCTACTAGGAAGGACAAAACAGG------A-A-TGAA
1 AACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAACATTGAA
* * *
25590 ATCAACACCTTCCGGCGGGGAAGGGCAAAACCA-GAATAAAACATTGAA
1 AACAACACCTTCCGACCGGGAAGGGCAAAA-CAGGAATAAAACATTGAA
*
25638 AACAACACCTTCCGACCGGGAAGGGCAAAAC------AAGA-A-TGAA
1 AACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAACATTGAA
* *** *
25678 ATCAACACCTTCCGGTGGGGAAGGGCAAAACAAGAATAAAACATTGAA
1 AACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAACATTGAA
* * * *
25726 AACAGCACCTTCCAACCGAGAAGGGCAAAAC----AT--GA-A-TGAA
1 AACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAACATTGAA
* *** *
25766 ATCAACACCTTCCGGTGGGGAAGGGCAAAACAGGAATGAAACATTGAA
1 AACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAACATTGAA
* * *
25814 AACAACACCTTTCTACCGGGAAGGGCAAAATAGG------A-A-TGAA
1 AACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAACATTGAA
* * *** *
25854 ATCAACACCTTTCGGTGGGGAAGGGCAAAACGGGAATAAAACATTGAA
1 AACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAACATTGAA
* **
25902 AACAACACCTTCCTACCGTAAAGGGCAAAACAGGAAT
1 AACAACACCTTCCGACCGGGAAGGGCAAAACAGGAAT
25939 GAAATCAACA
Statistics
Matches: 357, Mismatches: 74, Indels: 90
0.69 0.14 0.17
Matches are distributed among these distances:
38 1 0.00
39 26 0.07
40 119 0.33
41 7 0.02
42 7 0.02
43 2 0.01
44 5 0.01
45 1 0.00
46 7 0.02
47 6 0.02
48 173 0.48
49 3 0.01
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.13
Consensus pattern (48 bp):
AACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAACATTGAA
Found at i:25612 original size:40 final size:40
Alignment explanation
Indices: 25568--25972 Score: 243
Period size: 40 Copynumber: 9.3 Consensus size: 40
25558 CTTCCTACTA
*
25568 GGAAGGACAAAACAGGAATGAAATCAACACCTTCCGGCGG
1 GGAAGGGCAAAACAGGAATGAAATCAACACCTTCCGGCGG
* * * *
25608 GGAAGGGCAAAACCAGAATAAAACATTGAAAACAACACCTTCCGACCG
1 GGAAGGGCAAAA-CAG-----GA-A-TGAAATCAACACCTTCCGGCGG
* *
25656 GGAAGGGCAAAACAAGAATGAAATCAACACCTTCCGGTGG
1 GGAAGGGCAAAACAGGAATGAAATCAACACCTTCCGGCGG
* * * ** *
25696 GGAAGGGCAAAACAAGAATAAAACATTGAAAACAGCACCTTCCAACCG
1 GGAAGGGCAAAAC-AG-----GA-A-TGAAATCAACACCTTCCGGCGG
* * *
25744 AGAAGGGCAAAACATGAATGAAATCAACACCTTCCGGTGG
1 GGAAGGGCAAAACAGGAATGAAATCAACACCTTCCGGCGG
* ** *
25784 GGAAGGGCAAAACAGGAATGAAACATTGAAAACAACACCTTTCTACCG
1 GGAAGGGCAAAACAGGAATG-AA-A-T-----CAACACCTTCCGGCGG
* * *
25832 GGAAGGGCAAAATAGGAATGAAATCAACACCTTTCGGTGG
1 GGAAGGGCAAAACAGGAATGAAATCAACACCTTCCGGCGG
* * ** *
25872 GGAAGGGCAAAACGGGAATAAAACATTGAAAACAACACCTTCCTACCG
1 GGAAGGGCAAAACAGG------A-A-TGAAATCAACACCTTCCGGCGG
** *
25920 TAAAGGGCAAAACAGGAATGAAATCAACACCTTCCGGTGG
1 GGAAGGGCAAAACAGGAATGAAATCAACACCTTCCGGCGG
25960 GGAAGGGCAAAAC
1 GGAAGGGCAAAAC
25973 GGGTATATTG
Statistics
Matches: 275, Mismatches: 58, Indels: 64
0.69 0.15 0.16
Matches are distributed among these distances:
40 130 0.47
41 9 0.03
42 4 0.01
43 1 0.00
45 1 0.00
46 4 0.01
47 8 0.03
48 118 0.43
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (40 bp):
GGAAGGGCAAAACAGGAATGAAATCAACACCTTCCGGCGG
Found at i:25975 original size:88 final size:88
Alignment explanation
Indices: 25417--25972 Score: 769
Period size: 88 Copynumber: 6.3 Consensus size: 88
25407 GGAATAGGAA
* * * * * * *
25417 CAACTCCTTCCGATGGAGAAGGGCAAAACGGGAACAAAACATTGAAAATAACACCTTCCGACCGG
1 CAACACCTTCCGGTGGGGAAGGGCAAAACAGGAATAAAACATTGAAAACAACACCTTCCTACCGG
* * *
25482 GAAGGGCAAAACATGAAT-AAAA
66 AAAGGGCAAAACAGGAATGAAAT
* * * * * *
25504 CAACATCTTTCGCTGGGGAAAGGCAAAACAGGAATAAAACATTGAACACAACACCTTCCTACTAG
1 CAACACCTTCCGGTGGGGAAGGGCAAAACAGGAATAAAACATTGAAAACAACACCTTCCTAC-CG
*
25569 G-AAGGACAAAACAGGAATGAAAT
65 GAAAGGGCAAAACAGGAATGAAAT
* *
25592 CAACACCTTCCGGCGGGGAAGGGCAAAACCA-GAATAAAACATTGAAAACAACACCTTCCGACCG
1 CAACACCTTCCGGTGGGGAAGGGCAAAA-CAGGAATAAAACATTGAAAACAACACCTTCCTACCG
* *
25656 GGAAGGGCAAAACAAGAATGAAAT
65 GAAAGGGCAAAACAGGAATGAAAT
* * *
25680 CAACACCTTCCGGTGGGGAAGGGCAAAACAAGAATAAAACATTGAAAACAGCACCTTCCAACC-G
1 CAACACCTTCCGGTGGGGAAGGGCAAAACAGGAATAAAACATTGAAAACAACACCTTCCTACCGG
*
25744 AGAAGGGCAAAACATGAATGAAAT
66 A-AAGGGCAAAACAGGAATGAAAT
* *
25768 CAACACCTTCCGGTGGGGAAGGGCAAAACAGGAATGAAACATTGAAAACAACACCTTTCTACCGG
1 CAACACCTTCCGGTGGGGAAGGGCAAAACAGGAATAAAACATTGAAAACAACACCTTCCTACCGG
* *
25833 GAAGGGCAAAATAGGAATGAAAT
66 AAAGGGCAAAACAGGAATGAAAT
* * *
25856 CAACACCTTTCGGTGGGGAAGGGCAAAACGGGAATAAAACATTGAAAACAACACCTTCCTACCGT
1 CAACACCTTCCGGTGGGGAAGGGCAAAACAGGAATAAAACATTGAAAACAACACCTTCCTACCGG
25921 AAAGGGCAAAACAGGAATGAAAT
66 AAAGGGCAAAACAGGAATGAAAT
25944 CAACACCTTCCGGTGGGGAAGGGCAAAAC
1 CAACACCTTCCGGTGGGGAAGGGCAAAAC
25973 GGGTATATTG
Statistics
Matches: 416, Mismatches: 46, Indels: 13
0.88 0.10 0.03
Matches are distributed among these distances:
87 71 0.17
88 342 0.82
89 3 0.01
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (88 bp):
CAACACCTTCCGGTGGGGAAGGGCAAAACAGGAATAAAACATTGAAAACAACACCTTCCTACCGG
AAAGGGCAAAACAGGAATGAAAT
Found at i:26485 original size:50 final size:51
Alignment explanation
Indices: 26438--26538 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 51
26428 ACTTTTATTT
* * *
26438 CAAATTAATC-AAGAGTTCAATCTTTTAATTTAAAGATTTCATTTTTATCA
1 CAAATTAATCAAAAAATTCAATCTTTTAACTTAAAGATTTCATTTTTATCA
* * *
26488 CAAATTAATCAAAAAATTCATTTTTTTAGCTTAAAGATTTCATTTTTATCA
1 CAAATTAATCAAAAAATTCAATCTTTTAACTTAAAGATTTCATTTTTATCA
26539 TAAGCCAATC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 10 0.23
51 34 0.77
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.45
Consensus pattern (51 bp):
CAAATTAATCAAAAAATTCAATCTTTTAACTTAAAGATTTCATTTTTATCA
Found at i:26549 original size:51 final size:53
Alignment explanation
Indices: 26467--26568 Score: 145
Period size: 51 Copynumber: 2.0 Consensus size: 53
26457 ATCTTTTAAT
**
26467 TTAAAGATTTCATTTTTATCACAAATTAATCAAAAAATTCAT-TTT-TTTAGC
1 TTAAAGATTTCATTTTTATCACAAACCAATCAAAAAATTCATCTTTATTTAGC
* * *
26518 TTAAAGATTTCATTTTTATCATAAGCCAATCAAAAATTTCATCTTTATTTA
1 TTAAAGATTTCATTTTTATCACAAACCAATCAAAAAATTCATCTTTATTTA
26569 CAAATTAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 37 0.84
52 3 0.07
53 4 0.09
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.45
Consensus pattern (53 bp):
TTAAAGATTTCATTTTTATCACAAACCAATCAAAAAATTCATCTTTATTTAGC
Found at i:26718 original size:50 final size:50
Alignment explanation
Indices: 26558--27035 Score: 507
Period size: 50 Copynumber: 9.5 Consensus size: 50
26548 CAAAAATTTC
* * * * * *
26558 ATCTTTATTTACAAATTAATTAAAAGTTCAATATTTTAGCTTAAAGATTTC-
1 ATCTTTATTTACAAATTACTTAAAAGTTTAATCTTTTA-ATTAAA-AATCCA
* * * * *
26609 ATTTTTCTTTACAAATTGCTTAAAAGGTTTAATCTTTTCATGAAAAAATCCA
1 ATCTTTATTTACAAATTACTTAAAA-GTTTAATCTTTTAAT-TAAAAATCCA
* * *
26661 ATCTTTATTTACAAATTAATTAAAAGTTTGATCTTTTAATCAAAAATCCA
1 ATCTTTATTTACAAATTACTTAAAAGTTTAATCTTTTAATTAAAAATCCA
* * * *
26711 ATCTTTATTTACAAATTACTTAAAAGCTTCAAT-TTTTCACTTAAAGATTCA
1 ATCTTTATTTACAAATTACTTAAAAG-TTTAATCTTTT-AATTAAAAATCCA
* * * *
26762 ATCTTTATTCATAAATTACTTAAAAGTTTCATCTTTTAATCAAAAATCCA
1 ATCTTTATTTACAAATTACTTAAAAGTTTAATCTTTTAATTAAAAATCCA
* * * * *
26812 ACCTTTATTTACAAATTACTTAAAAGCTTCAAT-TTTCACTTAAAAATTCA
1 ATCTTTATTTACAAATTACTTAAAAG-TTTAATCTTTTAATTAAAAATCCA
* *
26862 ATCTTTATTTATAAATTACTTAAAAGTTTGATCTTTTAATTAAAAATCCA
1 ATCTTTATTTACAAATTACTTAAAAGTTTAATCTTTTAATTAAAAATCCA
* * * *
26912 A-CTTTTATTTACAAATTACTTAAAAGCTTCAAT-TTTCACTTAAAAATTCA
1 ATC-TTTATTTACAAATTACTTAAAAG-TTTAATCTTTTAATTAAAAATCCA
* * *
26962 ATCTTTATTCATAAATTACTTAAAAGTTTGATCTTTTAATTAAAAATCCA
1 ATCTTTATTTACAAATTACTTAAAAGTTTAATCTTTTAATTAAAAATCCA
*
27012 ACCTTTATTTACAAATTACTTAAA
1 ATCTTTATTTACAAATTACTTAAA
27036 GACTTCATCT
Statistics
Matches: 350, Mismatches: 65, Indels: 25
0.80 0.15 0.06
Matches are distributed among these distances:
49 9 0.03
50 219 0.63
51 88 0.25
52 34 0.10
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.43
Consensus pattern (50 bp):
ATCTTTATTTACAAATTACTTAAAAGTTTAATCTTTTAATTAAAAATCCA
Found at i:26901 original size:100 final size:101
Alignment explanation
Indices: 26616--27035 Score: 666
Period size: 100 Copynumber: 4.2 Consensus size: 101
26606 TTCATTTTTC
* * * * * * * *
26616 TTTACAAATTGCTTAAAAGGTTTAATCTTTTCA-TGAAAAAATCCAATCTTTATTTACAAATTAA
1 TTTACAAATTACTTAAAAGCTTCAAT-TTTTCACT-TAAAAATTCAATCTTTATTCATAAATTAC
*
26680 TTAAAAGTTTGATCTTTTAATCAAAAATCCAATCTTTA
64 TTAAAAGTTTGATCTTTTAATCAAAAATCCAACCTTTA
*
26718 TTTACAAATTACTTAAAAGCTTCAATTTTTCACTTAAAGATTCAATCTTTATTCATAAATTACTT
1 TTTACAAATTACTTAAAAGCTTCAATTTTTCACTTAAAAATTCAATCTTTATTCATAAATTACTT
*
26783 AAAAGTTTCATCTTTTAATCAAAAATCCAACCTTTA
66 AAAAGTTTGATCTTTTAATCAAAAATCCAACCTTTA
*
26819 TTTACAAATTACTTAAAAGCTTCAA-TTTTCACTTAAAAATTCAATCTTTATTTATAAATTACTT
1 TTTACAAATTACTTAAAAGCTTCAATTTTTCACTTAAAAATTCAATCTTTATTCATAAATTACTT
* *
26883 AAAAGTTTGATCTTTTAATTAAAAATCCAACTTTTA
66 AAAAGTTTGATCTTTTAATCAAAAATCCAACCTTTA
26919 TTTACAAATTACTTAAAAGCTTCAA-TTTTCACTTAAAAATTCAATCTTTATTCATAAATTACTT
1 TTTACAAATTACTTAAAAGCTTCAATTTTTCACTTAAAAATTCAATCTTTATTCATAAATTACTT
*
26983 AAAAGTTTGATCTTTTAATTAAAAATCCAACCTTTA
66 AAAAGTTTGATCTTTTAATCAAAAATCCAACCTTTA
27019 TTTACAAATTACTTAAA
1 TTTACAAATTACTTAAA
27036 GACTTCATCT
Statistics
Matches: 299, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
100 185 0.62
101 90 0.30
102 24 0.08
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.42
Consensus pattern (101 bp):
TTTACAAATTACTTAAAAGCTTCAATTTTTCACTTAAAAATTCAATCTTTATTCATAAATTACTT
AAAAGTTTGATCTTTTAATCAAAAATCCAACCTTTA
Found at i:30050 original size:8 final size:8
Alignment explanation
Indices: 30037--30064 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
30027 TAAGCTGATG
30037 CGAATAAA
1 CGAATAAA
30045 CGAATAAA
1 CGAATAAA
30053 CGAATAAA
1 CGAATAAA
30061 CGAA
1 CGAA
30065 GAGTAAGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.61, C:0.14, G:0.14, T:0.11
Consensus pattern (8 bp):
CGAATAAA
Found at i:30774 original size:29 final size:30
Alignment explanation
Indices: 30704--30774 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
30694 TATGTGTGTT
*
30704 TAATATTTTTTTTAATTATTTCTTATTTTC
1 TAATATTTTTTCTAATTATTTCTTATTTTC
* * *
30734 TAATCTTATTTTCTGATT-TTT-TTATTTTT
1 TAATATT-TTTTCTAATTATTTCTTATTTTC
30763 TAAATATTTTTT
1 T-AATATTTTTT
30775 ATTTCTCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
29 12 0.35
30 14 0.41
31 8 0.24
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.70
Consensus pattern (30 bp):
TAATATTTTTTCTAATTATTTCTTATTTTC
Done.