Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009912.1 Corchorus capsularis cultivar CVL-1 contig09933, 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: 27376
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:4928 original size:25 final size:25
Alignment explanation
Indices: 4894--4958 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
4884 TTTAATATAT
4894 TTTAAAATTTAAA-AACTATAATTAA
1 TTTAAAATTTAAATAA-TATAATTAA
*
4919 TTTAAGATTTAAATAATATAATTAA
1 TTTAAAATTTAAATAATATAATTAA
4944 TTT---ATTTAAATAATA
1 TTTAAAATTTAAATAATA
4959 CCCTTGCTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
22 12 0.32
25 24 0.63
26 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
TTTAAAATTTAAATAATATAATTAA
Found at i:6785 original size:29 final size:30
Alignment explanation
Indices: 6710--6790 Score: 94
Period size: 29 Copynumber: 2.7 Consensus size: 30
6700 CGGCTAAATA
*
6710 ACCAATTCAGGATATAACGTTTGTCCGAACG
1 ACCAATTCAGGATATAACG-TTGTCAGAACG
* **
6741 ATCAATTTGGGATATAACGTT-TCAGAAACG
1 ACCAATTCAGGATATAACGTTGTCAG-AACG
6771 -CCAATTCAGGATATAACGTT
1 ACCAATTCAGGATATAACGTT
6791 ATAGGAAACA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
29 20 0.48
30 6 0.14
31 16 0.38
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (30 bp):
ACCAATTCAGGATATAACGTTGTCAGAACG
Found at i:6926 original size:29 final size:30
Alignment explanation
Indices: 6890--6981 Score: 100
Period size: 29 Copynumber: 3.1 Consensus size: 30
6880 ATTTTATCCC
6890 AAATTGATCATTCTGAAACGTTATATCCTG
1 AAATTGATCATTCTGAAACGTTATATCCTG
* *
6920 AAA-TGAT-AGTTCTAAAACGTTATATCC-C
1 AAATTGATCA-TTCTGAAACGTTATATCCTG
* *
6948 AAATTGATCATGACAGCAAACGTTATATCCTG
1 AAATTGATCAT-TCTG-AAACGTTATATCCTG
6980 AA
1 AA
6982 TCGGTTATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
28 4 0.08
29 26 0.52
30 5 0.10
31 13 0.26
32 2 0.04
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (30 bp):
AAATTGATCATTCTGAAACGTTATATCCTG
Found at i:7163 original size:22 final size:22
Alignment explanation
Indices: 7135--7176 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
7125 GCAAAGAATC
*
7135 AAAACTAATTAAAGTACCAACT
1 AAAACTAATTAAAATACCAACT
7157 AAAACTAATTAAAATACCAA
1 AAAACTAATTAAAATACCAA
7177 TTCCTTTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.17, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAACTAATTAAAATACCAACT
Found at i:10367 original size:10 final size:10
Alignment explanation
Indices: 10352--10416 Score: 56
Period size: 10 Copynumber: 7.3 Consensus size: 10
10342 GTTCCTACTT
10352 TATGTACATA
1 TATGTACATA
10362 TATGT--A-A
1 TATGTACATA
*
10369 -ATGTATATA
1 TATGTACATA
10378 TATGTACATA
1 TATGTACATA
10388 TATGT--A-A
1 TATGTACATA
*
10395 -ATGTATATA
1 TATGTACATA
10404 TATGTACATA
1 TATGTACATA
10414 TAT
1 TAT
10417 ATATATATGT
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
6 8 0.18
7 2 0.04
8 4 0.09
9 2 0.04
10 29 0.64
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.43
Consensus pattern (10 bp):
TATGTACATA
Found at i:10378 original size:16 final size:16
Alignment explanation
Indices: 10353--10427 Score: 63
Period size: 16 Copynumber: 4.9 Consensus size: 16
10343 TTCCTACTTT
*
10353 ATGTACATATATGTAA
1 ATGTATATATATGTAA
10369 ATG--TATATA--T--
1 ATGTATATATATGTAA
*
10379 ATGTACATATATGTAA
1 ATGTATATATATGTAA
10395 ATGTATATATATGTACA
1 ATGTATATATATGTA-A
*
10412 TATATATATATATGTA
1 -ATGTATATATATGTA
10428 TATTCTTAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
10 3 0.06
12 6 0.13
14 6 0.13
16 17 0.36
17 1 0.02
18 14 0.30
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (16 bp):
ATGTATATATATGTAA
Found at i:10388 original size:26 final size:26
Alignment explanation
Indices: 10352--10430 Score: 131
Period size: 26 Copynumber: 3.0 Consensus size: 26
10342 GTTCCTACTT
10352 TATGTACATATATGTAAATGTATATA
1 TATGTACATATATGTAAATGTATATA
10378 TATGTACATATATGTAAATGTATATA
1 TATGTACATATATGTAAATGTATATA
*
10404 TATGTACATATATATATATATGTATAT
1 TATGTACATATATGTA-A-ATGTATAT
10431 TCTTAACATT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
26 41 0.82
27 1 0.02
28 8 0.16
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (26 bp):
TATGTACATATATGTAAATGTATATA
Found at i:12143 original size:31 final size:29
Alignment explanation
Indices: 12105--12168 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
12095 TCCGTTTAAA
* * *
12105 TATATCCTGAGTTGATCGTTTCATGTAACGT
1 TATATCCTGAATTG-GCGTTTC-TGAAACGT
12136 TATATCCTGAATTGGCGTTTCTGAAACGT
1 TATATCCTGAATTGGCGTTTCTGAAACGT
12165 TATA
1 TATA
12169 ACCCAAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 11 0.37
30 6 0.20
31 13 0.43
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (29 bp):
TATATCCTGAATTGGCGTTTCTGAAACGT
Found at i:12177 original size:29 final size:30
Alignment explanation
Indices: 12121--12178 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
12111 CTGAGTTGAT
* * **
12121 CGTTTCATGTAACGTTATATCCTGAATTGG
1 CGTTTCATGAAACGTTATAACCCAAATTGG
12151 CGTTTC-TGAAACGTTATAACCCAAATTG
1 CGTTTCATGAAACGTTATAACCCAAATTG
12179 ATCGTTCGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (30 bp):
CGTTTCATGAAACGTTATAACCCAAATTGG
Found at i:12665 original size:112 final size:115
Alignment explanation
Indices: 12538--12763 Score: 379
Period size: 112 Copynumber: 2.0 Consensus size: 115
12528 TTTTTCAATT
* *
12538 TATCTATATTATATATAAAACTACGAGTTTTGTTAAACTTTTTAATCGACCATTATACCCT-A-T
1 TATCTATACTATATATAAAACTACGAGTTTTGTGAAACTTTTTAATCGACCATTATACCCTCATT
*
12601 TTTTTTG-A-ATATTTCTTAAATGTCTTACTTAAACTATTGTAGTTTTATC
66 TTTTTTGAATATATTTCTT-AATGCCTTACTTAAACTATTGTAGTTTTATC
*
12650 TATCTATACTATATATAAAAGTACGAGTTTTGTGAAACTTTTTAATCGACCATTATACCCTCATT
1 TATCTATACTATATATAAAACTACGAGTTTTGTGAAACTTTTTAATCGACCATTATACCCTCATT
12715 TTTTTTGAATATATTTCTTAATGCCTTACTTAAACTATTGTAGTTTTAT
66 TTTTTTGAATATATTTCTTAATGCCTTACTTAAACTATTGTAGTTTTAT
12764 TCTACGAAAA
Statistics
Matches: 106, Mismatches: 4, Indels: 5
0.92 0.03 0.04
Matches are distributed among these distances:
112 58 0.55
113 1 0.01
114 8 0.08
115 30 0.28
116 9 0.08
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (115 bp):
TATCTATACTATATATAAAACTACGAGTTTTGTGAAACTTTTTAATCGACCATTATACCCTCATT
TTTTTTGAATATATTTCTTAATGCCTTACTTAAACTATTGTAGTTTTATC
Found at i:16026 original size:2 final size:2
Alignment explanation
Indices: 16019--16060 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
16009 TTATTATTAT
*
16019 TA TA TA TA TA TA -A TA TA TA TA TA TT 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 TA TA
16060 T
1 T
16061 GGGACATGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17135 original size:15 final size:16
Alignment explanation
Indices: 17105--17137 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
17095 CGATCCGAGT
17105 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
17121 CCGAACCCG-AAATAC
1 CCGAACCCGAAAATAC
17136 CC
1 CC
17138 CACCCGAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.39, C:0.42, G:0.12, T:0.06
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:17544 original size:33 final size:33
Alignment explanation
Indices: 17507--17931 Score: 431
Period size: 33 Copynumber: 12.8 Consensus size: 33
17497 AAAGAAGTGT
* *
17507 TCGAAGGGGTCAAAGGGGTGATTGGAACAACGC
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
**
17540 TCGAAGGGGCCAAAGGACTGACTGGAACAACGC
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
* * * *
17573 TCGGAGGAGCCAAA-GTGTGATTGGAACAACGC
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
* * * *
17605 TCAAAGGGGCCAAAGGGGTAACTGAAACAACGT
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
* * * *
17638 TGGAAGGGGTCAAAGGCGTGATTGGAACAACGC
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
* * *
17671 TCGACGGGGCCAATGGGGTAACTGGAACAACGC
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
* * ** *
17704 TCGAAGAGGCTAAAGACGTGAGTGGAACAACGC
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
*
17737 TCGAAGGGGCCAAAGGTGTGACTGGAACAACGC
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
* * *
17770 TTGAAGGGGCAAAAAGGGGTGACTAGAACAACGC
1 TCGAAGGGGC-CAAAGGGGTGACTGGAACAACGC
* * * *
17804 TCGAAGGGACC-AAGGGCATGAATATTGAAACAACGC
1 TCGAAGGGGCCAAAGGG-GTG---ACTGGAACAACGC
* * * *
17840 TGGTAGGGGCCAAAGGCGCGACTGGAACAACGC
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
* *
17873 TCGAAGGGGCTAAAGGCGTGACTGGAACAACGC
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
* *
17906 TTGAAGGGACCAAAGGGGTGACTGGA
1 TCGAAGGGGCCAAAGGGGTGACTGGA
17932 GGATGGTTTT
Statistics
Matches: 313, Mismatches: 72, Indels: 14
0.78 0.18 0.04
Matches are distributed among these distances:
32 31 0.10
33 231 0.74
34 28 0.09
36 19 0.06
37 4 0.01
ACGTcount: A:0.33, C:0.19, G:0.36, T:0.13
Consensus pattern (33 bp):
TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
Found at i:18503 original size:50 final size:49
Alignment explanation
Indices: 18381--18604 Score: 231
Period size: 49 Copynumber: 4.6 Consensus size: 49
18371 AATCATGGCA
* * * *
18381 AAACAACATCTTCCTATCGGGAAGGGCAAATC-AGGAATAAGACAAAATT
1 AAACAACACCTTCCGATGGGGAAGGGCAAAACGA-GAATAAGACAAAATT
**
18430 AAACAACACCTTCCGACCGGGAAGGGCAAAACGAGAATAAGACAAAATTT
1 AAACAACACCTTCCGATGGGGAAGGGCAAAACGAGAATAAGACAAAA-TT
* * * ** *
18480 AAACAACACCTTCTGGTGGGGAAGGGCAAAACGAGAAT--GAGATGACT
1 AAACAACACCTTCCGATGGGGAAGGGCAAAACGAGAATAAGACAAAATT
* * * * *
18527 AAACAACACCTTCTGATGGGGAAGGGCGAAACGGGAATAAGGC-AATTT
1 AAACAACACCTTCCGATGGGGAAGGGCAAAACGAGAATAAGACAAAATT
* *
18575 AAACAACACCTTCCGGTGAGGAAGGGCAAA
1 AAACAACACCTTCCGATGGGGAAGGGCAAA
18605 CTGGGAAACT
Statistics
Matches: 146, Mismatches: 25, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
47 36 0.25
48 31 0.21
49 42 0.29
50 37 0.25
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.15
Consensus pattern (49 bp):
AAACAACACCTTCCGATGGGGAAGGGCAAAACGAGAATAAGACAAAATT
Found at i:18547 original size:47 final size:45
Alignment explanation
Indices: 18399--18688 Score: 214
Period size: 47 Copynumber: 6.2 Consensus size: 45
18389 TCTTCCTATC
* * * ***
18399 GGGAAGGGCAAATCAGGAATAAGACAAAATTAAACAACACCTTCCGACC
1 GGGAAGGGCAAA-C-GGAATGAGAC--AACTAAACAACACCTTCTGGTG
* *
18448 GGGAAGGGCAAAACGAGAATAAGACAAAATTTAAACAACACCTTCTGGTG
1 GGGAAGGGC-AAACG-GAATGAGAC--AA-CTAAACAACACCTTCTGGTG
** *
18498 GGGAAGGGCAAAACGAGAATGAGATGACTAAACAACACCTTCTGATG
1 GGGAAGGGC-AAACG-GAATGAGACAACTAAACAACACCTTCTGGTG
* * * *
18545 GGGAAGGGCGAAACGGGAATAAGGCAATTTAAACAACACCTTCCGGTG
1 GGGAAGGGC-AAAC-GGAATGAGACAA-CTAAACAACACCTTCTGGTG
* * *
18593 AGGAAGGGCAAAC----TGGGA-AACTACACAACACCTTCCT-GTG
1 GGGAAGGGCAAACGGAATGAGACAACTAAACAACACCTT-CTGGTG
*
18633 GGGAAGGGCAAACTGGTAATTAGACAACTAAACAACACCTTCTGGTG
1 GGGAAGGGCAAAC-GG-AATGAGACAACTAAACAACACCTTCTGGTG
18680 GGGAAGGGC
1 GGGAAGGGC
18689 GAACTTAGAA
Statistics
Matches: 199, Mismatches: 28, Indels: 30
0.77 0.11 0.12
Matches are distributed among these distances:
40 27 0.14
41 3 0.02
42 2 0.01
46 5 0.03
47 69 0.35
48 28 0.14
49 23 0.12
50 42 0.21
ACGTcount: A:0.39, C:0.19, G:0.27, T:0.15
Consensus pattern (45 bp):
GGGAAGGGCAAACGGAATGAGACAACTAAACAACACCTTCTGGTG
Found at i:18638 original size:40 final size:39
Alignment explanation
Indices: 18574--18743 Score: 144
Period size: 40 Copynumber: 4.1 Consensus size: 39
18564 TAAGGCAATT
* *
18574 TAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAAC
1 TAAACAACACCTT-CTGTGGGGAAGGGCAAACTGGGAAAC
*
18614 TACACAACACCTTCCTGTGGGGAAGGGCAAACTGGTAATTAGACAAC
1 TAAACAACACCTT-CTGTGGGGAAGGGCAAACTGG------GA-AAC
* **
18661 TAAACAACACCTTCTGGTGGGGAAGGGCGAACTTAGAATA-
1 TAAACAACACCTTCT-GTGGGGAAGGGCAAACTGGGAA-AC
* * *
18701 AAAACAACACCTTCTGATCGGGAAGGGCAAACTAGGAAAC
1 TAAACAACACCTTCTG-TGGGGAAGGGCAAACTGGGAAAC
18741 TAA
1 TAA
18744 GAATAAGAAG
Statistics
Matches: 106, Mismatches: 13, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
39 2 0.02
40 66 0.62
41 3 0.03
46 4 0.04
47 31 0.29
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.16
Consensus pattern (39 bp):
TAAACAACACCTTCTGTGGGGAAGGGCAAACTGGGAAAC
Found at i:18868 original size:41 final size:41
Alignment explanation
Indices: 18753--19342 Score: 527
Period size: 41 Copynumber: 14.1 Consensus size: 41
18743 AGAATAAGAA
** *
18753 GAAA-CTAAACAACACCTTCCGACCG-GGAAGGGCGAACTGG
1 GAAATCTAAACAACACCTTCCG-GTGAGGAAGGGCAAACTGG
* * * *
18793 GAATAT-GAAGACAATACCTTCCGATGGGGAAGGGCAAACTGG
1 GAA-ATCTAA-ACAACACCTTCCGGTGAGGAAGGGCAAACTGG
* *
18835 GAAATCTAAACAACACCTTCCGGTGGGGTAGGGCAAACTGG
1 GAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGG
* * * *
18876 AAAATCTAAACAACACTTTCCAGTGGGGAAGGGCAAACTGG
1 GAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGG
* * * * *
18917 GAAATCTAAACAATACCTTCCGGTGAGGAAGGACGAACCGA
1 GAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGG
18958 GAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAAGA-TGG
1 GAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAA-ACTGG
* *
18999 GAAACGCAAACTTAAACAACACCTTCCGAT-ATGGAAGGGCAAACTGG
1 G--A---AATC-TAAACAACACCTTCCGGTGA-GGAAGGGCAAACTGG
* *
19046 GAAA-CTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGA
1 GAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGG
* * * *
19086 GAAGTCTAAACAACATCTTCCTGTGAGGAAGGGCAAGA-TGA
1 GAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAA-ACTGG
*
19127 GAAATGCAAACTTAAACAACACCTTCCGAT-ATGGAAGGGCAAACTGG
1 GAAAT-----C-TAAACAACACCTTCCGGTGA-GGAAGGGCAAACTGG
* *
19174 GAAA-CTAAAAAACACCTTCCAGTGAGGAAGGGCAAACTGG
1 GAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGG
* **
19214 G-AATTTAAACAACACCTTCCGACGAGGAAGGGCAAACTGG
1 GAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGG
* * *
19254 G-AATTTAAACAACACCTCCCGATGAGGAAGGGCAAACTGG
1 GAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGG
* * ** *
19294 GATTAAGCAACTAAAGAACACCTTCCGACGAGTAAGGGCAAACTGG
1 G---AA--ATCTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGG
19340 GAA
1 GAA
19343 TTAGACAAAG
Statistics
Matches: 460, Mismatches: 57, Indels: 63
0.79 0.10 0.11
Matches are distributed among these distances:
39 2 0.00
40 138 0.30
41 177 0.38
42 35 0.08
43 3 0.01
44 1 0.00
45 1 0.00
46 41 0.09
47 62 0.13
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (41 bp):
GAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGG
Found at i:19035 original size:47 final size:43
Alignment explanation
Indices: 18751--19478 Score: 305
Period size: 41 Copynumber: 16.9 Consensus size: 43
18741 TAAGAATAAG
** *
18751 AAGAAACTAAACAACACCTTCCGACCGGGAAGGGCGAACTGGGA
1 AAGAAACTAAACAACACCTTCCGA-TAGGAAGGGCAAACTGGGA
* * *
18795 ATATG--A--AGACAATACCTTCCGATGGGGAAGGGCAAACTGGG-
1 A-A-GAAACTAAACAACACCTTCCGAT-AGGAAGGGCAAACTGGGA
* * * *
18836 -A-AATCTAAACAACACCTTCCGGTGGGGTAGGGCAAACT-GG-
1 AAGAAACTAAACAACACCTTCCGAT-AGGAAGGGCAAACTGGGA
* * *
18876 AA-AATCTAAACAACACTTTCC-AGTGGGGAAGGGCAAACTGGG-
1 AAGAAACTAAACAACACCTTCCGA-T-AGGAAGGGCAAACTGGGA
* * * * * *
18918 -A-AATCTAAACAATACCTTCCGGTGAGGAAGGACGAAC--CG-
1 AAGAAACTAAACAACACCTTCCGAT-AGGAAGGGCAAACTGGGA
*
18957 -AGAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAAGA-TGGGA
1 AAGAAA-CTAAACAACACCTTCCGAT-AGGAAGGGCAA-ACTGGGA
19001 AACGCAAACTTAAACAACACCTTCCGATATGGAAGGGCAAACT-GG-
1 AA-G-AAAC-TAAACAACACCTTCCGATA-GGAAGGGCAAACTGGGA
* * *
19046 --GAAACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGAG-
1 AAGAAACTAAACAACACCTTCCGAT-AGGAAGGGCAAACTGGGA
* * *
19087 AAG--TCTAAACAACATCTTCCTG-TGAGGAAGGGCAAGA-TGAGA
1 AAGAAACTAAACAACACCTTCC-GAT-AGGAAGGGCAA-ACTGGGA
19129 AATGCAAACTTAAACAACACCTTCCGATATGGAAGGGCAAACT-GG-
1 AA-G-AAAC-TAAACAACACCTTCCGATA-GGAAGGGCAAACTGGGA
*
19174 --GAAACTAAAAAACACCTTCC-AGTGAGGAAGGGCAAACT-GG-
1 AAGAAACTAAACAACACCTTCCGA-T-AGGAAGGGCAAACTGGGA
** *
19214 --GAATTTAAACAACACCTTCCGACGAGGAAGGGCAAACT-GG-
1 AAGAAACTAAACAACACCTTCCGA-TAGGAAGGGCAAACTGGGA
** *
19254 --GAATTTAAACAACACCTCCCGATGAGGAAGGGCAAACTGGGA
1 AAGAAACTAAACAACACCTTCCGAT-AGGAAGGGCAAACTGGGA
* * * *
19296 TTAAGCAACTAAAGAACACCTTCCGACGAGTAAGGGCAAACTGGGA
1 --AAGAAACTAAACAACACCTTCCGA-TAGGAAGGGCAAACTGGGA
* *** *
19342 ATTAGACAAAGCTAGACAACACCTTCCAGCGGGGAAGGGCAAATTGGGA
1 A--AG--AAA-CTAAACAACACCTTCC-GATAGGAAGGGCAAACTGGGA
* * * * * * *
19391 ATTTGACAATTATACAACACCTTCCAACTGGGAAGGGCAAAATAGGA
1 A--AGA-AACTAAACAACACCTTCCGA-TAGGAAGGGCAAACTGGGA
* * *
19438 AATTGGCAACTAGACAACACCTTCCGACTGGGAAGGGCAAA
1 AA---GAAACTAAACAACACCTTCCGA-TAGGAAGGGCAAA
19479 ACCAAAAATC
Statistics
Matches: 555, Mismatches: 69, Indels: 117
0.75 0.09 0.16
Matches are distributed among these distances:
39 4 0.01
40 132 0.24
41 164 0.30
42 39 0.07
43 3 0.01
44 3 0.01
45 2 0.00
46 48 0.09
47 120 0.22
48 5 0.01
49 34 0.06
50 1 0.00
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.15
Consensus pattern (43 bp):
AAGAAACTAAACAACACCTTCCGATAGGAAGGGCAAACTGGGA
Found at i:19094 original size:128 final size:126
Alignment explanation
Indices: 18754--19295 Score: 583
Period size: 128 Copynumber: 4.3 Consensus size: 126
18744 GAATAAGAAG
** * * *
18754 AAACTAAACAACACCTTCCGACCGGGAAGGGCGAACTGGGAATA-TGAAGACAATACCTTCCGAT
1 AAACTAAACAACACCTTCCGATAGGGAAGGGCAAACTGGGAA-ACT-AA-ACAACACCTTCCGGT
* * * *
18818 GGGGAAGGGCAAACTGGGAAATCTAAACAACACCTTCCGGTGGGGTAGGGCAAACT-GG-AA--
63 GAGGAAGGGCAAACTGAGAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAAGC
* * * *
18878 AATCTAAACAACACTTTCC-AGTGGGGAAGGGCAAACTGGGAAATCTAAACAATACCTTCCGGTG
1 AAACTAAACAACACCTTCCGA-TAGGGAAGGGCAAACTGGGAAA-CTAAACAACACCTTCCGGTG
* * *
18942 AGGAAGGACGAACCGAGAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAAGA-TGGGAAACGC
64 AGGAAGGGCAAACTGAGAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAA-ACTGGGAAA-GC
* *
19006 AAACTTAAACAACACCTTCCGATATGGAAGGGCAAACTGGGAAACTAAACAACACCTTCCGGTGG
1 AAAC-TAAACAACACCTTCCGATAGGGAAGGGCAAACTGGGAAACTAAACAACACCTTCCGGTGA
* * * *
19071 GGAAGGGCAAACTGAGAAGTCTAAACAACATCTTCCTGTGAGGAAGGGCAAGA-TGAGAAATGC
65 GGAAGGGCAAACTGAGAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAA-ACTGGGAAA-GC
* * *
19134 AAACTTAAACAACACCTTCCGATATGGAAGGGCAAACTGGGAAACTAAAAAACACCTTCCAGTGA
1 AAAC-TAAACAACACCTTCCGATAGGGAAGGGCAAACTGGGAAACTAAACAACACCTTCCGGTGA
* * **
19199 GGAAGGGCAAACTG-GGAATTTAAACAACACCTTCCGACGAGGAAGGGCAAACT-GG---G-
65 GGAAGGGCAAACTGAGAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAAGC
** *
19255 AATTTAAACAACACCTCCCGAT-GAGGAAGGGCAAACTGGGA
1 AAACTAAACAACACCTTCCGATAG-GGAAGGGCAAACTGGGA
19296 TTAAGCAACT
Statistics
Matches: 363, Mismatches: 42, Indels: 30
0.83 0.10 0.07
Matches are distributed among these distances:
120 34 0.09
121 2 0.01
122 1 0.00
123 63 0.17
124 40 0.11
125 3 0.01
126 2 0.01
127 30 0.08
128 153 0.42
129 34 0.09
130 1 0.00
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (126 bp):
AAACTAAACAACACCTTCCGATAGGGAAGGGCAAACTGGGAAACTAAACAACACCTTCCGGTGAG
GAAGGGCAAACTGAGAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAAGC
Found at i:19138 original size:87 final size:87
Alignment explanation
Indices: 19047--19288 Score: 236
Period size: 80 Copynumber: 2.9 Consensus size: 87
19037 GCAAACTGGG
* * * * * *
19047 AAAC-TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGAGAAGTCTAAACAACATCTTCCTGTG
1 AAACTTAAACAACACCTTCCGATAGGGAAGGGCAAACTGAGAA-ACTAAAAAACACCTTCCAGTG
19111 AGGAAGGGCAAGATGAGAAATGC
65 AGGAAGGGCAAGATGAGAAATGC
* *
19134 AAACTTAAACAACACCTTCCGATATGGAAGGGCAAACTGGGAAACTAAAAAACACCTTCCAGTGA
1 AAACTTAAACAACACCTTCCGATAGGGAAGGGCAAACTGAGAAACTAAAAAACACCTTCCAGTGA
19199 GGAAGGGCAA-ACTG-G----G-
66 GGAAGGGCAAGA-TGAGAAATGC
* * * ** * *
19215 -AATTTAAACAACACCTTCCGA-CGAGGAAGGGCAAACTGGGAATTTAAACAACACC-TCCCGAT
1 AAACTTAAACAACACCTTCCGATAG-GGAAGGGCAAACTGAGAAACTAAAAAACACCTTCCAG-T
19277 GAGGAAGGGCAA
64 GAGGAAGGGCAA
19289 ACTGGGATTA
Statistics
Matches: 136, Mismatches: 15, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
79 4 0.03
80 61 0.45
82 1 0.01
86 2 0.01
87 34 0.25
88 34 0.25
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.15
Consensus pattern (87 bp):
AAACTTAAACAACACCTTCCGATAGGGAAGGGCAAACTGAGAAACTAAAAAACACCTTCCAGTGA
GGAAGGGCAAGATGAGAAATGC
Found at i:19280 original size:80 final size:79
Alignment explanation
Indices: 19138--19344 Score: 247
Period size: 80 Copynumber: 2.5 Consensus size: 79
19128 AAATGCAAAC
* ** *
19138 TTAAACAACACCTTCCGA-TATGGAAGGGCAAACTGGGAAACTAAAAAACACCTTCCAGTGAGGA
1 TTAAACAACACCTTCCGACGA-GGAAGGGCAAACTGGGAATTTAAAAAACACCTCCCAGTGAGGA
19202 AGGGCAAACTGGGAAT
65 AGGGCAAACTGGG-AT
*
19218 TTAAACAACACCTTCCGACGAGGAAGGGCAAACTGGGAATTTAAACAACACCTCCC-GATGAGGA
1 TTAAACAACACCTTCCGACGAGGAAGGGCAAACTGGGAATTTAAAAAACACCTCCCAG-TGAGGA
19282 AGGGCAAACTGGGAT
65 AGGGCAAACTGGGAT
* *
19297 TAAGCAACTAAAGAACACCTTCCGACGAGTAAGGGCAAACTGGGAATT
1 T-------TAAACAACACCTTCCGACGAGGAAGGGCAAACTGGGAATT
19345 AGACAAAGCT
Statistics
Matches: 111, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
79 4 0.04
80 68 0.61
81 1 0.01
86 38 0.34
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.16
Consensus pattern (79 bp):
TTAAACAACACCTTCCGACGAGGAAGGGCAAACTGGGAATTTAAAAAACACCTCCCAGTGAGGAA
GGGCAAACTGGGAT
Found at i:19479 original size:47 final size:47
Alignment explanation
Indices: 19262--19479 Score: 187
Period size: 47 Copynumber: 4.6 Consensus size: 47
19252 GGGAATTTAA
* * * *
19262 ACAACACCTCCCGA-TGAGGAAGGGCAAACTGG-GATTA-AGCAACTAA
1 ACAACACCTTCCGACTG-GGAAGGGCAAAATGGAAATTAGA-CAACTAG
* * * *
19308 AGAACACCTTCCGAC-GAGTAAGGGCAAACTGGGAATTAGACAAAGCTAG
1 ACAACACCTTCCGACTG-GGAAGGGCAAAATGGAAATTAGAC-AA-CTAG
* * * * * *
19357 ACAACACCTTCC-AGCGGGGAAGGGCAAATTGGGAATTTGACAATTAT
1 ACAACACCTTCCGA-CTGGGAAGGGCAAAATGGAAATTAGACAACTAG
* *
19404 ACAACACCTTCCAACTGGGAAGGGCAAAATAGGAAATT-GGCAACTAG
1 ACAACACCTTCCGACTGGGAAGGGCAAAAT-GGAAATTAGACAACTAG
19451 ACAACACCTTCCGACTGGGAAGGGCAAAA
1 ACAACACCTTCCGACTGGGAAGGGCAAAA
19480 CCAAAAATCA
Statistics
Matches: 145, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
46 28 0.19
47 67 0.46
48 13 0.09
49 36 0.25
50 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.15
Consensus pattern (47 bp):
ACAACACCTTCCGACTGGGAAGGGCAAAATGGAAATTAGACAACTAG
Found at i:20156 original size:31 final size:30
Alignment explanation
Indices: 20093--20154 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
20083 ATTTCATCAT
*
20093 TTACTAAAAGTTCAATCTTTATTTACAAAAA
1 TTACTAAAAGTTCAATCTTTAATTA-AAAAA
*
20124 TTACTTAAAAGTTCAATGTTTTAATTAAAAA
1 TTAC-TAAAAGTTCAAT-CTTTAATTAAAAA
20155 TTCAATCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 4 0.15
32 16 0.59
33 7 0.26
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (30 bp):
TTACTAAAAGTTCAATCTTTAATTAAAAAA
Found at i:20472 original size:51 final size:51
Alignment explanation
Indices: 20302--20470 Score: 241
Period size: 51 Copynumber: 3.3 Consensus size: 51
20292 AAGACCACAC
* ** * *
20302 TTTTATTTACAAATTAATCATCAA-TTCCATCATTTGGTTCAAAGATATCAT
1 TTTTATTTACAAATTAATCA-CAAGTTCAATCATTTAATTCAAAGCTCTCAT
*
20353 TTTTATTTAAAAATTAATCACAAGTTCAATCATTTAATTCAAAGCTCTCAT
1 TTTTATTTACAAATTAATCACAAGTTCAATCATTTAATTCAAAGCTCTCAT
* * *
20404 TTTTATTTACAAATTACTTACAAGTTCAATCATTTAATTCAAAGCTCTCGT
1 TTTTATTTACAAATTAATCACAAGTTCAATCATTTAATTCAAAGCTCTCAT
20455 TTTTATTTACAAATTA
1 TTTTATTTACAAATTA
20471 CTCAAAAGCT
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
50 3 0.03
51 104 0.97
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (51 bp):
TTTTATTTACAAATTAATCACAAGTTCAATCATTTAATTCAAAGCTCTCAT
Found at i:24704 original size:48 final size:47
Alignment explanation
Indices: 24652--24886 Score: 276
Period size: 48 Copynumber: 4.9 Consensus size: 47
24642 TCTCTCAATT
* * * *
24652 TTTTACTTACATTTTCTCAAAATGCCCTTCCCGGACGGAAGACACTTA
1 TTTTACTTGCTTTTTC-CAAAACGCCCTTCCCGGACGGAAGGCACTTA
* *
24700 TTTTACTTG-TTTCTTCCCAAAACGCCATTCCCAGACGGAAGGCACTTA
1 TTTTACTTGCTTT-TT-CCAAAACGCCCTTCCCGGACGGAAGGCACTTA
* * *
24748 TTTTACTTGCTTTTTCCCAAAACGTCCTTCCTGGACGGAAGGCACTTT
1 TTTTACTTGCTTTTT-CCAAAACGCCCTTCCCGGACGGAAGGCACTTA
* *
24796 TTTTACCTGCTATTTCCAAAAACGCCCTTCCCGGACGGAAGGCACTT-
1 TTTTACTTGCTTTTTCC-AAAACGCCCTTCCCGGACGGAAGGCACTTA
* *
24843 TTTTACCTGCTTTTTCCAAAAAACGCCCTTCCCGGATGGAAGGC
1 TTTTACTTGCTTTTTCC--AAAACGCCCTTCCCGGACGGAAGGC
24887 GTTAATGTTT
Statistics
Matches: 165, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
47 20 0.12
48 141 0.85
49 4 0.02
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (47 bp):
TTTTACTTGCTTTTTCCAAAACGCCCTTCCCGGACGGAAGGCACTTA
Found at i:26794 original size:6 final size:6
Alignment explanation
Indices: 26785--26817 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
26775 AAAGCAAAGC
26785 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
26818 GCAGATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Done.