Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012556.1 Corchorus capsularis cultivar CVL-1 contig12577, 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: 50970
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1658 original size:19 final size:20
Alignment explanation
Indices: 1620--1658 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1610 GCTTGGTCCC
* *
1620 TTTGCTTCCAAATTTCAATT
1 TTTGCTACCAAATCTCAATT
1640 TTTGCTACCAAA-CTCAATT
1 TTTGCTACCAAATCTCAATT
1659 CCAACTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (20 bp):
TTTGCTACCAAATCTCAATT
Found at i:7525 original size:5 final size:5
Alignment explanation
Indices: 7506--7537 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
7496 TTGCTTTAAA
7506 AAAAT -AAAT -AAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
7538 AATATTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:8637 original size:21 final size:21
Alignment explanation
Indices: 8611--8663 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
8601 GCACTGGAGT
* * * *
8611 ACATGGGTCGCGAGGCAAATC
1 ACATGGGGCGCCAAGCAAACC
8632 ACATGGGGCGCCAAGCAAACC
1 ACATGGGGCGCCAAGCAAACC
8653 ACAT-GGGCGCC
1 ACATGGGGCGCC
8664 CAGCGCTAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.28, C:0.30, G:0.32, T:0.09
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:15966 original size:8 final size:7
Alignment explanation
Indices: 15946--15978 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
15936 GAAATGTAAG
15946 CTTTTCTT
1 CTTTT-TT
15954 CTTTTTT
1 CTTTTTT
15961 CTTTTTT
1 CTTTTTT
15968 CTTTTTT
1 CTTTTTT
15975 -TTTT
1 CTTTT
15979 AATATTTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 4 0.16
7 16 0.64
8 5 0.20
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
CTTTTTT
Found at i:16381 original size:27 final size:27
Alignment explanation
Indices: 16309--16374 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
16299 AGTTGATCCA
*
16309 AAATGACCGAAATGCCCCTGAAGATGC
1 AAATGACCAAAATGCCCCTGAAGATGC
*
16336 AACTGACCAAAATGCCCCTGAATG-TGC
1 AAATGACCAAAATGCCCCTGAA-GATGC
16363 AAATGACCAAAA
1 AAATGACCAAAA
16375 CACCCCTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 34 0.97
28 1 0.03
ACGTcount: A:0.41, C:0.26, G:0.18, T:0.15
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAAGATGC
Found at i:16726 original size:23 final size:21
Alignment explanation
Indices: 16696--16739 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 21
16686 CAATCTTAAA
16696 AGAACTGTCTTCCGTGTATCCAT
1 AGAACTGTCTTCCG-GT-TCCAT
16719 AGAACTGTCTTCCGGTTCCAT
1 AGAACTGTCTTCCGGTTCCAT
16740 TTTAAAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.24
22 2 0.10
23 14 0.67
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.34
Consensus pattern (21 bp):
AGAACTGTCTTCCGGTTCCAT
Found at i:16731 original size:50 final size:50
Alignment explanation
Indices: 16666--17094 Score: 592
Period size: 50 Copynumber: 8.6 Consensus size: 50
16656 GAATCAACTT
* * *
16666 CTTCGAATTGTCTTCCAATTCAATCTTAAAAGAACTGTCTTCCG-TGTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCT-TATC
* * ** * * *
16716 CATAGAACTGTCTTCCGGTTCCATTTTAAAAGGACTGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* ** *
16766 CTTCGAACTATCTTCCAATTTGATCTTAAAAGGACCGTCTTCCACTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
*
16816 CTTCGAACTGTCTTCCAATTCAATCTTAGAAGGACCGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
16866 CTTCGAACTGTCTTCCAATTCCATCTTAAAAGGACTGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
16916 CTTCGAACTGTCTTCCAATTCCATCTTAAAAGTACCGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* * * *
16966 CTTTGACCTGTCTTCCAATTCAATCTTAAAAGGAACGTCTTCCGCTTAAC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
*
17016 CTTCGAACTGTCTTCCAATTCAAT-TTCAAAAGGACCGTTTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTT-AAAAGGACCGTCTTCCGCTTATC
* *
17066 CTTCGAACTATCTTCCAATTCCATCTTAA
1 CTTCGAACTGTCTTCCAATTCAATCTTAA
17095 TTTATCCTTT
Statistics
Matches: 335, Mismatches: 41, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
49 2 0.01
50 330 0.99
51 3 0.01
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (50 bp):
CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
Found at i:16902 original size:27 final size:27
Alignment explanation
Indices: 16870--16958 Score: 80
Period size: 27 Copynumber: 3.4 Consensus size: 27
16860 CTTATCCTTC
16870 GAACTGTCTTCCAATTCCATCTTAAAA
1 GAACTGTCTTCCAATTCCATCTTAAAA
* ** *
16897 GGACTGTCTTCCGCTT--ATCCTT---C
1 GAACTGTCTTCCAATTCCAT-CTTAAAA
16920 GAACTGTCTTCCAATTCCATCTTAAAA
1 GAACTGTCTTCCAATTCCATCTTAAAA
* *
16947 GTACCGTCTTCC
1 GAACTGTCTTCC
16959 GCTTATCCTT
Statistics
Matches: 46, Mismatches: 10, Indels: 12
0.68 0.15 0.18
Matches are distributed among these distances:
23 13 0.28
24 3 0.07
25 4 0.09
26 3 0.07
27 23 0.50
ACGTcount: A:0.24, C:0.30, G:0.11, T:0.35
Consensus pattern (27 bp):
GAACTGTCTTCCAATTCCATCTTAAAA
Found at i:19343 original size:29 final size:29
Alignment explanation
Indices: 19310--19371 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
19300 ACCCTATATC
*
19310 TTTTTATTTTTCG-TTAT-TTTCCTTTTTTA
1 TTTTTAGTTTT-GTTTATCTTTCC-TTTTTA
*
19339 TTTTTCGTTTTGTTTATCTTTCCTTTTTA
1 TTTTTAGTTTTGTTTATCTTTCCTTTTTA
19368 TTTT
1 TTTT
19372 CTTTGATACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 23 0.79
30 5 0.17
ACGTcount: A:0.08, C:0.11, G:0.05, T:0.76
Consensus pattern (29 bp):
TTTTTAGTTTTGTTTATCTTTCCTTTTTA
Found at i:23135 original size:6 final size:6
Alignment explanation
Indices: 23119--23149 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
23109 CTAAGCAAAG
23119 TAAAT- TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TA
23150 TGGCAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:24519 original size:11 final size:11
Alignment explanation
Indices: 24502--24533 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
24492 ATAGTCTTTA
24502 AATCTTCAAAT
1 AATCTTCAAAT
*
24513 TATCTTCAAAT
1 AATCTTCAAAT
24524 AATCTTCAAA
1 AATCTTCAAA
24534 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:27368 original size:15 final size:15
Alignment explanation
Indices: 27348--27388 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
27338 AGTTCAAGTT
*
27348 GCTCATCTTCTTGTG
1 GCTCATCTTCTGGTG
27363 GCTCATCTTCTGGTG
1 GCTCATCTTCTGGTG
27378 GCTCATCTTCT
1 GCTCATCTTCT
27389 AGCTTAGCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.07, C:0.29, G:0.20, T:0.44
Consensus pattern (15 bp):
GCTCATCTTCTGGTG
Found at i:28811 original size:6 final size:6
Alignment explanation
Indices: 28795--28825 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
28785 CTAAGCAAAG
28795 TAAAT- TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TA
28826 TGGCAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:30195 original size:11 final size:11
Alignment explanation
Indices: 30178--30209 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
30168 ATAGTCTTTA
30178 AATCTTCAAAT
1 AATCTTCAAAT
*
30189 TATCTTCAAAT
1 AATCTTCAAAT
30200 AATCTTCAAA
1 AATCTTCAAA
30210 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:34535 original size:18 final size:18
Alignment explanation
Indices: 34512--34547 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
34502 CAAGGACTGT
34512 AAGGAAGCATGGACAAGC
1 AAGGAAGCATGGACAAGC
* *
34530 AAGGAAGCGTGGATAAGC
1 AAGGAAGCATGGACAAGC
34548 TTAAAGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.14, G:0.36, T:0.08
Consensus pattern (18 bp):
AAGGAAGCATGGACAAGC
Found at i:34702 original size:43 final size:44
Alignment explanation
Indices: 34618--34704 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 44
34608 GCTTCCTTGT
34618 AATTCAAATCCCTTTTCATTTTGGGTCATTACTAAGTACATATC
1 AATTCAAATCCCTTTTCATTTTGGGTCATTACTAAGTACATATC
*
34662 AATTCAAATCTCTTTTCATTTT-GGTCATTACTAAGTACATATC
1 AATTCAAATCCCTTTTCATTTTGGGTCATTACTAAGTACATATC
34705 GTTCCTTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 21 0.50
44 21 0.50
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.43
Consensus pattern (44 bp):
AATTCAAATCCCTTTTCATTTTGGGTCATTACTAAGTACATATC
Found at i:38466 original size:39 final size:38
Alignment explanation
Indices: 38373--38504 Score: 117
Period size: 39 Copynumber: 3.5 Consensus size: 38
38363 TACCCCAATA
*
38373 AATTAAGAGTC-AAGATAATAGTAACCAGTGAATTAAGT
1 AATTAAGAGTCAAAG-TAATAGTAACCAGTAAATTAAGT
*
38411 AATTAAGAGTCAAAGTAATAGTAACCAGTAAAAATTGA-T
1 AATTAAGAGTCAAAGTAATAGTAACCAGT--AAATTAAGT
* * * ** * **
38450 ACTTAAGAATCAAAGTAATATTAATTAGTCAATCGA-T
1 AATTAAGAGTCAAAGTAATAGTAACCAGTAAATTAAGT
*
38487 GATTAAGAGTCAAAGTAA
1 AATTAAGAGTCAAAGTAA
38505 GAAGATTAAC
Statistics
Matches: 79, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
37 21 0.27
38 25 0.32
39 28 0.35
40 5 0.06
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.27
Consensus pattern (38 bp):
AATTAAGAGTCAAAGTAATAGTAACCAGTAAATTAAGT
Found at i:38576 original size:34 final size:33
Alignment explanation
Indices: 38538--38647 Score: 87
Period size: 34 Copynumber: 3.2 Consensus size: 33
38528 AGTTAAGGAA
38538 AAAAAATTAGTAATCAGTAAATCAGTAATTAAGT
1 AAAAAA-TAGTAATCAGTAAATCAGTAATTAAGT
* * * *
38572 AAAAAGAGATTAATCAGTAAAT-TGATAGTTAAGAGT
1 AAAAA-ATAGTAATCAGTAAATCAG-TAATT-A-AGT
** *
38608 CAAGGTAATAGTAATCAGTAAATCGGTAATTAAGT
1 -AA-AAAATAGTAATCAGTAAATCAGTAATTAAGT
38643 AAAAA
1 AAAAA
38648 GAGATTAATC
Statistics
Matches: 57, Mismatches: 12, Indels: 15
0.68 0.14 0.18
Matches are distributed among these distances:
33 2 0.04
34 24 0.42
35 5 0.09
36 4 0.07
37 20 0.35
38 2 0.04
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.27
Consensus pattern (33 bp):
AAAAAATAGTAATCAGTAAATCAGTAATTAAGT
Found at i:38767 original size:124 final size:124
Alignment explanation
Indices: 38545--38783 Score: 315
Period size: 124 Copynumber: 1.9 Consensus size: 124
38535 GAAAAAAAAT
* * * *
38545 TAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAGTTAAGAGTCA
1 TAGTAATCAGTAAATCACTAATAAAGTAAAAAGAGATTAATAAGTAAATTGATAATTAAGAGTCA
*** *
38610 AGGTAATAGTAATCAGTAAATCGGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAA
66 A-G-AATAGTAATCAGTAAATCAACAATTAAGTAAAAAGAGAGTAATCAGAGTCAAGGTAA
38671 TAGTAATCAGTAAATCACTAATAAAGT-AAAA-AGATTAATTAAGTAAATTGATAATTAAGGGAG
1 TAGTAATCAGTAAATCACTAATAAAGTAAAAAGAGATTAA-TAAGTAAATTGATAATTAA--GAG
*
38734 T-AA-AAGTAGTAATCAGTAAATCAACAATTAAGTAAAAAGATAGTAATCAG
63 TCAAGAA-TAGTAATCAGTAAATCAACAATTAAGTAAAAAGAGAGTAATCAG
38784 TAAATCGATA
Statistics
Matches: 100, Mismatches: 9, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
123 2 0.02
124 46 0.46
125 21 0.21
126 27 0.27
127 4 0.04
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (124 bp):
TAGTAATCAGTAAATCACTAATAAAGTAAAAAGAGATTAATAAGTAAATTGATAATTAAGAGTCA
AGAATAGTAATCAGTAAATCAACAATTAAGTAAAAAGAGAGTAATCAGAGTCAAGGTAA
Found at i:38783 original size:34 final size:34
Alignment explanation
Indices: 38670--38799 Score: 124
Period size: 34 Copynumber: 3.8 Consensus size: 34
38660 AGTCAAGGTA
*
38670 ATAGTAATCAGTAAATC-ACTAATAAAGTAAAAAG
1 ATAGTAATCAGTAAATCGAC-AATTAAGTAAAAAG
* * * *
38704 AT--TAATTAAGTAAATTGATAATTAAGGGAGTAAAAG
1 ATAGTAA-TCAGTAAATCGACAATTAA-GTA--AAAAG
*
38740 -TAGTAATCAGTAAATCAACAATTAAGTAAAAAG
1 ATAGTAATCAGTAAATCGACAATTAAGTAAAAAG
*
38773 ATAGTAATCAGTAAATCGATAATTAAG
1 ATAGTAATCAGTAAATCGACAATTAAG
38800 AGTCAAGGTA
Statistics
Matches: 76, Mismatches: 12, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
32 3 0.04
33 18 0.24
34 29 0.38
35 3 0.04
36 20 0.26
37 3 0.04
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (34 bp):
ATAGTAATCAGTAAATCGACAATTAAGTAAAAAG
Found at i:38819 original size:40 final size:41
Alignment explanation
Indices: 38768--38845 Score: 133
Period size: 40 Copynumber: 1.9 Consensus size: 41
38758 CAATTAAGTA
38768 AAAAGATAGTAATCAGTAAATC-GATAATTAAGAGTCAAGGT
1 AAAAGATAGTAATCAGTAAATCAG-TAATTAAGAGTCAAGGT
38809 AAAA-ATAGTAATCAGTAAATCAGTAATTAAGAGTCAA
1 AAAAGATAGTAATCAGTAAATCAGTAATTAAGAGTCAA
38846 TGGATTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
40 31 0.86
41 5 0.14
ACGTcount: A:0.51, C:0.08, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAAGATAGTAATCAGTAAATCAGTAATTAAGAGTCAAGGT
Found at i:38825 original size:74 final size:73
Alignment explanation
Indices: 38658--38839 Score: 211
Period size: 69 Copynumber: 2.6 Consensus size: 73
38648 GAGATTAATC
*
38658 AGAGTCAAGGT---AATAGTAATCAGTAAATC-ACTAATAAAGTAAAAAGATTAATTAAGTAAAT
1 AGAGTCAAGGTAAAAATAGTAATCAGTAAATCAAC-AATTAAGTAAAAAGATTAATTAAGTAAAT
*
38719 TGATAATTA
65 CGATAATTA
* * *
38728 AG-G--GA-GTAAAAGTAGTAATCAGTAAATCAACAATTAAGTAAAAAGATAGTAA-TCAGTAAA
1 AGAGTCAAGGTAAAAATAGTAATCAGTAAATCAACAATTAAGTAAAAAGAT--TAATTAAGTAAA
38788 TCGATAATTA
64 TCGATAATTA
**
38798 AGAGTCAAGGTAAAAATAGTAATCAGTAAATCAGTAATTAAG
1 AGAGTCAAGGTAAAAATAGTAATCAGTAAATCAACAATTAAG
38840 AGTCAATGGA
Statistics
Matches: 93, Mismatches: 9, Indels: 16
0.79 0.08 0.14
Matches are distributed among these distances:
66 2 0.02
67 1 0.01
69 33 0.35
70 22 0.24
71 4 0.04
73 1 0.01
74 30 0.32
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.26
Consensus pattern (73 bp):
AGAGTCAAGGTAAAAATAGTAATCAGTAAATCAACAATTAAGTAAAAAGATTAATTAAGTAAATC
GATAATTA
Found at i:38885 original size:74 final size:72
Alignment explanation
Indices: 38669--38901 Score: 233
Period size: 74 Copynumber: 3.2 Consensus size: 72
38659 GAGTCAAGGT
* *
38669 AATAGTAATCAGTAAATCACTAA-TAAAGTAAAAAGATTAATTAAGTAAATTGATAATTAA-GGG
1 AATAGTAATCAGTAAATCAATAATTAAAGTAAAAAGATTAA-TCAGTAAATTGATAATTAAGGGG
38732 --AGTAAA
65 AAAGTAAA
* * *
38738 AGTAGTAATCAGTAAATCAACAATT-AAGTAAAAAGATAGTAATCAGTAAATCGATAATTAAGAG
1 AATAGTAATCAGTAAATCAATAATTAAAGTAAAAAGAT--TAATCAGTAAATTGATAATTAAG-G
** *
38802 TCAAGGTAAA
63 GGAAAGTAAA
* * ** **
38812 AATAGTAATCAGTAAATCAGTAATTAAGAGTCAATGGATTAATCAGTAAATTGATACGTAAGGGA
1 AATAGTAATCAGTAAATCAATAATTAA-AGTAAAAAGATTAATCAGTAAATTGATAATTAAGGG-
38877 GAAAGTAAA
64 GAAAGTAAA
* *
38886 ATTAGTGATCAGTAAA
1 AATAGTAATCAGTAAA
38902 GAGAAAAATG
Statistics
Matches: 132, Mismatches: 22, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
69 32 0.24
70 18 0.14
71 3 0.02
72 1 0.01
73 1 0.01
74 68 0.52
75 1 0.01
76 8 0.06
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.26
Consensus pattern (72 bp):
AATAGTAATCAGTAAATCAATAATTAAAGTAAAAAGATTAATCAGTAAATTGATAATTAAGGGGA
AAGTAAA
Found at i:38965 original size:21 final size:21
Alignment explanation
Indices: 38940--38979 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
38930 TCAAGAGAGT
*
38940 AAAATAGTAATCAGTAAAGGA
1 AAAATAGTAAACAGTAAAGGA
* *
38961 AAAATGGTAAAGAGTAAAG
1 AAAATAGTAAACAGTAAAG
38980 AGTAATCAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.23, T:0.17
Consensus pattern (21 bp):
AAAATAGTAAACAGTAAAGGA
Found at i:38979 original size:7 final size:7
Alignment explanation
Indices: 38967--39069 Score: 50
Period size: 7 Copynumber: 14.6 Consensus size: 7
38957 AGGAAAAATG
38967 GTAAAGA
1 GTAAAGA
38974 GTAAAGA
1 GTAAAGA
**
38981 GTAATCA
1 GTAAAGA
*
38988 GTAAGGA
1 GTAAAGA
* **
38995 GTGATTA
1 GTAAAGA
39002 GTAAAGA
1 GTAAAGA
39009 GTAAA-A
1 GTAAAGA
*
39015 TGATAAAAA
1 -G-TAAAGA
39024 GTAAAGA
1 GTAAAGA
**
39031 GTAATCA
1 GTAAAGA
39038 GTAAAAGAA
1 GT-AAAG-A
*
39047 G-AATG-
1 GTAAAGA
*
39052 GTAAAAA
1 GTAAAGA
39059 GTAAAGA
1 GTAAAGA
39066 GTAA
1 GTAA
39070 TCGGTAAAGG
Statistics
Matches: 70, Mismatches: 19, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
5 1 0.01
6 3 0.04
7 56 0.80
8 7 0.10
9 3 0.04
ACGTcount: A:0.54, C:0.02, G:0.24, T:0.19
Consensus pattern (7 bp):
GTAAAGA
Found at i:39056 original size:50 final size:50
Alignment explanation
Indices: 38952--39063 Score: 129
Period size: 50 Copynumber: 2.3 Consensus size: 50
38942 AATAGTAATC
* * * * * *
38952 AGTAAAG-GAAAAATGGTAAAGAGTAAAGAGTAATCAGTAAGGAGTGATT
1 AGTAAAGAGTAAAATGATAAAAAGTAAAGAGTAATCAGTAAAGAGAGAAT
39001 AGTAAAGAGTAAAATGATAAAAAGTAAAGAGTAATCAGTAAA-AGAAGAAT
1 AGTAAAGAGTAAAATGATAAAAAGTAAAGAGTAATCAGTAAAGAG-AGAAT
* *
39051 GGTAAAAAGTAAA
1 AGTAAAGAGTAAA
39064 GAGTAATCGG
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
49 9 0.17
50 44 0.83
ACGTcount: A:0.55, C:0.02, G:0.24, T:0.19
Consensus pattern (50 bp):
AGTAAAGAGTAAAATGATAAAAAGTAAAGAGTAATCAGTAAAGAGAGAAT
Found at i:39063 original size:35 final size:35
Alignment explanation
Indices: 38987--39113 Score: 148
Period size: 35 Copynumber: 3.6 Consensus size: 35
38977 AAGAGTAATC
* * * *
38987 AGTAAGGAGTGATTAGTAAAGAGTAA-AATGATAAAA
1 AGTAAAGAGTAATCAGTAAA-AG-AAGAATGGTAAAA
39023 AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
1 AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
* * * *
39058 AGTAAAGAGTAATCGGTAAAGGAAGAATGGCAAAG
1 AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
*
39093 AGTAAAGGGTAATCAGTAAAA
1 AGTAAAGAGTAATCAGTAAAA
39114 AGTAAAAAGA
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
34 2 0.03
35 60 0.76
36 17 0.22
ACGTcount: A:0.53, C:0.03, G:0.26, T:0.18
Consensus pattern (35 bp):
AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
Found at i:39068 original size:28 final size:29
Alignment explanation
Indices: 39001--39069 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 29
38991 AGGAGTGATT
*
39001 AGTAAAGAGTAAAATGATAAAAAGTAAAG
1 AGTAAAGAGTAAAATGATAAAAAGTAAAA
** **
39030 AGTAATCAGTAAAA-GA-AGAATGGTAAAA
1 AGTAAAGAGTAAAATGATA-AAAAGTAAAA
39058 AGTAAAGAGTAA
1 AGTAAAGAGTAA
39070 TCGGTAAAGG
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
27 1 0.03
28 19 0.59
29 12 0.38
ACGTcount: A:0.59, C:0.01, G:0.22, T:0.17
Consensus pattern (29 bp):
AGTAAAGAGTAAAATGATAAAAAGTAAAA
Found at i:39130 original size:22 final size:22
Alignment explanation
Indices: 39100--39361 Score: 164
Period size: 22 Copynumber: 11.7 Consensus size: 22
39090 AAGAGTAAAG
39100 GGTAATCAGTAAAAAGTAAAAA
1 GGTAATCAGTAAAAAGTAAAAA
*
39122 GATAATCAGTAAAGAATGAAATAATAAAA
1 GGTAATCAGTAAA-AA-G---T-A-AAAA
* *
39151 GGTAATCAATAAAAAAGGT--AAT
1 GGTAATCAGT-AAAAA-GTAAAAA
* *
39173 GATAATCAGTAAAAGGTAAAATA
1 GGTAATCAGTAAAAAGTAAAA-A
* * *
39196 -GTAATCAGT-AAGAGCAAAAT
1 GGTAATCAGTAAAAAGTAAAAA
* * * *
39216 GGTAATCAGT-GAGAGCAAAAT
1 GGTAATCAGTAAAAAGTAAAAA
*
39237 GGTAATCAGTAAAGAGTAAAATA
1 GGTAATCAGTAAAAAGTAAAA-A
** *
39260 -GTAATCAGTAAAAACCAAGAA
1 GGTAATCAGTAAAAAGTAAAAA
*
39281 GGTAATCAGT-AAGAGTAAAATA
1 GGTAATCAGTAAAAAGTAAAA-A
* *
39303 -GTAACCAGTAAAAAGTAAGAA
1 GGTAATCAGTAAAAAGTAAAAA
*
39324 GGTAATCAGTAAAGAGTAAAATA
1 GGTAATCAGTAAAAAGTAAAA-A
39347 -GTAATCAGTAAAAAG
1 GGTAATCAGTAAAAAG
39362 CAATCAGTAA
Statistics
Matches: 188, Mismatches: 33, Indels: 38
0.73 0.13 0.15
Matches are distributed among these distances:
20 2 0.01
21 56 0.30
22 105 0.56
23 3 0.02
24 1 0.01
26 1 0.01
27 1 0.01
28 1 0.01
29 15 0.08
30 3 0.02
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.20
Consensus pattern (22 bp):
GGTAATCAGTAAAAAGTAAAAA
Found at i:39166 original size:16 final size:17
Alignment explanation
Indices: 39141--39172 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
39131 TAAAGAATGA
39141 AATAATAAAAGGTAATC
1 AATAATAAAAGGTAATC
39158 AATAA-AAAAGGTAAT
1 AATAATAAAAGGTAAT
39173 GATAATCAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.22
Consensus pattern (17 bp):
AATAATAAAAGGTAATC
Found at i:39177 original size:29 final size:29
Alignment explanation
Indices: 39118--39177 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 29
39108 GTAAAAAGTA
* * *
39118 AAAAGATAATCAGTAAAGAATGAAATAAT
1 AAAAGATAATCAATAAAAAAGGAAATAAT
* * *
39147 AAAAGGTAATCAATAAAAAAGGTAATGAT
1 AAAAGATAATCAATAAAAAAGGAAATAAT
39176 AA
1 AA
39178 TCAGTAAAAG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.62, C:0.03, G:0.15, T:0.20
Consensus pattern (29 bp):
AAAAGATAATCAATAAAAAAGGAAATAAT
Found at i:39222 original size:43 final size:41
Alignment explanation
Indices: 39175--39453 Score: 255
Period size: 43 Copynumber: 6.7 Consensus size: 41
39165 AAGGTAATGA
* * *
39175 TAATCAGTAAAAGGTAAAATAGTAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAAA-GTAAAA-GGTAATCAGTAAGAGTAAAATAG
* * *
39218 TAATCAGTGAGAGCAAAATGGTAATCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAAGTAAAA-GGTAATCAGT-AAGAGTAAAATAG
**
39261 TAATCAGTAAAAACCAAGAAGGTAATCAGTAAGAGTAAAATAG
1 TAATCAGT-AAAAGTAA-AAGGTAATCAGTAAGAGTAAAATAG
*
39304 TAACCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAATAG
1 TAATCAGT-AAAAGTAA-AAGGTAATCAGT-AAGAGTAAAATAG
* * *
39348 TAATCAGT---A--AAAA-GCAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAAAGTAAAAGGTAATCAGTAAGAGTAAAATAG
* * * * *
39383 TAATCAATGAGAGCAAAATGGTAATTAGTAAGAGTAAAATAG
1 TAATCAGTAAAAGTAAAA-GGTAATCAGTAAGAGTAAAATAG
*
39425 TAATCAGTAAAGAGTAAAAGGTGATCAGT
1 TAATCAGTAAA-AGTAAAAGGTAATCAGT
39454 GATTTAAAGA
Statistics
Matches: 197, Mismatches: 27, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
35 18 0.09
36 8 0.04
37 2 0.01
38 3 0.02
40 5 0.03
42 49 0.25
43 75 0.38
44 35 0.18
45 2 0.01
ACGTcount: A:0.51, C:0.08, G:0.21, T:0.20
Consensus pattern (41 bp):
TAATCAGTAAAAGTAAAAGGTAATCAGTAAGAGTAAAATAG
Found at i:39312 original size:15 final size:15
Alignment explanation
Indices: 39294--39359 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
39284 AATCAGTAAG
*
39294 AGTAAAATAGTAACC
1 AGTAAAATAGTAAAC
39309 AGTAAAA-AGTAAGA-
1 AGTAAAATAGTAA-AC
*
39323 AGGT--AATCAGTAAAG
1 A-GTAAAAT-AGTAAAC
*
39338 AGTAAAATAGTAATC
1 AGTAAAATAGTAAAC
39353 AGTAAAA
1 AGTAAAA
39360 AGCAATCAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
13 2 0.05
14 9 0.22
15 27 0.66
16 3 0.07
ACGTcount: A:0.56, C:0.06, G:0.18, T:0.20
Consensus pattern (15 bp):
AGTAAAATAGTAAAC
Found at i:39313 original size:65 final size:64
Alignment explanation
Indices: 39179--39357 Score: 193
Period size: 65 Copynumber: 2.8 Consensus size: 64
39169 TAATGATAAT
* * * * *
39179 CAGTAAAAGGTAAAATAGTAATCAGT-AAGAGCAAAATGGTAATCAGTGAGAGCAAAATGGTAAT
1 CAGTAAAA-GTAAAATAGTAATCAGTAAAAACCAAAATGGTAATCAGTAAGAGCAAAATAGTAAC
*
39243 CAGTAAAGAGTAAAATAGTAATCAGTAAAAACCAAGAA-GGTAATCAGTAAGAGTAAAATAGTAA
1 CAGTAAA-AGTAAAATAGTAATCAGTAAAAACCAA-AATGGTAATCAGTAAGAGCAAAATAGTAA
39307 C
64 C
* * ** *
39308 CAGTAAAAAGTAAGAA-GGTAATCAGTAAAGAGTAAAATAGTAATCAGTAA
1 CAGT-AAAAGTAA-AATAGTAATCAGTAAAAACCAAAATGGTAATCAGTAA
39358 AAAGCAATCA
Statistics
Matches: 98, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
64 26 0.27
65 65 0.66
66 7 0.07
ACGTcount: A:0.52, C:0.08, G:0.21, T:0.20
Consensus pattern (64 bp):
CAGTAAAAGTAAAATAGTAATCAGTAAAAACCAAAATGGTAATCAGTAAGAGCAAAATAGTAAC
Found at i:39387 original size:21 final size:21
Alignment explanation
Indices: 39363--39453 Score: 103
Period size: 21 Copynumber: 4.3 Consensus size: 21
39353 AGTAAAAAGC
39363 AATCAGTAAGAGCAAAATGGT
1 AATCAGTAAGAGCAAAATGGT
* *
39384 AATCAATGAGAGCAAAATGGT
1 AATCAGTAAGAGCAAAATGGT
* * *
39405 AATTAGTAAGAGTAAAATAGT
1 AATCAGTAAGAGCAAAATGGT
*
39426 AATCAGTAAAGAGTAAAA-GGT
1 AATCAGT-AAGAGCAAAATGGT
*
39447 GATCAGT
1 AATCAGT
39454 GATTTAAAGA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
21 49 0.83
22 10 0.17
ACGTcount: A:0.48, C:0.07, G:0.23, T:0.22
Consensus pattern (21 bp):
AATCAGTAAGAGCAAAATGGT
Found at i:40285 original size:18 final size:18
Alignment explanation
Indices: 40258--40295 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40248 ATCAAGGAGT
*
40258 GCAAGTAAGCATGGACAA
1 GCAAGGAAGCATGGACAA
*
40276 GCAAGGAAGCGTGGACAA
1 GCAAGGAAGCATGGACAA
40294 GC
1 GC
40296 TTAAAGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.18, G:0.34, T:0.08
Consensus pattern (18 bp):
GCAAGGAAGCATGGACAA
Found at i:41781 original size:13 final size:13
Alignment explanation
Indices: 41748--41783 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
41738 TCTACTCCCT
*
41748 TAAGTGGCATAGC
1 TAAGTGGTATAGC
41761 TAAGTGGTATAGC
1 TAAGTGGTATAGC
*
41774 TAGGTGGTAT
1 TAAGTGGTAT
41784 GAGTGAGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.28, C:0.08, G:0.33, T:0.31
Consensus pattern (13 bp):
TAAGTGGTATAGC
Found at i:44865 original size:156 final size:155
Alignment explanation
Indices: 44556--44921 Score: 384
Period size: 156 Copynumber: 2.3 Consensus size: 155
44546 CCGAACCTCT
* * *
44556 CACCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGA
1 CACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGCTG-
* * * *
44621 AACTTTTCCAAGGGACTTAGATTATCTCCATGAGACTATTGAAAAAATTCTAAGTAAAACCGAGC
65 AACTTTTCCAAGAGACTTAGATTATCTCCATGAGACTATGGAAAAAATTCTAAGTAAAACAGAAC
* * * *
44686 TCCCATTGATGGTGAACTAGGTTTCT
130 TCCCATAGATAGAGAACTAGGTTTCA
* ** **
44712 CTCCCTGAGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAAGCTG
1 CACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACG-AGCTG
*
44776 -A-TTTTCCACCAGTAGACTTAGATTAT-TCCCATGA-AGCTATGGGAAAAATTCTAAGTAAAAC
65 AACTTTTCCA--AG-AGACTTAGATTATCT-CCATGAGA-CTATGGAAAAAATTCTAAGTAAAAC
* * * *
44837 AGAACTCTC-TAGCATAGAGAAGTTGGTTTGA
125 AGAACTCCCATAG-ATAGAGAACTAGGTTTCA
* * * * *
44868 CACCCCAAACTGTCCTTAACTGAAAAACTTGCAAAAGTTTTTCATACAAAGTCT
1 CACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCT
44922 GTTTGAGATG
Statistics
Matches: 171, Mismatches: 31, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
153 7 0.04
154 1 0.01
155 9 0.05
156 154 0.90
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (155 bp):
CACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGCTGA
ACTTTTCCAAGAGACTTAGATTATCTCCATGAGACTATGGAAAAAATTCTAAGTAAAACAGAACT
CCCATAGATAGAGAACTAGGTTTCA
Done.