Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017651.1 Corchorus olitorius cultivar O-4 contig17684, 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: 84416
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:283 original size:15 final size:15
Alignment explanation
Indices: 259--298 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
249 TTTCCTTGGG
* *
259 TCATTCGGGTTCCGC
1 TCATTTGGGTTCAGC
*
274 TCATTTGGGTTCAGG
1 TCATTTGGGTTCAGC
289 TCATTTGGGT
1 TCATTTGGGT
299 CTCGGGTCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.10, C:0.20, G:0.30, T:0.40
Consensus pattern (15 bp):
TCATTTGGGTTCAGC
Found at i:2721 original size:161 final size:161
Alignment explanation
Indices: 2518--2958 Score: 699
Period size: 161 Copynumber: 2.7 Consensus size: 161
2508 AGTTTTACTC
*
2518 AACTATAAACTCTA-TTT-TTATTTAATTAAATATAATATCCTTATAACTATTTAATTTTTACCA
1 AACTAAAAACTCTATTTTATTATTTAATTAAATATAATATCCTTATAACTATTTAATTTTTACCA
2581 TTTTACTATTTTAATTAAAAATATATATATTAGAATTTTTTAAATGTATTTTTATAGTTTTACTT
66 TTTTACTATTTTAATTAAAAATATATATATTAGAATTTTTTAAATGTATTTTTATAGTTTTACTT
2646 AACTAAAAACTCTATTTTTTGGC-AAAAAAA
131 AACTAAAAACTCTATTTTTTGGCAAAAAAAA
2676 AACTAAAAACTCTATTTTTATTATTTAATTAAATATAATATCCTTATAACTATTTAATTTTTACC
1 AACTAAAAACTCTA-TTTTATTATTTAATTAAATATAATATCCTTATAACTATTTAATTTTTACC
*
2741 ATTTTACTATTTTAATTAAAAATATATATATTAGAATTTTTTAAATGTATTTTTGTAGTTTTACT
65 ATTTTACTATTTTAATTAAAAATATATATATTAGAATTTTTTAAATGTATTTTTATAGTTTTACT
2806 TAACTAAAAACTCTATTTTTTGGCAAAAAAAAA
130 TAACTAAAAACTCTATTTTTTGGC-AAAAAAAA
* * * * *
2839 AACTAAAAACTCTACTTTTATTATTTAATTAAATCTAATATCCTTATACCTGTTTTATTTTTATC
1 AACTAAAAACTCTA-TTTTATTATTTAATTAAATATAATATCCTTATAACTATTTAATTTTTACC
* * * * *
2904 AATTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAATATATTT
65 ATTTTACTATTTTAATT-AAAAA--TATATATATTAGAATTTTTTAAATGTATTT
2959 CTTAAATGAC
Statistics
Matches: 262, Mismatches: 13, Indels: 8
0.93 0.05 0.03
Matches are distributed among these distances:
158 13 0.05
160 3 0.01
161 133 0.51
163 81 0.31
164 5 0.02
166 27 0.10
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.48
Consensus pattern (161 bp):
AACTAAAAACTCTATTTTATTATTTAATTAAATATAATATCCTTATAACTATTTAATTTTTACCA
TTTTACTATTTTAATTAAAAATATATATATTAGAATTTTTTAAATGTATTTTTATAGTTTTACTT
AACTAAAAACTCTATTTTTTGGCAAAAAAAA
Found at i:6370 original size:32 final size:31
Alignment explanation
Indices: 6300--6375 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 31
6290 ACGATGACAA
*
6300 AACTGGTCATTCTCCAGTCTTGTCGCTGAAT
1 AACTGGTCATTCTCCAGTCTTGTCGCGGAAT
* *
6331 AATTGGTCATGT-TCCAGTCTTTGTCGCGGCAT
1 AACTGGTCAT-TCTCCAGTC-TTGTCGCGGAAT
6363 AACTGGTCCATTC
1 AACTGGT-CATTC
6376 CAGTTTTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
31 16 0.43
32 18 0.49
33 3 0.08
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (31 bp):
AACTGGTCATTCTCCAGTCTTGTCGCGGAAT
Found at i:6377 original size:31 final size:31
Alignment explanation
Indices: 6300--6384 Score: 86
Period size: 31 Copynumber: 2.7 Consensus size: 31
6290 ACGATGACAA
* *
6300 AACTGGTCATTCTCCAGTC-TTGTCGCTGAAT
1 AACTGGTCAGT-TCCAGTCTTTGTCGCGGAAT
* *
6331 AATTGGTCATGTTCCAGTCTTTGTCGCGGCAT
1 AACTGGTCA-GTTCCAGTCTTTGTCGCGGAAT
6363 AACTGGTCCA-TTCCAGT-TTTGT
1 AACTGGT-CAGTTCCAGTCTTTGT
6385 TTTTTTTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
30 5 0.11
31 22 0.48
32 17 0.37
33 2 0.04
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.38
Consensus pattern (31 bp):
AACTGGTCAGTTCCAGTCTTTGTCGCGGAAT
Found at i:10447 original size:19 final size:19
Alignment explanation
Indices: 10423--10459 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
10413 AAAAAAAAAA
10423 ACCTCATTTGTTTTTATGC
1 ACCTCATTTGTTTTTATGC
10442 ACCTCATTTGTTTTTATG
1 ACCTCATTTGTTTTTATG
10460 TATACAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.19, G:0.11, T:0.54
Consensus pattern (19 bp):
ACCTCATTTGTTTTTATGC
Found at i:20712 original size:2 final size:2
Alignment explanation
Indices: 20667--20693 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20657 TGATATGGGA
20667 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
20694 CTTTATACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28300 original size:23 final size:23
Alignment explanation
Indices: 28229--28300 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 23
28219 TATATATATA
28229 TATTATGTTTA-TTACTAATG-TG
1 TATTATGTTTATTTA-TAATGTTG
* *
28251 ATATTTAT-ATTATTAAT-ATGTAT-
1 -TA-TTATGTTTATTTATAATGT-TG
28274 TATTATGTTTATTTATAATGTTG
1 TATTATGTTTATTTATAATGTTG
28297 TATT
1 TATT
28301 TATTGATACT
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
21 4 0.11
22 13 0.34
23 14 0.37
24 7 0.18
ACGTcount: A:0.31, C:0.01, G:0.10, T:0.58
Consensus pattern (23 bp):
TATTATGTTTATTTATAATGTTG
Found at i:28863 original size:42 final size:41
Alignment explanation
Indices: 28804--28883 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 41
28794 TAAGGATCAG
28804 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAA-TTACAAAGAATTTTCTAT
*
28846 GATTTGAGTTGAGTATTTCTTAATTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTACAAAGAATTTTC
28884 AAGACTTAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
41 14 0.38
42 23 0.62
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.46
Consensus pattern (41 bp):
GATTTGAGTTGAGTATTTCTTAATTACAAAGAATTTTCTAT
Found at i:43044 original size:1 final size:1
Alignment explanation
Indices: 43033--43068 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
43023 TCTCTCTCTC
* *
43033 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
43069 GGAATTGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.03, G:0.03, T:0.94
Consensus pattern (1 bp):
T
Found at i:50495 original size:67 final size:67
Alignment explanation
Indices: 50390--50523 Score: 189
Period size: 67 Copynumber: 2.0 Consensus size: 67
50380 CTTATATATA
* * *
50390 ATTTGCGGTCCACCGAGACTTGCAAAGATTGATGGTGAAATTGATGCAATGTCCCTTATGAATAA
1 ATTTGCGGTCCACCGAGACTTGCAAAGATTGATCGTGAAATCGATACAATGTCCCTTATGAATAA
50455 TT
66 TT
** * *
50457 ATTTGCGGTCCATTGAGACTTGCAAA-AGTTGGTCGTGAAATCGATACAATGTCCCTTTTGAATA
1 ATTTGCGGTCCACCGAGACTTGCAAAGA-TTGATCGTGAAATCGATACAATGTCCCTTATGAATA
50521 ATT
65 ATT
50524 GCAGTCTATT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
66 1 0.02
67 58 0.98
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (67 bp):
ATTTGCGGTCCACCGAGACTTGCAAAGATTGATCGTGAAATCGATACAATGTCCCTTATGAATAA
TT
Found at i:50628 original size:44 final size:44
Alignment explanation
Indices: 50580--50694 Score: 212
Period size: 44 Copynumber: 2.6 Consensus size: 44
50570 TGTCCCAAAA
50580 AATTTGCAGTCCTTTGGACTTGCAAATTGATGTCCCGTATGAAT
1 AATTTGCAGTCCTTTGGACTTGCAAATTGATGTCCCGTATGAAT
50624 AATTTGCAGTCCTTTGGACTTGCAAATTGATGTCCCGTATGAAT
1 AATTTGCAGTCCTTTGGACTTGCAAATTGATGTCCCGTATGAAT
*
50668 AATTTGCAGTCCATTGAGACTTGCAAA
1 AATTTGCAGTCCTTTG-GACTTGCAAA
50695 GGTTTATTGT
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
44 59 0.86
45 10 0.14
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (44 bp):
AATTTGCAGTCCTTTGGACTTGCAAATTGATGTCCCGTATGAAT
Found at i:50651 original size:24 final size:24
Alignment explanation
Indices: 50579--50651 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 24
50569 ATGTCCCAAA
50579 AAATTTGCAGTCCTTTGGACTTGC
1 AAATTTGCAGTCCTTTGGACTTGC
* * *
50603 AAA-TTG-ATGTCC--CGTA--TGA
1 AAATTTGCA-GTCCTTTGGACTTGC
50622 ATAATTTGCAGTCCTTTGGACTTGC
1 A-AATTTGCAGTCCTTTGGACTTGC
50647 AAATT
1 AAATT
50652 GATGTCCCGT
Statistics
Matches: 35, Mismatches: 6, Indels: 16
0.61 0.11 0.28
Matches are distributed among these distances:
19 3 0.09
20 2 0.06
21 9 0.26
22 2 0.06
23 9 0.26
24 7 0.20
25 3 0.09
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (24 bp):
AAATTTGCAGTCCTTTGGACTTGC
Found at i:51307 original size:110 final size:110
Alignment explanation
Indices: 51145--51393 Score: 360
Period size: 110 Copynumber: 2.3 Consensus size: 110
51135 AGTCTATTAT
* * * *
51145 TGAGACTTGCAAAGGTTTATTGCTGGAATTGATGCAATGTCCCGAAAAATTTGCAGTCCTTTGGA
1 TGAGACTTGCAAAGGTTTATTGTTGGAATTGATACAATGTCCCGAAAAATTTGCAGTCCTCTAGA
* *
51210 CTTGCAAACTGATGCAATGTCCCCTA-TGAATAATTTGCAGTCCAC
66 CTTGCAAACTGATGCAATGT-CCCGAGTGAACAATTTGCAGTCCAC
51255 TGAGACTTGCAAAGGTTTATTGTTGGAATTGATACAATGTCCC-AAATAATTTGCAGTCCTCTAG
1 TGAGACTTGCAAAGGTTTATTGTTGGAATTGATACAATGTCCCGAAA-AATTTGCAGTCCTCTAG
* *
51319 ATTTGCAAATTGATGCAATGTCCCGAGTGAACAATTTGCAGTCCAC
65 ACTTGCAAACTGATGCAATGTCCCGAGTGAACAATTTGCAGTCCAC
* * *
51365 CGAGACTTGCAAA-GTTTAATGTTGAAATT
1 TGAGACTTGCAAAGGTTTATTGTTGGAATT
51394 TATGCATGGT
Statistics
Matches: 126, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
109 21 0.17
110 105 0.83
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (110 bp):
TGAGACTTGCAAAGGTTTATTGTTGGAATTGATACAATGTCCCGAAAAATTTGCAGTCCTCTAGA
CTTGCAAACTGATGCAATGTCCCGAGTGAACAATTTGCAGTCCAC
Found at i:52431 original size:67 final size:67
Alignment explanation
Indices: 52315--52447 Score: 178
Period size: 67 Copynumber: 2.0 Consensus size: 67
52305 GTCTTTATGG
* * *
52315 TTTGCGGTCCACAGAGACTTACAAAGATTGATGGTGAAATTGATGCAATGTCCCTTATGAATAAT
1 TTTGCGGTCCACAGAGACTTACAAAGATTGATCGTGAAATCGATACAATGTCCCTTATGAATAAT
52380 TA
66 TA
** * * *
52382 TTTGCGGTCCATTGAGACTTGCAAA-AGTTGGTCGTGAAATCGATACAATGTCCCTTTTGAATAA
1 TTTGCGGTCCACAGAGACTTACAAAGA-TTGATCGTGAAATCGATACAATGTCCCTTATGAATAA
52446 TT
65 TT
52448 GCAGTCTATT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 1 0.02
67 56 0.98
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (67 bp):
TTTGCGGTCCACAGAGACTTACAAAGATTGATCGTGAAATCGATACAATGTCCCTTATGAATAAT
TA
Found at i:52567 original size:105 final size:105
Alignment explanation
Indices: 52429--53031 Score: 760
Period size: 105 Copynumber: 5.6 Consensus size: 105
52419 AATCGATACA
* * * * *
52429 ATGTCCCTTTTGAATAA-TTGCAGTCTATTGAGACTTGCAAAGGTTTATTTTTGGCATTGATGCA
1 ATGTCCCGTATGAATAATTTGCAGTCCATTGAGACTTGCAAAGGTTTATTGTTGGAATTGATGCA
*
52493 ATTTCCCAAAAAATTTGCAGTCCTCTGGACTTGCAAACTG
66 ATGTCCCAAAAAATTTGCAGTCCTCTGGACTTGCAAACTG
*
52533 ATGTCCCGTATGAATAATTTGCAGTCCATTGAGACTTTCAAAGGTTTATTGTTGGAATTGATGCA
1 ATGTCCCGTATGAATAATTTGCAGTCCATTGAGACTTGCAAAGGTTTATTGTTGGAATTGATGCA
52598 ATGTCCCAAAAAATTTGCAGTCCTCTGGACTTGCAAACTG
66 ATGTCCCAAAAAATTTGCAGTCCTCTGGACTTGCAAACTG
*
52638 ATGTCCCGTATGAATAATTTGCAGTCCATTGAGACTTTCAAAGGTTTATTGTTGGAATTGATGCA
1 ATGTCCCGTATGAATAATTTGCAGTCCATTGAGACTTGCAAAGGTTTATTGTTGGAATTGATGCA
* * * * * *
52703 ATGTCCCGAATAATTTGCGGTCCTCTGCAAAAGTTGGTCGTGAAATCGATACA
66 ATGTCCCAAAAAATTTGCAGTCCTCTG---GACTT-G-C---AAA-C--T--G
* * * * *
52756 ATGTCCCTTTTGAATAA-TTGCAGTCTATTGAGACTTGCAAAGGTTTATTTTTGGCATTGATGCA
1 ATGTCCCGTATGAATAATTTGCAGTCCATTGAGACTTGCAAAGGTTTATTGTTGGAATTGATGCA
52820 ATGTCCCAAAAAATTTGCAGTCCTCTGGACTTGCAAACTG
66 ATGTCCCAAAAAATTTGCAGTCCTCTGGACTTGCAAACTG
* *
52860 ATGTCCCGTATGAATAATTTGCATTCCATTGAGACTTTCAAAGGTTTATTGTTGGAATTGATGCA
1 ATGTCCCGTATGAATAATTTGCAGTCCATTGAGACTTGCAAAGGTTTATTGTTGGAATTGATGCA
* * * * *
52925 ATGTCCCGAATAATTTGCGGTCCTCTGGATTTGCAAATTGATG
66 ATGTCCCAAAAAATTTGCAGTCCTCTGGACTTGCAAA---CTG
* * * *
52968 CAATGTCCCGTATGAATAATTTGCAGTCCATTGAGACCTGCAAAAGTTTAATGTTGAAATTGAT
1 --ATGTCCCGTATGAATAATTTGCAGTCCATTGAGACTTGCAAAGGTTTATTGTTGGAATTGAT
53032 CCATGGTCCC
Statistics
Matches: 436, Mismatches: 43, Indels: 34
0.85 0.08 0.07
Matches are distributed among these distances:
104 30 0.07
105 246 0.56
106 1 0.00
108 6 0.01
109 4 0.01
110 57 0.13
112 1 0.00
113 4 0.01
114 4 0.01
116 1 0.00
117 67 0.15
118 15 0.03
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (105 bp):
ATGTCCCGTATGAATAATTTGCAGTCCATTGAGACTTGCAAAGGTTTATTGTTGGAATTGATGCA
ATGTCCCAAAAAATTTGCAGTCCTCTGGACTTGCAAACTG
Found at i:52937 original size:222 final size:223
Alignment explanation
Indices: 52533--53031 Score: 800
Period size: 222 Copynumber: 2.3 Consensus size: 223
52523 TTGCAAACTG
*
52533 ATGTCCCGTATGAATAATTTGCAGTCCATTGAGACTTTCAAAGGTTTATTGTTGGAATTGATGCA
1 ATGTCCCGTATGAATAATTTGCAGTCCATTGAGACTTGCAAAGGTTTATTGTTGGAATTGATGCA
52598 ATGTCCCAAAAAATTTGCAGTCCTCTGGACTTGCAAACTGATGTCCCGTATGAATAATTTGCAGT
66 ATGTCCCAAAAAATTTGCAGTCCTCTGGACTTGCAAACTGATGTCCCGTATGAATAATTTGCAGT
52663 CCATTGAGACTTTCAAAGGTTTATTGTTGGAATTGATGCAATGTCCCGAATAATTTGCGGTCCTC
131 CCATTGAGACTTTCAAAGGTTTATTGTTGGAATTGATGCAATGTCCCGAATAATTTGCGGTCCTC
52728 TGCAAAAGTTGGTCGTGAAATCGATACA
196 TGCAAAAGTTGGTCGTGAAATCGATACA
* * * * *
52756 ATGTCCCTTTTGAATAA-TTGCAGTCTATTGAGACTTGCAAAGGTTTATTTTTGGCATTGATGCA
1 ATGTCCCGTATGAATAATTTGCAGTCCATTGAGACTTGCAAAGGTTTATTGTTGGAATTGATGCA
*
52820 ATGTCCCAAAAAATTTGCAGTCCTCTGGACTTGCAAACTGATGTCCCGTATGAATAATTTGCATT
66 ATGTCCCAAAAAATTTGCAGTCCTCTGGACTTGCAAACTGATGTCCCGTATGAATAATTTGCAGT
52885 CCATTGAGACTTTCAAAGGTTTATTGTTGGAATTGATGCAATGTCCCGAATAATTTGCGGTCCTC
131 CCATTGAGACTTTCAAAGGTTTATTGTTGGAATTGATGCAATGTCCCGAATAATTTGCGGTCCTC
* * * *
52950 TG---GA-TT--T-G-CAAATTGATGCA
196 TGCAAAAGTTGGTCGTGAAATCGATACA
* * * *
52970 ATGTCCCGTATGAATAATTTGCAGTCCATTGAGACCTGCAAAAGTTTAATGTTGAAATTGAT
1 ATGTCCCGTATGAATAATTTGCAGTCCATTGAGACTTGCAAAGGTTTATTGTTGGAATTGAT
53032 CCATGGTCCC
Statistics
Matches: 255, Mismatches: 20, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
214 24 0.09
215 38 0.15
216 1 0.00
218 2 0.01
219 1 0.00
222 174 0.68
223 15 0.06
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (223 bp):
ATGTCCCGTATGAATAATTTGCAGTCCATTGAGACTTGCAAAGGTTTATTGTTGGAATTGATGCA
ATGTCCCAAAAAATTTGCAGTCCTCTGGACTTGCAAACTGATGTCCCGTATGAATAATTTGCAGT
CCATTGAGACTTTCAAAGGTTTATTGTTGGAATTGATGCAATGTCCCGAATAATTTGCGGTCCTC
TGCAAAAGTTGGTCGTGAAATCGATACA
Found at i:53458 original size:45 final size:47
Alignment explanation
Indices: 53408--53501 Score: 120
Period size: 49 Copynumber: 2.0 Consensus size: 47
53398 TTGTTGGAAT
*
53408 TGATGCAATGTCCC-GAATAATTTGCAATCCTCTG-GACTTGCAAAC
1 TGATGCAATGTCCCAGAATAATTTGCAATCCACTGAGACTTGCAAAC
* *
53453 TGATGCAGTGTCCCATATGAATAATTTGCAGTCCACTGAGACTTGCAAA
1 TGATGCAATGTCCC--A-GAATAATTTGCAATCCACTGAGACTTGCAAA
53502 GGTTTATTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
45 13 0.32
49 18 0.44
50 10 0.24
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (47 bp):
TGATGCAATGTCCCAGAATAATTTGCAATCCACTGAGACTTGCAAAC
Found at i:57923 original size:58 final size:59
Alignment explanation
Indices: 57825--57940 Score: 164
Period size: 58 Copynumber: 2.0 Consensus size: 59
57815 ATGTCCCATA
* * * *
57825 CGAATAATTTGCAGTCCACGAGACTTGTAAAGGTTAATGTTGAAATTGATGCAATGTCC
1 CGAATAATTTGCAGTCCACGAGACTCGCAAAGATTAATGTTAAAATTGATGCAATGTCC
*
57884 CGAATAATTTG-TGTCCACTG-GACTCGCAAAGATTAATGTTAAAATTGATGCAATGTC
1 CGAATAATTTGCAGTCCAC-GAGACTCGCAAAGATTAATGTTAAAATTGATGCAATGTC
57941 TTGTATGAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
58 39 0.76
59 12 0.24
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (59 bp):
CGAATAATTTGCAGTCCACGAGACTCGCAAAGATTAATGTTAAAATTGATGCAATGTCC
Found at i:57986 original size:55 final size:55
Alignment explanation
Indices: 57837--58000 Score: 172
Period size: 58 Copynumber: 2.9 Consensus size: 55
57827 AATAATTTGC
* *
57837 AGTCCAC-GAGACTTGTAAAGGTTAATGTTGAAATTGATGCAATGTCCCGAATAATTTG
1 AGTCCACTGAGACTTGCAAAGGTTAATGTTGAAATTGATGCAATGTCCTG--T-A-TTG
* * * * *
57895 TGTCCACTG-GACTCGCAAAGATTAATGTTAAAATTGATGCAATGTCTTGTA-TG
1 AGTCCACTGAGACTTGCAAAGGTTAATGTTGAAATTGATGCAATGTCCTGTATTG
* * *
57948 AAGTCTACTGAGACTTGCAAAGGTTAATGTTGATATTGATGCATTGTCCTGTA
1 -AGTCCACTGAGACTTGCAAAGGTTAATGTTGAAATTGATGCAATGTCCTGTA
58001 CTAGAAGGTT
Statistics
Matches: 88, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
53 2 0.02
54 7 0.08
55 37 0.42
56 1 0.01
58 40 0.45
59 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (55 bp):
AGTCCACTGAGACTTGCAAAGGTTAATGTTGAAATTGATGCAATGTCCTGTATTG
Found at i:66709 original size:174 final size:175
Alignment explanation
Indices: 66365--66725 Score: 573
Period size: 174 Copynumber: 2.1 Consensus size: 175
66355 TACATTCAAA
* * *
66365 TTCA-CAAAGGAAATGGTGAAGTGACCATAAAACATATTATTACAACCCAAGAAAAAGAGAATCA
1 TTCAGCAAAGAAAATGGTGAAGTGAACATAAAACATATTATTACAACCAAAGAAAAAGAGAATCA
* * *
66429 AATAGATCGAAGCCTCAATAAGCAAGGTCATCACAAGGAGTACAGACTAAACCCCACAGTCCACA
66 AATAAATCGAAGCCTCAACAAGCAAGGTCATCACAAGGAGCACAGACTAAACCCCACAGTCCACA
*
66494 AACTAAAGACACCTAAAACTGGCAGACCTAAAAAAACCAATATAC
131 AAATAAAGACACCTAAAACTGGCAGACCTAAAAAAACCAATATAC
* * * * *
66539 TTCAGCAAAGAAAATGGTGAAGTGAACATGAAACATATTATTATAATCAAAGAAAAAGAGAGTCG
1 TTCAGCAAAGAAAATGGTGAAGTGAACATAAAACATATTATTACAACCAAAGAAAAAGAGAATCA
* *
66604 AATAAATTGAAGCCTCAACAAGCAAGGTCATCA-AAGGAGCACAGACTAAACCCCACGGTCCACA
66 AATAAATCGAAGCCTCAACAAGCAAGGTCATCACAAGGAGCACAGACTAAACCCCACAGTCCACA
*
66668 AAATAAAGACACCTAAAACTGGCAGACTTAAAAAAACCAATATAC
131 AAATAAAGACACCTAAAACTGGCAGACCTAAAAAAACCAATATAC
66713 TTCAGCAAAGAAA
1 TTCAGCAAAGAAA
66726 TGCTGCCGAG
Statistics
Matches: 171, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
174 89 0.52
175 82 0.48
ACGTcount: A:0.48, C:0.20, G:0.15, T:0.16
Consensus pattern (175 bp):
TTCAGCAAAGAAAATGGTGAAGTGAACATAAAACATATTATTACAACCAAAGAAAAAGAGAATCA
AATAAATCGAAGCCTCAACAAGCAAGGTCATCACAAGGAGCACAGACTAAACCCCACAGTCCACA
AAATAAAGACACCTAAAACTGGCAGACCTAAAAAAACCAATATAC
Found at i:69163 original size:40 final size:40
Alignment explanation
Indices: 69104--69185 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
69094 TACAATACCG
*
69104 AAATGACCGAAATGTTAATCCCAACAAACAAACCCAGTGA
1 AAATGACCGAAATGCTAATCCCAACAAACAAACCCAGTGA
69144 AAATGACCGAAATGCTAATCCCAACAAACAAACCCAGTGA
1 AAATGACCGAAATGCTAATCCCAACAAACAAACCCAGTGA
69184 AA
1 AA
69186 TTTACAACCG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.49, C:0.26, G:0.12, T:0.13
Consensus pattern (40 bp):
AAATGACCGAAATGCTAATCCCAACAAACAAACCCAGTGA
Found at i:75145 original size:31 final size:31
Alignment explanation
Indices: 75108--75172 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
75098 TAACAGATGT
*
75108 TTTAATTTGTGACTAAATTGTTCTAATATAA
1 TTTAATTTGTGACTAAATTGTACTAATATAA
75139 TTTAATTTGTGACTAAATTGTACTAATATAA
1 TTTAATTTGTGACTAAATTGTACTAATATAA
75170 TTT
1 TTT
75173 TTTTGAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.49
Consensus pattern (31 bp):
TTTAATTTGTGACTAAATTGTACTAATATAA
Found at i:75277 original size:31 final size:30
Alignment explanation
Indices: 75242--75346 Score: 115
Period size: 31 Copynumber: 3.5 Consensus size: 30
75232 ATACCCTACA
75242 GGTCCCTCTACTTATAAAAAAGGATCAATTT
1 GGTCCCTCTACTTATAAAAAAGG-TCAATTT
**
75273 GGTCCCTCTAC-TATAAAAACTGTCAATTT
1 GGTCCCTCTACTTATAAAAAAGGTCAATTT
* ***
75302 GGTCCCTCTACTTACAATTTAGTGTCAA-TT
1 GGTCCCTCTACTTATAAAAAAG-GTCAATTT
75332 GAGTCCCTCTACTTA
1 G-GTCCCTCTACTTA
75347 ACAAAATCCG
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
29 18 0.29
30 16 0.25
31 29 0.46
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (30 bp):
GGTCCCTCTACTTATAAAAAAGGTCAATTT
Found at i:75300 original size:29 final size:30
Alignment explanation
Indices: 75242--75313 Score: 110
Period size: 29 Copynumber: 2.4 Consensus size: 30
75232 ATACCCTACA
75242 GGTCCCTCTACTTATAAAAAAGGATCAATTT
1 GGTCCCTCTAC-TATAAAAAAGGATCAATTT
**
75273 GGTCCCTCTACTATAAAAACTG-TCAATTT
1 GGTCCCTCTACTATAAAAAAGGATCAATTT
75302 GGTCCCTCTACT
1 GGTCCCTCTACT
75314 TACAATTTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 19 0.49
30 9 0.23
31 11 0.28
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (30 bp):
GGTCCCTCTACTATAAAAAAGGATCAATTT
Found at i:75657 original size:29 final size:31
Alignment explanation
Indices: 75611--75687 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 31
75601 TGACACCAAA
* *
75611 TTATAAGTATAGGGACCAAATTGA-CAGTTT
1 TTATAAGTAGAAGGACCAAATTGATCAGTTT
**
75641 TTAT-AGTAGAAGGACCAAATTGATCCTTTT
1 TTATAAGTAGAAGGACCAAATTGATCAGTTT
*
75671 TTATAAGTAGAGGGACC
1 TTATAAGTAGAAGGACC
75688 TGTACGGTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 17 0.43
30 12 0.30
31 11 0.28
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (31 bp):
TTATAAGTAGAAGGACCAAATTGATCAGTTT
Found at i:77503 original size:15 final size:17
Alignment explanation
Indices: 77469--77505 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
77459 ATGAAGGGGA
*
77469 AAAAATGAAGAACTAAC
1 AAAAATGAAGAACCAAC
77486 AAAAATG-A-AACCAAC
1 AAAAATGAAGAACCAAC
77501 AAAAA
1 AAAAA
77506 ATTTTTTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 11 0.58
16 1 0.05
17 7 0.37
ACGTcount: A:0.70, C:0.14, G:0.08, T:0.08
Consensus pattern (17 bp):
AAAAATGAAGAACCAAC
Done.