Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016215.1 Corchorus capsularis cultivar CVL-1 contig16236, 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: 47553
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:5509 original size:11 final size:12
Alignment explanation
Indices: 5484--5522 Score: 64
Period size: 11 Copynumber: 3.4 Consensus size: 12
5474 ACACCCTTAG
5484 GAAAAACTAGAA
1 GAAAAACTAGAA
5496 GAAAAACTAG-A
1 GAAAAACTAGAA
5507 GAAAAA-TAGAA
1 GAAAAACTAGAA
5518 GAAAA
1 GAAAA
5523 GAAATTGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 3 0.12
11 13 0.50
12 10 0.38
ACGTcount: A:0.69, C:0.05, G:0.18, T:0.08
Consensus pattern (12 bp):
GAAAAACTAGAA
Found at i:8250 original size:21 final size:21
Alignment explanation
Indices: 8226--8266 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
8216 ACTGGCGGGC
8226 TTTACTTGCTGAGGAAGGCGT
1 TTTACTTGCTGAGGAAGGCGT
8247 TTTACTTGCTGAGGAAGGCG
1 TTTACTTGCTGAGGAAGGCG
8267 AACTCTTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.15, G:0.34, T:0.32
Consensus pattern (21 bp):
TTTACTTGCTGAGGAAGGCGT
Found at i:8453 original size:17 final size:17
Alignment explanation
Indices: 8415--8447 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
8405 CTCGTAGTAC
8415 CTAGGTAGTATGAGGTA
1 CTAGGTAGTATGAGGTA
8432 CTAGGTAGTATGAGGT
1 CTAGGTAGTATGAGGT
8448 GATAGGCCGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.36, T:0.30
Consensus pattern (17 bp):
CTAGGTAGTATGAGGTA
Found at i:9037 original size:156 final size:155
Alignment explanation
Indices: 8799--9162 Score: 400
Period size: 156 Copynumber: 2.3 Consensus size: 155
8789 GAGCTTCTCA
* * *
8799 CCTCAAAATGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAA
1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGCTG-AA
* * * *
8864 TTTTTCCAAGGGTCTTAGAATAT-ACACAT-GAGACTATGGAAAAAATTCTAAGTAAAACCGAGC
65 TTTTTCCAAGAGACTTAGAATATCAC-CATAAAG-CTATGGAAAAAATTCTAAGTAAAACCGAAC
* * * *
8927 TCCCCTTG-ATGGTGAACTAGGTTTCTCT
128 T-CCCTAGCATAGAGAACTAGGTTTCACT
* **
8955 CC-CTGAGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAAGCTG-
1 CCTC-AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACG-AGCTGA
* *
9017 A-TTTTCCACCAGTAGACTTAGATTATCACCATAAAGCTATGGGAAAAATTCTAAGTAAAACCGA
64 ATTTTTCCA--AG-AGACTTAGAATATCACCATAAAGCTATGGAAAAAATTCTAAGTAAAACCGA
* * * *
9081 ACTCTCTAGCATAGAGAAGTTGGTTTGACT
126 ACTCCCTAGCATAGAGAACTAGGTTTCACT
* *
9111 CCTCAAACTGTCCTTAATTGAAAAACTAGCATAAGTTTTTCATACTAAGTCT
1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCT
9163 GTTTGAGATG
Statistics
Matches: 174, Mismatches: 24, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
153 7 0.04
154 1 0.01
155 10 0.06
156 151 0.87
157 5 0.03
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.31
Consensus pattern (155 bp):
CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGCTGAAT
TTTTCCAAGAGACTTAGAATATCACCATAAAGCTATGGAAAAAATTCTAAGTAAAACCGAACTCC
CTAGCATAGAGAACTAGGTTTCACT
Found at i:10615 original size:26 final size:26
Alignment explanation
Indices: 10586--10649 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
10576 TAGTCTCGAT
10586 TGGTGTGCCCATGAGCACAGTGAACC
1 TGGTGTGCCCATGAGCACAGTGAACC
10612 TGGTGTGCCCATGAGCACAGTGAACC
1 TGGTGTGCCCATGAGCACAGTGAACC
10638 TGGTGTGCCCAT
1 TGGTGTGCCCAT
10650 CCGCCTGGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.20, C:0.27, G:0.31, T:0.22
Consensus pattern (26 bp):
TGGTGTGCCCATGAGCACAGTGAACC
Found at i:12358 original size:15 final size:15
Alignment explanation
Indices: 12338--12367 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12328 CACCCAATAC
12338 AAATACTCAACTGGT
1 AAATACTCAACTGGT
*
12353 AAATACTCACCTGGT
1 AAATACTCAACTGGT
12368 GCAATGCTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (15 bp):
AAATACTCAACTGGT
Found at i:12393 original size:16 final size:16
Alignment explanation
Indices: 12354--12395 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
12344 TCAACTGGTA
*
12354 AATACTCACCTGGTGC
1 AATACTCACCTGATGC
*
12370 AATGCTCACCTGATG-
1 AATACTCACCTGATGC
12385 AGATACTCACC
1 A-ATACTCACC
12396 CCCACTCACC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 1 0.05
16 21 0.95
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.24
Consensus pattern (16 bp):
AATACTCACCTGATGC
Found at i:12420 original size:16 final size:16
Alignment explanation
Indices: 12399--12453 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
12389 ACTCACCCCC
*
12399 ACTCACCCAGTACAAT
1 ACTCACCTAGTACAAT
* *
12415 ACTCACTTGGTA-AAT
1 ACTCACCTAGTACAAT
*
12430 ACTCACCTAGTGCAAT
1 ACTCACCTAGTACAAT
12446 ACTCACCT
1 ACTCACCT
12454 GGTGAGATAC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
15 12 0.38
16 20 0.62
ACGTcount: A:0.33, C:0.33, G:0.09, T:0.25
Consensus pattern (16 bp):
ACTCACCTAGTACAAT
Found at i:12432 original size:15 final size:16
Alignment explanation
Indices: 12412--12468 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
12402 CACCCAGTAC
*
12412 AATACTCACTTGGT-A
1 AATACTCACCTGGTGA
* *
12427 AATACTCACCTAGTGC
1 AATACTCACCTGGTGA
12443 AATACTCACCTGGTGA
1 AATACTCACCTGGTGA
*
12459 GATACTCACC
1 AATACTCACC
12469 CACACTCACC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
15 12 0.34
16 23 0.66
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (16 bp):
AATACTCACCTGGTGA
Found at i:12432 original size:73 final size:74
Alignment explanation
Indices: 12325--12478 Score: 240
Period size: 73 Copynumber: 2.1 Consensus size: 74
12315 TTCCTACCTT
* *
12325 ACTCACCCAATACAAATACTCAACTGGTAAATACTCACCTGGTGCAATGCTCACCTGATGAGATA
1 ACTCACCCAATACAAATACTCAACTGGTAAATACTCACCTAGTGCAATACTCACCTGATGAGATA
*
12390 CTCACCCCC
66 CTCACCCAC
* *
12399 ACTCACCCAGTAC-AATACTC-ACTTGGTAAATACTCACCTAGTGCAATACTCACCTGGTGAGAT
1 ACTCACCCAATACAAATACTCAAC-TGGTAAATACTCACCTAGTGCAATACTCACCTGATGAGAT
12462 ACTCACCCAC
65 ACTCACCCAC
12472 ACTCACC
1 ACTCACC
12479 TACTATATAC
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
72 2 0.03
73 60 0.81
74 12 0.16
ACGTcount: A:0.32, C:0.34, G:0.12, T:0.22
Consensus pattern (74 bp):
ACTCACCCAATACAAATACTCAACTGGTAAATACTCACCTAGTGCAATACTCACCTGATGAGATA
CTCACCCAC
Found at i:12446 original size:31 final size:32
Alignment explanation
Indices: 12399--12470 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 32
12389 ACTCACCCCC
*
12399 ACTCACCCAGTACAATACTCACTTGGT-AAAT
1 ACTCACCCAGTACAATACTCACCTGGTGAAAT
* * *
12430 ACTCACCTAGTGCAATACTCACCTGGTGAGAT
1 ACTCACCCAGTACAATACTCACCTGGTGAAAT
12462 ACTCACCCA
1 ACTCACCCA
12471 CACTCACCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 24 0.69
32 11 0.31
ACGTcount: A:0.32, C:0.32, G:0.12, T:0.24
Consensus pattern (32 bp):
ACTCACCCAGTACAATACTCACCTGGTGAAAT
Found at i:12502 original size:73 final size:73
Alignment explanation
Indices: 12325--12509 Score: 194
Period size: 73 Copynumber: 2.5 Consensus size: 73
12315 TTCCTACCTT
* ** * *
12325 ACTCACCCAATACAAATACTCA-ACTGGTAAATACTCACCTGGTGCAATGCTCACCTGATGAGAT
1 ACTCACCCACTAC-AATACTCACAC-AATAAATACTCACCTAGTGCAATACTCACCTGATGAGAT
*
12389 ACTCACCCCC
64 ACTCACCCAC
* **** *
12399 ACTCACCCAGTACAATACTCACTTGGTAAATACTCACCTAGTGCAATACTCACCTGGTGAGATAC
1 ACTCACCCACTACAATACTCACACAATAAATACTCACCTAGTGCAATACTCACCTGATGAGATAC
12464 TCACCCAC
66 TCACCCAC
* * *
12472 ACTCACCTACTA-TATACTATACACAATAAATACTCACC
1 ACTCACCCACTACAATACT-CACACAATAAATACTCACC
12510 AAATACTTAT
Statistics
Matches: 94, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
72 5 0.05
73 77 0.82
74 12 0.13
ACGTcount: A:0.34, C:0.33, G:0.10, T:0.23
Consensus pattern (73 bp):
ACTCACCCACTACAATACTCACACAATAAATACTCACCTAGTGCAATACTCACCTGATGAGATAC
TCACCCAC
Found at i:13760 original size:36 final size:36
Alignment explanation
Indices: 13712--13803 Score: 121
Period size: 36 Copynumber: 2.6 Consensus size: 36
13702 GTAATGTCGT
* *
13712 TGGCCTTGGTCGCCCAATACTTGGCTATAACGCTGC
1 TGGCCTTAGTCGCCCAATACTTGGCTATAACGCCGC
** *
13748 TGGCCTTAGTCGCCCAATGTTTGGCTATAATGCCGC
1 TGGCCTTAGTCGCCCAATACTTGGCTATAACGCCGC
* *
13784 TGACCTTAGTCGCCTAATAC
1 TGGCCTTAGTCGCCCAATAC
13804 ATAATTGGCT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.29
Consensus pattern (36 bp):
TGGCCTTAGTCGCCCAATACTTGGCTATAACGCCGC
Found at i:14865 original size:14 final size:13
Alignment explanation
Indices: 14848--14905 Score: 64
Period size: 14 Copynumber: 4.3 Consensus size: 13
14838 ACCTATCTTT
14848 AAAAAAAAAGAAGG
1 AAAAAAAAAGAA-G
14862 AAAAAAAAAGAAG
1 AAAAAAAAAGAAG
* *
14875 -AAAAAGAATAAG
1 AAAAAAAAAGAAG
14887 AAAAACAAAAGAAAG
1 AAAAA-AAAAG-AAG
14902 AAAA
1 AAAA
14906 TAAATTACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
12 10 0.27
13 5 0.14
14 15 0.41
15 7 0.19
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.02
Consensus pattern (13 bp):
AAAAAAAAAGAAG
Found at i:14907 original size:23 final size:24
Alignment explanation
Indices: 14863--14908 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
14853 AAAAGAAGGA
14863 AAAAAAAAGAAGAAAAAGAATAAG
1 AAAAAAAAGAAGAAAAAGAATAAG
*
14887 AAAAACAA-AAGAAAGAA-AATAA
1 AAAAAAAAGAAGAAA-AAGAATAA
14909 ATTACTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.04
Consensus pattern (24 bp):
AAAAAAAAGAAGAAAAAGAATAAG
Found at i:15482 original size:106 final size:107
Alignment explanation
Indices: 15210--15479 Score: 404
Period size: 114 Copynumber: 2.5 Consensus size: 107
15200 CTATTATAGT
* *
15210 TTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTTT
1 TTTATTCTACTA-AAACTCTATTTTCATTTAATTAAA-T---TCTAATATCTTTATAATTACTTT
*
15275 ATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAAT
61 A-TTTTACC-AAAAATTTGGATATACTAAAATTTTTTCTAATATACAAC
15324 TTTATTCTACTAAAAACTCTATTTTCATTTAATTAAA-TCTAATATCTTTATAATTACTTTATTT
1 TTTATTCTACT-AAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATAATTACTTTATTT
*
15388 TACCAAAAATTTGGATATATTAAAA-TTTTTCTAATATACAAC
65 TACCAAAAATTTGGATATACTAAAATTTTTTCTAATATACAAC
15430 TTTATTCTACTAAAACTCTATTTTCATTTAATTAAATTC-AATAT-TTTATA
1 TTTATTCTACTAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATA
15480 TAAGTTTTTT
Statistics
Matches: 150, Mismatches: 4, Indels: 14
0.89 0.02 0.08
Matches are distributed among these distances:
104 6 0.04
105 30 0.20
106 29 0.19
107 20 0.13
108 7 0.05
109 24 0.16
114 33 0.22
115 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (107 bp):
TTTATTCTACTAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATAATTACTTTATTTT
ACCAAAAATTTGGATATACTAAAATTTTTTCTAATATACAAC
Found at i:16409 original size:36 final size:36
Alignment explanation
Indices: 16351--16428 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 36
16341 TGGGGCACGC
16351 CCCCCCTTCCAATCTAATATGGGGCAG-GT-GTTACG
1 CCCCCCTTCCAATCTAATATGGGG-AGAGTCGTTACG
*
16386 CCCCCCTTCCAAATACTTA-ATGGGGAGACGTCGTTACG
1 CCCCCCTTCC-AAT-CTAATATGGGGAGA-GTCGTTACG
16424 CCCCC
1 CCCCC
16429 TTTCAATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
35 12 0.32
36 9 0.24
37 5 0.14
38 11 0.30
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.23
Consensus pattern (36 bp):
CCCCCCTTCCAATCTAATATGGGGAGAGTCGTTACG
Found at i:16679 original size:33 final size:33
Alignment explanation
Indices: 16642--16944 Score: 374
Period size: 33 Copynumber: 9.1 Consensus size: 33
16632 AGGGGAGACA
*
16642 CCTCAGGGGAGACTCCCTTGCTACGCGAGACTT
1 CCTCAGGGGAGACTCCCTTGCTACGCGAGACTC
* ** *
16675 CCTCAGGGGAGACTCTCTTATTATGCGAGACTC
1 CCTCAGGGGAGACTCCCTTGCTACGCGAGACTC
* *
16708 CCTCAGGGGAGACTCCCTTGCTATGCGAGACTT
1 CCTCAGGGGAGACTCCCTTGCTACGCGAGACTC
* *
16741 CCTCAGGGGAGACTCCCTTACTATGCGAGACTC
1 CCTCAGGGGAGACTCCCTTGCTACGCGAGACTC
*
16774 CCTCAGGGGAGACTCCTTTGCTACGCGAGAGTACTC
1 CCTCAGGGGAGACTCCCTTGCTACGC--GAG-ACTC
* * *
16810 CCTCAAGGGAGACTCCCTTACTATGCGAGACTC
1 CCTCAGGGGAGACTCCCTTGCTACGCGAGACTC
* **
16843 CCTCAGGGGAGACTCCCTTTGCTGCGAAAGACTC
1 CCTCAGGGGAGACTCCC-TTGCTACGCGAGACTC
* *
16877 CCTCAGGGGAGACTCCCTTACTACGTG-GACTC
1 CCTCAGGGGAGACTCCCTTGCTACGCGAGACTC
* * *
16909 CCTCAGGGGAGACTCCTTTGCTACGTGACACTC
1 CCTCAGGGGAGACTCCCTTGCTACGCGAGACTC
16942 CCT
1 CCT
16945 TTGTGACGCC
Statistics
Matches: 234, Mismatches: 31, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
32 30 0.13
33 144 0.62
34 31 0.13
35 3 0.01
36 26 0.11
ACGTcount: A:0.20, C:0.32, G:0.25, T:0.23
Consensus pattern (33 bp):
CCTCAGGGGAGACTCCCTTGCTACGCGAGACTC
Found at i:16748 original size:66 final size:66
Alignment explanation
Indices: 16642--16944 Score: 428
Period size: 66 Copynumber: 4.5 Consensus size: 66
16632 AGGGGAGACA
* * *
16642 CCTCAGGGGAGACTCCCTTGCTACGCGAGACTTCCTCAGGGGAGACTCTCTTATTATGCGAGACT
1 CCTCAGGGGAGACTCCCTTGCTACGCGAGACTCCCTCAGGGGAGACTCCCTTACTATGCGAGACT
16707 C
66 C
* *
16708 CCTCAGGGGAGACTCCCTTGCTATGCGAGACTTCCTCAGGGGAGACTCCCTTACTATGCGAGACT
1 CCTCAGGGGAGACTCCCTTGCTACGCGAGACTCCCTCAGGGGAGACTCCCTTACTATGCGAGACT
16773 C
66 C
* *
16774 CCTCAGGGGAGACTCCTTTGCTACGCGAGAGTACTCCCTCAAGGGAGACTCCCTTACTATGCGAG
1 CCTCAGGGGAGACTCCCTTGCTACGC--GAG-ACTCCCTCAGGGGAGACTCCCTTACTATGCGAG
16839 ACTC
63 ACTC
* ** * *
16843 CCTCAGGGGAGACTCCCTTTGCTGCGAAAGACTCCCTCAGGGGAGACTCCCTTACTACGTG-GAC
1 CCTCAGGGGAGACTCCC-TTGCTACGCGAGACTCCCTCAGGGGAGACTCCCTTACTATGCGAGAC
16907 TC
65 TC
* * *
16909 CCTCAGGGGAGACTCCTTTGCTACGTGACACTCCCT
1 CCTCAGGGGAGACTCCCTTGCTACGCGAGACTCCCT
16945 TTGTGACGCC
Statistics
Matches: 214, Mismatches: 19, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
65 15 0.07
66 108 0.50
67 28 0.13
68 5 0.02
69 51 0.24
70 7 0.03
ACGTcount: A:0.20, C:0.32, G:0.25, T:0.23
Consensus pattern (66 bp):
CCTCAGGGGAGACTCCCTTGCTACGCGAGACTCCCTCAGGGGAGACTCCCTTACTATGCGAGACT
C
Found at i:16908 original size:135 final size:131
Alignment explanation
Indices: 16642--16944 Score: 439
Period size: 135 Copynumber: 2.3 Consensus size: 131
16632 AGGGGAGACA
* * * * *
16642 CCTCAGGGGAGACTCCCTTGCTACGCGAGACTTCCTCAGGGGAGACTCTCTTATTATGCGAGACT
1 CCTCAGGGGAGACTCCTTTGCTACGCGAGACTCCCTCAAGGGAGACTCCCTTACTATGCGAGACT
* *
16707 CCCTCAGGGGAGACTCCCTTGCTATGCGAGACTTCCTCAGGGGAGACTCCCTTACTATGCGAGAC
66 CCCTCAGGGGAGACTCCCTTGC-ATGCGAGACTCCCTCAGGGGAGACTCCCTTACTACGCGAGAC
16772 TC
130 TC
16774 CCTCAGGGGAGACTCCTTTGCTACGCGAGAGTACTCCCTCAAGGGAGACTCCCTTACTATGCGAG
1 CCTCAGGGGAGACTCCTTTGCTACGC--GAG-ACTCCCTCAAGGGAGACTCCCTTACTATGCGAG
*
16839 ACTCCCTCAGGGGAGACTCCCTTTGC-TGCGAAAGACTCCCTCAGGGGAGACTCCCTTACTACGT
63 ACTCCCTCAGGGGAGACTCCC-TTGCATGCG--AGACTCCCTCAGGGGAGACTCCCTTACTACGC
16903 G-GACTC
125 GAGACTC
* *
16909 CCTCAGGGGAGACTCCTTTGCTACGTGACACTCCCT
1 CCTCAGGGGAGACTCCTTTGCTACGCGAGACTCCCT
16945 TTGTGACGCC
Statistics
Matches: 155, Mismatches: 10, Indels: 12
0.88 0.06 0.07
Matches are distributed among these distances:
132 32 0.21
133 2 0.01
134 7 0.05
135 80 0.52
136 34 0.22
ACGTcount: A:0.20, C:0.32, G:0.25, T:0.23
Consensus pattern (131 bp):
CCTCAGGGGAGACTCCTTTGCTACGCGAGACTCCCTCAAGGGAGACTCCCTTACTATGCGAGACT
CCCTCAGGGGAGACTCCCTTGCATGCGAGACTCCCTCAGGGGAGACTCCCTTACTACGCGAGACT
C
Found at i:17276 original size:181 final size:180
Alignment explanation
Indices: 16943--17289 Score: 642
Period size: 181 Copynumber: 1.9 Consensus size: 180
16933 GTGACACTCC
16943 CTTTGTGACGCCCCAAGATCCCACATCAGGAGGATGTGGTGATCTATTGTGGTTTAAAATATAGA
1 CTTTGTGACGCCCCAAGATCCCACATCAGGAGGATGTGGTGATCTATTGTGGTTTAAAATATAGA
17008 GATCCAACCCAAACTTGTGAGGCGCCTTTTGGGAAGGGCAAACCCGTGAGGCCTTTGGGCCAAAG
66 GATCCAACCCAAACTTGTGAGGCGCCTTTTGGGAAGGGCAAACCCGTGAGGCCTTTGGGCCAAAG
17073 CGGACAATACCTCGCAGGTTGGGCCGGGTCTCTACAGTTGGTAATCAGAG
131 CGGACAATACCTCGCAGGTTGGGCCGGGTCTCTACAGTTGGTAATCAGAG
*
17123 CTTTGTGACGCCCCAAGATCCCACATCAGGAGGATGTGGTGATCTATTGTGGTTT-ATATAATAG
1 CTTTGTGACGCCCCAAGATCCCACATCAGGAGGATGTGGTGATCTATTGTGGTTTAAAAT-ATAG
* *
17187 AGATCTAACCCAAACCTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGCCTTTGGGCCAA
65 AGATCCAACCCAAA-CTTGTGAGGCGCCTTTTGGGAAGGGCAAACCCGTGAGGCCTTTGGGCCAA
17252 AGCGGACAATACCTCGCAGGTTGGGCCGGGTCTCTACA
129 AGCGGACAATACCTCGCAGGTTGGGCCGGGTCTCTACA
17290 CCCTTAGGGG
Statistics
Matches: 162, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
179 3 0.02
180 72 0.44
181 87 0.54
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (180 bp):
CTTTGTGACGCCCCAAGATCCCACATCAGGAGGATGTGGTGATCTATTGTGGTTTAAAATATAGA
GATCCAACCCAAACTTGTGAGGCGCCTTTTGGGAAGGGCAAACCCGTGAGGCCTTTGGGCCAAAG
CGGACAATACCTCGCAGGTTGGGCCGGGTCTCTACAGTTGGTAATCAGAG
Found at i:17793 original size:23 final size:23
Alignment explanation
Indices: 17759--17841 Score: 107
Period size: 23 Copynumber: 3.6 Consensus size: 23
17749 AATTCCCTTT
17759 GCTCTTGCGCGGAGGCTCACCTA
1 GCTCTTGCGCGGAGGCTCACCTA
* *
17782 GCTCTTGAGCGGAGCGCTCCCCT-
1 GCTCTTGCGCGGAG-GCTCACCTA
*
17805 GCT-TTCGGGCGGAGGCTCACCTA
1 GCTCTT-GCGCGGAGGCTCACCTA
17828 GCTCTTGCGCGGAG
1 GCTCTTGCGCGGAG
17842 CTCTCCCCAG
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
22 9 0.18
23 33 0.65
24 9 0.18
ACGTcount: A:0.11, C:0.34, G:0.34, T:0.22
Consensus pattern (23 bp):
GCTCTTGCGCGGAGGCTCACCTA
Found at i:18261 original size:16 final size:16
Alignment explanation
Indices: 18220--18277 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
18210 CACCCAATAC
18220 AAATACTCACCTGGT-
1 AAATACTCACCTGGTG
18235 AAATACTCACCTGGTG
1 AAATACTCACCTGGTG
* *
18251 CAATGCTCACCTGGTG
1 AAATACTCACCTGGTG
*
18267 AGATACTCACC
1 AAATACTCACC
18278 CACACTCACC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
15 15 0.41
16 22 0.59
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (16 bp):
AAATACTCACCTGGTG
Found at i:18302 original size:42 final size:42
Alignment explanation
Indices: 18251--18351 Score: 184
Period size: 42 Copynumber: 2.4 Consensus size: 42
18241 TCACCTGGTG
* *
18251 CAATGCTCACCTGGTGAGATACTCACCCACACTCACCCAGTA
1 CAATACTCACCTGGTGAGATACTCACCCACACTCAACCAGTA
18293 CAATACTCACCTGGTGAGATACTCACCCACACTCAACCAGTA
1 CAATACTCACCTGGTGAGATACTCACCCACACTCAACCAGTA
18335 CAATACTCACCTGGTGA
1 CAATACTCACCTGGTGA
18352 TGCCATGCTC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.31, C:0.36, G:0.14, T:0.20
Consensus pattern (42 bp):
CAATACTCACCTGGTGAGATACTCACCCACACTCAACCAGTA
Found at i:18987 original size:58 final size:58
Alignment explanation
Indices: 18859--18977 Score: 238
Period size: 58 Copynumber: 2.1 Consensus size: 58
18849 TGTCTTTTAT
18859 ATACGACATTTTTACTTAATTTTCAATAATAATGAAATATAGTTCCGGTCAAATAAAA
1 ATACGACATTTTTACTTAATTTTCAATAATAATGAAATATAGTTCCGGTCAAATAAAA
18917 ATACGACATTTTTACTTAATTTTCAATAATAATGAAATATAGTTCCGGTCAAATAAAA
1 ATACGACATTTTTACTTAATTTTCAATAATAATGAAATATAGTTCCGGTCAAATAAAA
18975 ATA
1 ATA
18978 ATGGATTTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (58 bp):
ATACGACATTTTTACTTAATTTTCAATAATAATGAAATATAGTTCCGGTCAAATAAAA
Found at i:21847 original size:108 final size:108
Alignment explanation
Indices: 21658--21896 Score: 442
Period size: 108 Copynumber: 2.2 Consensus size: 108
21648 GATACCAATT
* * *
21658 TGAGCATCCTGATGATATAAGTTTTACAACGTGGGAAATCAATTCTATTTAAAAGAAATTAAGCC
1 TGAGCATCCCGATGATATAAGTTTTACAACGTGGGAAATCAATTCGACTTAAAAGAAATTAAGCC
*
21723 AATTTTGGCTTTATCATCGACACCAATCAATTGGTCCTGATGG
66 AATATTGGCTTTATCATCGACACCAATCAATTGGTCCTGATGG
21766 TGAGCATCCCGATGATATAAGTTTTACAACGTGGGAAATCAATTCGACTTAAAAGAAATTAAGCC
1 TGAGCATCCCGATGATATAAGTTTTACAACGTGGGAAATCAATTCGACTTAAAAGAAATTAAGCC
21831 AATATTGGCTTTATCATCGACACCAATCAATTGGTCCTGATGG
66 AATATTGGCTTTATCATCGACACCAATCAATTGGTCCTGATGG
21874 TGAGCATCCCGATGATATAAGTT
1 TGAGCATCCCGATGATATAAGTT
21897 GGCTTTTGGA
Statistics
Matches: 127, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 127 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (108 bp):
TGAGCATCCCGATGATATAAGTTTTACAACGTGGGAAATCAATTCGACTTAAAAGAAATTAAGCC
AATATTGGCTTTATCATCGACACCAATCAATTGGTCCTGATGG
Found at i:22049 original size:55 final size:55
Alignment explanation
Indices: 21987--22108 Score: 217
Period size: 55 Copynumber: 2.2 Consensus size: 55
21977 AATAAATCAA
*
21987 TCCTGATGGTGTTGCCTTCAATTTATCATTCACACCATTGGGACTAATAAATTGG
1 TCCTGATGGTGTTGCCTTCAATTTATCATTCACACCATCGGGACTAATAAATTGG
* *
22042 TCTTGATGGTGTTGCCTTCCATTTATCATTCACACCATCGGGACTAATAAATTGG
1 TCCTGATGGTGTTGCCTTCAATTTATCATTCACACCATCGGGACTAATAAATTGG
22097 TCCTGATGGTGT
1 TCCTGATGGTGT
22109 AAATGAAATA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 63 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (55 bp):
TCCTGATGGTGTTGCCTTCAATTTATCATTCACACCATCGGGACTAATAAATTGG
Found at i:23167 original size:24 final size:25
Alignment explanation
Indices: 23132--23183 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
23122 AAAAAAAATA
23132 CTCTTTGCCTTTCTTTGGGGTC-AT
1 CTCTTTGCCTTTCTTTGGGGTCAAT
* *
23156 CTCTTTGGCTTTCTTTGGGTTCAAT
1 CTCTTTGCCTTTCTTTGGGGTCAAT
23181 CTC
1 CTC
23184 ACATGTATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (25 bp):
CTCTTTGCCTTTCTTTGGGGTCAAT
Found at i:27185 original size:27 final size:27
Alignment explanation
Indices: 27155--27225 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 27
27145 AGGGTCATAG
**
27155 AGGGGCATTTTGGTCATTTTTACACTA
1 AGGGGCATTTTGGTCATTTGCACACTA
* * *
27182 A-GGGCATTTCGGTCATTTGCACATTC
1 AGGGGCATTTTGGTCATTTGCACACTA
27208 AGGGGCATTTTGGTCATT
1 AGGGGCATTTTGGTCATT
27226 CTTAGTACAC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
26 21 0.57
27 16 0.43
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGCACACTA
Found at i:34321 original size:21 final size:21
Alignment explanation
Indices: 34262--34321 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
34252 TGAATTAAAT
34262 CATCAAGAACC-AA-AATCAAC
1 CATCAA-AACCAAATAATCAAC
**
34282 CATCAAAACCAGTTAATCAAC
1 CATCAAAACCAAATAATCAAC
* *
34303 CATCAAAACGAAATCATCA
1 CATCAAAACCAAATAATCA
34322 TCACCAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
19 4 0.12
20 6 0.19
21 22 0.69
ACGTcount: A:0.52, C:0.28, G:0.05, T:0.15
Consensus pattern (21 bp):
CATCAAAACCAAATAATCAAC
Found at i:35453 original size:111 final size:111
Alignment explanation
Indices: 35265--35475 Score: 395
Period size: 111 Copynumber: 1.9 Consensus size: 111
35255 CTGGGCTTCA
35265 TGGGCCAAAATGGACCGAAATCAGTAGTTTCACCAAATTGCTCCAAATCTTCATCCTCTTAAACA
1 TGGGCCAAAATGGACCGAAATCAGTAGTTTCACCAAATTGCTCCAAATCTTCATCCTCTTAAACA
*
35330 ATAGCTCTAAATGGGCCTAAAATAACAAAGATGATGATGGGCCTAT
66 ATAGCTCCAAATGGGCCTAAAATAACAAAGATGATGATGGGCCTAT
* *
35376 TGGGCCAAAATGGGCCGAAATCAGTAGTTTCACCAAATTGCTCTAAATCTTCATCCTCTTAAACA
1 TGGGCCAAAATGGACCGAAATCAGTAGTTTCACCAAATTGCTCCAAATCTTCATCCTCTTAAACA
35441 ATAGCTCCAAATGGGCCTAAAATAACAAAGATGAT
66 ATAGCTCCAAATGGGCCTAAAATAACAAAGATGAT
35476 AAATATAAGG
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 97 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (111 bp):
TGGGCCAAAATGGACCGAAATCAGTAGTTTCACCAAATTGCTCCAAATCTTCATCCTCTTAAACA
ATAGCTCCAAATGGGCCTAAAATAACAAAGATGATGATGGGCCTAT
Found at i:45940 original size:17 final size:17
Alignment explanation
Indices: 45918--45959 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
45908 GAAACTTCAG
45918 GGGCAAAATTGGCTATT
1 GGGCAAAATTGGCTATT
45935 GGGCAAAATTGGCTATT
1 GGGCAAAATTGGCTATT
45952 GGGCAAAA
1 GGGCAAAA
45960 CACGAAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.31, T:0.24
Consensus pattern (17 bp):
GGGCAAAATTGGCTATT
Found at i:47395 original size:3 final size:3
Alignment explanation
Indices: 47387--47430 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
47377 CCAAGTAGCT
*
47387 AAG AAG AAG AAG CAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
47431 AATGTGGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Done.