Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006868.1 Corchorus capsularis cultivar CVL-1 contig06889, 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: 21417
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:874 original size:14 final size:14
Alignment explanation
Indices: 857--883 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
847 TCCTTTTCTA
857 TTTCTCTACAGGTC
1 TTTCTCTACAGGTC
871 TTTCTCTACAGGT
1 TTTCTCTACAGGT
884 GACATGTGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.26, G:0.15, T:0.44
Consensus pattern (14 bp):
TTTCTCTACAGGTC
Found at i:3532 original size:79 final size:79
Alignment explanation
Indices: 3346--3673 Score: 433
Period size: 79 Copynumber: 4.0 Consensus size: 79
3336 ATCTTGAAGA
* * *
3346 AATAATGCACCGCATTAACTTGATTCACCGAATCACCCTGAACTGTTTGAGAAT-AGCTGCACCG
1 AATAATGCACCGCATTAACTTGATTCACCGAATCACCCTGAACTATTTGAAAATGTGCTGCACCG
3410 AGCTCACCGAATCC
66 AGCTCACCGAATCC
* *
3424 AATAATGCACCGCATTAACTTGATTCACCGAATCACCCTGAACTGTTTGAGAATGTGCTGCACCG
1 AATAATGCACCGCATTAACTTGATTCACCGAATCACCCTGAACTATTTGAAAATGTGCTGCACCG
3489 AGCTCACCGAATCC
66 AGCTCACCGAATCC
* ** *
3503 AATAATGCACCGCATTATCTTGATTCACCGAATCGTCATGAACTATTTGAAAATGTGCTGCACCG
1 AATAATGCACCGCATTAACTTGATTCACCGAATCACCCTGAACTATTTGAAAATGTGCTGCACCG
3568 AGCTCACCGAATCCAAC
66 AGCTCACCGAAT-C--C
* ** *
3585 TTTGAAGAAATAATGCACTGCATTAACTTGATTCACCGAATCGTCCTGAACTATTTGAAAATATG
1 --------AATAATGCACCGCATTAACTTGATTCACCGAATCACCCTGAACTATTTGAAAATGTG
3650 CTGCACCGAGCTCACCGAATCC
58 CTGCACCGAGCTCACCGAATCC
3672 AA
1 AA
3674 CTTTGAAGAT
Statistics
Matches: 227, Mismatches: 11, Indels: 23
0.87 0.04 0.09
Matches are distributed among these distances:
78 54 0.24
79 96 0.42
80 1 0.00
82 1 0.00
87 1 0.00
89 1 0.00
90 73 0.32
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (79 bp):
AATAATGCACCGCATTAACTTGATTCACCGAATCACCCTGAACTATTTGAAAATGTGCTGCACCG
AGCTCACCGAATCC
Found at i:3656 original size:90 final size:90
Alignment explanation
Indices: 3503--3682 Score: 324
Period size: 90 Copynumber: 2.0 Consensus size: 90
3493 CACCGAATCC
* *
3503 AATAATGCACCGCATTATCTTGATTCACCGAATCGTCATGAACTATTTGAAAATGTGCTGCACCG
1 AATAATGCACCGCATTAACTTGATTCACCGAATCGTCATGAACTATTTGAAAATATGCTGCACCG
3568 AGCTCACCGAATCCAACTTTGAAGA
66 AGCTCACCGAATCCAACTTTGAAGA
* *
3593 AATAATGCACTGCATTAACTTGATTCACCGAATCGTCCTGAACTATTTGAAAATATGCTGCACCG
1 AATAATGCACCGCATTAACTTGATTCACCGAATCGTCATGAACTATTTGAAAATATGCTGCACCG
3658 AGCTCACCGAATCCAACTTTGAAGA
66 AGCTCACCGAATCCAACTTTGAAGA
3683 TGCTACATTG
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (90 bp):
AATAATGCACCGCATTAACTTGATTCACCGAATCGTCATGAACTATTTGAAAATATGCTGCACCG
AGCTCACCGAATCCAACTTTGAAGA
Found at i:3713 original size:43 final size:43
Alignment explanation
Indices: 3661--3951 Score: 397
Period size: 43 Copynumber: 6.8 Consensus size: 43
3651 TGCACCGAGC
** *
3661 TCACCGAATCCAACTTTGAAGATGCTACATTGAGTCATCGGAT
1 TCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATCTGAT
* * *
3704 TCACCGAATCGAACTTTGAAGATGCTCCACTGAGTCATCTGAT
1 TCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATCTGAT
* *
3747 TCACCGAATCCAACTTTGAAGATGTTACACCGAGTCATTTGATTT
1 TCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATCTGA--T
*
3792 TCA-CGAATCCAAC-TTGTAGATGCTACACCGAGTCATCTGAT
1 TCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATCTGAT
** *
3833 TCACTAAATCCAACTTTGAAGATGCTACACCGAATCATCTGAT
1 TCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATCTGAT
* *
3876 TCACTGAATCCAACTTTGAAGATGCTACACCGAGTCATCTGGT
1 TCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATCTGAT
* * *
3919 TCACCAAATCCAACTTAGAAGATGCTTCACCGA
1 TCACCGAATCCAACTTTGAAGATGCTACACCGA
3952 ATCCAACCTA
Statistics
Matches: 221, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
41 4 0.02
42 8 0.04
43 195 0.88
44 10 0.05
45 4 0.02
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (43 bp):
TCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATCTGAT
Found at i:3954 original size:26 final size:26
Alignment explanation
Indices: 3918--3977 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
3908 AGTCATCTGG
* *
3918 TTCACCAAATCCAACTTAGAAGATGC
1 TTCACCGAATCCAACCTAGAAGATGC
*
3944 TTCACCGAATCCAACCTAGAAGATGT
1 TTCACCGAATCCAACCTAGAAGATGC
3970 TTCACCGA
1 TTCACCGA
3978 GTCGTCTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.23
Consensus pattern (26 bp):
TTCACCGAATCCAACCTAGAAGATGC
Found at i:3991 original size:69 final size:66
Alignment explanation
Indices: 3875--4007 Score: 167
Period size: 69 Copynumber: 2.0 Consensus size: 66
3865 AATCATCTGA
* * * *
3875 TTCACTGAATCCAACTTTGAAGATGCTACACCGAGTCATCTGGTTCACCAAATCCAACTTAGAAG
1 TTCACCGAATCCAACCTAGAAGATGCTACACCGAGTCATCTGATTCACCAAA-CC-ACTT-GAAG
3940 ATGC
63 ATGC
* * * *
3944 TTCACCGAATCCAACCTAGAAGATGTTTCACCGAGTCGTCTGATTCACCGAACCACTTGAAGAT
1 TTCACCGAATCCAACCTAGAAGATGCTACACCGAGTCATCTGATTCACCAAACCACTTGAAGAT
4008 ATACTCAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
66 6 0.11
67 4 0.07
68 2 0.04
69 44 0.79
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.26
Consensus pattern (66 bp):
TTCACCGAATCCAACCTAGAAGATGCTACACCGAGTCATCTGATTCACCAAACCACTTGAAGATG
C
Found at i:4082 original size:54 final size:54
Alignment explanation
Indices: 3997--4598 Score: 873
Period size: 54 Copynumber: 11.1 Consensus size: 54
3987 TTCACCGAAC
* * * * * * *
3997 CACTTGAAGATATACTCAAATCACTGAAAACTTCCTTGACTGACCGCACTGTAT
1 CACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGAT
*
4051 CACTTGAAGATAAATTTAAACCACTGGAAACTCTT-TTGATTGACCGCACTGGAT
1 CACTTGAAGATAAACTTAAACCACTGGAAACT-TTCTTGATTGACCGCACTGGAT
* *
4105 CACTTGAAGATAAATTTAAACCACTAGAAACTTTCTTGATTGACCGCACTGGAT
1 CACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGAT
* *
4159 CACTTGAAGATAAACTTAAACCACTGGAAACTTGCTTGATTGACCGTACTGGAT
1 CACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGAT
* * * *
4213 CACTTGAAGATAAACTTAAACCATTGTAAACTTTCTTGACTGACCGCACTCGAT
1 CACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGAT
* *
4267 CACTTGAAGATAAACTTAATACCACTGGAAACTTTCTTGACTGATCGCACTGGAT
1 CACTTGAAGATAAACTTAA-ACCACTGGAAACTTTCTTGATTGACCGCACTGGAT
* *
4322 CACTCGAAGATGAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGAT
1 CACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGAT
*
4376 CACTTGAAGATAAACTTAATACAACTGGAAACTTTCTTGATTGACCGCACTGGAT
1 CACTTGAAGATAAACTTAA-ACCACTGGAAACTTTCTTGATTGACCGCACTGGAT
* * * *
4431 TACTTGAAGATAAACTTAAACAACTGTAAACTTTCTTGACTGACCGCACTGGAT
1 CACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGAT
* * * *
4485 CACTTGAAGATAAACTTAAACAACTGTAAACTTTCTTGACTGACCACACTGGAT
1 CACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGAT
* * *
4539 CACTTGAAAATAAACTTAATACCACTGGAAACTTTCTTGATTGACCACACTAGAT
1 CACTTGAAGATAAACTTAA-ACCACTGGAAACTTTCTTGATTGACCGCACTGGAT
4594 CACTT
1 CACTT
4599 TGAAATTCGG
Statistics
Matches: 503, Mismatches: 40, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
53 2 0.00
54 364 0.72
55 137 0.27
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (54 bp):
CACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGAT
Found at i:4343 original size:109 final size:108
Alignment explanation
Indices: 3997--4598 Score: 873
Period size: 109 Copynumber: 5.5 Consensus size: 108
3987 TTCACCGAAC
* * * * * *
3997 CACTTGAAGATATACTCAAATCACTGAAAACTTCCTTGACTGACCGCACTGTATCACTTGAAGAT
1 CACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGACTGACCGCACTGGATCACTTGAAGAT
*
4062 AAATTTAAACCACTGGAAACTCTT-TTGATTGACCGCACTGGAT
66 AAACTTAAACCACTGGAAACT-TTCTTGATTGACCGCACTGGAT
* * *
4105 CACTTGAAGATAAATTTAAACCACTAGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGAT
1 CACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGACTGACCGCACTGGATCACTTGAAGAT
* *
4170 AAACTTAAACCACTGGAAACTTGCTTGATTGACCGTACTGGAT
66 AAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGAT
* * *
4213 CACTTGAAGATAAACTTAAACCATTGTAAACTTTCTTGACTGACCGCACTCGATCACTTGAAGAT
1 CACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGACTGACCGCACTGGATCACTTGAAGAT
* *
4278 AAACTTAATACCACTGGAAACTTTCTTGACTGATCGCACTGGAT
66 AAACTTAA-ACCACTGGAAACTTTCTTGATTGACCGCACTGGAT
* * *
4322 CACTCGAAGATGAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGAT
1 CACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGACTGACCGCACTGGATCACTTGAAGAT
*
4387 AAACTTAATACAACTGGAAACTTTCTTGATTGACCGCACTGGAT
66 AAACTTAA-ACCACTGGAAACTTTCTTGATTGACCGCACTGGAT
* * *
4431 TACTTGAAGATAAACTTAAACAACTGTAAACTTTCTTGACTGACCGCACTGGATCACTTGAAGAT
1 CACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGACTGACCGCACTGGATCACTTGAAGAT
* * * *
4496 AAACTTAAACAACTGTAAACTTTCTTGACTGACCACACTGGAT
66 AAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGAT
* * * *
4539 CACTTGAAAATAAACTTAATACCACTGGAAACTTTCTTGATTGACCACACTAGATCACTT
1 CACTTGAAGATAAACTTAA-ACCACTGGAAACTTTCTTGACTGACCGCACTGGATCACTT
4599 TGAAATTCGG
Statistics
Matches: 444, Mismatches: 47, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
107 1 0.00
108 210 0.47
109 233 0.52
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (108 bp):
CACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGACTGACCGCACTGGATCACTTGAAGAT
AAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGAT
Found at i:4362 original size:163 final size:163
Alignment explanation
Indices: 3997--4598 Score: 886
Period size: 163 Copynumber: 3.7 Consensus size: 163
3987 TTCACCGAAC
* * * * * *
3997 CACTTGAAGATATACTCAAATCACTGAAAACTTCCTTGACTGACCGCACTGTATCACTTGAAGAT
1 CACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGACTGACCGCACTGGATCACTTGAAGAT
* *
4062 AAATTTAA-ACCACTGGAAACTCTT-TTGATTGACCGCACTGGATCACTTGAAGATAAATTTAAA
66 AAACTTAATACCACTGGAAACT-TTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAA
* *
4125 CCACTAGAAACTTTCTTGATTGACCGCACTGGAT
130 CCACTGGAAACTTTCTTGACTGACCGCACTGGAT
* * *
4159 CACTTGAAGATAAACTTAAACCACTGGAAACTTGCTTGATTGACCGTACTGGATCACTTGAAGAT
1 CACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGACTGACCGCACTGGATCACTTGAAGAT
* * * *
4224 AAACTTAA-ACCATTGTAAACTTTCTTGACTGACCGCACTCGATCACTTGAAGATAAACTTAATA
66 AAACTTAATACCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAA-A
*
4288 CCACTGGAAACTTTCTTGACTGATCGCACTGGAT
130 CCACTGGAAACTTTCTTGACTGACCGCACTGGAT
* * *
4322 CACTCGAAGATGAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGAT
1 CACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGACTGACCGCACTGGATCACTTGAAGAT
* *
4387 AAACTTAATACAACTGGAAACTTTCTTGATTGACCGCACTGGATTACTTGAAGATAAACTTAAAC
66 AAACTTAATACCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
* *
4452 AACTGTAAACTTTCTTGACTGACCGCACTGGAT
131 CACTGGAAACTTTCTTGACTGACCGCACTGGAT
* * * *
4485 CACTTGAAGATAAACTTAAACAACTGTAAACTTTCTTGACTGACCACACTGGATCACTTGAAAAT
1 CACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGACTGACCGCACTGGATCACTTGAAGAT
* *
4550 AAACTTAATACCACTGGAAACTTTCTTGATTGACCACACTAGATCACTT
66 AAACTTAATACCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTT
4599 TGAAATTCGG
Statistics
Matches: 396, Mismatches: 41, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
161 2 0.01
162 110 0.28
163 236 0.60
164 48 0.12
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (163 bp):
CACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGACTGACCGCACTGGATCACTTGAAGAT
AAACTTAATACCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
CACTGGAAACTTTCTTGACTGACCGCACTGGAT
Found at i:6321 original size:13 final size:13
Alignment explanation
Indices: 6305--6334 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6295 CTGAGTTTTT
6305 TTCTTTTTCTTTC
1 TTCTTTTTCTTTC
*
6318 TTCTTTTTTTTTC
1 TTCTTTTTCTTTC
6331 TTCT
1 TTCT
6335 CTTTGAGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTCTTTTTCTTTC
Found at i:6337 original size:18 final size:18
Alignment explanation
Indices: 6303--6337 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
6293 GGCTGAGTTT
6303 TTTTCTTTTTCTTTCTTC
1 TTTTCTTTTTCTTTCTTC
6321 TTTT-TTTTTCTTCTCTT
1 TTTTCTTTTTCTT-TCTT
6338 TGAGTTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTTCTTTCTTC
Found at i:7056 original size:14 final size:14
Alignment explanation
Indices: 7037--7075 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
7027 ACTCAAAACC
7037 TTTTTGAAAACTCA
1 TTTTTGAAAACTCA
*
7051 TTTTTGAAAA-TCT
1 TTTTTGAAAACTCA
7064 TTTCTTGAAAAC
1 TTT-TTGAAAAC
7076 AATTTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (14 bp):
TTTTTGAAAACTCA
Found at i:7739 original size:3 final size:3
Alignment explanation
Indices: 7731--7773 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
7721 TCAGCAAATT
7731 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
7774 ACAAATGAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:8507 original size:40 final size:40
Alignment explanation
Indices: 8404--8507 Score: 129
Period size: 39 Copynumber: 2.6 Consensus size: 40
8394 ATCTATGCAT
* * * * *
8404 TGCATGATCATATATAAGATGGAATGTATAATGCATGATGGA
1 TGCATGAACATATACAA-AT-GAATGGATAATGCATCATCGA
*
8446 TGCATG-ACATATACAAATGAATGGATAATGTATCATCGA
1 TGCATGAACATATACAAATGAATGGATAATGCATCATCGA
8485 TGCATGAACATATACAAATGAAT
1 TGCATGAACATATACAAATGAAT
8508 ATCATGATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
39 23 0.42
40 18 0.33
41 8 0.15
42 6 0.11
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (40 bp):
TGCATGAACATATACAAATGAATGGATAATGCATCATCGA
Found at i:9873 original size:6 final size:6
Alignment explanation
Indices: 9862--9894 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
9852 ATCCTAAATG
9862 CTTAAT CTTAAT CTTAAT CTTAAT CTTAAT CTT
1 CTTAAT CTTAAT CTTAAT CTTAAT CTTAAT CTT
9895 TTTGTATTTT
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:0.30, C:0.18, G:0.00, T:0.52
Consensus pattern (6 bp):
CTTAAT
Found at i:10161 original size:67 final size:66
Alignment explanation
Indices: 10072--10455 Score: 420
Period size: 67 Copynumber: 5.7 Consensus size: 66
10062 CTAGACTCAG
* * * *
10072 ATGCAAAAAGACGAAAATGACCCTTCGACCGGAAGGGTGTTTTTTGGAAATGAAGATACTAAACT
1 ATGC-AAAAGACGAAAATGACCCTTCGACCGAAAGGGT-ATTTTTGGAAAAGAAAATACTAAACT
*
10137 TGA
64 TAA
* * * *
10140 ATACAAAAGAC-AACAATGACCCTTTGACCGAAAGGGTACTCTTGGGAAAAGAAAATACTAAACT
1 ATGCAAAAGACGAA-AATGACCCTTCGACCGAAAGGGTA-TTTTTGGAAAAGAAAATACTAAACT
10204 TAA
64 TAA
* * * *
10207 ATGCAAAGGACGAAAATGACCCTTTC-ACCGAAAGGGTATTTTTGGGAATGAGAATACTAAACTT
1 ATGCAAAAGACGAAAATGACCC-TTCGACCGAAAGGGTATTTTTGGAAAAGAAAATACTAAACTT
*
10271 GA
65 AA
* * * *
10273 ATGCAAAAGAC-AATACTGACCCTTTGATCGAAAGGGTATTTTTGGGAAAAGAAAATA-TCATAC
1 ATGCAAAAGACGAA-AATGACCCTTCGACCGAAAGGGTATTTTT-GGAAAAGAAAATACT-AAAC
*
10336 CTAA
63 TTAA
* *
10340 ATGCAAAAGACAAAAATGACCCTTTC-ACCGAAAGGGTA-TTTTCGAGAAAGAAAATACTAAACT
1 ATGCAAAAGACGAAAATGACCC-TTCGACCGAAAGGGTATTTTTGGA-AAAGAAAATACTAAACT
10403 TAA
64 TAA
* *
10406 ATACGAAAAGACGAAAATAACCCTTCGACCGAAAGGGTATTTTTGGAAAA
1 ATGC-AAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAA
10456 ACAAAATAAA
Statistics
Matches: 263, Mismatches: 38, Indels: 31
0.79 0.11 0.09
Matches are distributed among these distances:
65 6 0.02
66 84 0.32
67 156 0.59
68 17 0.06
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.22
Consensus pattern (66 bp):
ATGCAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAGAAAATACTAAACTTA
A
Found at i:10269 original size:133 final size:131
Alignment explanation
Indices: 10072--10463 Score: 491
Period size: 133 Copynumber: 2.9 Consensus size: 131
10062 CTAGACTCAG
* * *
10072 ATGCAAAAAGACGAAAATGACCC-TTCGACCGGAAGGGTGTTTTTTGGAAATGAAGATACTAAAC
1 ATGC-AAAAGACGAAAATGACCCTTTC-ACCGAAAGGGT-ATTTTTGGGAATGAA-ATACTAAAC
* *
10136 TTGAATACAAAAGACAACAATGACCCTTTGACCGAAAGGGTACTCTTGGGAAAAGAAAATA-CTA
62 TTGAATACAAAAGACAA-AATGACCCTTTGACCGAAAGGGTATTTTTGGGAAAAGAAAATATC-A
*
10200 AACTTAA
125 AACCTAA
*
10207 ATGCAAAGGACGAAAATGACCCTTTCACCGAAAGGGTATTTTTGGGAATGAGAATACTAAACTTG
1 ATGCAAAAGACGAAAATGACCCTTTCACCGAAAGGGTATTTTTGGGAATGA-AATACTAAACTTG
* * * *
10272 AATGCAAAAGACAATACTGACCCTTTGATCGAAAGGGTATTTTTGGGAAAAGAAAATATCATACC
65 AATACAAAAGACAA-AATGACCCTTTGACCGAAAGGGTATTTTTGGGAAAAGAAAATATCAAACC
10337 TAA
129 TAA
* * * * *
10340 ATGCAAAAGACAAAAATGACCCTTTCACCGAAAGGGTATTTTCGAGAAAGAAAATACTAAACTTA
1 ATGCAAAAGACGAAAATGACCCTTTCACCGAAAGGGTATTTTTGGGAATG-AAATACTAAACTTG
* * * *
10405 AATACGAAAAGACGAAAATAACCCTTCGACCGAAAGGGTATTTTTGGAAAAACAAAATA
65 AATAC-AAAAGAC-AAAATGACCCTTTGACCGAAAGGGTATTTTTGGGAAAAGAAAATA
10464 AAACTTTACT
Statistics
Matches: 226, Mismatches: 25, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
133 143 0.63
134 74 0.33
135 9 0.04
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (131 bp):
ATGCAAAAGACGAAAATGACCCTTTCACCGAAAGGGTATTTTTGGGAATGAAATACTAAACTTGA
ATACAAAAGACAAAATGACCCTTTGACCGAAAGGGTATTTTTGGGAAAAGAAAATATCAAACCTA
A
Found at i:10505 original size:7 final size:6
Alignment explanation
Indices: 10468--10504 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
10458 AAAATAAAAC
10468 TTTACTT TTTATT TTTATT TTTATT TTTATCT TTTAT
1 TTTA-TT TTTATT TTTATT TTTATT TTTAT-T TTTAT
10505 CAACTCTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 19 0.66
7 10 0.34
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:11105 original size:33 final size:33
Alignment explanation
Indices: 11063--11174 Score: 152
Period size: 33 Copynumber: 3.4 Consensus size: 33
11053 CGGCTACATG
* ** * *
11063 ACCGGCCACATGACTTGGAGATGCCTGGCCACC
1 ACCGGCCACATGACTCGGCCATGCCCGGCCACA
*
11096 ACCGGCCACATGACTCGGCCATGCCCGGCTACA
1 ACCGGCCACATGACTCGGCCATGCCCGGCCACA
*
11129 ACCAGCCACATGACTCGGCCATGCCCGGCCACA
1 ACCGGCCACATGACTCGGCCATGCCCGGCCACA
*
11162 ACTGGCCACATGA
1 ACCGGCCACATGA
11175 TCCTTTAACT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.23, C:0.40, G:0.24, T:0.12
Consensus pattern (33 bp):
ACCGGCCACATGACTCGGCCATGCCCGGCCACA
Found at i:13799 original size:6 final size:6
Alignment explanation
Indices: 13788--13814 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
13778 AAAGCAAAGC
13788 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
13815 GCAGAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:14625 original size:12 final size:12
Alignment explanation
Indices: 14608--14651 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
14598 TTGATTCACT
14608 TTTGATTTGAAC
1 TTTGATTTGAAC
*
14620 TTTGATTTAAAC
1 TTTGATTTGAAC
*
14632 TTTGATTCGAAC
1 TTTGATTTGAAC
14644 TTTGATTT
1 TTTGATTT
14652 CAATTATTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.25, C:0.09, G:0.14, T:0.52
Consensus pattern (12 bp):
TTTGATTTGAAC
Found at i:14983 original size:15 final size:16
Alignment explanation
Indices: 14965--15003 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
14955 AAACTCATTT
14965 TTGAAAAACC-TTTTC
1 TTGAAAAACCATTTTC
*
14980 TTG-AAGACCATTTTC
1 TTGAAAAACCATTTTC
14995 TTGAAAAAC
1 TTGAAAAAC
15004 GTCTCTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
14 5 0.25
15 11 0.55
16 4 0.20
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (16 bp):
TTGAAAAACCATTTTC
Found at i:19986 original size:19 final size:18
Alignment explanation
Indices: 19953--19988 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19943 TTGAAATAAT
19953 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
19971 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
19989 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Done.