Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007516.1 Corchorus capsularis cultivar CVL-1 contig07537, 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: 52225
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Found at i:1322 original size:10 final size:10
Alignment explanation
Indices: 1284--1326 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
1274 CTGGCATGGA
1284 ATATTATATT
1 ATATTATATT
1294 ATA-TATATAT
1 ATATTATAT-T
1304 ATATATATATT
1 ATAT-TATATT
*
1315 ACATTATATT
1 ATATTATATT
1325 AT
1 AT
1327 GATTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
9 5 0.18
10 14 0.50
11 4 0.14
12 5 0.18
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (10 bp):
ATATTATATT
Found at i:3315 original size:37 final size:37
Alignment explanation
Indices: 3265--3347 Score: 139
Period size: 37 Copynumber: 2.2 Consensus size: 37
3255 CATATCTTTC
3265 TCTTTCTCCATTTCTGAATTTCTGTATTGAAGACTCT
1 TCTTTCTCCATTTCTGAATTTCTGTATTGAAGACTCT
* *
3302 TCTTTCTCTATTTCTGCATTTCTGTATTGAAGACTCT
1 TCTTTCTCCATTTCTGAATTTCTGTATTGAAGACTCT
*
3339 TATTTCTCC
1 TCTTTCTCC
3348 TTTTTTGCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.17, C:0.23, G:0.10, T:0.51
Consensus pattern (37 bp):
TCTTTCTCCATTTCTGAATTTCTGTATTGAAGACTCT
Found at i:3357 original size:37 final size:37
Alignment explanation
Indices: 3267--3359 Score: 134
Period size: 37 Copynumber: 2.5 Consensus size: 37
3257 TATCTTTCTC
* * *
3267 TTTCTCCATTTCTGAATTTCTGTATTGAAGACTCTTC
1 TTTCTCCTTTTCTGCATTTCTGTATTGAAGACTCTTA
3304 TTTCT-CTATTTCTGCATTTCTGTATTGAAGACTCTTA
1 TTTCTCCT-TTTCTGCATTTCTGTATTGAAGACTCTTA
*
3341 TTTCTCCTTTTTTGCATTT
1 TTTCTCCTTTTCTGCATTT
3360 TTTGACAGGA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
36 1 0.02
37 47 0.94
38 2 0.04
ACGTcount: A:0.16, C:0.20, G:0.10, T:0.54
Consensus pattern (37 bp):
TTTCTCCTTTTCTGCATTTCTGTATTGAAGACTCTTA
Found at i:4142 original size:30 final size:31
Alignment explanation
Indices: 4106--4189 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 31
4096 GTTTTGTGCT
*
4106 TAAAAAT-CAATTCAGGGTATAAAGTTTGCC
1 TAAAAATGCAATTCAGGATATAAAGTTTGCC
* * * *
4136 TAAAAATGCATTTCAAGATTTAAGGTTTGCC
1 TAAAAATGCAATTCAGGATATAAAGTTTGCC
*
4167 TGAAAATGCAATTCAGGATATAA
1 TAAAAATGCAATTCAGGATATAA
4190 GGTTACAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 7 0.16
31 37 0.84
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (31 bp):
TAAAAATGCAATTCAGGATATAAAGTTTGCC
Found at i:4400 original size:29 final size:30
Alignment explanation
Indices: 4345--4424 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
4335 TCGGATCTGG
**
4345 AAACGTTATATCCTTCATTAGCATTTTT-G-
1 AAACGTTATATCCTGAATT-GCATTTTTGGC
* *
4374 TAACGTTATATCCTGAATTGCGTTTTTTGGC
1 AAACGTTATATCCTGAATTGC-ATTTTTGGC
*
4405 AAACCTTATATCCTGAATTG
1 AAACGTTATATCCTGAATTG
4425 ATTATTTAGC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
28 2 0.05
29 21 0.50
30 1 0.02
31 18 0.43
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.42
Consensus pattern (30 bp):
AAACGTTATATCCTGAATTGCATTTTTGGC
Found at i:11213 original size:16 final size:16
Alignment explanation
Indices: 11181--11256 Score: 55
Period size: 16 Copynumber: 4.8 Consensus size: 16
11171 GTCGGGTTGA
* *
11181 TCGGGTTCTGGTCATT
1 TCGGGTTCGGGTAATT
* *
11197 TTGGGTTTGGGTAATT
1 TCGGGTTCGGGTAATT
**
11213 TCGGGTTCGGGTTGTT
1 TCGGGTTCGGGTAATT
* * * *
11229 T-GGATTTGAGTCATT
1 TCGGGTTCGGGTAATT
11244 TCGGGTTCGGGTA
1 TCGGGTTCGGGTA
11257 CCCAAAAATT
Statistics
Matches: 42, Mismatches: 17, Indels: 2
0.69 0.28 0.03
Matches are distributed among these distances:
15 10 0.24
16 32 0.76
ACGTcount: A:0.09, C:0.11, G:0.37, T:0.43
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Found at i:11245 original size:31 final size:31
Alignment explanation
Indices: 11196--11255 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
11186 TTCTGGTCAT
* *
11196 TTTGGGTTTGGGTAATTTCGGGTTCGGGTTG
1 TTTGGATTTGAGTAATTTCGGGTTCGGGTTG
*
11227 TTTGGATTTGAGTCATTTCGGGTTCGGGT
1 TTTGGATTTGAGTAATTTCGGGTTCGGGT
11256 ACCCAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.08, C:0.08, G:0.38, T:0.45
Consensus pattern (31 bp):
TTTGGATTTGAGTAATTTCGGGTTCGGGTTG
Found at i:15164 original size:2 final size:2
Alignment explanation
Indices: 15159--15191 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15149 TATGTATAGG
15159 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15192 GATGTTAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18705 original size:2 final size:2
Alignment explanation
Indices: 18698--18726 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18688 ACCAGCCTAT
18698 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
18727 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:22026 original size:25 final size:26
Alignment explanation
Indices: 21998--22048 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
21988 GAAAAAAACA
21998 TTTGAGCGTTA-CTAGTCACCTAAAT
1 TTTGAGCGTTACCTAGTCACCTAAAT
22023 TTTGAGCGTTACTCTAGTCACCTAAA
1 TTTGAGCGTTAC-CTAGTCACCTAAA
22049 CTTTCAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 11 0.46
27 13 0.54
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (26 bp):
TTTGAGCGTTACCTAGTCACCTAAAT
Found at i:23902 original size:25 final size:26
Alignment explanation
Indices: 23874--23964 Score: 148
Period size: 25 Copynumber: 3.5 Consensus size: 26
23864 TATTAGTATA
23874 ATAATAATAATAATAATAATATATA-
1 ATAATAATAATAATAATAATATATAT
23899 ATAATAATAATAATAATAATATATAT
1 ATAATAATAATAATAATAATATATAT
* *
23925 ATATATAATAATAATAACAATACATAT
1 ATA-ATAATAATAATAATAATATATAT
23952 ATAATAATAATAA
1 ATAATAATAATAA
23965 AAACTATAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
25 25 0.40
26 13 0.21
27 24 0.39
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
ATAATAATAATAATAATAATATATAT
Found at i:23976 original size:3 final size:3
Alignment explanation
Indices: 23871--23964 Score: 125
Period size: 3 Copynumber: 29.3 Consensus size: 3
23861 AGTTATTAGT
23871 ATA ATA ATA ATA ATA ATA ATA ATA TATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA
*
23917 ATA TATA TATA TATA ATA ATA ATA ACA ATA CATA TATA ATA ATA ATA
1 ATA -ATA -ATA -ATA ATA ATA ATA ATA ATA -ATA -ATA ATA ATA ATA
23964 A
1 A
23965 AAACTATAAT
Statistics
Matches: 85, Mismatches: 3, Indels: 6
0.90 0.03 0.06
Matches are distributed among these distances:
3 65 0.76
4 20 0.24
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:36851 original size:13 final size:13
Alignment explanation
Indices: 36833--36857 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36823 AGTAGCCTGT
36833 GTTCATTAAGCAG
1 GTTCATTAAGCAG
36846 GTTCATTAAGCA
1 GTTCATTAAGCA
36858 CTTTCCGGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
GTTCATTAAGCAG
Found at i:40334 original size:30 final size:31
Alignment explanation
Indices: 40300--40366 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 31
40290 AAGAAGGGGC
40300 AATCAGCAATTAAGTTCAATAAGAAA-AAGT
1 AATCAGCAATTAAGTTCAATAAGAAAGAAGT
** *
40330 AATCAGTGATTAAGTTCAATAAGAAAGATGT
1 AATCAGCAATTAAGTTCAATAAGAAAGAAGT
40361 AATCAG
1 AATCAG
40367 TAAAAGGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 24 0.73
31 9 0.27
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.25
Consensus pattern (31 bp):
AATCAGCAATTAAGTTCAATAAGAAAGAAGT
Found at i:40366 original size:31 final size:30
Alignment explanation
Indices: 40308--40367 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
40298 GCAATCAGCA
40308 ATTAAGTTCAATAAGAAAAAGTAATCAGTG
1 ATTAAGTTCAATAAGAAAAAGTAATCAGTG
*
40338 ATTAAGTTCAATAAGAAAGATGTAATCAGT
1 ATTAAGTTCAATAAGAAA-AAGTAATCAGT
40368 AAAAGGTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (30 bp):
ATTAAGTTCAATAAGAAAAAGTAATCAGTG
Found at i:40386 original size:22 final size:23
Alignment explanation
Indices: 40361--40420 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
40351 AGAAAGATGT
*
40361 AATCAGTAAAAG-GTAAAGCGGC
1 AATCAGTAAAAGAGTAAAGCGAC
* *
40383 AATCAGT-AAAGAGTAAAGTGAT
1 AATCAGTAAAAGAGTAAAGCGAC
40405 AATCAGT-AAAGAGTAA
1 AATCAGTAAAAGAGTAA
40421 TAGAAATCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 4 0.12
22 30 0.88
ACGTcount: A:0.50, C:0.08, G:0.23, T:0.18
Consensus pattern (23 bp):
AATCAGTAAAAGAGTAAAGCGAC
Found at i:40529 original size:107 final size:109
Alignment explanation
Indices: 40404--40608 Score: 360
Period size: 107 Copynumber: 1.9 Consensus size: 109
40394 AGTAAAGTGA
*
40404 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAA-A-ATTAATTAGAGTC
1 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTC
*
40467 AAGGTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAAT
66 AAAGTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAAT
40511 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTC
1 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTC
* *
40576 AAAGTAATAGTAATCAGTAAATCGATAATTAAG
66 AAAGTAATAGAAATCAGTAAATCAATAATTAAG
40609 AGTTAAAATG
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
107 49 0.53
108 1 0.01
109 42 0.46
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (109 bp):
TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTC
AAAGTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAAT
Found at i:40543 original size:54 final size:53
Alignment explanation
Indices: 40404--40608 Score: 263
Period size: 54 Copynumber: 3.8 Consensus size: 53
40394 AGTAAAGTGA
*
40404 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAA-AAAT
1 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGTAAAAGAAAT
* *
40456 TAATTAGAGTCAAG-GTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAAT
1 TAA-T-CAGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGT-AAAAGAAAT
* *
40511 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
1 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGT-AAAAGAAAT
* * *
40565 TAATCAGAGTCAA-AGTAATAGTAATCAGTAAATCGATAATTAAG
1 TAATC--AGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAG
40609 AGTTAAAATG
Statistics
Matches: 134, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
52 3 0.02
53 37 0.28
54 54 0.40
55 35 0.26
56 5 0.04
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (53 bp):
TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGTAAAAGAAAT
Found at i:40896 original size:43 final size:41
Alignment explanation
Indices: 40846--41086 Score: 214
Period size: 43 Copynumber: 5.6 Consensus size: 41
40836 TAATCAGTAA
* *
40846 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAACCAAC
1 AAGAGTAAAA-AGTAATCAGTAAAAAGTAA-AAGGTAATCAGC
* *
40889 AAGAGTAAAATAGTAGTCAGTAAAAAGTAAATA-GTAATCAGT
1 AAGAGTAAAA-AGTAATCAGTAAAAAGTAAA-AGGTAATCAGC
* * * *
40931 AAGAGTAAAAAAAGTAATAAGTAAGAAGTAAAAGGAAATCAGT
1 AAGAGT--AAAAAGTAATCAGTAAAAAGTAAAAGGTAATCAGC
* * *
40974 AAGAGTAAAAAGGTGATCAGTAAAGAGTAAAAAGCTAATCAGC
1 AAGAGTAAAAA-GTAATCAGTAAAAAGT-AAAAGGTAATCAGC
* * * *
41017 AAGAAGTAAAAAGATAATCATTAAAACGAAAAAGGTAATCAGTA
1 AAG-AGTAAAAAG-TAATCAGTAAAAAGTAAAAGGTAATCAG-C
* *
41061 AAAACTAAAAGAGTAATCAGTAAAAA
1 AAGAGTAAAA-AGTAATCAGTAAAAA
41087 AGGAGCAGAA
Statistics
Matches: 162, Mismatches: 26, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
41 5 0.03
42 26 0.16
43 105 0.65
44 26 0.16
ACGTcount: A:0.57, C:0.07, G:0.19, T:0.18
Consensus pattern (41 bp):
AAGAGTAAAAAGTAATCAGTAAAAAGTAAAAGGTAATCAGC
Found at i:40922 original size:21 final size:22
Alignment explanation
Indices: 40829--41242 Score: 263
Period size: 22 Copynumber: 18.8 Consensus size: 22
40819 TGAAAGGGTA
*
40829 AAAAGAGTAATCAGTAAAAGAGT
1 AAAATAGTAATCAGTAAAA-AGT
40852 AAAATAGTAATCAGTAAAAAGT
1 AAAATAGTAATCAGTAAAAAGT
* * *
40874 AAGAA-GGTAACCA--ACAAGAGT
1 AA-AATAGTAATCAGTA-AAAAGT
*
40895 AAAATAGTAGTCAGTAAAAAGT
1 AAAATAGTAATCAGTAAAAAGT
*
40917 -AAATAGTAATCAGT-AAGAGT
1 AAAATAGTAATCAGTAAAAAGT
* * *
40937 AAAAAAAGTAATAAGTAAGAAGT
1 -AAAATAGTAATCAGTAAAAAGT
* * *
40960 AAAA-GGAAATCAGT-AAGAGT
1 AAAATAGTAATCAGTAAAAAGT
* *
40980 AAAA-AGGTGATCAGTAAAGAGT
1 AAAATA-GTAATCAGTAAAAAGT
* *
41002 AAAA-AGCTAATCAGCAAGAAGT
1 AAAATAG-TAATCAGTAAAAAGT
* *
41024 AAAA-AGATAATCATTAAAACG-
1 AAAATAG-TAATCAGTAAAAAGT
*
41045 AAAA-AGGTAATCAGTAAAAACT
1 AAAATA-GTAATCAGTAAAAAGT
* *
41067 AAAAGAGTAATCAGTAAAAAAGGAGCAG
1 AAAATAGTAATCAGT--AAAA--AG--T
41095 AAAATAGTAATCAGTAAAAGAGT
1 AAAATAGTAATCAGTAAAA-AGT
*
41118 AAAATGGTAATCAGTAAAAGAGT
1 AAAATAGTAATCAGTAAAA-AGT
*
41141 AAAATGGTAATCAGTAAAAAGT
1 AAAATAGTAATCAGTAAAAAGT
* *
41163 AAGAA-GGTAATCA--ACAAGAGT
1 AA-AATAGTAATCAGTA-AAAAGT
*
41184 AAAATAGTAATCAGTACAAAGT
1 AAAATAGTAATCAGTAAAAAGT
*
41206 AAAGA-A-TAATCAGTGAAATAGT
1 AAA-ATAGTAATCAGT-AAAAAGT
*
41228 --AATGGTAATCAGTAA
1 AAAATAGTAATCAGTAA
41243 TCCAGTAAAA
Statistics
Matches: 316, Mismatches: 46, Indels: 61
0.75 0.11 0.14
Matches are distributed among these distances:
19 1 0.00
20 22 0.07
21 86 0.27
22 110 0.35
23 71 0.22
24 4 0.01
25 3 0.01
26 5 0.02
28 14 0.04
ACGTcount: A:0.55, C:0.07, G:0.19, T:0.19
Consensus pattern (22 bp):
AAAATAGTAATCAGTAAAAAGT
Found at i:41084 original size:15 final size:15
Alignment explanation
Indices: 41066--41119 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
41056 CAGTAAAAAC
41066 TAAAAGAGTAATCAG
1 TAAAAGAGTAATCAG
* * *
41081 TAAAAAAG-GAGCAG
1 TAAAAGAGTAATCAG
*
41095 -AAAATAGTAATCAG
1 TAAAAGAGTAATCAG
41109 TAAAAGAGTAA
1 TAAAAGAGTAA
41120 AATGGTAATC
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 6 0.20
14 8 0.27
15 16 0.53
ACGTcount: A:0.57, C:0.06, G:0.20, T:0.17
Consensus pattern (15 bp):
TAAAAGAGTAATCAG
Found at i:41251 original size:139 final size:137
Alignment explanation
Indices: 40821--41064 Score: 88
Period size: 128 Copynumber: 1.8 Consensus size: 137
40811 AAGGTACCTG
* * * * *
40821 AAAGGGTAAAAAGAGTAATCAGTAAAAGAGTAAAATAG-TAATCAGTAAAAAGTAAGAAGGTAAC
1 AAAGAGTAAAAAG-GTAATCAGT-AAAGAGTAAAA-AGCTAATCAGCAAAAAGTAAAAAGATAAT
* * * * *
40885 CAACAAGA-GTAAAATA-GTAGTCAGTAAAAAGTAAATAG--TAATCAGT--AAGAGTA-A-AAA
63 CAACAAAACG-AAAA-AGGTAATCAGTAAAAACTAAA-AGAATAATCAGTAAAAAAGGACAGAAA
*
40942 A-AGTAATAAGTA
125 ATAGTAATCAGTA
* * * * * * * *
40954 AGA-AGT-AAAAGGAAATCAGT-AAGAGTAAAAAGGTGATCAGTAAAGAGTAAAAAGCTAATCAG
1 AAAGAGTAAAAAGGTAATCAGTAAAGAGTAAAAAGCTAATCAGCAAAAAGTAAAAAGATAATCAA
* * * *
41016 CAAGAA-GTAAAAAGATAATCA-TTAAAACGAAAA-AGGTAATCAGTAAAAA
66 CAA-AACG-AAAAAGGTAATCAGTAAAAACTAAAAGA-ATAATCAGTAAAAA
41065 CTAAAAGAGT
Statistics
Matches: 87, Mismatches: 16, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
127 3 0.03
128 45 0.52
129 20 0.23
130 8 0.09
131 7 0.08
132 2 0.02
133 2 0.02
ACGTcount: A:0.57, C:0.06, G:0.20, T:0.18
Consensus pattern (137 bp):
AAAGAGTAAAAAGGTAATCAGTAAAGAGTAAAAAGCTAATCAGCAAAAAGTAAAAAGATAATCAA
CAAAACGAAAAAGGTAATCAGTAAAAACTAAAAGAATAATCAGTAAAAAAGGACAGAAAATAGTA
ATCAGTA
Found at i:41254 original size:139 final size:137
Alignment explanation
Indices: 40967--41219 Score: 309
Period size: 139 Copynumber: 1.9 Consensus size: 137
40957 AGTAAAAGGA
* *
40967 AATCAGT--AAGAGTAAAAAGGTGATCAGTAAAGAGTAAAAAGCTAATCAGCAAGAAGTAAAAAG
1 AATCAGTAAAAGAGTAAAAAGGTAATCAGTAAAGAGTAAAAAGCTAATCAGCAAAAAGTAAAAAG
** *
41030 ATAATCATTAAAACGAAAAAGGTAATCAGTAAAAACTAAAAGAGTAATCAGTAAAAAAGGAGCAG
66 ATAATCAACAAAACGAAAAAGGTAATCAGTAAAAACTAAAAGAATAATCAGTAAAAAAGGA-CAG
41095 AAAATAGT
130 AAAATAGT
* * * * *
41103 AATCAGTAAAAGAGTAAAATGGTAATCAGTAAAAGAGTAAAATGGTAATCAGTAAAAAGTAAGAA
1 AATCAGTAAAAGAGTAAAAAGGTAATCAGT-AAAGAGTAAAAAGCTAATCAGCAAAAAGTAAAAA
* * * *
41168 GGTAATCAACAAGA-GTAAAATA-GTAATCAGTACAAAGT-AAAGAATAATCAGT
65 GATAATCAACAAAACG-AAAA-AGGTAATCAGTAAAAACTAAAAGAATAATCAGT
41220 GAAATAGTAA
Statistics
Matches: 98, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
136 7 0.07
138 33 0.34
139 57 0.58
140 1 0.01
ACGTcount: A:0.55, C:0.08, G:0.19, T:0.19
Consensus pattern (137 bp):
AATCAGTAAAAGAGTAAAAAGGTAATCAGTAAAGAGTAAAAAGCTAATCAGCAAAAAGTAAAAAG
ATAATCAACAAAACGAAAAAGGTAATCAGTAAAAACTAAAAGAATAATCAGTAAAAAAGGACAGA
AAATAGT
Found at i:48838 original size:3 final size:3
Alignment explanation
Indices: 48826--48860 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
48816 GAAGTAAGCT
48826 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
48861 ATGTCACGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:51495 original size:25 final size:25
Alignment explanation
Indices: 51461--51512 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
51451 ACGATGAATT
51461 TAGGCTTAATC-CTTTAGATTAAAAC
1 TAGGCTTAATCTC-TTAGATTAAAAC
* *
51486 TAGGCTTAATTTCTTGGATTAAAAC
1 TAGGCTTAATCTCTTAGATTAAAAC
51511 TA
1 TA
51513 ATTCAAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (25 bp):
TAGGCTTAATCTCTTAGATTAAAAC
Found at i:52113 original size:25 final size:25
Alignment explanation
Indices: 52079--52130 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
52069 ACGATGAATT
52079 TAGGCTTAATC-CTTTAGATTAAAAC
1 TAGGCTTAATCTC-TTAGATTAAAAC
* *
52104 TAGGCTTAATTTCTTGGATTAAAAC
1 TAGGCTTAATCTCTTAGATTAAAAC
52129 TA
1 TA
52131 ATTCAAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (25 bp):
TAGGCTTAATCTCTTAGATTAAAAC
Done.