Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019049.1 Corchorus olitorius cultivar O-4 contig19082, 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: 39481
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:851 original size:32 final size:32
Alignment explanation
Indices: 815--878 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
805 ACAGCTTAAT
815 GAAAATACAAAAATATAACAATGTTCCTACAA
1 GAAAATACAAAAATATAACAATGTTCCTACAA
847 GAAAATACAAAAATATAACAATGTTCCTACAA
1 GAAAATACAAAAATATAACAATGTTCCTACAA
879 TTTTCCTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.56, C:0.16, G:0.06, T:0.22
Consensus pattern (32 bp):
GAAAATACAAAAATATAACAATGTTCCTACAA
Found at i:4122 original size:28 final size:28
Alignment explanation
Indices: 4029--4134 Score: 85
Period size: 28 Copynumber: 3.7 Consensus size: 28
4019 TCTGTAAAGA
*
4029 GTAAAGAGTAATCAGTAAAAATGGTAATG
1 GTAAAGAGTAATCAGT-AAAATGGCAATG
* *
4058 GTAATTCAGAGTAAT---TAAAAT-TCAAAG
1 GTAA---AGAGTAATCAGTAAAATGGCAATG
4085 AAGTAAAGAGTAATCAGTAAAATGGCAATG
1 --GTAAAGAGTAATCAGTAAAATGGCAATG
**
4115 GTAAAGAGTAAAGAGTAAAA
1 GTAAAGAGTAATCAGTAAAA
4135 GAGGAATAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
26 8 0.13
27 3 0.05
28 23 0.38
29 15 0.25
30 4 0.07
32 8 0.13
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.23
Consensus pattern (28 bp):
GTAAAGAGTAATCAGTAAAATGGCAATG
Found at i:4182 original size:15 final size:15
Alignment explanation
Indices: 4160--4213 Score: 74
Period size: 15 Copynumber: 3.6 Consensus size: 15
4150 GTAAAAGAAT
4160 AAAGAGTAATCTATA
1 AAAGAGTAATCTATA
* *
4175 AAATAGTAATCTGTA
1 AAAGAGTAATCTATA
4190 AAAGAGTAATC-AGTA
1 AAAGAGTAATCTA-TA
4205 AAAGAGTAA
1 AAAGAGTAA
4214 AGAGTAAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.24
Consensus pattern (15 bp):
AAAGAGTAATCTATA
Found at i:4194 original size:30 final size:30
Alignment explanation
Indices: 4160--4229 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
4150 GTAAAAGAAT
* * *
4160 AAAGAGTAATCTA-TAAAATAGTAATCTGTA
1 AAAGAGTAATC-AGTAAAAGAGTAAACAGTA
*
4190 AAAGAGTAATCAGTAAAAGAGTAAAGAGTA
1 AAAGAGTAATCAGTAAAAGAGTAAACAGTA
4220 AAAGAGTAAT
1 AAAGAGTAAT
4230 AATAGTTAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 1 0.03
30 34 0.97
ACGTcount: A:0.54, C:0.04, G:0.19, T:0.23
Consensus pattern (30 bp):
AAAGAGTAATCAGTAAAAGAGTAAACAGTA
Found at i:4219 original size:15 final size:15
Alignment explanation
Indices: 4160--4228 Score: 68
Period size: 15 Copynumber: 4.6 Consensus size: 15
4150 GTAAAAGAAT
*
4160 AAAGAGTAATCTA-TA
1 AAAGAGTAAAC-AGTA
* * *
4175 AAATAGTAATCTGTA
1 AAAGAGTAAACAGTA
*
4190 AAAGAGTAATCAGTA
1 AAAGAGTAAACAGTA
*
4205 AAAGAGTAAAGAGTA
1 AAAGAGTAAACAGTA
4220 AAAGAGTAA
1 AAAGAGTAA
4229 TAATAGTTAG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.55, C:0.04, G:0.19, T:0.22
Consensus pattern (15 bp):
AAAGAGTAAACAGTA
Found at i:4268 original size:28 final size:28
Alignment explanation
Indices: 4187--4269 Score: 78
Period size: 28 Copynumber: 2.9 Consensus size: 28
4177 ATAGTAATCT
* *
4187 GTAAAAGAGTAATCAGTAAAAGAGTAAAGA
1 GTAAAAGAGTAATAAG--AGAGAGTAAAGA
* **
4217 GTAAAAGAGTAATAATAGTTAGTAAAGA
1 GTAAAAGAGTAATAAGAGAGAGTAAAGA
*
4245 GT-AAAGAGTAATCAAGGGAGAGTAA
1 GTAAAAGAGTAAT-AAGAGAGAGTAA
4270 TAGTAATCGG
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
27 10 0.23
28 19 0.44
30 14 0.33
ACGTcount: A:0.53, C:0.02, G:0.25, T:0.19
Consensus pattern (28 bp):
GTAAAAGAGTAATAAGAGAGAGTAAAGA
Found at i:4287 original size:21 final size:21
Alignment explanation
Indices: 4194--4347 Score: 87
Period size: 21 Copynumber: 7.6 Consensus size: 21
4184 TCTGTAAAAG
4194 AGTAATCAGTAAAAGAGTAA-
1 AGTAATCAGTAAAAGAGTAAT
4214 AG-----AGTAAAAGAGTAAT
1 AGTAATCAGTAAAAGAGTAAT
* * * *
4230 AATAGTTAGT-AAAGAGTAAAG
1 AGTAATCAGTAAAAGAGT-AAT
**
4251 AGTAATCA--AGGGAGAGTAAT
1 AGTAATCAGTA-AAAGAGTAAT
* *
4271 AGTAATCGGTAAAAGAGTAAAC
1 AGTAATCAGTAAAAGAGT-AAT
*
4293 AGTAAACAGTAAAATGA-TAAT
1 AGTAATCAGTAAAA-GAGTAAT
4314 AGTAATCAGTAAAA-AGTAAAAT
1 AGTAATCAGTAAAAGAGT--AAT
*
4336 GGTAATCAGTAA
1 AGTAATCAGTAA
4348 GAGTAAAATG
Statistics
Matches: 101, Mismatches: 17, Indels: 30
0.68 0.11 0.20
Matches are distributed among these distances:
15 13 0.13
16 1 0.01
19 1 0.01
20 19 0.19
21 35 0.35
22 30 0.30
23 2 0.02
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (21 bp):
AGTAATCAGTAAAAGAGTAAT
Found at i:4317 original size:28 final size:29
Alignment explanation
Indices: 4286--4355 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 29
4276 TCGGTAAAAG
*
4286 AGTAAACAGTAAACAGTAAAATGATAAT-
1 AGTAAACAGTAAAAAGTAAAATGATAATC
* *
4314 AGTAATCAGTAAAAAGTAAAATGGTAATC
1 AGTAAACAGTAAAAAGTAAAATGATAATC
*
4343 AGT-AAGAGTAAAA
1 AGTAAACAGTAAAA
4356 TGGTACAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
28 33 0.92
29 3 0.08
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.21
Consensus pattern (29 bp):
AGTAAACAGTAAAAAGTAAAATGATAATC
Found at i:4380 original size:57 final size:60
Alignment explanation
Indices: 4319--4438 Score: 194
Period size: 60 Copynumber: 2.0 Consensus size: 60
4309 ATAATAGTAA
4319 TCAGTAAAAAGTAAAATGGTAATC-A-GT-AAGAGTAAAATGGTACAAT-AGTAATTAAAT
1 TCAGTAAAAAGTAAAATGGTAATCAATGTAAAGAGTAAAATGGTA-AATCAGTAATTAAAT
*
4376 TCAGTAAAAAGTAAAATGGTAATCAATTTAAAGAGTAAAATGGTAAATCAGTAATTAAAT
1 TCAGTAAAAAGTAAAATGGTAATCAATGTAAAGAGTAAAATGGTAAATCAGTAATTAAAT
4436 TCA
1 TCA
4439 AAGAGTAAGA
Statistics
Matches: 58, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
57 24 0.41
58 1 0.02
59 4 0.07
60 29 0.50
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.28
Consensus pattern (60 bp):
TCAGTAAAAAGTAAAATGGTAATCAATGTAAAGAGTAAAATGGTAAATCAGTAATTAAAT
Found at i:4629 original size:26 final size:26
Alignment explanation
Indices: 4593--4643 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
4583 AAAAAAGAAG
*
4593 AAGAGTAAAAAATGGTAATAAGTAAA
1 AAGAATAAAAAATGGTAATAAGTAAA
*
4619 AAGAATAAAAAATGGTAATCAGTAA
1 AAGAATAAAAAATGGTAATAAGTAA
4644 TCAAGAAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.61, C:0.02, G:0.18, T:0.20
Consensus pattern (26 bp):
AAGAATAAAAAATGGTAATAAGTAAA
Found at i:5137 original size:35 final size:35
Alignment explanation
Indices: 5097--5171 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
5087 AGTTCGTTTA
*
5097 TGTTCACGAACAGGCTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
5132 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
5167 TGTTC
1 TGTTC
5172 GTTTATATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (35 bp):
TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
Found at i:5234 original size:16 final size:16
Alignment explanation
Indices: 5213--5244 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5203 TATAATTATT
5213 TATATATTAATAATAA
1 TATATATTAATAATAA
*
5229 TATATATTATTAATAA
1 TATATATTAATAATAA
5245 AAATAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATTAATAATAA
Found at i:5239 original size:19 final size:19
Alignment explanation
Indices: 5197--5249 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
5187 GAACGTTCGT
* *
5197 TTATTATATAATTATTTATA
1 TTATTA-ATAATAATATATA
5217 -TATTAATAATAATATATA
1 TTATTAATAATAATATATA
*
5235 TTATTAATAAAAATA
1 TTATTAATAATAATA
5250 ATAATATTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 11 0.38
19 18 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATTAATAATAATATATA
Found at i:5251 original size:25 final size:27
Alignment explanation
Indices: 5221--5270 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
5211 TTTATATATT
5221 AATAATAATA-TATATTAT-TAATAAA
1 AATAATAATATTATATTATCTAATAAA
*
5246 AATAATAATATTCTATTATCTAATA
1 AATAATAATATTATATTATCTAATA
5271 TATTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 7 0.32
27 5 0.23
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (27 bp):
AATAATAATATTATATTATCTAATAAA
Found at i:5391 original size:18 final size:18
Alignment explanation
Indices: 5364--5398 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5354 AATTATTATA
5364 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
5382 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
5399 CAATTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:8930 original size:36 final size:36
Alignment explanation
Indices: 8885--9067 Score: 140
Period size: 36 Copynumber: 4.9 Consensus size: 36
8875 CCCTCTCCCT
* * *
8885 CTGAATCTGAGCAGCAACAGTAGCCTCTCTCTCACG
1 CTGACTCTGAGCAGCAGCAGAAGCCTCTCTCTCACG
* * *
8921 CTGACTCTGAGCAGCAGTAGAAGCCTCTCTCCCTCCCT
1 CTGACTCTGAGCAGCAGCAGAAGCCTCTCT--CTCACG
**
8959 CTCCCTCTGAATTTG-AGCAGCAGAAGTAGCCTCTCTCTCACG
1 CTGACTCTG-A---GCAGCAGCAG-A--AGCCTCTCTCTCACG
* *
9001 CTGACTCTGAGCAGCAGTAGAAGCCTCTCTC-C-CT
1 CTGACTCTGAGCAGCAGCAGAAGCCTCTCTCTCACG
* *
9035 ATGACTCTTAGCAGCAGCA-ACAGCCTCTCTCTC
1 CTGACTCTGAGCAGCAGCAGA-AGCCTCTCTCTC
9068 CCTTTAACTG
Statistics
Matches: 117, Mismatches: 18, Indels: 25
0.73 0.11 0.16
Matches are distributed among these distances:
33 1 0.01
34 27 0.23
35 2 0.02
36 36 0.31
38 13 0.11
39 8 0.07
41 8 0.07
42 13 0.11
44 9 0.08
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.24
Consensus pattern (36 bp):
CTGACTCTGAGCAGCAGCAGAAGCCTCTCTCTCACG
Found at i:8995 original size:80 final size:80
Alignment explanation
Indices: 8864--9034 Score: 303
Period size: 80 Copynumber: 2.2 Consensus size: 80
8854 TCAACATCTC
8864 AGCCTCTCT--CTCCCTCTCCCTCTGAATCTGAGCAGCAACAGTAGCCTCTCTCTCACGCTGACT
1 AGCCTCTCTCCCTCCCTCTCCCTCTGAATCTGAGCAGCAACAGTAGCCTCTCTCTCACGCTGACT
8927 CTGAGCAGCAGTAGA
66 CTGAGCAGCAGTAGA
*
8942 AGCCTCTCTCCCTCCCTCTCCCTCTGAATTTGAGCAGCAGA-AGTAGCCTCTCTCTCACGCTGAC
1 AGCCTCTCTCCCTCCCTCTCCCTCTGAATCTGAGCAGCA-ACAGTAGCCTCTCTCTCACGCTGAC
9006 TCTGAGCAGCAGTAGA
65 TCTGAGCAGCAGTAGA
9022 AGCCTCTCTCCCT
1 AGCCTCTCTCCCT
9035 ATGACTCTTA
Statistics
Matches: 89, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
78 9 0.10
80 79 0.89
81 1 0.01
ACGTcount: A:0.19, C:0.38, G:0.18, T:0.25
Consensus pattern (80 bp):
AGCCTCTCTCCCTCCCTCTCCCTCTGAATCTGAGCAGCAACAGTAGCCTCTCTCTCACGCTGACT
CTGAGCAGCAGTAGA
Found at i:9040 original size:34 final size:34
Alignment explanation
Indices: 8957--9065 Score: 112
Period size: 34 Copynumber: 3.1 Consensus size: 34
8947 CTCTCCCTCC
* * *
8957 CTCTCCCTCTGAATTTGAGCAGCAGAAGTAGCCT
1 CTCTCCCTCTGACTCTGAGCAGCAGAAGAAGCCT
* *
8991 CTCTCTCACGCTGACTCTGAGCAGCAGTAGAAGCCT
1 CTCTC-C-CTCTGACTCTGAGCAGCAGAAGAAGCCT
* * *
9027 CTCTCCCTATGACTCTTAGCAGCAGCAA-CAGCCT
1 CTCTCCCTCTGACTCTGAGCAGCAG-AAGAAGCCT
9061 CTCTC
1 CTCTC
9066 TCCCTTTAAC
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
34 31 0.50
35 3 0.05
36 28 0.45
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.25
Consensus pattern (34 bp):
CTCTCCCTCTGACTCTGAGCAGCAGAAGAAGCCT
Found at i:9296 original size:18 final size:17
Alignment explanation
Indices: 9243--9296 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
9233 ATTAATCGTA
9243 AATAAACTAATT--AAT
1 AATAAACTAATTAAAAT
* *
9258 TATAAACTAAGTAAAACT
1 AATAAACTAATTAAAA-T
9276 AATAAACTAATTAAGAAT
1 AATAAACTAATTAA-AAT
9294 AAT
1 AAT
9297 TAATTTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
15 10 0.32
17 2 0.06
18 17 0.55
19 2 0.06
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (17 bp):
AATAAACTAATTAAAAT
Found at i:9666 original size:24 final size:24
Alignment explanation
Indices: 9590--9675 Score: 75
Period size: 24 Copynumber: 3.4 Consensus size: 24
9580 CTTGAAGATT
* *
9590 GTTTAAAGAAAATGAAGGTTGA-A
1 GTTTGAAGAAAATGAAAGTTGAGA
* *
9613 GGTTGAAGAAAATGAAGTAAAGATTAAGA
1 GTTTGAAGAAAAT---G-AAAG-TTGAGA
9642 GTTTGAAGAAAATGAAAGTTGAGA
1 GTTTGAAGAAAATGAAAGTTGAGA
*
9666 GTTTTAAGAA
1 GTTTGAAGAA
9676 GTTGTTAGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
23 11 0.22
24 14 0.28
25 4 0.08
26 2 0.04
27 3 0.06
28 3 0.06
29 13 0.26
ACGTcount: A:0.48, C:0.00, G:0.27, T:0.26
Consensus pattern (24 bp):
GTTTGAAGAAAATGAAAGTTGAGA
Found at i:10105 original size:2 final size:2
Alignment explanation
Indices: 10098--10149 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
10088 AGGCGTCCTA
* * *
10098 AT AT AT AT AC AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10140 AT AT AT AT AT
1 AT AT AT AT AT
10150 GGTTTGGCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:12155 original size:30 final size:30
Alignment explanation
Indices: 12107--12165 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
12097 GTTTATTAAT
12107 GAAACTTGAAATTAAAAGCCATAAAATAAAG
1 GAAACTTGAAATTAAAAG-CATAAAATAAAG
*
12138 GAAA-TTGAAAATT-AAAGCATAAACTAAA
1 GAAACTTG-AAATTAAAAGCATAAAATAAA
12166 TAACTAATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 10 0.38
30 7 0.27
31 9 0.35
ACGTcount: A:0.59, C:0.08, G:0.12, T:0.20
Consensus pattern (30 bp):
GAAACTTGAAATTAAAAGCATAAAATAAAG
Found at i:25245 original size:19 final size:18
Alignment explanation
Indices: 25212--25247 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
25202 TTCAGATAAT
25212 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
25230 TCTTCATATTATCTTCAA
1 TCTTCA-ATGATCTTCAA
25248 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:25255 original size:11 final size:10
Alignment explanation
Indices: 25200--25258 Score: 50
Period size: 11 Copynumber: 5.7 Consensus size: 10
25190 AATTCTTGCT
25200 TCTTCAGATAA
1 TCTTCA-ATAA
*
25211 TTCTTCAATGA
1 -TCTTCAATAA
25222 TCTTC-A-AA
1 TCTTCAATAA
*
25230 TCTTCATATTA
1 TCTTCA-ATAA
25241 TCTTCAATAA
1 TCTTCAATAA
25251 GTCTTCAA
1 -TCTTCAA
25259 ACACGAACTT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
8 6 0.15
9 1 0.03
10 9 0.23
11 17 0.44
12 6 0.15
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.42
Consensus pattern (10 bp):
TCTTCAATAA
Found at i:33261 original size:17 final size:17
Alignment explanation
Indices: 33239--33271 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
33229 CCAACCTAAT
*
33239 TAAAACGTGCACGTGAC
1 TAAAACGTACACGTGAC
33256 TAAAACGTACACGTGA
1 TAAAACGTACACGTGA
33272 ATGAATCGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (17 bp):
TAAAACGTACACGTGAC
Found at i:34210 original size:50 final size:50
Alignment explanation
Indices: 34067--34238 Score: 299
Period size: 50 Copynumber: 3.4 Consensus size: 50
34057 TTCCTTGGAT
* * *
34067 TGTCTTCCAATCCAATATTAAAAGGACCGTCTTCCGTTTATCCTTTGAAC
1 TGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAAC
*
34117 TGTCTTCCAATTCAATCTTTAAAAGGACCATCTTCCGCTTATCCTTTGAAC
1 TGTCTTCCAATTCAATC-TTAAAAGGACCGTCTTCCGCTTATCCTTTGAAC
34168 TGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAAC
1 TGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAAC
34218 TGTCTTCCAATTCAATCTTAA
1 TGTCTTCCAATTCAATCTTAA
34239 GAAAATCATC
Statistics
Matches: 116, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
50 68 0.59
51 48 0.41
ACGTcount: A:0.26, C:0.27, G:0.10, T:0.37
Consensus pattern (50 bp):
TGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAAC
Found at i:34705 original size:64 final size:64
Alignment explanation
Indices: 34464--34885 Score: 515
Period size: 64 Copynumber: 6.6 Consensus size: 64
34454 CCGGTGCATC
* * * ** * * * *
34464 TCTTAACAAGATCATCTTCCGATCAACTTCTGAAACCTTTTCAAGAAACTATCTTCTAGTGTGCT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAA-ATTTTTGAGAAACCATCTTCTGGCGTACT
* *
34529 TTTTAACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCTGGCGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCTGGCGTACT
* * * * * * * *
34593 TTTTGACAAGATCATC-TCCGAACAACTTTTGAAGATTGTTGAGAAACCATTTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCTGGCGTACT
** * *
34656 TCTTGATGAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCTGGCGTACT
* * *
34720 TCTTGACAAGATCGTCTTCCGATCATCTTCTGGAAATTTTTGAGAAACCATCTTCTAGCGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCTGGCGTACT
*
34784 TCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAATTTTTGAGAAACCATCTTCTGGCGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCTGGCGTACT
* * ** * *
34848 CCTTAATGAGATTGTCTTCCAATCAACATT-TGAAAATT
1 TCTTGACAAGATCGTCTTCCGATCAAC-TTCTGAAAATT
34886 CTTTCTAGCA
Statistics
Matches: 314, Mismatches: 41, Indels: 5
0.87 0.11 0.01
Matches are distributed among these distances:
63 53 0.17
64 226 0.72
65 35 0.11
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (64 bp):
TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCTGGCGTACT
Found at i:34941 original size:36 final size:36
Alignment explanation
Indices: 34899--35019 Score: 120
Period size: 36 Copynumber: 3.3 Consensus size: 36
34889 TCTAGCAAAC
34899 CGTCTTCCGGTGTTCTTCTAAAATCCTCTAAGGAAA
1 CGTCTTCCGGTGTTCTTCTAAAATCCTCTAAGGAAA
** ** * * *
34935 CGTCTTCCGGATCATCTT-TGATTATCCTTTGAA-CATTAC
1 CGTCTTCCGG-TGTTCTTCT-AAAATCCTCT-AAGGA--AA
34974 CGTCTTCCGGTGTTCTTCTAAAATCCTCTAAGGAAA
1 CGTCTTCCGGTGTTCTTCTAAAATCCTCTAAGGAAA
35010 CGTCTTCCGG
1 CGTCTTCCGG
35020 ATCATCTTTG
Statistics
Matches: 64, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
36 22 0.34
37 15 0.23
38 15 0.23
39 12 0.19
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (36 bp):
CGTCTTCCGGTGTTCTTCTAAAATCCTCTAAGGAAA
Found at i:34984 original size:75 final size:75
Alignment explanation
Indices: 34897--35048 Score: 304
Period size: 75 Copynumber: 2.0 Consensus size: 75
34887 TTTCTAGCAA
34897 ACCGTCTTCCGGTGTTCTTCTAAAATCCTCTAAGGAAACGTCTTCCGGATCATCTTTGATTATCC
1 ACCGTCTTCCGGTGTTCTTCTAAAATCCTCTAAGGAAACGTCTTCCGGATCATCTTTGATTATCC
34962 TTTGAACATT
66 TTTGAACATT
34972 ACCGTCTTCCGGTGTTCTTCTAAAATCCTCTAAGGAAACGTCTTCCGGATCATCTTTGATTATCC
1 ACCGTCTTCCGGTGTTCTTCTAAAATCCTCTAAGGAAACGTCTTCCGGATCATCTTTGATTATCC
35037 TTTGAACATT
66 TTTGAACATT
35047 AC
1 AC
35049 TTTCCGAGTG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (75 bp):
ACCGTCTTCCGGTGTTCTTCTAAAATCCTCTAAGGAAACGTCTTCCGGATCATCTTTGATTATCC
TTTGAACATT
Found at i:35037 original size:37 final size:37
Alignment explanation
Indices: 34921--35037 Score: 114
Period size: 37 Copynumber: 3.1 Consensus size: 37
34911 TTCTTCTAAA
34921 ATCCTCTAAGGAAACGTCTTCCGGATCATCTTTGATT
1 ATCCTCTAAGGAAACGTCTTCCGGATCATCTTTGATT
* * * ** **
34958 ATCCTTTGAA-CATTACCGTCTTCCGG-TGTTCTTCT-AAA
1 ATCCTCT-AAGGA--AACGTCTTCCGGATCATCTT-TGATT
34996 ATCCTCTAAGGAAACGTCTTCCGGATCATCTTTGATT
1 ATCCTCTAAGGAAACGTCTTCCGGATCATCTTTGATT
35033 ATCCT
1 ATCCT
35038 TTGAACATTA
Statistics
Matches: 59, Mismatches: 14, Indels: 14
0.68 0.16 0.16
Matches are distributed among these distances:
36 12 0.20
37 20 0.34
38 15 0.25
39 12 0.20
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.37
Consensus pattern (37 bp):
ATCCTCTAAGGAAACGTCTTCCGGATCATCTTTGATT
Done.