Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024789.1 Corchorus olitorius cultivar O-4 contig24822, 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: 106336
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3699 original size:14 final size:14
Alignment explanation
Indices: 3680--3718 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
3670 TTTTTAGTTG
3680 AGTAAAACTA-TAAA
1 AGTAAAA-TAGTAAA
3694 AGTAAAATAGTAAA
1 AGTAAAATAGTAAA
*
3708 AATAAAATAGT
1 AGTAAAATAGT
3719 TATAAGGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 2 0.09
14 21 0.91
ACGTcount: A:0.64, C:0.03, G:0.10, T:0.23
Consensus pattern (14 bp):
AGTAAAATAGTAAA
Found at i:3851 original size:31 final size:31
Alignment explanation
Indices: 3815--3877 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
3805 ATATTCGAAA
*
3815 AATAAGCGTATGATAGGCGATTCAAAAGTTT
1 AATAAGCGTATAATAGGCGATTCAAAAGTTT
* *
3846 AATAAGTGTATAATAGGTGATTCAAAAGTTT
1 AATAAGCGTATAATAGGCGATTCAAAAGTTT
3877 A
1 A
3878 CTATCTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (31 bp):
AATAAGCGTATAATAGGCGATTCAAAAGTTT
Found at i:4121 original size:55 final size:54
Alignment explanation
Indices: 4050--4386 Score: 169
Period size: 55 Copynumber: 6.3 Consensus size: 54
4040 ACCATCATCC
* *
4050 TTTGGGGTTTGTCCATGCATGTACAATGATGTTTTTGGAGGTTTGACTATTAAAA
1 TTTGGGGTTTGACCATGCAT-TACAATGATGTTTTTGGAGGTTTGACTATCAAAA
* * * *
4105 TTTGGGGTTTGACCATGCATATACAATTAAATG-TTTT-GTGGTTTGACTATCGAAT
1 TTTGGGGTTTGACCATGCAT-TACAA-T-GATGTTTTTGGAGGTTTGACTATCAAAA
* ** ** **** * ** * * ***
4160 TTTGGGGTTTGACCAT-CA-TCCTTTGGGGTTTGACCATGCATGTACAATGATGT
1 TTTGGGGTTTGACCATGCATTACAATGATGTTTTTGGAGGTTTG-ACTATCAAAA
* * * * *
4213 TTTGGGGTTTGATCATGCA-TA-AATG--CTTTTTGTGA--TATGACTATCGAAC
1 TTTGGGGTTTGACCATGCATTACAATGATGTTTTTG-GAGGTTTGACTATCAAAA
* ** *
4262 TTTGGGGATTGATTATGCATGTACAATGATGTTTTTGGAGGTTTGACTATTAAAA
1 TTTGGGGTTTGACCATGCAT-TACAATGATGTTTTTGGAGGTTTGACTATCAAAA
* * * *
4317 TTT-GGGTTTGACCATGCATAAACAATGAAATG-TTTT-GTGGTTTGACTATCGAAC
1 TTTGGGGTTTGACCATGCAT-TACAATG--ATGTTTTTGGAGGTTTGACTATCAAAA
4371 TTTGGGGTTTGACCAT
1 TTTGGGGTTTGACCAT
4387 CATCCTTTGG
Statistics
Matches: 208, Mismatches: 57, Indels: 34
0.70 0.19 0.11
Matches are distributed among these distances:
49 21 0.10
50 4 0.02
51 8 0.04
52 10 0.05
53 24 0.12
54 47 0.23
55 83 0.40
56 8 0.04
57 3 0.01
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.40
Consensus pattern (54 bp):
TTTGGGGTTTGACCATGCATTACAATGATGTTTTTGGAGGTTTGACTATCAAAA
Found at i:4168 original size:21 final size:19
Alignment explanation
Indices: 4138--4196 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 19
4128 CAATTAAATG
* *
4138 TTTTGTGGTTTGACTATCGAA
1 TTTTGGGGTTTGACCATC--A
4159 TTTTGGGGTTTGACCATCA
1 TTTTGGGGTTTGACCATCA
4178 TCCTTTGGGGTTTGACCAT
1 T--TTTGGGGTTTGACCAT
4197 GCATGTACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.06
21 32 0.94
ACGTcount: A:0.15, C:0.15, G:0.25, T:0.44
Consensus pattern (19 bp):
TTTTGGGGTTTGACCATCA
Found at i:4169 original size:76 final size:75
Alignment explanation
Indices: 4082--4224 Score: 189
Period size: 76 Copynumber: 1.9 Consensus size: 75
4072 ACAATGATGT
* * *
4082 TTTTGGAGGTTTGACTATTAAAATTTGGGGTTTGACCATGCATATACAATTAAATGTTTTGTGGT
1 TTTTGGAGGTTTGACCATCAAAATTTGGGGTTTGACCATGCATATACAA-T-AATGTTTTGGGGT
4147 TTGACTATCGAA
64 TTGACTATCGAA
*** * *
4159 TTTTGG-GGTTTGACCATCATCCTTTGGGGTTTGACCATGCATGTACAATGATGTTTTGGGGTTT
1 TTTTGGAGGTTTGACCATCAAAATTTGGGGTTTGACCATGCATATACAATAATGTTTTGGGGTTT
4223 GA
66 GA
4225 TCATGCATAA
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
74 15 0.26
75 1 0.02
76 36 0.62
77 6 0.10
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.41
Consensus pattern (75 bp):
TTTTGGAGGTTTGACCATCAAAATTTGGGGTTTGACCATGCATATACAATAATGTTTTGGGGTTT
GACTATCGAA
Found at i:4379 original size:21 final size:21
Alignment explanation
Indices: 4350--4407 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
4340 AATGAAATGT
* *
4350 TTTGTGGTTTGACTATCGA-AC
1 TTTGGGGTTTGACCATC-ATAC
*
4371 TTTGGGGTTTGACCATCATCC
1 TTTGGGGTTTGACCATCATAC
4392 TTTGGGGTTTGACCAT
1 TTTGGGGTTTGACCAT
4408 GCATGTATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.16, C:0.17, G:0.26, T:0.41
Consensus pattern (21 bp):
TTTGGGGTTTGACCATCATAC
Found at i:4453 original size:33 final size:34
Alignment explanation
Indices: 4392--4462 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 34
4382 ACCATCATCC
* * *
4392 TTTGGGGTTTGACCATGCATGTATAATG-ATGTT
1 TTTGGGGATTGACCATGCATATACAATGAATGTT
* *
4425 TTTGGGGATTGATCATTCATATACAATGAAATGTT
1 TTTGGGGATTGACCATGCATATACAATG-AATGTT
4460 TTT
1 TTT
4463 TGTGATATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 23 0.74
35 8 0.26
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (34 bp):
TTTGGGGATTGACCATGCATATACAATGAATGTT
Found at i:4545 original size:53 final size:55
Alignment explanation
Indices: 4425--4822 Score: 192
Period size: 57 Copynumber: 7.2 Consensus size: 55
4415 TAATGATGTT
* * * * * * *
4425 TTTGGGGATTGATCATTCATATACAATGAAATGTTTTTT-GTGATATGAAT-ATCGAAC
1 TTTGGGGTTTGACCATACATATACAATG-AATGTTTTTTAG-G-TTTGACTAAT-AAAG
*
4482 TTTGGGGTTTGACCATACATGTACAATG-ATG-TTTTTAGGTTTGACTAATAAAG
1 TTTGGGGTTTGACCATACATATACAATGAATGTTTTTTAGGTTTGACTAATAAAG
* * * *
4535 TTTGGGGTTTGACCATGCATATACAATGACATGTTTTTTTGGTTTGACTATTGAAG
1 TTTGGGGTTTGACCATACATATACAATGA-ATGTTTTTTAGGTTTGACTAATAAAG
** * ** ** *** * ** ***
4591 TTTGGGGTTAAACCAT-CATCT--TTTG-GGGTTTGACCATGCATGTA-TAATGGTG
1 TTTGGGGTTTGACCATACATATACAATGAATGTTT-TTTAGGTTTG-ACTAATAAAG
* * * *
4643 TTTTTGGGGATTGATCATTCATATACAATGAAATGTTTTTT--GTAATATGACT-ATCAAAC
1 --TTTGGGGTTTGACCATACATATACAATG-AATGTTTTTTAGGT--T-TGACTAAT-AAAG
* *
4702 TTTGAGGTTTGACCATACATGTACAATG-ATGTTTTTTGAGGTTTGACTAATAAAG
1 TTTGGGGTTTGACCATACATATACAATGAATGTTTTTT-AGGTTTGACTAATAAAG
* * * * * *
4757 TTTAGGGTTTGACCATGCATATACAATGACATATTTTTTTTGGTTTGACTATTGAAG
1 TTTGGGGTTTGACCATACATATACAATGA-AT-GTTTTTTAGGTTTGACTAATAAAG
4814 TTTGGGGTT
1 TTTGGGGTT
4823 AAACCATCAT
Statistics
Matches: 252, Mismatches: 63, Indels: 52
0.69 0.17 0.14
Matches are distributed among these distances:
51 4 0.02
52 8 0.03
53 36 0.14
54 20 0.08
55 56 0.22
56 37 0.15
57 73 0.29
58 11 0.04
59 7 0.03
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (55 bp):
TTTGGGGTTTGACCATACATATACAATGAATGTTTTTTAGGTTTGACTAATAAAG
Found at i:4580 original size:220 final size:220
Alignment explanation
Indices: 4049--4872 Score: 1139
Period size: 220 Copynumber: 3.8 Consensus size: 220
4039 GACCATCATC
* * *
4049 CTTTGGGGTTTGTCCATGCATGTACAATGATGTTTTTGGAGGTTTGACTATTAAAATTTGGGGTT
1 CTTTGGGGTTTGACCATACATGTACAATGATGTTTTT-GAGGTTTGACTAATAAAATTTGGGGTT
* * **
4114 TGACCATGCATATACAATTAAATGTTTTGTGGTTTGACTATCGAATTTTGGGGTTTGACCATCAT
65 TGACCATGCATATACAATGAAATGTTTTGTGGTTTGACTATCGAAGTTTGGGGTTAAACCATCAT
* *
4179 CCTTTGGGGTTTGACCATGCATGTACAATGATG-TTTTGGGG-TT--TGA-TC--ATGC-AT-AA
130 CCTTTGGGGTTTGACCATGCATGTACAATGATGTTTTTGGGGATTGATCATTCATATACAATGAA
*
4235 ATGCTTTTTGTGATATGACTATCGAA
195 ATGTTTTTTGTGATATGACTATCGAA
* ** * *
4261 CTTTGGGGATTGATTATGCATGTACAATGATGTTTTTGGAGGTTTGACTATTAAAATTT-GGGTT
1 CTTTGGGGTTTGACCATACATGTACAATGATGTTTTT-GAGGTTTGACTAATAAAATTTGGGGTT
* * **
4325 TGACCATGCATAAACAATGAAATGTTTTGTGGTTTGACTATCGAACTTTGGGGTTTGACCATCAT
65 TGACCATGCATATACAATGAAATGTTTTGTGGTTTGACTATCGAAGTTTGGGGTTAAACCATCAT
*
4390 CCTTTGGGGTTTGACCATGCATGTATAATGATGTTTTTGGGGATTGATCATTCATATACAATGAA
130 CCTTTGGGGTTTGACCATGCATGTACAATGATGTTTTTGGGGATTGATCATTCATATACAATGAA
*
4455 ATGTTTTTTGTGATATGAATATCGAA
195 ATGTTTTTTGTGATATGACTATCGAA
*
4481 CTTTGGGGTTTGACCATACATGTACAATGATGTTTTT-AGGTTTGACTAATAAAGTTTGGGGTTT
1 CTTTGGGGTTTGACCATACATGTACAATGATGTTTTTGAGGTTTGACTAATAAAATTTGGGGTTT
* * *
4545 GACCATGCATATACAATGACATGTTTTTTTGGTTTGACTATTGAAGTTTGGGGTTAAACCATCAT
66 GACCATGCATATACAATGAAATG-TTTTGTGGTTTGACTATCGAAGTTTGGGGTTAAACCATCAT
* * *
4610 CTTTTGGGGTTTGACCATGCATGTATAATGGTGTTTTTGGGGATTGATCATTCATATACAATGAA
130 CCTTTGGGGTTTGACCATGCATGTACAATGATGTTTTTGGGGATTGATCATTCATATACAATGAA
* *
4675 ATGTTTTTTGTAATATGACTATCAAA
195 ATGTTTTTTGTGATATGACTATCGAA
* * *
4701 CTTTGAGGTTTGACCATACATGTACAATGATGTTTTTTGAGGTTTGACTAATAAAGTTTAGGGTT
1 CTTTGGGGTTTGACCATACATGTACAATGATG-TTTTTGAGGTTTGACTAATAAAATTTGGGGTT
* * *
4766 TGACCATGCATATACAATGACATATTTTTTTTGGTTTGACTATTGAAGTTTGGGGTTAAACCATC
65 TGACCATGCATATACAATGA-A-ATGTTTTGTGGTTTGACTATCGAAGTTTGGGGTTAAACCATC
** * * * *
4831 ATCCTTTAAGATTTTACCATACATGTACAATGGTGTTTTTGG
128 ATCCTTTGGGGTTTGACCATGCATGTACAATGATGTTTTTGG
4873 ATAACAATGC
Statistics
Matches: 556, Mismatches: 41, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
211 99 0.18
212 63 0.11
213 2 0.00
215 2 0.00
216 2 0.00
218 21 0.04
219 29 0.05
220 212 0.38
221 5 0.01
222 45 0.08
223 74 0.13
224 2 0.00
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (220 bp):
CTTTGGGGTTTGACCATACATGTACAATGATGTTTTTGAGGTTTGACTAATAAAATTTGGGGTTT
GACCATGCATATACAATGAAATGTTTTGTGGTTTGACTATCGAAGTTTGGGGTTAAACCATCATC
CTTTGGGGTTTGACCATGCATGTACAATGATGTTTTTGGGGATTGATCATTCATATACAATGAAA
TGTTTTTTGTGATATGACTATCGAA
Found at i:4749 original size:55 final size:55
Alignment explanation
Indices: 4653--4808 Score: 138
Period size: 55 Copynumber: 2.8 Consensus size: 55
4643 TTTTTGGGGA
* * * * *
4653 TTGATCATTCATATACAATGAAATGTTTTTTGTA-ATATGACTATCAAACTTT-GAGGT
1 TTGACCATACATATACAATG-AATATTTTTTG-AGGTTTGACTAT-AAACTTTAG-GGT
* * *
4710 TTGACCATACATGTACAATG-ATGTTTTTTGAGGTTTGACTAATAAAGTTTAGGGT
1 TTGACCATACATATACAATGAATATTTTTTGAGGTTTGACT-ATAAACTTTAGGGT
* **
4765 TTGACCATGCATATACAATGACATATTTTTTTTGGTTTGACTAT
1 TTGACCATACATATACAATGA-ATATTTTTTGAGGTTTGACTAT
4809 TGAAGTTTGG
Statistics
Matches: 83, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
54 1 0.01
55 43 0.52
56 5 0.06
57 34 0.41
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (55 bp):
TTGACCATACATATACAATGAATATTTTTTGAGGTTTGACTATAAACTTTAGGGT
Found at i:5817 original size:7 final size:6
Alignment explanation
Indices: 5800--5830 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
5790 CTGATATCTC
5800 CTTTTT CTTTTT CTTTTT CTTATTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTT-TTT CTTTTT
5831 TTGTTCCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:10490 original size:21 final size:22
Alignment explanation
Indices: 10445--10491 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
10435 TCGCTAAATT
*
10445 TTTTACAAAGAAATCCCCCTGA
1 TTTTACAAAGAAATCCCCCTAA
* *
10467 TTTT-CAAAGAAATCCTCTTAA
1 TTTTACAAAGAAATCCCCCTAA
10488 TTTT
1 TTTT
10492 TGGTTTTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.38
Consensus pattern (22 bp):
TTTTACAAAGAAATCCCCCTAA
Found at i:11633 original size:53 final size:54
Alignment explanation
Indices: 11542--11652 Score: 199
Period size: 54 Copynumber: 2.1 Consensus size: 54
11532 GCAGATTCTC
11542 ATTAACAAATTCTTAATGTTAAAAAAGAAAAAGAAAAAAAAATA-CATGAAAGG
1 ATTAACAAATTCTTAATGTTAAAAAAGAAAAAGAAAAAAAAATATCATGAAAGG
11595 ATTAACAAATTCTTAATTGTTAAAAAAGAAAAAG-AAAAAAAATATCATGAAAGG
1 ATTAACAAATTCTTAA-TGTTAAAAAAGAAAAAGAAAAAAAAATATCATGAAAGG
11649 ATTA
1 ATTA
11653 CGGTGATGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
53 26 0.46
54 30 0.54
ACGTcount: A:0.60, C:0.05, G:0.11, T:0.23
Consensus pattern (54 bp):
ATTAACAAATTCTTAATGTTAAAAAAGAAAAAGAAAAAAAAATATCATGAAAGG
Found at i:11733 original size:1 final size:1
Alignment explanation
Indices: 11727--11752 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
11717 TTTGAAAGAG
11727 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
11753 GTCATGAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:19434 original size:11 final size:11
Alignment explanation
Indices: 19418--19442 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19408 TTTTTTTTTT
19418 AATGACTATAG
1 AATGACTATAG
19429 AATGACTATAG
1 AATGACTATAG
19440 AAT
1 AAT
19443 TTCTTGAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (11 bp):
AATGACTATAG
Found at i:20007 original size:17 final size:17
Alignment explanation
Indices: 19985--20020 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
19975 TGATTTGTAA
19985 AGTTTGTTATACCAGAT
1 AGTTTGTTATACCAGAT
*
20002 AGTTTGTTATACTAGAT
1 AGTTTGTTATACCAGAT
20019 AG
1 AG
20021 CTCTTTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (17 bp):
AGTTTGTTATACCAGAT
Found at i:23386 original size:36 final size:36
Alignment explanation
Indices: 23346--23439 Score: 109
Period size: 36 Copynumber: 2.6 Consensus size: 36
23336 TGCTGGATCA
* * * *
23346 TACAACAAGATCGACTATGGTGGCTGCAGCAAC-GAC
1 TACAACAAGAGCAACTATGGTGGCAGCAACAACAG-C
*
23382 TACAACAAGGGCAACTATGGTGGCAGCAACAACAGC
1 TACAACAAGAGCAACTATGGTGGCAGCAACAACAGC
* *
23418 TACAACATGGGCAACTATGGTG
1 TACAACAAGAGCAACTATGGTG
23440 CTAGATCATA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
36 50 0.98
37 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.26, T:0.16
Consensus pattern (36 bp):
TACAACAAGAGCAACTATGGTGGCAGCAACAACAGC
Found at i:24285 original size:81 final size:81
Alignment explanation
Indices: 24196--24510 Score: 533
Period size: 81 Copynumber: 3.9 Consensus size: 81
24186 GATCATTGCT
** * * *
24196 ACAAATATGAGGAGAGTGACAACGATGAAGGAGAATGATGTGAAGATTCTGCATATTCTGGGGAC
1 ACAAATATGAGGAGAGCAACGACGATGAAGGAGAAGGATGCGAAGATTCTGCATATTCTGGGGAC
24261 TCTGATGATCAC-TACA
66 TCTGATGATC-CTTACA
** * *
24277 ACAAATATGAGGAGAGTGACGACGATGAAAGAGAAGGATGCGGAGATTCTGCATATTCTGGGGAC
1 ACAAATATGAGGAGAGCAACGACGATGAAGGAGAAGGATGCGAAGATTCTGCATATTCTGGGGAC
24342 TCTGATGATCCTTACA
66 TCTGATGATCCTTACA
24358 ACAAATATGAGGAGAGCAACGACGATGAAGGAGAAGGATGCGAAGATTCTGCATATTCTGGGGAC
1 ACAAATATGAGGAGAGCAACGACGATGAAGGAGAAGGATGCGAAGATTCTGCATATTCTGGGGAC
24423 TCTGATGATCCTTACA
66 TCTGATGATCCTTACA
24439 ACAAATATGAGGAGAGCAACGACGATGAAGGAGAAGGATGCGAAGATTCTGCATATTCTGGGGAC
1 ACAAATATGAGGAGAGCAACGACGATGAAGGAGAAGGATGCGAAGATTCTGCATATTCTGGGGAC
24504 TCTGATG
66 TCTGATG
24511 GTTATGATTC
Statistics
Matches: 224, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
80 1 0.00
81 223 1.00
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.22
Consensus pattern (81 bp):
ACAAATATGAGGAGAGCAACGACGATGAAGGAGAAGGATGCGAAGATTCTGCATATTCTGGGGAC
TCTGATGATCCTTACA
Found at i:25102 original size:16 final size:16
Alignment explanation
Indices: 25081--25112 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
25071 AGGAAGCATA
25081 AGAGAGAATGCTTATG
1 AGAGAGAATGCTTATG
25097 AGAGAGAATGCTTATG
1 AGAGAGAATGCTTATG
25113 TGATGCCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.31, T:0.25
Consensus pattern (16 bp):
AGAGAGAATGCTTATG
Found at i:37284 original size:2 final size:2
Alignment explanation
Indices: 37277--37309 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
37267 CATTTAAAAT
37277 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
37310 CATTGTTCTT
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:37988 original size:12 final size:12
Alignment explanation
Indices: 37971--38002 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
37961 TGTGGAGGCT
37971 ATGATTACCCAG
1 ATGATTACCCAG
*
37983 ATGATTACCCGG
1 ATGATTACCCAG
37995 ATGATTAC
1 ATGATTAC
38003 ACGAATGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (12 bp):
ATGATTACCCAG
Found at i:44993 original size:76 final size:73
Alignment explanation
Indices: 44857--44996 Score: 185
Period size: 76 Copynumber: 1.9 Consensus size: 73
44847 GGACTATGAA
*
44857 CAAAGGAATGATGAGTTTTAATCAAAATTTTTCAAAAATCAGTTTTAGTCAAAACTATGATTTCG
1 CAAAGGAATGATGAGTTTTAATCAAAATTTTTCAAAAA-CAGTTTTAGTCAAAACAATGATTTCG
44922 AGTTGTGAG
65 AGTTGTGAG
* *
44931 CAAAGGAATGATGGAGTTTTAATCAAAAGATGTTTT--AAAACAAGTTTTTGTCAAAGCAATGAT
1 CAAAGGAATGAT-GAGTTTTAATC-AAA-AT-TTTTCAAAAAC-AGTTTTAGTCAAAACAATGAT
44994 TTC
61 TTC
44997 AAGGAGGCTG
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
74 12 0.21
75 12 0.21
76 28 0.48
77 2 0.03
78 4 0.07
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (73 bp):
CAAAGGAATGATGAGTTTTAATCAAAATTTTTCAAAAACAGTTTTAGTCAAAACAATGATTTCGA
GTTGTGAG
Found at i:46425 original size:50 final size:50
Alignment explanation
Indices: 46347--46550 Score: 304
Period size: 50 Copynumber: 4.1 Consensus size: 50
46337 AGAACAATAA
* * *
46347 TTTTTATAATAAGATTGCATTCCGTTTGTGAGTCTAAGGTCAAAATTCGC
1 TTTTTATAATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGC
*
46397 TTTTTATAATAAGATTGCATTCCATTTGTGAGTCCAAGGTCAAAATTCG-
1 TTTTTATAATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGC
*
46446 TTTTTGATAATAAGATTGCATTCCATTGGTGAGTCCAAGATCAAAATTCGC
1 TTTTT-ATAATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGC
* * *
46497 TTTTCA-AAGTAAGATTGCATTCCATTTGTGAGTCCAAGACCAAAGTTCGC
1 TTTTTATAA-TAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGC
46547 TTTT
1 TTTT
46551 CGAAGGGTAT
Statistics
Matches: 143, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
49 7 0.05
50 132 0.92
51 4 0.03
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (50 bp):
TTTTTATAATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGC
Found at i:53212 original size:99 final size:99
Alignment explanation
Indices: 53021--53202 Score: 240
Period size: 99 Copynumber: 1.8 Consensus size: 99
53011 ATGCTACCAT
* * * *
53021 TGGCTATGGTGGTGGCAACTAGATAATTACCTACAACTATCAATCAAAGCCAATTGGGTAGTCCA
1 TGGCTATGGTGGTGGCAACTAGATAACTACCTACAAATATCAATCAAAGCCAATAGGGCAGTCCA
*
53086 ACTACATTCAGACTACTACAACTGTGAAAAATTA
66 ACTACAATCAGACTACTACAACTGTGAAAAATTA
* * ** *
53120 TGGCTATGGTGGTGGCAAGC-AGATCACTACCTTCAAATATCAATCAAAGCTGATAGGGCAGTTC
1 TGGCTATGGTGGTGGCAA-CTAGATAACTACCTACAAATATCAATCAAAGCCAATAGGGCAGTCC
**
53184 GGCTACAATCAGACTACTA
65 AACTACAATCAGACTACTA
53203 GTGCTGTGAA
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
99 69 0.99
100 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (99 bp):
TGGCTATGGTGGTGGCAACTAGATAACTACCTACAAATATCAATCAAAGCCAATAGGGCAGTCCA
ACTACAATCAGACTACTACAACTGTGAAAAATTA
Found at i:55623 original size:88 final size:88
Alignment explanation
Indices: 55474--55650 Score: 336
Period size: 88 Copynumber: 2.0 Consensus size: 88
55464 TTAATTACAA
*
55474 GTGGATCGGCCCACGCTGATGCGTTGGGCGTTCAGCAATTTATTTCTTTGAACATTTTTCTATTC
1 GTGGATCGGCCCACGCTGACGCGTTGGGCGTTCAGCAATTTATTTCTTTGAACATTTTTCTATTC
55539 GAATTAAATTGTTTGATACGTAG
66 GAATTAAATTGTTTGATACGTAG
*
55562 GTGGATCGGCCCACGCTGGCGCGTTGGGCGTTCAGCAATTTATTTCTTTGAACATTTTTCTATTC
1 GTGGATCGGCCCACGCTGACGCGTTGGGCGTTCAGCAATTTATTTCTTTGAACATTTTTCTATTC
55627 GAATTAAATTGTTTGATACGTAG
66 GAATTAAATTGTTTGATACGTAG
55650 G
1 G
55651 AAATTTCGAA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.38
Consensus pattern (88 bp):
GTGGATCGGCCCACGCTGACGCGTTGGGCGTTCAGCAATTTATTTCTTTGAACATTTTTCTATTC
GAATTAAATTGTTTGATACGTAG
Found at i:66591 original size:13 final size:12
Alignment explanation
Indices: 66573--66606 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
66563 TCGACCCATA
66573 TCTTCTTTTTTCT
1 TCTTCTTTTTT-T
66586 TCTTCTTTTTTT
1 TCTTCTTTTTTT
66598 T-TTCTTTTT
1 TCTTCTTTTT
66607 CCTTTCTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.38
12 2 0.10
13 11 0.52
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TCTTCTTTTTTT
Found at i:69163 original size:67 final size:67
Alignment explanation
Indices: 69053--69187 Score: 200
Period size: 67 Copynumber: 2.0 Consensus size: 67
69043 TTCAGAGCCG
* * *
69053 AGTCTCTCGTTGGATAGCGATTAGGAGAAATTTTTCCAGCACATATTTTTTGAACTCCTCCCACT
1 AGTCTCTCGTCGGATAGCGATTAGGAGAAATTTTCCCAACACATATTTTTTGAACTCCTCCCACT
69118 TA
66 TA
* * *
69120 AGTCTCTCGTCGGATTA-CGATTGGGTGAAATTTTCCCAACACATATTTTTTGAACTTCTCCCAC
1 AGTCTCTCGTCGGA-TAGCGATTAGGAGAAATTTTCCCAACACATATTTTTTGAACTCCTCCCAC
69184 TTA
65 TTA
69187 A
1 A
69188 AACAATAGGT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
67 59 0.97
68 2 0.03
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (67 bp):
AGTCTCTCGTCGGATAGCGATTAGGAGAAATTTTCCCAACACATATTTTTTGAACTCCTCCCACT
TA
Found at i:74390 original size:11 final size:11
Alignment explanation
Indices: 74374--74400 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
74364 AACTATTAGT
74374 TTGTATTTAAA
1 TTGTATTTAAA
74385 TTGTATTTAAA
1 TTGTATTTAAA
74396 TTGTA
1 TTGTA
74401 ACAGCTTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (11 bp):
TTGTATTTAAA
Found at i:76452 original size:19 final size:20
Alignment explanation
Indices: 76402--76461 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
76392 GCTGCTCTAA
*
76402 TAATCTCATTTGTACAGTACC
1 TAATCTCATCTGTACAGTA-C
* * *
76423 TAATTTGATCTGTACAGT-G
1 TAATCTCATCTGTACAGTAC
76442 TAATCTCATCTGTACAGTAC
1 TAATCTCATCTGTACAGTAC
76462 ATAAAAAGTG
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
19 16 0.52
21 15 0.48
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTAC
Found at i:92374 original size:2 final size:2
Alignment explanation
Indices: 92367--92396 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
92357 TTTCTAGTCT
92367 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
92397 AAAGTATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:98852 original size:27 final size:29
Alignment explanation
Indices: 98813--98866 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
98803 CAATACAATA
*
98813 TAATAATTTAATT-CTTTAAT-TTTTTAT
1 TAATAATTCAATTACTTTAATATTTTTAT
*
98840 TAATAATTCAATTATTTTAATATTTTT
1 TAATAATTCAATTACTTTAATATTTTT
98867 TATTTAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 12 0.52
28 6 0.26
29 5 0.22
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (29 bp):
TAATAATTCAATTACTTTAATATTTTTAT
Found at i:101152 original size:34 final size:34
Alignment explanation
Indices: 101113--101181 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
101103 TGCTGATCCA
* *
101113 TAGAGCATCCCTCTTCCTTTGATGAATCTTATCT
1 TAGAGCATCCATCTTCCTTTGATAAATCTTATCT
*
101147 TAGAGCATCCATCTTCGTTTGATAAATCTTATCT
1 TAGAGCATCCATCTTCCTTTGATAAATCTTATCT
101181 T
1 T
101182 TGTTGGTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (34 bp):
TAGAGCATCCATCTTCCTTTGATAAATCTTATCT
Found at i:104379 original size:34 final size:34
Alignment explanation
Indices: 104336--104402 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
104326 TTGAAAGACC
*
104336 ACCTAAGGCTTCACAAATGAAGATAAGATTTACT
1 ACCTAAGGCTTCACAAACGAAGATAAGATTTACT
104370 ACCTAAGGCTTCACAAACGAAGATAAGATTTAC
1 ACCTAAGGCTTCACAAACGAAGATAAGATTTAC
104403 CAAACCTAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (34 bp):
ACCTAAGGCTTCACAAACGAAGATAAGATTTACT
Done.