Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017374.1 Corchorus olitorius cultivar O-4 contig17407, 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: 83511
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:78 original size:30 final size:30
Alignment explanation
Indices: 44--177 Score: 88
Period size: 30 Copynumber: 4.1 Consensus size: 30
34 CCCACCACCC
44 CCTCCAGTCTACAAGTACAAGTCCCCTCCA
1 CCTCCAGTCTACAAGTACAAGTCCCCTCCA
* * * * *
74 CCTCCAATTTATAAGTACAAGTCTCCTCCT
1 CCTCCAGTCTACAAGTACAAGTCCCCTCCA
* *
104 CCTCCTAAGGAGCCATACAAGTACAAGTCTCCCCCACCA
1 CCTCC-----AGTC-TACAAGTACAAG--T-CCCCTCCA
*
143 CCCCCTCCAGTCTACAAGTACAAGTCTCCTCCA
1 ---CCTCCAGTCTACAAGTACAAGTCCCCTCCA
176 CC
1 CC
178 ACCACCACCT
Statistics
Matches: 77, Mismatches: 15, Indels: 24
0.66 0.13 0.21
Matches are distributed among these distances:
30 32 0.42
33 6 0.08
34 1 0.01
35 1 0.01
36 23 0.30
37 3 0.04
38 1 0.01
39 5 0.06
42 5 0.06
ACGTcount: A:0.27, C:0.42, G:0.10, T:0.22
Consensus pattern (30 bp):
CCTCCAGTCTACAAGTACAAGTCCCCTCCA
Found at i:198 original size:42 final size:36
Alignment explanation
Indices: 17--183 Score: 125
Period size: 36 Copynumber: 4.8 Consensus size: 36
7 CAAGGAGCCA
* *
17 TACAAGTACAAATCTCCCCCACCACCCCCTCCAGTC
1 TACAAGTACAAGTCTCCCCCACCACCACCTCCAGTC
* * *
53 TACAAGTACAAG--T---CC-CCTCCACCTCCAATT
1 TACAAGTACAAGTCTCCCCCACCACCACCTCCAGTC
* * * * *** *
83 TATAAGTACAAGTCTCCTCCTCCTCCTA--AGGAGCC
1 TACAAGTACAAGTCTCCCCCACCACC-ACCTCCAGTC
*
118 ATACAAGTACAAGTCTCCCCCACCACCCCCTCCAGTC
1 -TACAAGTACAAGTCTCCCCCACCACCACCTCCAGTC
*
155 TACAAGTACAAGTCTCCTCCACCACCACC
1 TACAAGTACAAGTCTCCCCCACCACCACC
184 ACCTCACTAT
Statistics
Matches: 98, Mismatches: 23, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
30 22 0.22
31 2 0.02
32 1 0.01
34 1 0.01
35 3 0.03
36 65 0.66
37 4 0.04
ACGTcount: A:0.28, C:0.44, G:0.08, T:0.20
Consensus pattern (36 bp):
TACAAGTACAAGTCTCCCCCACCACCACCTCCAGTC
Found at i:4458 original size:28 final size:29
Alignment explanation
Indices: 4426--4484 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
4416 AATCTGGTAA
4426 GCATTGGATCC-AACATCTCGATCATAAT
1 GCATTGGATCCTAACATCTCGATCATAAT
* *
4454 GCATTGGTTCCTCACATCTCGATCATAAT
1 GCATTGGATCCTAACATCTCGATCATAAT
4483 GC
1 GC
4485 CATGGCCGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (29 bp):
GCATTGGATCCTAACATCTCGATCATAAT
Found at i:5912 original size:21 final size:20
Alignment explanation
Indices: 5886--5925 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5876 ATTGAGCTAA
*
5886 CTGATCCATCCTTTGCGCCAG
1 CTGATCCATCCATT-CGCCAG
*
5907 CTGATCGATCCATTCGCCA
1 CTGATCCATCCATTCGCCA
5926 ATAGTTCGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.17, C:0.38, G:0.17, T:0.28
Consensus pattern (20 bp):
CTGATCCATCCATTCGCCAG
Found at i:7158 original size:30 final size:32
Alignment explanation
Indices: 7122--7189 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
7112 AATTGTCCTC
* *
7122 AATTTCAC-TT-TTTTCAAAGTATAGGGATTA
1 AATTTCACATTCTTTTCAAAGTATACGGACTA
7152 AATTTCACTAATTCTTTTCAAAGTATACGGACTA
1 AATTTCAC--ATTCTTTTCAAAGTATACGGACTA
7186 AATT
1 AATT
7190 GCAATTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 8 0.25
33 2 0.06
34 22 0.69
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.41
Consensus pattern (32 bp):
AATTTCACATTCTTTTCAAAGTATACGGACTA
Found at i:7589 original size:17 final size:17
Alignment explanation
Indices: 7567--7599 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
7557 CACGTTTTCA
7567 TATTTTCTATCAATAAC
1 TATTTTCTATCAATAAC
7584 TATTTTCTATCAATAA
1 TATTTTCTATCAATAA
7600 TTCGCCAAAT
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:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTTTCTATCAATAAC
Found at i:7916 original size:16 final size:16
Alignment explanation
Indices: 7852--7919 Score: 84
Period size: 16 Copynumber: 4.3 Consensus size: 16
7842 GAATCTGAAG
7852 CCGAAAAAACTCGAAC
1 CCGAAAAAACTCGAAC
* * *
7868 CTGAAAAAACTAGAAT
1 CCGAAAAAACTCGAAC
*
7884 CC-AAAAAACTCAAAC
1 CCGAAAAAACTCGAAC
*
7899 CCGAAAAAACCCGAAC
1 CCGAAAAAACTCGAAC
7915 CCGAA
1 CCGAA
7920 TCCGAAAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
15 12 0.29
16 30 0.71
ACGTcount: A:0.53, C:0.29, G:0.10, T:0.07
Consensus pattern (16 bp):
CCGAAAAAACTCGAAC
Found at i:8691 original size:66 final size:66
Alignment explanation
Indices: 8609--8740 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
8599 ATTTAGCATT
*
8609 GGCTAACTGTGCTTTTGGAAATGTGAAAATATACTAAATATGAGCAACTAATAGAAACCTCAATA
1 GGCTAACTGTGCTTTTGGAAATGTGAAAATATACTAAATATAAGCAACTAATAGAAACCTCAATA
8674 A
66 A
8675 GGCTAACTGTGCTTTTGGAAATGTGAAAATATACTAAATATAAGCAACTAATAGAAACCTCAATA
1 GGCTAACTGTGCTTTTGGAAATGTGAAAATATACTAAATATAAGCAACTAATAGAAACCTCAATA
8740 A
66 A
8741 AAAGGAAGTC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (66 bp):
GGCTAACTGTGCTTTTGGAAATGTGAAAATATACTAAATATAAGCAACTAATAGAAACCTCAATA
A
Found at i:9428 original size:57 final size:57
Alignment explanation
Indices: 9335--9446 Score: 197
Period size: 57 Copynumber: 2.0 Consensus size: 57
9325 TTAATCTTCA
*
9335 ATTTAGCCTTTAAGTAATTTCCATAATCACTAAAAATAATATATAGTATATATATAT
1 ATTTAGCCTTTAAGTAATTTACATAATCACTAAAAATAATATATAGTATATATATAT
* *
9392 ATTTGGCCTTTAAGTAATTTACATAGTCACTAAAAATAATATATAGTATATATAT
1 ATTTAGCCTTTAAGTAATTTACATAATCACTAAAAATAATATATAGTATATATAT
9447 CTCTTACTTG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (57 bp):
ATTTAGCCTTTAAGTAATTTACATAATCACTAAAAATAATATATAGTATATATATAT
Found at i:11390 original size:2 final size:2
Alignment explanation
Indices: 11383--11429 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
11373 CGTCTCTAGA
*
11383 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11425 AT AT A
1 AT AT A
11430 ATAGTCTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11545 original size:22 final size:21
Alignment explanation
Indices: 11490--11545 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 21
11480 AATACTTCTA
*
11490 TAAATTTAAGAACCACACTAT
1 TAAATTTAATAACCACACTAT
* *
11511 GAAACTTTGATAACCTA-ACTAT
1 TAAA-TTTAATAACC-ACACTAT
11533 TAAATTTTAATAA
1 TAAA-TTTAATAA
11546 ACTTTTCTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
21 3 0.11
22 23 0.85
23 1 0.04
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.34
Consensus pattern (21 bp):
TAAATTTAATAACCACACTAT
Found at i:11861 original size:21 final size:22
Alignment explanation
Indices: 11749--11898 Score: 103
Period size: 22 Copynumber: 6.9 Consensus size: 22
11739 TTCCTACTTA
* * *
11749 CTATGAAATTTTGATAATCTTG
1 CTATGAAATTTTGATAACCATC
*
11771 CTAT-ATTATTTTGATAACC-TC
1 CTATGA-AATTTTGATAACCATC
* * *
11792 TCTAAGAAATTGTGATAATC-TCC
1 -CTATGAAATTTTGATAACCAT-C
* *
11815 CTGTGAAACTTTGATAACCA-C
1 CTATGAAATTTTGATAACCATC
*
11836 ACTATTAAATTTTGAT-ACCATC
1 -CTATGAAATTTTGATAACCATC
*
11858 CTATGAAATTTTGATAACCATA
1 CTATGAAATTTTGATAACCATC
* * *
11880 CTATAAAACTGTGATAACC
1 CTATGAAATTTTGATAACC
11899 TCTATATGAA
Statistics
Matches: 100, Mismatches: 20, Indels: 16
0.74 0.15 0.12
Matches are distributed among these distances:
21 21 0.21
22 77 0.77
23 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCATC
Found at i:12012 original size:22 final size:22
Alignment explanation
Indices: 11987--12029 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
11977 CTATGAAATT
11987 TTGATAACCTCCCTATAGAATG
1 TTGATAACCTCCCTATAGAATG
*
12009 TTGATAACTTCCCTATAGAAT
1 TTGATAACCTCCCTATAGAAT
12030 TTCGTTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.35
Consensus pattern (22 bp):
TTGATAACCTCCCTATAGAATG
Found at i:12239 original size:22 final size:22
Alignment explanation
Indices: 12211--12261 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
12201 GAGATTTCGA
12211 GAAATTTTGACAACCACATTAT
1 GAAATTTTGACAACCACATTAT
* * * *
12233 GAAATTTTGATAGCTACCTTAT
1 GAAATTTTGACAACCACATTAT
12255 GAAATTT
1 GAAATTT
12262 CGATAATCTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (22 bp):
GAAATTTTGACAACCACATTAT
Found at i:12945 original size:20 final size:21
Alignment explanation
Indices: 12880--12961 Score: 60
Period size: 20 Copynumber: 4.0 Consensus size: 21
12870 ATAATTACCT
* **
12880 ATGAAATTGTGATAAACTCCAT
1 ATGAAATT-TGATAACCTCCCC
* ** *
12902 ATG-ACTTTGATAACCTAACT
1 ATGAAATTTGATAACCTCCCC
12922 ATGAAATTTG-TAACCTCCCC
1 ATGAAATTTGATAACCTCCCC
**
12942 ATGAGTTTTGATAACCTCCC
1 ATGAAATTTGATAACCTCCC
12962 TATAAGATTT
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
20 27 0.57
21 17 0.36
22 3 0.06
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (21 bp):
ATGAAATTTGATAACCTCCCC
Found at i:12982 original size:22 final size:22
Alignment explanation
Indices: 12820--12998 Score: 81
Period size: 22 Copynumber: 8.4 Consensus size: 22
12810 TTTTTATGAA
*
12820 ATTTTGAT-ATCTACCCTATTAA-
1 ATTTTGATAACCT-CCCTA-TAAG
* ** *
12842 ATTTTGATAACCACGTTATAAA
1 ATTTTGATAACCTCCCTATAAG
* *
12864 ATTTTGATAA-TTACCTATGAA-
1 ATTTTGATAACCTCCCTAT-AAG
* * *
12885 ATTGTGATAAACT-CC-ATATG
1 ATTTTGATAACCTCCCTATAAG
* **
12905 ACTTTGATAACCTAACTATGAA-
1 ATTTTGATAACCTCCCTAT-AAG
* *
12927 A-TTTG-TAACCTCCCCATGAG
1 ATTTTGATAACCTCCCTATAAG
12947 -TTTTGATAACCTCCCTATAAG
1 ATTTTGATAACCTCCCTATAAG
* * *
12968 ATTTTGTTAATCTCCCTATAAT
1 ATTTTGATAACCTCCCTATAAG
*
12990 TTTTTGATA
1 ATTTTGATA
12999 CTATAGTATA
Statistics
Matches: 117, Mismatches: 28, Indels: 24
0.69 0.17 0.14
Matches are distributed among these distances:
19 2 0.02
20 25 0.21
21 35 0.30
22 52 0.44
23 3 0.03
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.40
Consensus pattern (22 bp):
ATTTTGATAACCTCCCTATAAG
Found at i:19880 original size:27 final size:26
Alignment explanation
Indices: 19834--19885 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
19824 TTTTTACTTT
*
19834 TTTTTAAAGATTAATAATTAGTTATTA
1 TTTTTAAAAATTAATAATTA-TTATTA
* *
19861 TTTTTAAAAATTAGTTATTATTATT
1 TTTTTAAAAATTAATAATTATTATT
19886 TTATATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (26 bp):
TTTTTAAAAATTAATAATTATTATTA
Found at i:19895 original size:23 final size:20
Alignment explanation
Indices: 19844--19896 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
19834 TTTTTAAAGA
19844 TTAATAATTAGTTATTATTT
1 TTAATAATTAGTTATTATTT
*
19864 TTAAAAATTAGTTATTATTATT
1 TTAATAATTAGTTATTA-T-TT
19886 TTATATAATTA
1 TTA-ATAATTA
19897 TTTTGGCCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 16 0.57
21 1 0.04
22 5 0.18
23 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (20 bp):
TTAATAATTAGTTATTATTT
Found at i:20219 original size:15 final size:15
Alignment explanation
Indices: 20199--20240 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
20189 AATCCAGTTA
* *
20199 AAAAATTAGTTAATT
1 AAAAATTAATTAATG
20214 AAAAATTAATTAATG
1 AAAAATTAATTAATG
20229 -AAAATTAATTAA
1 AAAAATTAATTAA
20241 AAATGTAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (15 bp):
AAAAATTAATTAATG
Found at i:20232 original size:14 final size:15
Alignment explanation
Indices: 20199--20240 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
20189 AATCCAGTTA
*
20199 AAAAATTAGTTAATT
1 AAAAATTAATTAATT
20214 AAAAATTAATTAA-T
1 AAAAATTAATTAATT
*
20228 GAAAATTAATTAA
1 AAAAATTAATTAA
20241 AAATGTAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (15 bp):
AAAAATTAATTAATT
Found at i:23323 original size:45 final size:45
Alignment explanation
Indices: 23272--23368 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
23262 AACAACAATT
* *
23272 AATATTAGCTTTACTTTGATGAATTATATAGAGATGGAGGACTAG
1 AATATTAGCTTTACTTTGATGAATTACATAGAAATGGAGGACTAG
* * *
23317 AATATTAGCTTTATTTTGATGAATTACCTAGAAATGGAGGAGTAG
1 AATATTAGCTTTACTTTGATGAATTACATAGAAATGGAGGACTAG
23362 AAT-TTAG
1 AATATTAG
23369 GTAATGCACT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 4 0.09
45 43 0.91
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (45 bp):
AATATTAGCTTTACTTTGATGAATTACATAGAAATGGAGGACTAG
Found at i:26037 original size:21 final size:21
Alignment explanation
Indices: 26013--26054 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
26003 GCACCTTAGG
26013 CAACTCCAATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
*
26034 CAACTCCGATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
26055 TTCTTTGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.29, G:0.17, T:0.19
Consensus pattern (21 bp):
CAACTCCAATGAGCTTGAAAC
Found at i:32317 original size:22 final size:23
Alignment explanation
Indices: 32290--32335 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
32280 CTCGAGAAAA
*
32290 ATCGAGCCGAACTCGAGTA-TTC
1 ATCGAGCCGAACCCGAGTAGTTC
*
32312 ATCGAGCCGAGCCCGAGTAGTTC
1 ATCGAGCCGAACCCGAGTAGTTC
32335 A
1 A
32336 CAAGTAGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
ATCGAGCCGAACCCGAGTAGTTC
Found at i:33281 original size:21 final size:21
Alignment explanation
Indices: 33257--33298 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
33247 GCACCTTAGG
33257 CAACTCCAATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
*
33278 CAACTCCGATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
33299 TTCTTTGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.29, G:0.17, T:0.19
Consensus pattern (21 bp):
CAACTCCAATGAGCTTGAAAC
Found at i:41804 original size:2 final size:2
Alignment explanation
Indices: 41792--41860 Score: 66
Period size: 2 Copynumber: 33.0 Consensus size: 2
41782 AGGTATAAAG
* ** * *
41792 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT TT GAT GG AA AG
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
41836 AT AT CAT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT
41861 TTTATGGAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
2 51 0.91
3 5 0.09
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (2 bp):
AT
Found at i:41852 original size:36 final size:35
Alignment explanation
Indices: 41801--41871 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
41791 GATATCATAT
41801 ATATATATATATATATATATATATTTGATGGAAAG
1 ATATATATATATATATATATATATTTGATGGAAAG
*
41836 ATATCATATATATATATATATATATTTTATGGAAAG
1 ATAT-ATATATATATATATATATATTTGATGGAAAG
41872 TCTACATGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 4 0.12
36 30 0.88
ACGTcount: A:0.45, C:0.01, G:0.10, T:0.44
Consensus pattern (35 bp):
ATATATATATATATATATATATATTTGATGGAAAG
Found at i:43294 original size:16 final size:17
Alignment explanation
Indices: 43273--43309 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
43263 TTTTGACAAA
43273 AAAAAAGCA-AAGA-AAT
1 AAAAAAG-AGAAGAGAAT
43289 AAAAAAGAGAAGAGAAT
1 AAAAAAGAGAAGAGAAT
43306 AAAA
1 AAAA
43310 GACCTAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 1 0.05
16 11 0.58
17 7 0.37
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (17 bp):
AAAAAAGAGAAGAGAAT
Found at i:45434 original size:51 final size:51
Alignment explanation
Indices: 45358--45461 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
45348 AGTAAGAGAT
*
45358 ATATATACTATATATTATTTTTAGTGACTATGTAAATTACTTAAAGGCCAA
1 ATATATACTATATATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAA
*
45409 ATATATACTATATATTATTTTTAGTGATTATGGAAATTACTTAAAGGCCAA
1 ATATATACTATATATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAA
45460 AT
1 AT
45462 TGAAGATTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (51 bp):
ATATATACTATATATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAA
Found at i:46131 original size:66 final size:66
Alignment explanation
Indices: 46055--46186 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 66
46045 GACGTCCTTT
* * *
46055 TTATTTAGGTTTTTATTAGTTGCTTATATTTAGTATATTTTCACATTTCCAAAAGCACAGTTAGC
1 TTATTGAGGTTTCTATTAGTTGCTCATATTTAGTATATTTTCACATTTCCAAAAGCACAGTTAGC
46120 C
66 C
46121 TTATTGAGGTTTCTATTAGTTGCTCATATTTAGTATATTTTCACATTTCCAAAAGCACAGTTAGC
1 TTATTGAGGTTTCTATTAGTTGCTCATATTTAGTATATTTTCACATTTCCAAAAGCACAGTTAGC
46186 C
66 C
46187 AATGCTAAGT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (66 bp):
TTATTGAGGTTTCTATTAGTTGCTCATATTTAGTATATTTTCACATTTCCAAAAGCACAGTTAGC
C
Found at i:46242 original size:12 final size:12
Alignment explanation
Indices: 46225--46249 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46215 ATTGTATAAA
46225 TTGCAAATGCTC
1 TTGCAAATGCTC
46237 TTGCAAATGCTC
1 TTGCAAATGCTC
46249 T
1 T
46250 CAACTAATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (12 bp):
TTGCAAATGCTC
Found at i:47923 original size:109 final size:109
Alignment explanation
Indices: 47732--47949 Score: 382
Period size: 109 Copynumber: 2.0 Consensus size: 109
47722 TAGTCATTTT
47732 GGTGCTTATATTTTTCTTTAAATCCAATAGTTCATTCCACTTTGTATTGTTTGGTATGTGTGCTT
1 GGTGCTTATATTTTTCTTTAAATCCAATAGTTCATTCCACTTTGTATTGTTTGGTATGTGTGCTT
*
47797 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
66 ATTTAATAAGTTCAATTGAATAAACAACACAATTAATAATAATA
* * * *
47841 GGTGCTTGTATTTTTCTTTAAATGCAATAGTTCATTGCATTTTGTATTGTTTGGTATGTGTGCTT
1 GGTGCTTATATTTTTCTTTAAATCCAATAGTTCATTCCACTTTGTATTGTTTGGTATGTGTGCTT
*
47906 ATTTAATAAGTTCAATTGAATAAACCACACAATTAATAATAATA
66 ATTTAATAAGTTCAATTGAATAAACAACACAATTAATAATAATA
47950 TATATAATAG
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
109 103 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.44
Consensus pattern (109 bp):
GGTGCTTATATTTTTCTTTAAATCCAATAGTTCATTCCACTTTGTATTGTTTGGTATGTGTGCTT
ATTTAATAAGTTCAATTGAATAAACAACACAATTAATAATAATA
Found at i:48350 original size:42 final size:43
Alignment explanation
Indices: 48299--48392 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
48289 AGTGCATTAT
*
48299 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAA
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
*
48340 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
48385 CTAATATT
1 CTAATATT
48393 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:55554 original size:31 final size:31
Alignment explanation
Indices: 55516--55579 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
55506 CCAAAGAATA
*
55516 AGAAGAAAACTTATCTATGGATGAGAATAAG
1 AGAAGAAAACTTATCTATGGATGAGAAGAAG
*
55547 AGAAGAAAACTTATCTATTGATGAGAAGAAG
1 AGAAGAAAACTTATCTATGGATGAGAAGAAG
55578 AG
1 AG
55580 GGGGCGGCGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.06, G:0.23, T:0.22
Consensus pattern (31 bp):
AGAAGAAAACTTATCTATGGATGAGAAGAAG
Found at i:56449 original size:23 final size:23
Alignment explanation
Indices: 56419--56466 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
56409 CTATTGTGTT
** *
56419 TTCCTCTCTGCAATGGTTGGTTC
1 TTCCTCTCTAAAATGGTTGCTTC
56442 TTCCTCTCTAAAATGGTTGCTTC
1 TTCCTCTCTAAAATGGTTGCTTC
56465 TT
1 TT
56467 TTCTCCCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (23 bp):
TTCCTCTCTAAAATGGTTGCTTC
Found at i:71112 original size:144 final size:144
Alignment explanation
Indices: 70841--71113 Score: 323
Period size: 144 Copynumber: 1.9 Consensus size: 144
70831 GTAGAATAGA
* * *
70841 CTCAAGAGAAGAGTTATCTTGAATTTCTTGAGCTACATACTGCAATCTTGGGCAACTTGATATAT
1 CTCAAGAGAAGAGTTATCTTGAATTTCTTGAGCTACATACTCCAATCTTGGACAACTTGATATAC
* * * * * * * **
70906 TCAGTTCCTTCAGACTCGTGGGTAACTCACCTCTGGATGATAAGGACACAAGCGATGCACAATCT
66 TCAATTCCTTAACACCCATGGGTAACTCAACTCTGGATGATAAAGACACAAAAGATGCACAATCT
70971 TCTATACTCAGTTT
131 TCTATACTCAGTTT
* * * * * * *
70985 CTCAAGAGAAGTGTTCTGTTGAATTTCTTGGGCTACATACTCC-AGCTTTGGACAATTTGATATG
1 CTCAAGAGAAGAGTTATCTTGAATTTCTTGAGCTACATACTCCAATC-TTGGACAACTTGATATA
* * * *
71049 CTCAATTTCTTAACACCCATGGGTAACTCAACTTTGGATGATAAAGATACAAAAGATGGACAATC
65 CTCAATTCCTTAACACCCATGGGTAACTCAACTCTGGATGATAAAGACACAAAAGATGCACAATC
71114 AGAAATACAC
Statistics
Matches: 105, Mismatches: 23, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
143 2 0.02
144 103 0.98
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (144 bp):
CTCAAGAGAAGAGTTATCTTGAATTTCTTGAGCTACATACTCCAATCTTGGACAACTTGATATAC
TCAATTCCTTAACACCCATGGGTAACTCAACTCTGGATGATAAAGACACAAAAGATGCACAATCT
TCTATACTCAGTTT
Found at i:76486 original size:26 final size:26
Alignment explanation
Indices: 76432--76486 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
76422 TGGATCTTCT
*
76432 TTCAATAATTCCCCAATAACTGGGGC
1 TTCAATAATTCCCCAATAACTGGAGC
* * * *
76458 TTCAGTAATTCTCCAATAATTGGATC
1 TTCAATAATTCCCCAATAACTGGAGC
76484 TTC
1 TTC
76487 TTTGAAAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.35
Consensus pattern (26 bp):
TTCAATAATTCCCCAATAACTGGAGC
Found at i:78449 original size:26 final size:23
Alignment explanation
Indices: 78419--78465 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
78409 CTAGAAAATT
78419 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAAC-TTGAT-GAT-AGATGGA
78445 TGAAAAACTTGATGATAGATG
1 TGAAAAACTTGATGATAGATG
78466 AATAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (23 bp):
TGAAAAACTTGATGATAGATGGA
Found at i:80325 original size:67 final size:65
Alignment explanation
Indices: 80168--80353 Score: 250
Period size: 67 Copynumber: 2.8 Consensus size: 65
80158 GTGCTCCAAA
* *
80168 TTTTGTCTAAGTCGTCCTTTGCAGGATTTTCAACTTAGCGAGAC--TTTTTTTTTTTCGCTCTAA
1 TTTTGCCTAAGTCGTCCTTTACAGGATTTTCAACTTAGCGAG-CTTTTTTTTTTTTTCGCTCTAA
80231 C
65 C
* **
80232 TTTTGCTTAAGTCGTTTTTTACAGGATTTTCAACTTAGCGAGCTTTTTCTTTTTTTTTCGCTCTA
1 TTTTGCCTAAGTCGTCCTTTACAGGATTTTCAACTTAGCGAGC-TTTT-TTTTTTTTTCGCTCTA
80297 AC
64 AC
* * * *
80299 TTTTGCCTAAGCCGTCCTTTATAGGATTTTCAATTTAGCGAGCTCTTTTTTTTTT
1 TTTTGCCTAAGTCGTCCTTTACAGGATTTTCAACTTAGCGAGCTTTTTTTTTTTT
80354 GGCAGTTTAG
Statistics
Matches: 106, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
63 1 0.01
64 37 0.35
65 8 0.08
66 5 0.05
67 55 0.52
ACGTcount: A:0.17, C:0.19, G:0.15, T:0.50
Consensus pattern (65 bp):
TTTTGCCTAAGTCGTCCTTTACAGGATTTTCAACTTAGCGAGCTTTTTTTTTTTTTCGCTCTAAC
Found at i:83402 original size:19 final size:19
Alignment explanation
Indices: 83384--83420 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
83374 TATTAATTAT
*
83384 TTTA-ATATTATATTTTTA
1 TTTATATATTACATTTTTA
83402 TTTATATATTACATTTTTA
1 TTTATATATTACATTTTTA
83421 CTTAAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTACATTTTTA
Done.