Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019383.1 Corchorus olitorius cultivar O-4 contig19416, 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: 131948
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--87 Score: 88
Period size: 3 Copynumber: 29.7 Consensus size: 3
* *
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAG TAT TAG TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
48 TAG TA- TAT TAG TAT TAG TAT TAG TAT TAG TAT TAG TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
88 GTATAGTATT
Statistics
Matches: 67, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
2 4 0.06
3 63 0.94
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:88 original size:6 final size:6
Alignment explanation
Indices: 4--102 Score: 130
Period size: 6 Copynumber: 16.5 Consensus size: 6
1 TAT
* * * *
4 TATTAT TATTAT TATTAT TATTAT TATTA- TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
51 TATATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TA-TAG TATTAG
1 --TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
100 TAT
1 TAT
103 ATATATGATA
Statistics
Matches: 89, Mismatches: 0, Indels: 8
0.92 0.00 0.08
Matches are distributed among these distances:
5 10 0.11
6 73 0.82
8 6 0.07
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (6 bp):
TATTAG
Found at i:4389 original size:90 final size:92
Alignment explanation
Indices: 4233--4412 Score: 292
Period size: 90 Copynumber: 2.0 Consensus size: 92
4223 AATTCCGAAG
*
4233 ATCTCTCACCATAAATTCAAATTTTTATCACTTAAACTAGTCGTCATCAATTACACACCCAAATT
1 ATCTCTCACCATAAATTCAAATCTTTATCACTTAAACTAG-CGTCATCAATTACACACCCAAATT
*
4298 ATTCGATGTGAGAGAATCAACTCCAGAT
65 ATTCGATATGAGAGAATCAACTCCAGAT
* * *
4326 ATCTCTCACCATATATTCATA-CTTTATCACTTAAACTA-CGTCATCAGTTACACACCCAAATTA
1 ATCTCTCACCATAAATTCAAATCTTTATCACTTAAACTAGCGTCATCAATTACACACCCAAATTA
4389 TTCGATATGAGAGAATCAACTCCA
66 TTCGATATGAGAGAATCAACTCCA
4413 CAGTGTGAGG
Statistics
Matches: 82, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
90 47 0.57
92 16 0.20
93 19 0.23
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.31
Consensus pattern (92 bp):
ATCTCTCACCATAAATTCAAATCTTTATCACTTAAACTAGCGTCATCAATTACACACCCAAATTA
TTCGATATGAGAGAATCAACTCCAGAT
Found at i:7847 original size:13 final size:14
Alignment explanation
Indices: 7829--7860 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
7819 TCTTTATTAC
7829 ATTTATTTTA-TTT
1 ATTTATTTTACTTT
7842 ATTTA-TTTACTTT
1 ATTTATTTTACTTT
7855 ATTTAT
1 ATTTAT
7861 ATGTTGTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (14 bp):
ATTTATTTTACTTT
Found at i:10210 original size:39 final size:39
Alignment explanation
Indices: 10151--10227 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
10141 ACGGAGGGGA
*
10151 GGACGGTAGCTTTGATTTTGATTTTATTTTGGTGAATTC
1 GGACGGTAGCTTTGAGTTTGATTTTATTTTGGTGAATTC
10190 GGACGGTAGCTTTGAGTTTGATTTTATTTTGGTGAATT
1 GGACGGTAGCTTTGAGTTTGATTTTATTTTGGTGAATT
10228 TATTTAGAGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.18, C:0.06, G:0.27, T:0.48
Consensus pattern (39 bp):
GGACGGTAGCTTTGAGTTTGATTTTATTTTGGTGAATTC
Found at i:27696 original size:16 final size:16
Alignment explanation
Indices: 27675--27706 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
27665 AAAACCTAAA
27675 ATATTGAATATTTTGT
1 ATATTGAATATTTTGT
27691 ATATTGAATATTTTGT
1 ATATTGAATATTTTGT
27707 CAGGAAAAAA
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:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (16 bp):
ATATTGAATATTTTGT
Found at i:38281 original size:20 final size:20
Alignment explanation
Indices: 38256--38293 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38246 AAGTTTTTCA
*
38256 GAAAAGATTCAACAGAGCAT
1 GAAAAGATTAAACAGAGCAT
38276 GAAAAGATTAAACAGAGC
1 GAAAAGATTAAACAGAGC
38294 TGTTTACAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.13, G:0.21, T:0.13
Consensus pattern (20 bp):
GAAAAGATTAAACAGAGCAT
Found at i:50235 original size:146 final size:145
Alignment explanation
Indices: 49953--50244 Score: 469
Period size: 146 Copynumber: 2.0 Consensus size: 145
49943 AAATCATATT
* *
49953 AACCCGGCCCAACCCGGTATGGGTCAACTGTTGGTCAAACAGGTTATTGACCGAGTCTTGACTGG
1 AACCCGGCCCAACCCGGTATGGGTCAACTGTCGGTCAAACAGGTTATTGACCGAGTCTTGACCGG
* **
50018 GCCAAACCTCCCCGGTTAACCCCCTCTCCGGACCGGAAAGGCCTCCGAGCTCTGTTGAATCGGTC
66 GCCAAACCTCCCCGGTTAACCCCCTCTCCGGACCGGAAAGGCCTCCGAGCCCCATTGAATCGGTC
50083 TAGGGTTTGAAAACAC
131 -AGGGTTTGAAAACAC
*
50099 AACCCGGCCCAACCCGGTCTGGGTCAACTGTCGGTCAAACAGGTTATTGACCGAGTCTTGACCGG
1 AACCCGGCCCAACCCGGTATGGGTCAACTGTCGGTCAAACAGGTTATTGACCGAGTCTTGACCGG
* * *
50164 GCCAAACCTCCCCGGTTAACCCCCCTTTCCGGACCGGACAGGCCTCCGGGCCCCATTGAATCGGT
66 GCCAAACCTCCCCGGTTAA-CCCCCTCTCCGGACCGGAAAGGCCTCCGAGCCCCATTGAATCGGT
50229 -ACGGGTTTGAAAACAC
130 CA-GGGTTTGAAAACAC
50245 TACTTGTGAT
Statistics
Matches: 135, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
145 1 0.01
146 95 0.70
147 39 0.29
ACGTcount: A:0.22, C:0.33, G:0.25, T:0.20
Consensus pattern (145 bp):
AACCCGGCCCAACCCGGTATGGGTCAACTGTCGGTCAAACAGGTTATTGACCGAGTCTTGACCGG
GCCAAACCTCCCCGGTTAACCCCCTCTCCGGACCGGAAAGGCCTCCGAGCCCCATTGAATCGGTC
AGGGTTTGAAAACAC
Found at i:50522 original size:129 final size:127
Alignment explanation
Indices: 50301--50557 Score: 442
Period size: 129 Copynumber: 2.0 Consensus size: 127
50291 TATAGGTTAG
* *
50301 AGCTCAGCTAAGAATGGGCCCCGTGTCCGTAGTGGTCTAACAAAATCTGTCTTGTTATTATAGTA
1 AGCTCAGCTAAGAATGGGCCCCGTGTCCGTAGTGATCTAACAAAATCTATCTTGTTATTATAGTA
*
50366 GAAAGACCAATTGACCCTGGACCCAAAATGGGCCGAACACCCACATTGTGAAATTTGGGGCT
66 GAAAGACCAATTGACCCTGGACCCAAAATGGCCCGAACACCCACATTGTGAAATTTGGGGCT
50428 AGCTCAGCTAAGAATGGGCCCCGTGTCCGTAGTGATCTAACAAAATCTTTATCTTGTTATTATAG
1 AGCTCAGCTAAGAATGGGCCCCGTGTCCGTAGTGATCTAACAAAATC--TATCTTGTTATTATAG
* * *
50493 TAGAAAGATCAATTGACCCTGGACTCAAAATGGCCCGAACACCCATATTGTGAAATTTGGGGCT
64 TAGAAAGACCAATTGACCCTGGACCCAAAATGGCCCGAACACCCACATTGTGAAATTTGGGGCT
50557 A
1 A
50558 AACTTACCTA
Statistics
Matches: 122, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
127 46 0.38
129 76 0.62
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (127 bp):
AGCTCAGCTAAGAATGGGCCCCGTGTCCGTAGTGATCTAACAAAATCTATCTTGTTATTATAGTA
GAAAGACCAATTGACCCTGGACCCAAAATGGCCCGAACACCCACATTGTGAAATTTGGGGCT
Found at i:53824 original size:100 final size:99
Alignment explanation
Indices: 53651--53845 Score: 302
Period size: 100 Copynumber: 2.0 Consensus size: 99
53641 CTCCTTTAGC
* * *
53651 GAATAGTTTTGAATTACAGAAACAAAATTAATCAAGAAAATGTGTATGTATCAACTTCTTAATCC
1 GAATAGTTTTGAATTACAAAAACAAAATTAATCAAAAAAATGTGTATGTATCAACTTCTTAACCC
53716 GCTTGTAGAGTCCAAAAGTTACACTTGATAGAATG
66 GCTTGTAGAGTCCAAAAGTTACA-TTGATAGAATG
**
53751 GAATAGTTTTGAATTTTAAAAACAAAATTAATCAAAAAAATGTGTATG-AGTCAACTTCTTAACC
1 GAATAGTTTTGAATTACAAAAACAAAATTAATCAAAAAAATGTGTATGTA-TCAACTTCTTAACC
* *
53815 CGCTTGTAGAGTTCAAAATTTACATTGATAG
65 CGCTTGTAGAGTCCAAAAGTTACATTGATAG
53846 TGTATTATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
99 8 0.09
100 79 0.91
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (99 bp):
GAATAGTTTTGAATTACAAAAACAAAATTAATCAAAAAAATGTGTATGTATCAACTTCTTAACCC
GCTTGTAGAGTCCAAAAGTTACATTGATAGAATG
Found at i:53940 original size:21 final size:20
Alignment explanation
Indices: 53911--53949 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53901 AAGACACAAA
*
53911 TACTATTATGAATGGAAAGCT
1 TACTATTAT-AAAGGAAAGCT
*
53932 TACTTTTATAAAGGAAAG
1 TACTATTATAAAGGAAAG
53950 GGTAATTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (20 bp):
TACTATTATAAAGGAAAGCT
Found at i:57842 original size:276 final size:272
Alignment explanation
Indices: 57370--57871 Score: 752
Period size: 276 Copynumber: 1.8 Consensus size: 272
57360 CTCTAAAGAG
* * * * * * *
57370 ACACATGTCGACCCTTTAACCCTAACCCTGCATGTGCAGTCTGCTAAATTTCACTAATGGTGGAT
1 ACACATGTCAACCCTTTAACCCTAACCCTGCATGTGCAATCAGCTAAACTTCACTAACGATGCAT
* ** * *
57435 AAAATAATTTTCCTTGAAAAATATACACGAAAAAGATGCATGCCAATCCTTTAACCCCGTTTGTA
66 AAAATAATTTTCCTTAAAAAATATACACGAAAAAGACACATGCCAAACCTTTAACCCCATTTGTA
* **
57500 CAATCTAATAGTAAACTACACTAATAGTGGATGTGATTATTTTACTTTTTTTAATAACCATAAAC
131 CAATCTAATAGTAAACTACACTAATAGTGGATGTGATAATTTTACTTTTCGTAATAACCATAAAC
*
57565 ACTTTTAGGTTTAATTTAAGTAACATTATTATGGCTTTTTACTTAATTAATGTTCAAAAATCAAA
196 ACTTTTAAG--T--TTTAAGTAACATTATTATGGCTTTTTACTTAATTAATGTTCAAAAATCAAA
57630 ACTAATCCCTAAGGGT
257 ACTAATCCCTAAGGGT
*
57646 ACACATGTCAACCCTTTAACCGTAACCCTGCATGTGCAATCAGCTAAACTTCACTAACGATGCAT
1 ACACATGTCAACCCTTTAACCCTAACCCTGCATGTGCAATCAGCTAAACTTCACTAACGATGCAT
* * * * *
57711 AAAATATTTTTCCTTAAAAAATATACACTAAAAAGACACATGTCAAACTTTTAACCCTATTTGTA
66 AAAATAATTTTCCTTAAAAAATATACACGAAAAAGACACATGCCAAACCTTTAACCCCATTTGTA
*
57776 CAATCTAATAGTAAACTACACTGATAGTGGATGTGATAATTTTACTTTTCGTAATAACCATAAAC
131 CAATCTAATAGTAAACTACACTAATAGTGGATGTGATAATTTTACTTTTCGTAATAACCATAAAC
*
57841 ACTTTTAAGTTTTAAGTAACATTATTGTGGC
196 ACTTTTAAGTTTTAAGTAACATTATTATGGC
57872 AAAACTTTAG
Statistics
Matches: 202, Mismatches: 24, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
272 20 0.10
274 1 0.00
276 181 0.90
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (272 bp):
ACACATGTCAACCCTTTAACCCTAACCCTGCATGTGCAATCAGCTAAACTTCACTAACGATGCAT
AAAATAATTTTCCTTAAAAAATATACACGAAAAAGACACATGCCAAACCTTTAACCCCATTTGTA
CAATCTAATAGTAAACTACACTAATAGTGGATGTGATAATTTTACTTTTCGTAATAACCATAAAC
ACTTTTAAGTTTTAAGTAACATTATTATGGCTTTTTACTTAATTAATGTTCAAAAATCAAAACTA
ATCCCTAAGGGT
Found at i:59798 original size:18 final size:20
Alignment explanation
Indices: 59777--59825 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
59767 ATTTTACCAC
59777 TAATAATAA-TTAAT-ATAA
1 TAATAATAAGTTAATAATAA
*
59795 TAATAATAAGTTTAATAATTA
1 TAATAATAAG-TTAATAATAA
59816 TAATAATAAG
1 TAATAATAAG
59826 AGATTTAACG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 9 0.33
20 5 0.19
21 13 0.48
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (20 bp):
TAATAATAAGTTAATAATAA
Found at i:59810 original size:15 final size:14
Alignment explanation
Indices: 59777--59820 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
59767 ATTTTACCAC
59777 TAATAATAATTAATA
1 TAATAATAA-TAATA
*
59792 TAATAATAATAAGTT
1 TAATAATAATAA-TA
*
59807 TAATAATTATAATA
1 TAATAATAATAATA
59821 ATAAGAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:64242 original size:14 final size:13
Alignment explanation
Indices: 64223--64261 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
64213 AAATTGTAAA
64223 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
64236 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
64250 ATTTAAAAAATT
1 ATTTAAAAAATT
64262 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:64489 original size:124 final size:127
Alignment explanation
Indices: 64247--64503 Score: 412
Period size: 124 Copynumber: 2.0 Consensus size: 127
64237 ATTTAAGAAA
*
64247 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATTAAAATAGTAAAATGGT---AATAAA
*
64312 ATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAA
63 AT--GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAA
64377 AG
126 AG
*
64379 TATATTTAAAAAATTCTAATATATATACGTTTTTTAAATTAAAATAGTAAAATGGT-A-AAAAT-
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATTAAAATAGTAAAATGGTAATAAAATG
*
64441 TATAATGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
66 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
64503 T
1 T
64504 TTAAACAATG
Statistics
Matches: 121, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
124 61 0.50
127 5 0.04
128 1 0.01
132 54 0.45
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATTAAAATAGTAAAATGGTAATAAAATG
TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:64887 original size:22 final size:22
Alignment explanation
Indices: 64862--64904 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
64852 AAAACCTGTA
64862 AACAGAGTTCCT-TTAACCCATC
1 AACAGAGTTCCTATT-ACCCATC
*
64884 AACAGATTTCCTATTACCCAT
1 AACAGAGTTCCTATTACCCAT
64905 AAAACCATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (22 bp):
AACAGAGTTCCTATTACCCATC
Found at i:80633 original size:27 final size:27
Alignment explanation
Indices: 80603--80681 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 27
80593 ATATTCTACA
80603 CACATACAAATATTCCACACACACATT
1 CACATACAAATATTCCACACACACATT
** *
80630 CACATATGAATATT-----C-TACA--
1 CACATACAAATATTCCACACACACATT
80649 CACATACAAATATTCCACACACACATT
1 CACATACAAATATTCCACACACACATT
80676 CACATA
1 CACATA
80682 TGAATATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
19 12 0.32
21 3 0.08
22 1 0.03
24 1 0.03
25 3 0.08
27 18 0.47
ACGTcount: A:0.44, C:0.30, G:0.01, T:0.24
Consensus pattern (27 bp):
CACATACAAATATTCCACACACACATT
Found at i:80641 original size:46 final size:46
Alignment explanation
Indices: 80584--80702 Score: 220
Period size: 46 Copynumber: 2.6 Consensus size: 46
80574 GCACCACACA
80584 CACATATGAATATTCTACACACATACAAATATTCCACACACACATT
1 CACATATGAATATTCTACACACATACAAATATTCCACACACACATT
80630 CACATATGAATATTCTACACACATACAAATATTCCACACACACATT
1 CACATATGAATATTCTACACACATACAAATATTCCACACACACATT
* *
80676 CACATATGAATATTTTGCACACATACA
1 CACATATGAATATTCTACACACATACA
80703 GAGTACTACA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.43, C:0.27, G:0.03, T:0.27
Consensus pattern (46 bp):
CACATATGAATATTCTACACACATACAAATATTCCACACACACATT
Found at i:80682 original size:21 final size:21
Alignment explanation
Indices: 80577--80674 Score: 78
Period size: 19 Copynumber: 4.6 Consensus size: 21
80567 TACAACTGCA
**
80577 CCACACACACATATGAATATT
1 CCACACACACATACAAATATT
*
80598 -C-TACACACATACAAATATT
1 CCACACACACATACAAATATT
80617 CCACACACACATTCACATATGAATATT
1 CCACACACACA-T-AC--A--AATATT
*
80644 -C-TACACACATACAAATATT
1 CCACACACACATACAAATATT
80663 CCACACACACAT
1 CCACACACACAT
80675 TCACATATGA
Statistics
Matches: 61, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
19 21 0.34
20 3 0.05
21 16 0.26
22 1 0.02
23 4 0.07
24 1 0.02
25 8 0.13
26 1 0.02
27 6 0.10
ACGTcount: A:0.44, C:0.31, G:0.02, T:0.23
Consensus pattern (21 bp):
CCACACACACATACAAATATT
Found at i:91720 original size:6 final size:6
Alignment explanation
Indices: 91709--91735 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
91699 AGAACAAGAT
91709 CAATAG CAATAG CAATAG CAATAG CAA
1 CAATAG CAATAG CAATAG CAATAG CAA
91736 GAAGAGGAAG
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:0.52, C:0.19, G:0.15, T:0.15
Consensus pattern (6 bp):
CAATAG
Found at i:105697 original size:20 final size:20
Alignment explanation
Indices: 105672--105710 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
105662 ACTCACAGTA
105672 ATGCATTTAACACCTTGTCC
1 ATGCATTTAACACCTTGTCC
105692 ATGCATTTAACACCTTGTC
1 ATGCATTTAACACCTTGTC
105711 AAATATTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.28, G:0.10, T:0.36
Consensus pattern (20 bp):
ATGCATTTAACACCTTGTCC
Found at i:109942 original size:33 final size:33
Alignment explanation
Indices: 109905--110002 Score: 196
Period size: 33 Copynumber: 3.0 Consensus size: 33
109895 TGTATTCTTG
109905 AAAATTTTAGTAACCTTAAAACAATTTTATTTA
1 AAAATTTTAGTAACCTTAAAACAATTTTATTTA
109938 AAAATTTTAGTAACCTTAAAACAATTTTATTTA
1 AAAATTTTAGTAACCTTAAAACAATTTTATTTA
109971 AAAATTTTAGTAACCTTAAAACAATTTTATTT
1 AAAATTTTAGTAACCTTAAAACAATTTTATTT
110003 TAGTTCAAGA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 65 1.00
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (33 bp):
AAAATTTTAGTAACCTTAAAACAATTTTATTTA
Found at i:119246 original size:24 final size:24
Alignment explanation
Indices: 119218--119267 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
119208 TCGTAGCCTT
* *
119218 CTTAAGCTTAGGAAGATTACGAAG
1 CTTAAGCTTAGCAAGATTACAAAG
*
119242 CTTAATCTTAGCAAGATTACAAAG
1 CTTAAGCTTAGCAAGATTACAAAG
119266 CT
1 CT
119268 CATGTGCACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (24 bp):
CTTAAGCTTAGCAAGATTACAAAG
Found at i:126565 original size:40 final size:40
Alignment explanation
Indices: 126521--126600 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
126511 ATAGAAGGAT
126521 GCCACTAATTTGCACCCTC-TTTTTCTATTTTCATCTTCTG
1 GCCACTAATTTGCACCCTCTTTTTTC-ATTTTCATCTTCTG
*
126561 GCCACTAATTTGCACCCTCTTTTTTCATTTTGATCTTCTG
1 GCCACTAATTTGCACCCTCTTTTTTCATTTTCATCTTCTG
126601 TATTTTGATT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 32 0.84
41 6 0.16
ACGTcount: A:0.15, C:0.29, G:0.09, T:0.47
Consensus pattern (40 bp):
GCCACTAATTTGCACCCTCTTTTTTCATTTTCATCTTCTG
Found at i:131494 original size:120 final size:120
Alignment explanation
Indices: 131284--131641 Score: 623
Period size: 120 Copynumber: 3.0 Consensus size: 120
131274 ACCCGAACCT
* * * * *
131284 GAATCTCCAGCTTTCTCCTCAGCTGAATCTAAAG---CATCCTCACCAGAAACTAAAGCTTCATC
1 GAATCTCCAACTTTTTCCTCACCAGAATCTAAAGCTTCCTCCTCACCAGAAACTAAAGCTTCATC
131346 GGAAGCCTTATTCTCAGCTTCAGAAGCCTTTCCTTCAGAAGGCTTGTCTCCATTG
66 GGAAGCCTTATTCTCAGCTTCAGAAGCCTTTCCTTCAGAAGGCTTGTCTCCATTG
* *
131401 GAATCTCCAACTTTTTCCTCACCGGAATCTAAAGCTTCCTCCTCACCAGAAACTAAAGTTTCATC
1 GAATCTCCAACTTTTTCCTCACCAGAATCTAAAGCTTCCTCCTCACCAGAAACTAAAGCTTCATC
131466 GGAAGCCTTATTCTCAGCTTCAGAAGCCTTTCCTTCAGAAGGCTTGTCTCCATTG
66 GGAAGCCTTATTCTCAGCTTCAGAAGCCTTTCCTTCAGAAGGCTTGTCTCCATTG
*
131521 GAAACTCCAACTTTTTCCTCACCAGAATCTAAAGCTTCCTCCTCACCAGAAACTAAAGCTTCATC
1 GAATCTCCAACTTTTTCCTCACCAGAATCTAAAGCTTCCTCCTCACCAGAAACTAAAGCTTCATC
131586 GGAAGCCTTATTCTCAGCTTCAGAAGCCTTTCCTTCAGAAGGCTTGTCTCCATTG
66 GGAAGCCTTATTCTCAGCTTCAGAAGCCTTTCCTTCAGAAGGCTTGTCTCCATTG
131641 G
1 G
131642 CGCTGGAAGA
Statistics
Matches: 229, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
117 30 0.13
120 199 0.87
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.30
Consensus pattern (120 bp):
GAATCTCCAACTTTTTCCTCACCAGAATCTAAAGCTTCCTCCTCACCAGAAACTAAAGCTTCATC
GGAAGCCTTATTCTCAGCTTCAGAAGCCTTTCCTTCAGAAGGCTTGTCTCCATTG
Found at i:131565 original size:24 final size:24
Alignment explanation
Indices: 131536--131582 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
131526 TCCAACTTTT
*
131536 TCCTCACCAGAATCTAAAGCTTCC
1 TCCTCACCAGAAACTAAAGCTTCC
131560 TCCTCACCAGAAACTAAAGCTTC
1 TCCTCACCAGAAACTAAAGCTTC
131583 ATCGGAAGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.09, T:0.23
Consensus pattern (24 bp):
TCCTCACCAGAAACTAAAGCTTCC
Done.