Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017276.1 Corchorus olitorius cultivar O-4 contig17309, 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: 57364
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1336 original size:28 final size:30
Alignment explanation
Indices: 1293--1369 Score: 90
Period size: 28 Copynumber: 2.7 Consensus size: 30
1283 ACAAGGTTAA
*
1293 AAGGGTAAAACTGTAAATTTAAC-C-TTCT
1 AAGGGTAAAACGGTAAATTTAACTCATTCT
*
1321 AAGGATAAAACGGT-AATTT-ACTCATTCT
1 AAGGGTAAAACGGTAAATTTAACTCATTCT
* *
1349 TAGGGTAAAACGGTAATTTTA
1 AAGGGTAAAACGGTAAATTTA
1370 TGCCTATACA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 2 0.05
27 6 0.15
28 28 0.70
29 4 0.10
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (30 bp):
AAGGGTAAAACGGTAAATTTAACTCATTCT
Found at i:2051 original size:27 final size:27
Alignment explanation
Indices: 2020--2079 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
2010 TCTCTTCTAT
* * *
2020 GGGTAGTTTCGTAA-TTTAACAACTTAA
1 GGGTAATTTAGTAATTTTAAC-ACCTAA
2047 GGGTAATTTAGTAATTTTAACACCTAA
1 GGGTAATTTAGTAATTTTAACACCTAA
2074 GGGTAA
1 GGGTAA
2080 AATGGTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 23 0.79
28 6 0.21
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (27 bp):
GGGTAATTTAGTAATTTTAACACCTAA
Found at i:6708 original size:72 final size:75
Alignment explanation
Indices: 6619--6768 Score: 209
Period size: 77 Copynumber: 2.0 Consensus size: 75
6609 AAAAAAATGT
** *
6619 CAGTTTCATTTT-CCCC-C-TCTGTCGAAGAACCATTGAAATCCTTAGCTTCTTTTCTTTTC-AA
1 CAGTTTCATTTTCCCCCTCATCTGTCGAAGAACCACCGAAATCCCTAGCTTCTTTTC-TTTCGAA
6680 ATCCCTAACGC
65 ATCCCTAACGC
*
6691 CAGTTTCATTTTTCCCCTCTAATCTGTCGAAGAACCACCGAAATCCCTAGCTTCTTTTCTTTCGA
1 CAGTTTCA-TTTTCCCC-CTCATCTGTCGAAGAACCACCGAAATCCCTAGCTTCTTTTCTTTCGA
6756 AATCCCTAACGC
64 AATCCCTAACGC
6768 C
1 C
6769 TTCTACCCAA
Statistics
Matches: 68, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
72 8 0.12
73 4 0.06
74 3 0.04
75 1 0.01
76 4 0.06
77 48 0.71
ACGTcount: A:0.23, C:0.32, G:0.10, T:0.35
Consensus pattern (75 bp):
CAGTTTCATTTTCCCCCTCATCTGTCGAAGAACCACCGAAATCCCTAGCTTCTTTTCTTTCGAAA
TCCCTAACGC
Found at i:9848 original size:2 final size:2
Alignment explanation
Indices: 9841--9879 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
9831 CCCTTGTTAC
9841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9880 AGATAAGGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9999 original size:43 final size:43
Alignment explanation
Indices: 9952--10230 Score: 372
Period size: 43 Copynumber: 6.6 Consensus size: 43
9942 GAAATGCCTT
* *
9952 TGTGTTACATATGTGTTTGAGGACTTTGTAATAGAGATGCCCC
1 TGTGTTATATATGTGTTTGGGGACTTTGTAATAGAGATGCCCC
* * *
9995 TGTGTTATATATGTGTTTGGGGACTTTG-ATATGGAGATGCTCT
1 TGTGTTATATATGTGTTTGGGGACTTTGTA-ATAGAGATGCCCC
* * *
10038 TGTGTTATATATGTGTTTGGGGAC-TT-TAATATAAATGCCTC
1 TGTGTTATATATGTGTTTGGGGACTTTGTAATAGAGATGCCCC
* *
10079 TGTGTTATATATGTGTTTGAGGACTTTGGAATAGAGATG-CCC
1 TGTGTTATATATGTGTTTGGGGACTTTGTAATAGAGATGCCCC
* *
10121 TGTGTTATATATGTGTTTGGGGAC-TT-TAATATAGATGCCTC
1 TGTGTTATATATGTGTTTGGGGACTTTGTAATAGAGATGCCCC
* * *
10162 TGTTTTATATATGTGTTTGAGGACTTTGGAATAGAGATGCCCC
1 TGTGTTATATATGTGTTTGGGGACTTTGTAATAGAGATGCCCC
10205 TGTGTTATATATGTGTTTGGGGACTT
1 TGTGTTATATATGTGTTTGGGGACTT
10231 CTTGTTATTG
Statistics
Matches: 202, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
40 9 0.04
41 56 0.28
42 33 0.16
43 104 0.51
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.42
Consensus pattern (43 bp):
TGTGTTATATATGTGTTTGGGGACTTTGTAATAGAGATGCCCC
Found at i:10160 original size:83 final size:83
Alignment explanation
Indices: 9952--10230 Score: 425
Period size: 83 Copynumber: 3.3 Consensus size: 83
9942 GAAATGCCTT
* * * * *
9952 TGTGTTACATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTGTTTGGGG
1 TGTGTTATATATGTGTTTGGGGAC-TT-TAATATAGATGCCTCTGTGTTATATATGTGTTTGAGG
* *
10017 ACTTT-GATATGGAGATGCTCT
64 ACTTTGGA-ATAGAGATGC-CC
*
10038 TGTGTTATATATGTGTTTGGGGACTTTAATATAAATGCCTCTGTGTTATATATGTGTTTGAGGAC
1 TGTGTTATATATGTGTTTGGGGACTTTAATATAGATGCCTCTGTGTTATATATGTGTTTGAGGAC
10103 TTTGGAATAGAGATGCCC
66 TTTGGAATAGAGATGCCC
*
10121 TGTGTTATATATGTGTTTGGGGACTTTAATATAGATGCCTCTGTTTTATATATGTGTTTGAGGAC
1 TGTGTTATATATGTGTTTGGGGACTTTAATATAGATGCCTCTGTGTTATATATGTGTTTGAGGAC
10186 TTTGGAATAGAGATGCCCC
66 TTTGGAATAGAGATG-CCC
10205 TGTGTTATATATGTGTTTGGGGACTT
1 TGTGTTATATATGTGTTTGGGGACTT
10231 CTTGTTATTG
Statistics
Matches: 181, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
83 79 0.44
84 76 0.42
85 4 0.02
86 22 0.12
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.42
Consensus pattern (83 bp):
TGTGTTATATATGTGTTTGGGGACTTTAATATAGATGCCTCTGTGTTATATATGTGTTTGAGGAC
TTTGGAATAGAGATGCCC
Found at i:15485 original size:225 final size:225
Alignment explanation
Indices: 15094--15544 Score: 839
Period size: 225 Copynumber: 2.0 Consensus size: 225
15084 ACCAACGCTG
*
15094 AAAAAATCGATTCTGCCAAAATCTTTGGCGAAGCAATACACAGTTTTTATAAGCCATTAAAATCC
1 AAAAAATCGATTCTGCCAAAATCTTTGGCCAAGCAATACACAGTTTTTATAAGCCATTAAAATCC
15159 ATTTTTCTTTTGGTTTTAATCCTAGCCATTGGATCATCTCTTCATCATCAAATCATGACCATCCA
66 ATTTTTCTTTTGGTTTTAATCCTAGCCATTGGATCATCTCTTCATCATCAAATCATGACCATCCA
*
15224 AATTCATTAAACCATATGGGCCACCATAAGCCCAAATGCAATACCAAATGGGGTTGGACCCCAAT
131 AATTCATTAAACCATATGGGCCACCATAAGCCCAAATGCAATACCAAATGGGGTTGGACCCCAAC
15289 GGGCTATAAGCCCAACAATCTCCCCCACCA
196 GGGCTATAAGCCCAACAATCTCCCCCACCA
* * *
15319 AAAAAATTGATTCTGCCAAAATCTTTGGCCAAGCAATACACGGTTTTTTTAAGCCATTAAAATCC
1 AAAAAATCGATTCTGCCAAAATCTTTGGCCAAGCAATACACAGTTTTTATAAGCCATTAAAATCC
*
15384 CTTTTTCTTTTGGTTTTAATCCTAGCCATTGGATCATCTCTTCATCATCAAATCATGACCATCCA
66 ATTTTTCTTTTGGTTTTAATCCTAGCCATTGGATCATCTCTTCATCATCAAATCATGACCATCCA
15449 AATTCATTAAACCATATGGGCCACCATAAGCCCAAATGCAATACCAAATGGGGTTGGACCCCAAC
131 AATTCATTAAACCATATGGGCCACCATAAGCCCAAATGCAATACCAAATGGGGTTGGACCCCAAC
*
15514 GGGCTATAAGCCCAACAATCTCCCCCTCCA
196 GGGCTATAAGCCCAACAATCTCCCCCACCA
15544 A
1 A
15545 CCCCATACAG
Statistics
Matches: 219, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
225 219 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.28
Consensus pattern (225 bp):
AAAAAATCGATTCTGCCAAAATCTTTGGCCAAGCAATACACAGTTTTTATAAGCCATTAAAATCC
ATTTTTCTTTTGGTTTTAATCCTAGCCATTGGATCATCTCTTCATCATCAAATCATGACCATCCA
AATTCATTAAACCATATGGGCCACCATAAGCCCAAATGCAATACCAAATGGGGTTGGACCCCAAC
GGGCTATAAGCCCAACAATCTCCCCCACCA
Found at i:17713 original size:79 final size:79
Alignment explanation
Indices: 17582--17743 Score: 306
Period size: 79 Copynumber: 2.1 Consensus size: 79
17572 TTTTGATCCC
* *
17582 TTTATTCTATCTTGCCTTCCCATGTTCTTTTTGAGGCTCATATATGTCCCTATATTTCTTTACTT
1 TTTATTCCATCTTGCCTTCCCATGTTCTTTTTAAGGCTCATATATGTCCCTATATTTCTTTACTT
17647 TGATTTGCTTGCCA
66 TGATTTGCTTGCCA
17661 TTTATTCCATCTTGCCTTCCCATGTTCTTTTTAAGGCTCATATATGTCCCTATATTTCTTTACTT
1 TTTATTCCATCTTGCCTTCCCATGTTCTTTTTAAGGCTCATATATGTCCCTATATTTCTTTACTT
17726 TGATTTGCTTGCCA
66 TGATTTGCTTGCCA
17740 TTTA
1 TTTA
17744 GATAAACCGA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.16, C:0.23, G:0.10, T:0.51
Consensus pattern (79 bp):
TTTATTCCATCTTGCCTTCCCATGTTCTTTTTAAGGCTCATATATGTCCCTATATTTCTTTACTT
TGATTTGCTTGCCA
Found at i:18783 original size:136 final size:136
Alignment explanation
Indices: 18539--18812 Score: 530
Period size: 136 Copynumber: 2.0 Consensus size: 136
18529 GAGGTGGGAT
18539 TAACGAGACGATCAAACACCCAGCTTTTAAAAGTGGTCCCTCCTTTGTATTACCTGTACAGACAG
1 TAACGAGACGATCAAACACCCAGCTTTTAAAAGTGGTCCCTCCTTTGTATTACCTGTACAGACAG
18604 GGAAAGAGCAAAATTAGGAGGCCTGGCAGTGGGTTTGTGGCACTATAAGCATAAGTTAACAGCAG
66 GGAAAGAGCAAAATTAGGAGGCCTGGCAGTGGGTTTGTGGCACTATAAGCATAAGTTAACAGCAG
18669 GTAAAG
131 GTAAAG
* *
18675 TAACGAGACGATCAAACACCCAGCTTTTGAAAGTGGTCCCTCCTTTGTATTACCTGTACAGATAG
1 TAACGAGACGATCAAACACCCAGCTTTTAAAAGTGGTCCCTCCTTTGTATTACCTGTACAGACAG
18740 GGAAAGAGCAAAATTAGGAGGCCTGGCAGTGGGTTTGTGGCACTATAAGCATAAGTTAACAGCAG
66 GGAAAGAGCAAAATTAGGAGGCCTGGCAGTGGGTTTGTGGCACTATAAGCATAAGTTAACAGCAG
18805 GTAAAG
131 GTAAAG
18811 TA
1 TA
18813 CAAGAAAACA
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 136 1.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (136 bp):
TAACGAGACGATCAAACACCCAGCTTTTAAAAGTGGTCCCTCCTTTGTATTACCTGTACAGACAG
GGAAAGAGCAAAATTAGGAGGCCTGGCAGTGGGTTTGTGGCACTATAAGCATAAGTTAACAGCAG
GTAAAG
Found at i:21004 original size:18 final size:19
Alignment explanation
Indices: 20981--21017 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
20971 TTTGGGCCTT
20981 ATTGTT-TTTAGGCTTGAG
1 ATTGTTATTTAGGCTTGAG
*
20999 ATTGTTATTTAGGGTTGAG
1 ATTGTTATTTAGGCTTGAG
21018 TTGATCGGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.19, C:0.03, G:0.30, T:0.49
Consensus pattern (19 bp):
ATTGTTATTTAGGCTTGAG
Found at i:21201 original size:15 final size:16
Alignment explanation
Indices: 21177--21216 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
21167 AGAGGTTGAA
*
21177 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
21192 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
21208 AGAAAACAA
1 AGAAAACAA
21217 AGCAAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:22937 original size:2 final size:2
Alignment explanation
Indices: 22930--22957 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22920 TATTACATAC
22930 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
22958 TTACTAGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34485 original size:17 final size:17
Alignment explanation
Indices: 34463--34500 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
34453 AATTATTAAT
34463 AAATAATAATAATTTTG
1 AAATAATAATAATTTTG
34480 AAATAATAATAATTTTG
1 AAATAATAATAATTTTG
34497 AAAT
1 AAAT
34501 TATTATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (17 bp):
AAATAATAATAATTTTG
Found at i:38052 original size:2 final size:2
Alignment explanation
Indices: 38045--38072 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38035 GTTAAACTAC
38045 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
38073 ACTTATAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39165 original size:31 final size:31
Alignment explanation
Indices: 39094--39165 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
39084 GTCTATCATC
*
39094 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
39125 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
39155 GTTTTAATTTG
1 -TTTTAATTTG
39166 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:39455 original size:13 final size:12
Alignment explanation
Indices: 39419--39465 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
39409 TCAATCTTTA
*
39419 TATATATTGATAA
1 TATATATT-ATAT
*
39432 TA-ATGTTATAT
1 TATATATTATAT
39443 TATATTATTATAT
1 TATA-TATTATAT
39456 TATATATTAT
1 TATATATTAT
39466 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:40128 original size:11 final size:11
Alignment explanation
Indices: 40108--40142 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
40098 TTGACAGTGC
40108 AACAAAAACAA
1 AACAAAAACAA
*
40119 AACGAAAACAA
1 AACAAAAACAA
40130 AACAAAAACAA
1 AACAAAAACAA
40141 AA
1 AA
40143 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:42678 original size:40 final size:40
Alignment explanation
Indices: 42622--42699 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
42612 TGTTTTTTCT
*
42622 TTTTATCTCACCTAGGGTTTA-ATGTATTTTTTAGGGTTCC
1 TTTTATCTCACCTAGGGTTTATAT-TATTTGTTAGGGTTCC
* *
42662 TTTTATCTCACTTAGGGTTTATATTGTTTGTTAGGGTT
1 TTTTATCTCACCTAGGGTTTATATTATTTGTTAGGGTT
42700 TGGCTTTCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 32 0.94
41 2 0.06
ACGTcount: A:0.17, C:0.12, G:0.19, T:0.53
Consensus pattern (40 bp):
TTTTATCTCACCTAGGGTTTATATTATTTGTTAGGGTTCC
Found at i:42936 original size:109 final size:107
Alignment explanation
Indices: 42802--43018 Score: 398
Period size: 109 Copynumber: 2.0 Consensus size: 107
42792 AGATTTCATA
42802 TCATGTCAATTTTTTTTTGTCTATAACAATCCTTAGGTAATTTTGTCATTTAATTAGTCTATAAC
1 TCATGTCAATTTTTTTTTGTCTATAACAATCCTTAGGTAATTTTGTCATTTAATTAGTCTATAAC
*
42867 AAATGATTGTTGGGTTTAGGGTTTGTTTAGTTTTTGGCATGC
66 AAATGATTGTTGGGTTTAGGGTTTGTTTAGTTTTTAGCATGC
*
42909 TCATGTCAATCTGTTTTTTTGTCTATAACAATCCTTAGGTAATTTTGTCATTTAATTTGTCTATA
1 TCATGTCAAT-T-TTTTTTTGTCTATAACAATCCTTAGGTAATTTTGTCATTTAATTAGTCTATA
42974 ACAAATGATTGTTGGGTTTAGGGTTTGTTTAGTTTTTAGCATGC
64 ACAAATGATTGTTGGGTTTAGGGTTTGTTTAGTTTTTAGCATGC
43018 T
1 T
43019 TAATTAGGAC
Statistics
Matches: 106, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
107 10 0.09
108 1 0.01
109 95 0.90
ACGTcount: A:0.23, C:0.11, G:0.18, T:0.49
Consensus pattern (107 bp):
TCATGTCAATTTTTTTTTGTCTATAACAATCCTTAGGTAATTTTGTCATTTAATTAGTCTATAAC
AAATGATTGTTGGGTTTAGGGTTTGTTTAGTTTTTAGCATGC
Found at i:43741 original size:40 final size:42
Alignment explanation
Indices: 43697--43782 Score: 131
Period size: 43 Copynumber: 2.1 Consensus size: 42
43687 ATATTACCTA
* *
43697 AATTCTACT-T-CATCTCTAGGTAATTCATCAAACTAAAGCT
1 AATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAGCT
43737 AATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCT
1 AATTCTACT-CTCCATCTCTAGATAATTCATCAAAATAAAGCT
43780 AAT
1 AAT
43783 ATTAATTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
40 9 0.22
42 1 0.02
43 31 0.76
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (42 bp):
AATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAGCT
Found at i:44935 original size:31 final size:31
Alignment explanation
Indices: 44900--44976 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
44890 TAAATTATTT
* *
44900 TTTAGGCTCAAATTGAGCAAATTTTGAAAGG
1 TTTAGGCTCAAATTGAGCAAAATTTGAAAGA
44931 TTTAGGCTCAAATTGAGCAAAATTTGAAAGA
1 TTTAGGCTCAAATTGAGCAAAATTTGAAAGA
*
44962 TTTAGTCTCAAATTG
1 TTTAGGCTCAAATTG
44977 GTCAACTTGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.34
Consensus pattern (31 bp):
TTTAGGCTCAAATTGAGCAAAATTTGAAAGA
Found at i:50558 original size:6 final size:6
Alignment explanation
Indices: 50543--50576 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
50533 TGACCTTTAA
*
50543 TTTT-T TTTTCT TTTTCT TTTTCC TTTTCT TTTTC
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
50577 CCTCTTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:51206 original size:28 final size:28
Alignment explanation
Indices: 51165--51219 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
51155 GACTCAAAGC
* *
51165 AAAGGCAAGCCAAGCTATCCACCAACTA
1 AAAGCCAAACCAAGCTATCCACCAACTA
* *
51193 AAAGCCAAACCAAGTTATCCACTAACT
1 AAAGCCAAACCAAGCTATCCACCAACT
51220 CTTCCTTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.44, C:0.31, G:0.11, T:0.15
Consensus pattern (28 bp):
AAAGCCAAACCAAGCTATCCACCAACTA
Found at i:53100 original size:26 final size:24
Alignment explanation
Indices: 53053--53126 Score: 60
Period size: 26 Copynumber: 2.9 Consensus size: 24
53043 TAACACATTA
* *
53053 TCTTACTATTGATTACTC-TTTTAC
1 TCTTATTACTGATTAC-CATTTTAC
53077 TTCTTGATTACTGATTACCATTTTTTAC
1 -TCTT-ATTACTGATTACCA--TTTTAC
* *
53105 TCTTTTTACTTATTACCATTTT
1 TCTTATTACTGATTACCATTTT
53127 TTACTCTTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
24 4 0.10
25 5 0.12
26 22 0.54
27 4 0.10
28 6 0.15
ACGTcount: A:0.20, C:0.19, G:0.04, T:0.57
Consensus pattern (24 bp):
TCTTATTACTGATTACCATTTTAC
Found at i:53127 original size:26 final size:26
Alignment explanation
Indices: 53084--53135 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
53074 TACTTCTTGA
53084 TTACTGATTACCATTTTTTACTCTTT
1 TTACTGATTACCATTTTTTACTCTTT
*
53110 TTACTTATTACCATTTTTTACTCTTT
1 TTACTGATTACCATTTTTTACTCTTT
53136 CTAATTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.02, T:0.60
Consensus pattern (26 bp):
TTACTGATTACCATTTTTTACTCTTT
Found at i:53320 original size:24 final size:25
Alignment explanation
Indices: 53293--53349 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 25
53283 TTTTACTCTA
53293 TTTACTTATTACCA-TTTTCCCTTT
1 TTTACTTATTACCATTTTTCCCTTT
** * *
53317 TTTACTGGTTTCCATTTTTTGCCTTT
1 TTTACTTATTACCA-TTTTTCCCTTT
53343 TTTACTT
1 TTTACTT
53350 TAATTACTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 11 0.42
26 15 0.58
ACGTcount: A:0.12, C:0.21, G:0.05, T:0.61
Consensus pattern (25 bp):
TTTACTTATTACCATTTTTCCCTTT
Found at i:53367 original size:35 final size:36
Alignment explanation
Indices: 53328--53414 Score: 135
Period size: 35 Copynumber: 2.5 Consensus size: 36
53318 TTACTGGTTT
* *
53328 CCATTTTTTGC-CTTTTTTACTTTAATTACTGAGTA
1 CCATTTTTTACTCTTTTTTACTTTAATTACTGAATA
53363 CCA-TTTTTACTCTTTTTTACTTTAATTACTGAATA
1 CCATTTTTTACTCTTTTTTACTTTAATTACTGAATA
53398 CCA-TTTTTACTCTTTTT
1 CCATTTTTTACTCTTTTT
53415 ACCACTTTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
34 6 0.12
35 43 0.88
ACGTcount: A:0.21, C:0.18, G:0.05, T:0.56
Consensus pattern (36 bp):
CCATTTTTTACTCTTTTTTACTTTAATTACTGAATA
Found at i:53423 original size:18 final size:18
Alignment explanation
Indices: 53396--53430 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53386 AATTACTGAA
*
53396 TACCATTTTTACTCTTTT
1 TACCACTTTTACTCTTTT
53414 TACCACTTTTACTCTTT
1 TACCACTTTTACTCTTT
53431 GAATTTTAAT
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:0.17, C:0.26, G:0.00, T:0.57
Consensus pattern (18 bp):
TACCACTTTTACTCTTTT
Found at i:53466 original size:21 final size:20
Alignment explanation
Indices: 53440--53546 Score: 67
Period size: 21 Copynumber: 5.0 Consensus size: 20
53430 TGAATTTTAA
53440 TTACTGATTATTATTACCATT
1 TTACTGATTATTATTACC-TT
53461 TTACTGATTACTCT-TTA-CTCT
1 TTACTGATTA-T-TATTACCT-T
** *
53482 TTACTGATTGCTATGACCATT
1 TTACTGATTATTATTACC-TT
*
53503 TTACTGTTTACTGT-TTACTCTT
1 TTACTGATTA-T-TATTAC-CTT
*
53525 TTACTGATTACTATTACTCTT
1 TTACTGATTATTATTAC-CTT
53546 T
1 T
53547 CTTGATTACT
Statistics
Matches: 67, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
19 1 0.01
20 4 0.06
21 40 0.60
22 19 0.28
23 3 0.04
ACGTcount: A:0.21, C:0.19, G:0.07, T:0.52
Consensus pattern (20 bp):
TTACTGATTATTATTACCTT
Found at i:53514 original size:7 final size:7
Alignment explanation
Indices: 53502--53569 Score: 50
Period size: 7 Copynumber: 9.7 Consensus size: 7
53492 CTATGACCAT
53502 TTTACTG
1 TTTACTG
53509 TTTACTG
1 TTTACTG
*
53516 TTTACTCT
1 TTTACT-G
53524 TTTACTG
1 TTTACTG
*
53531 ATTACT-
1 TTTACTG
* *
53537 ATTACTC
1 TTTACTG
53544 TTT-CTTG
1 TTTAC-TG
* *
53551 ATTACTC
1 TTTACTG
53558 TTTACTG
1 TTTACTG
53565 TTTAC
1 TTTAC
53570 AGACTATTAT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
6 7 0.15
7 34 0.71
8 7 0.15
ACGTcount: A:0.18, C:0.19, G:0.07, T:0.56
Consensus pattern (7 bp):
TTTACTG
Found at i:53581 original size:41 final size:41
Alignment explanation
Indices: 53440--53669 Score: 243
Period size: 41 Copynumber: 5.5 Consensus size: 41
53430 TGAATTTTAA
*
53440 TTACTGATTATTATTAC-CATTT-TACTGATTACTCTTTACTCT
1 TTACTGACTATTATTACTC-TTTCT--TGATTACTCTTTACTCT
* ** * * *
53482 TTACTGATTGCTATGAC-CATTT-TACTGTTTACTGTTTACTCTT
1 TTACTGACTATTATTACTC-TTTCT--TGATTACTCTTTACTC-T
* * *
53525 TTACTGATTACTATTACTCTTTCTTGATTACTCTTTACTGT
1 TTACTGACTATTATTACTCTTTCTTGATTACTCTTTACTCT
*
53566 TTACAGACTATTATTACTCTTTCTTGATTACTCTTTACTCT
1 TTACTGACTATTATTACTCTTTCTTGATTACTCTTTACTCT
*
53607 TTACTGACTATTATTACTCTTTCTTGACTACTCTTTACTCT
1 TTACTGACTATTATTACTCTTTCTTGATTACTCTTTACTCT
* *
53648 TTACTTACTACTATTACTCTTT
1 TTACTGACTATTATTACTCTTT
53670 TACTCTTTAC
Statistics
Matches: 167, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
41 97 0.58
42 49 0.29
43 19 0.11
44 2 0.01
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.52
Consensus pattern (41 bp):
TTACTGACTATTATTACTCTTTCTTGATTACTCTTTACTCT
Found at i:53647 original size:7 final size:7
Alignment explanation
Indices: 53635--53747 Score: 51
Period size: 7 Copynumber: 16.3 Consensus size: 7
53625 CTTTCTTGAC
53635 TACTCTT
1 TACTCTT
53642 TACTCTT
1 TACTCTT
53649 TA--C-T
1 TACTCTT
53653 TACTACTAT
1 TACT-CT-T
53662 TACTCTTT
1 TACTC-TT
53670 TACTCTT
1 TACTCTT
*
53677 TAC-CGAT
1 TACTC-TT
*
53684 TACT-AT
1 TACTCTT
53690 TAC-CATTT
1 TACTC--TT
**
53698 TACTGAT
1 TACTCTT
53705 TACTCTT
1 TACTCTT
*
53712 CACTCTT
1 TACTCTT
**
53719 TACTGAT
1 TACTCTT
*
53726 TACT-AT
1 TACTCTT
53732 TACTCTT
1 TACTCTT
53739 TACTCTT
1 TACTCTT
53746 TA
1 TA
53748 ACATTACCAT
Statistics
Matches: 82, Mismatches: 11, Indels: 26
0.69 0.09 0.22
Matches are distributed among these distances:
4 3 0.04
5 1 0.01
6 12 0.15
7 49 0.60
8 11 0.13
9 6 0.07
ACGTcount: A:0.22, C:0.25, G:0.03, T:0.50
Consensus pattern (7 bp):
TACTCTT
Found at i:53671 original size:21 final size:21
Alignment explanation
Indices: 53517--53673 Score: 84
Period size: 21 Copynumber: 7.6 Consensus size: 21
53507 TGTTTACTGT
* *
53517 TTACTCTTTTACTGATTACTA
1 TTACTCTTTTACTTACTACTA
53538 TTACTCTTTCTTGA-TTACT-CT-
1 TTACTC-TT-TT-ACTTACTACTA
* ** *
53559 TTACT-GTTTACAGACTATTA
1 TTACTCTTTTACTTACTACTA
53579 TTACTCTTTCTTGA-TTACT-CT-
1 TTACTC-TT-TT-ACTTACTACTA
* *
53600 TTACTC-TTTACTGACTATTA
1 TTACTCTTTTACTTACTACTA
*
53620 TTACTC-TTT-CTTGACTACTCT
1 TTACTCTTTTACTT-ACTACT-A
53641 TTACTC-TTTACTTACTACTA
1 TTACTCTTTTACTTACTACTA
53661 TTACTCTTTTACT
1 TTACTCTTTTACT
53674 CTTTACCGAT
Statistics
Matches: 103, Mismatches: 16, Indels: 34
0.67 0.10 0.22
Matches are distributed among these distances:
17 2 0.02
18 11 0.11
19 6 0.06
20 25 0.24
21 38 0.37
22 9 0.09
23 10 0.10
24 2 0.02
ACGTcount: A:0.20, C:0.22, G:0.04, T:0.53
Consensus pattern (21 bp):
TTACTCTTTTACTTACTACTA
Found at i:53671 original size:28 final size:28
Alignment explanation
Indices: 53635--53701 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
53625 CTTTCTTGAC
**
53635 TACTC-TTTACTCTTTACTTACTACTAT
1 TACTCTTTTACTCTTTACCGACTACTAT
*
53662 TACTCTTTTACTCTTTACCGATTACTAT
1 TACTCTTTTACTCTTTACCGACTACTAT
53690 TAC-CATTTTACT
1 TACTC-TTTTACT
53702 GATTACTCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.17
28 29 0.83
ACGTcount: A:0.22, C:0.25, G:0.01, T:0.51
Consensus pattern (28 bp):
TACTCTTTTACTCTTTACCGACTACTAT
Found at i:53705 original size:21 final size:21
Alignment explanation
Indices: 53669--53770 Score: 90
Period size: 21 Copynumber: 5.0 Consensus size: 21
53659 TATTACTCTT
*
53669 TTAC-TCTTTACCGATTACTA
1 TTACATCTTTACTGATTACTA
*
53689 TTACCAT-TTTACTGATTACTC
1 TTA-CATCTTTACTGATTACTA
53710 TT-CACTCTTTACTGATTACTA
1 TTACA-TCTTTACTGATTACTA
**
53731 TTAC-TCTTTACTCTTTAAC-A
1 TTACATCTTTACTGATT-ACTA
53751 TTACCAT-TTTACTGATTACT
1 TTA-CATCTTTACTGATTACT
53771 CTTTACTTCT
Statistics
Matches: 66, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
19 2 0.03
20 20 0.30
21 41 0.62
22 3 0.05
ACGTcount: A:0.25, C:0.24, G:0.04, T:0.48
Consensus pattern (21 bp):
TTACATCTTTACTGATTACTA
Found at i:55428 original size:16 final size:16
Alignment explanation
Indices: 55407--55438 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
55397 AAAAGGAGAT
55407 TAATATAATGAATTTA
1 TAATATAATGAATTTA
*
55423 TAATATAATGACTTTA
1 TAATATAATGAATTTA
55439 ATACCAATCA
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:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (16 bp):
TAATATAATGAATTTA
Done.