Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008106.1 Corchorus capsularis cultivar CVL-1 contig08127, 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: 21962
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:8829 original size:6 final size:6
Alignment explanation
Indices: 8813--8853 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
8803 GGCAACGTAG
*
8813 CAAAAA C-AAAA CAAAAA C-GAAA CAAAAA CAAAAAA CAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA C-AAAAA CAAAAA
8854 AACGAAAGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 9 0.30
6 15 0.50
7 6 0.20
ACGTcount: A:0.80, C:0.17, G:0.02, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:8829 original size:11 final size:11
Alignment explanation
Indices: 8813--8845 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
8803 GGCAACGTAG
8813 CAAAAACAAAA
1 CAAAAACAAAA
*
8824 CAAAAACGAAA
1 CAAAAACAAAA
8835 CAAAAACAAAA
1 CAAAAACAAAA
8846 AACAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.79, C:0.18, G:0.03, T:0.00
Consensus pattern (11 bp):
CAAAAACAAAA
Found at i:8941 original size:33 final size:32
Alignment explanation
Indices: 8882--8964 Score: 114
Period size: 34 Copynumber: 2.5 Consensus size: 32
8872 CGACCCCTAA
*
8882 GATTTTGAGTTTTGAACATGAAATGCAGATTCTG
1 GATTTTGAGTTTTGAA-ATGAAATGCAAATT-TG
8916 GATTTTGAGTTTTGAAATGAAATGCAAATTTG
1 GATTTTGAGTTTTGAAATGAAATGCAAATTTG
*
8948 AATTTTGA-TTTTCGAAA
1 GATTTTGAGTTTT-GAAA
8965 GGAATGCTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
31 4 0.09
32 13 0.28
33 13 0.28
34 16 0.35
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (32 bp):
GATTTTGAGTTTTGAAATGAAATGCAAATTTG
Found at i:9145 original size:148 final size:147
Alignment explanation
Indices: 8884--9370 Score: 752
Period size: 148 Copynumber: 3.3 Consensus size: 147
8874 ACCCCTAAGA
* * * * * * *
8884 TTTTGAGTTTTGAA-CATGAAATGCAGATTCTGGATTTTGAGTTTTG-A-AATGAAATGCAAATT
1 TTTTGAATTTTGAACCATGAGATGCTGATTTTGAATTTTGATTTTTGAATAATGAAATGCAATTT
* * *
8946 TGAATTTTGATTTTCG-A-AA-GGAATGCTGAAATATAAGTTTTGAATTTTGACTTTTGAAGAAT
66 TGAACTTTGATTTTCGAAGAATAGAATGCTGAAATGTAAGTTTTGAATTTTGACTTTTGAAGAAT
*
9008 GAACCGTGAAATGCAGG
131 GAACCATGAAATGCAGG
* *
9025 TTTTGAATTTTGAGCCATGAGATGCTGATTTTGAACTTTGATTTTTGAATAATGAAATGCGAATT
1 TTTTGAATTTTGAACCATGAGATGCTGATTTTGAATTTTGATTTTTGAATAATGAAATGC-AATT
* *
9090 TTGAACTTTAATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAA
65 TTGAACTTTGATTTTCGAAGAATAGAATGCTGAAATGTAAGTTTTGAATTTTGACTTTTGAAGAA
9155 TGAACCATGAAATGCAGG
130 TGAACCATGAAATGCAGG
*
9173 TTTTGAATTTTGAACCATGAGATGCTGATTTTGATTTTTGATTTTTGAATAATGAAATGCAAATT
1 TTTTGAATTTTGAACCATGAGATGCTGATTTTGAATTTTGATTTTTGAATAATGAAATGC-AATT
* *
9238 TTGAACTTTGATTTTCGAAGGATAGAATGTTGAAATGTAAGTTTTGAATTTTGACTTTTGAAGAA
65 TTGAACTTTGATTTTCGAAGAATAGAATGCTGAAATGTAAGTTTTGAATTTTGACTTTTGAAGAA
9303 TGAACCATGAAATGCAGG
130 TGAACCATGAAATGCAGG
9321 TTTTGAATTTTGAACCATGAGATGCTGATTTTGAATTTTGATTTTTGAAT
1 TTTTGAATTTTGAACCATGAGATGCTGATTTTGAATTTTGATTTTTGAAT
9371 TTTGAAGACT
Statistics
Matches: 315, Mismatches: 24, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
141 12 0.04
142 26 0.08
143 1 0.00
144 10 0.03
145 18 0.06
146 1 0.00
147 2 0.01
148 245 0.78
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.40
Consensus pattern (147 bp):
TTTTGAATTTTGAACCATGAGATGCTGATTTTGAATTTTGATTTTTGAATAATGAAATGCAATTT
TGAACTTTGATTTTCGAAGAATAGAATGCTGAAATGTAAGTTTTGAATTTTGACTTTTGAAGAAT
GAACCATGAAATGCAGG
Found at i:9153 original size:43 final size:43
Alignment explanation
Indices: 9076--9186 Score: 131
Period size: 42 Copynumber: 2.6 Consensus size: 43
9066 TTTTTGAATA
* *
9076 ATGAAATGCGAA-TTTTGAACTTT-AATTTTCGAAGAATAGAATGC
1 ATGAAATGC-AAGTTTTGAATTTTGAATTTTCGAAGAAT-GAA-CC
*
9120 -TGAAATGCAAGTTTTGAATTTTGACTTTT-GAAGAATGAACC
1 ATGAAATGCAAGTTTTGAATTTTGAATTTTCGAAGAATGAACC
*
9161 ATGAAATGCAGGTTTTGAATTTTGAA
1 ATGAAATGCAAGTTTTGAATTTTGAA
9187 CCATGAGATG
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
41 1 0.02
42 28 0.47
43 25 0.42
44 5 0.08
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (43 bp):
ATGAAATGCAAGTTTTGAATTTTGAATTTTCGAAGAATGAACC
Found at i:9176 original size:28 final size:28
Alignment explanation
Indices: 9145--9206 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
9135 GAATTTTGAC
*
9145 TTTTGAAGAATGAACCATGAAATGCAGG
1 TTTTGAAGAATGAACCATGAAATGCAGA
*** * *
9173 TTTTGAATTTTGAACCATGAGATGCTGA
1 TTTTGAAGAATGAACCATGAAATGCAGA
9201 TTTTGA
1 TTTTGA
9207 TTTTTGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (28 bp):
TTTTGAAGAATGAACCATGAAATGCAGA
Found at i:9211 original size:28 final size:28
Alignment explanation
Indices: 9155--9213 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
9145 TTTTGAAGAA
*
9155 TGAACCATGAAATGCAGGTTTTGAATTT
1 TGAACCATGAAATGCAGATTTTGAATTT
* * *
9183 TGAACCATGAGATGCTGATTTTGATTTT
1 TGAACCATGAAATGCAGATTTTGAATTT
9211 TGA
1 TGA
9214 TTTTTGAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (28 bp):
TGAACCATGAAATGCAGATTTTGAATTT
Found at i:9239 original size:35 final size:35
Alignment explanation
Indices: 8883--9252 Score: 126
Period size: 35 Copynumber: 10.3 Consensus size: 35
8873 GACCCCTAAG
* * * *
8883 ATTTTGAGTTTTGAAC-ATGAAATGCAGATTCTGG
1 ATTTTGATTTTTGAACAATGAAATGCAAATTTTGA
*
8917 ATTTTGAGTTTTG-A-AATGAAATGCAAA-TTTGA
1 ATTTTGATTTTTGAACAATGAAATGCAAATTTTGA
* * ** *
8949 ATTTTGATTTTCGAAAGGAATGCTGAAATATAAGTTTTGA
1 ATTTTGATTTTTG-AA-CAA---TGAAATGCAAATTTTGA
* * * ***
8989 ATTTTGACTTTTGAAGAATGAACCGTG-AAATGCAG-
1 ATTTTGATTTTTGAACAATGAA--ATGCAAATTTTGA
* * * * * **
9024 GTTTTGAATTTTGAGCCATGAGATGCTGATTTTGA
1 ATTTTGATTTTTGAACAATGAAATGCAAATTTTGA
* * *
9059 ACTTTGATTTTTGAATAATGAAATGCGAATTTTGA
1 ATTTTGATTTTTGAACAATGAAATGCAAATTTTGA
* * * * *
9094 ACTTTAATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGA
1 ATTTTGATTTT---TG-A-ACAA---TGAAATGCAAATTTTGA
* * ***
9137 ATTTTGACTTTTGAAGAATGAACCATG-AAATGCAG-
1 ATTTTGATTTTTGAACAATGAA--ATGCAAATTTTGA
* * * * **
9172 GTTTTGAATTTTGAACCATGAGATGCTGATTTTGA
1 ATTTTGATTTTTGAACAATGAAATGCAAATTTTGA
* *
9207 TTTTTGATTTTTGAATAATGAAATGCAAATTTTGA
1 ATTTTGATTTTTGAACAATGAAATGCAAATTTTGA
*
9242 ACTTTGATTTT
1 ATTTTGATTTT
9253 CGAAGGATAG
Statistics
Matches: 242, Mismatches: 69, Indels: 49
0.67 0.19 0.14
Matches are distributed among these distances:
32 14 0.06
33 17 0.07
34 20 0.08
35 114 0.47
36 10 0.04
37 4 0.02
38 8 0.03
39 12 0.05
40 20 0.08
43 23 0.10
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (35 bp):
ATTTTGATTTTTGAACAATGAAATGCAAATTTTGA
Found at i:9324 original size:28 final size:28
Alignment explanation
Indices: 9293--9355 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
9283 GAATTTTGAC
*
9293 TTTTGAAGAATGAACCATGAAATGCAGG
1 TTTTGAAGAATGAACCATGAAATGCAGA
*** * *
9321 TTTTGAATTTTGAACCATGAGATGCTGA
1 TTTTGAAGAATGAACCATGAAATGCAGA
9349 TTTTGAA
1 TTTTGAA
9356 TTTTGATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (28 bp):
TTTTGAAGAATGAACCATGAAATGCAGA
Found at i:9324 original size:42 final size:43
Alignment explanation
Indices: 9224--9333 Score: 125
Period size: 43 Copynumber: 2.6 Consensus size: 43
9214 TTTTTGAATA
* * * **
9224 ATGAAATGCAAATTTTGAACTTTGATTTTCGAAGGATAGAATG
1 ATGAAATGCAAGTTTTGAATTTTGATTTTCGAAGAATAGAACC
* *
9267 TTGAAATGTAAGTTTTGAATTTTGACTTTT-GAAGAAT-GAACC
1 ATGAAATGCAAGTTTTGAATTTTGA-TTTTCGAAGAATAGAACC
*
9309 ATGAAATGCAGGTTTTGAATTTTGA
1 ATGAAATGCAAGTTTTGAATTTTGA
9334 ACCATGAGAT
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
42 25 0.45
43 27 0.48
44 4 0.07
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (43 bp):
ATGAAATGCAAGTTTTGAATTTTGATTTTCGAAGAATAGAACC
Found at i:9356 original size:28 final size:28
Alignment explanation
Indices: 9303--9361 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
9293 TTTTGAAGAA
*
9303 TGAACCATGAAATGCAGGTTTTGAATTT
1 TGAACCATGAAATGCAGATTTTGAATTT
* *
9331 TGAACCATGAGATGCTGATTTTGAATTT
1 TGAACCATGAAATGCAGATTTTGAATTT
9359 TGA
1 TGA
9362 TTTTTGAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (28 bp):
TGAACCATGAAATGCAGATTTTGAATTT
Found at i:9368 original size:14 final size:14
Alignment explanation
Indices: 9349--9375 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9339 GAGATGCTGA
9349 TTTTGAATTTTGAT
1 TTTTGAATTTTGAT
9363 TTTTGAATTTTGA
1 TTTTGAATTTTGA
9376 AGACTTTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (14 bp):
TTTTGAATTTTGAT
Found at i:9544 original size:37 final size:37
Alignment explanation
Indices: 9502--9958 Score: 395
Period size: 37 Copynumber: 12.4 Consensus size: 37
9492 TGGTTTTCGA
*
9502 ACACCTAAACAGGGAACATAAACAA-GATTTTGATAAG
1 ACACCTAAACAGGGAACTTAAACAAGGA-TTTGATAAG
*
9539 ACACCTAAACAGGG-ACTTTAAATAAGGATTTGATAAG
1 ACACCTAAACAGGGAAC-TTAAACAAGGATTTGATAAG
* * * * * *
9576 A-ACTCTAAACAGGCATCTT-GACTAAGGTTTTGATGAC
1 ACAC-CTAAACAGGGAACTTAAAC-AAGGATTTGATAAG
* *
9613 ACACCTAAACAGGTACCTTAAACAAGGATTTTGATAAG
1 ACACCTAAACAGGGAACTTAAACAAGGA-TTTGATAAG
* * * *
9651 AAACCTAAATA-GGAATCTTGAAGAA-GATTTTGAT--G
1 ACACCTAAACAGGGAA-CTTAAACAAGGA-TTTGATAAG
* * *
9686 ACACCTAAATAGGGACCTTAAACAAGGA-TTAATAAG
1 ACACCTAAACAGGGAACTTAAACAAGGATTTGATAAG
* * *
9722 AAACCTAAACA-GGAATTTTAAACAA-GATTTTGATGAG
1 ACACCTAAACAGGGAA-CTTAAACAAGGA-TTTGATAAG
* *
9759 ACACCTAAACAGTGACCTTAAACAAGGATTTGATAAG
1 ACACCTAAACAGGGAACTTAAACAAGGATTTGATAAG
* *
9796 AAACCTAAA-AAGGAATCTTAAACAA-GATTTTGATGAA-
1 ACACCTAAACAGGGAA-CTTAAACAAGGA-TTTGAT-AAG
*
9833 ACACCTAAACAGGGAGCTTAAACAAGGATTTGATAAG
1 ACACCTAAACAGGGAACTTAAACAAGGATTTGATAAG
* * * *
9870 ACACCTAAACAGGCACCTTAAATAAGGATTTAATAAG
1 ACACCTAAACAGGGAACTTAAACAAGGATTTGATAAG
* * *
9907 ACACCTAAACA-TGAACCTTAAACATGGATTTGACAAG
1 ACACCTAAACAGGGAA-CTTAAACAAGGATTTGATAAG
*
9944 AAACCTAAACAGGGA
1 ACACCTAAACAGGGA
9959 TCTTGGGATC
Statistics
Matches: 337, Mismatches: 57, Indels: 51
0.76 0.13 0.11
Matches are distributed among these distances:
34 4 0.01
35 23 0.07
36 36 0.11
37 230 0.68
38 44 0.13
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (37 bp):
ACACCTAAACAGGGAACTTAAACAAGGATTTGATAAG
Found at i:9634 original size:74 final size:73
Alignment explanation
Indices: 9504--10065 Score: 535
Period size: 74 Copynumber: 7.5 Consensus size: 73
9494 GTTTTCGAAC
* * * *
9504 ACCTAAACAGGGAA-CATAAACAAGATTTTGATAAGACACCTAAACAGGGACTTTAAATAAGGAT
1 ACCTAAACA-GGAATC-TTAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGAT
9568 TTGATAAG-A
64 TTGATAAGAA
* * * * *
9577 ACTCTAAACAGGCATCTTGACTAAGGTTTTGATGACACACCTAAACAGGTACCTTAAACAAGGAT
1 AC-CTAAACAGGAATCTTAAC-AAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGA-
9642 TTTGATAAGAA
63 TTTGATAAGAA
* * *
9653 ACCTAAATAGGAATCTTGAAGAAGATTTTGAT--GACACCTAAATAGGGACCTTAAACAAGGA-T
1 ACCTAAACAGGAATCTT-AACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
*
9715 TAATAAGAA
65 TGATAAGAA
* *
9724 ACCTAAACAGGAATTTTAAACAAGATTTTGATGAGACACCTAAACAGTGACCTTAAACAAGGATT
1 ACCTAAACAGGAATCTT-AACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
9789 TGATAAGAA
65 TGATAAGAA
* * *
9798 ACCTAAAAAGGAATCTTAAACAAGATTTTGATGAAACACCTAAACAGGGAGCTTAAACAAGGATT
1 ACCTAAACAGGAATCTT-AACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
*
9863 TGATAAGAC
65 TGATAAGAA
* * * * * * * *
9872 ACCTAAACAGGCACCTTAAATAAGGA-TTTAATAAGACACCTAAACATGAACCTTAAACATGGAT
1 ACCTAAACAGGAATCTT-AACAA-GATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGAT
*
9936 TTGACAAGAA
64 TTGATAAGAA
* * * * **
9946 ACCTAAACAGGGATCTTGGGATCTTGAACAAGGATTTTTATGAAACACCTAAATAAGGATTTTAA
1 ACCTAAACA-GGA-------ATCTT-AACAA-GATTTTGATGAGACACCTAAACAGGGACCTTAA
* *
10011 ATAAGGATTTGATAAGAC
56 ACAAGGATTTGATAAGAA
* *
10029 ACTTAAACAGAAATCTTGAACAATG-TTTTGATGAGAC
1 ACCTAAACAGGAATCTT-AACAA-GATTTTGATGAGAC
10066 TGAATTTTTT
Statistics
Matches: 405, Mismatches: 65, Indels: 37
0.80 0.13 0.07
Matches are distributed among these distances:
71 37 0.09
73 61 0.15
74 198 0.49
75 48 0.12
76 4 0.01
82 13 0.03
83 44 0.11
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (73 bp):
ACCTAAACAGGAATCTTAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTT
GATAAGAA
Found at i:9939 original size:111 final size:110
Alignment explanation
Indices: 9501--10062 Score: 455
Period size: 111 Copynumber: 5.0 Consensus size: 110
9491 TTGGTTTTCG
* *
9501 AACACCTAAACAGGGAACATAAACAAGATTTTGATAAGACACCTAAACAGGGACTTTAAATAAGG
1 AACACCTAAACAGGGAACTTAAACAAGATTTTGATAAGACACCTAAACA-GGACCTTAAATAAGG
* * * *
9566 ATTTGATAAGA-ACTCTAAACAGGCATCTT-GACTAAGGTTTTGATGA
65 ATTTGATAAGACAC-CTAAACAGGAACCTTAAAC-AAGGATTTGATGA
* * * * * * * *
9612 CACACCTAAACAGGTACCTTAAACAAGGATTTTGATAAGAAACCTAAATAGGAATCTTGAAGAA-
1 AACACCTAAACAGGGAACTTAAACAA-GATTTTGATAAGACACCTAAACAGG-ACCTTAAATAAG
* * *
9676 GATTTTGAT--GACACCTAAATAGGGACCTTAAACAAGGA-TTAAT-A
64 GA-TTTGATAAGACACCTAAACAGGAACCTTAAACAAGGATTTGATGA
* * * *
9720 AGAAACCTAAACA-GGAATTTTAAACAAGATTTTGATGAGACACCTAAACAGTGACCTTAAACAA
1 A-ACACCTAAACAGGGAA-CTTAAACAAGATTTTGATAAGACACCTAAACAG-GACCTTAAATAA
* * *
9784 GGATTTGATAAGAAACCTAAAAAGGAATCTTAAACAA-GATTTTGATGA
63 GGATTTGATAAGACACCTAAACAGGAACCTTAAACAAGGA-TTTGATGA
*
9832 AACACCTAAACAGGGAGCTTAAACAAGGA-TTTGATAAGACACCTAAACAGGCACCTTAAATAAG
1 AACACCTAAACAGGGAACTTAAACAA-GATTTTGATAAGACACCTAAACAGG-ACCTTAAATAAG
* * * *
9896 GATTTAATAAGACACCTAAACATGAACCTTAAACATGGATTTGA-CA
64 GATTTGATAAGACACCTAAACAGGAACCTTAAACAAGGATTTGATGA
* * * * *
9942 AGAAACCTAAACAGGGATCTTGGGATCTTGAACAAGGATTTTTATGAA-ACACCTAAATAAGGAT
1 A-ACACCTAAACAGGGA-------A-CTTAAACAA-GATTTTGAT-AAGACACCTAAA-CAGGAC
* * * * * * *
10006 TTTAAATAAGGATTTGATAAGACACTTAAACAGAAATCTTGAACAATGTTTTGATGA
54 CTTAAATAAGGATTTGATAAGACACCTAAACAGGAACCTTAAACAAGGATTTGATGA
10063 GACTGAATTT
Statistics
Matches: 359, Mismatches: 61, Indels: 52
0.76 0.13 0.11
Matches are distributed among these distances:
108 38 0.11
109 27 0.08
110 43 0.12
111 132 0.37
112 43 0.12
119 11 0.03
120 59 0.16
121 6 0.02
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.25
Consensus pattern (110 bp):
AACACCTAAACAGGGAACTTAAACAAGATTTTGATAAGACACCTAAACAGGACCTTAAATAAGGA
TTTGATAAGACACCTAAACAGGAACCTTAAACAAGGATTTGATGA
Found at i:10013 original size:13 final size:13
Alignment explanation
Indices: 9995--10020 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9985 ATGAAACACC
9995 TAAATAAGGATTT
1 TAAATAAGGATTT
10008 TAAATAAGGATTT
1 TAAATAAGGATTT
10021 GATAAGACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
TAAATAAGGATTT
Found at i:10241 original size:6 final size:6
Alignment explanation
Indices: 10232--10259 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
10222 GTAAATGTTG
10232 ATGATT ATGATT ATGATT ATGATT ATGA
1 ATGATT ATGATT ATGATT ATGATT ATGA
10260 GATGCAATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (6 bp):
ATGATT
Found at i:11118 original size:8 final size:8
Alignment explanation
Indices: 11107--11163 Score: 62
Period size: 8 Copynumber: 7.1 Consensus size: 8
11097 TTGATTTCTC
11107 TTTCTTTT
1 TTTCTTTT
*
11115 TTTCCTTT
1 TTTCTTTT
11123 TTT-TTTT
1 TTTCTTTT
**
11130 TTTCGCTT
1 TTTCTTTT
*
11138 TCTCTTTT
1 TTTCTTTT
11146 TTTCTTTTT
1 TTTC-TTTT
11155 TTTCTTTT
1 TTTCTTTT
11163 T
1 T
11164 AGTATTGCTT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
7 6 0.15
8 25 0.64
9 8 0.21
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (8 bp):
TTTCTTTT
Found at i:11128 original size:12 final size:14
Alignment explanation
Indices: 11101--11157 Score: 55
Period size: 15 Copynumber: 4.1 Consensus size: 14
11091 GAACCTTTGA
11101 TTTCTCTTTCTTTT
1 TTTCTCTTTCTTTT
* *
11115 TTTCCTTTTTTTTTT
1 TTT-CTCTTTCTTTT
*
11130 TTTCGCTTTCTCTTT
1 TTTCTCTTTCT-TTT
11145 TTT-TCTTT-TTTT
1 TTTCTCTTTCTTTT
11157 T
1 T
11158 CTTTTTAGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
12 4 0.11
13 1 0.03
14 12 0.34
15 18 0.51
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.81
Consensus pattern (14 bp):
TTTCTCTTTCTTTT
Found at i:11145 original size:29 final size:31
Alignment explanation
Indices: 11101--11163 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
11091 GAACCTTTGA
*
11101 TTTCTCTTTCT-TTTTTTCCTTTTTTTT-TT
1 TTTCGCTTTCTCTTTTTTCCTTTTTTTTCTT
*
11130 TTTCGCTTTCTCTTTTTTTCTTTTTTTTCTT
1 TTTCGCTTTCTCTTTTTTCCTTTTTTTTCTT
11161 TTT
1 TTT
11164 AGTATTGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 10 0.33
30 15 0.50
31 5 0.17
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (31 bp):
TTTCGCTTTCTCTTTTTTCCTTTTTTTTCTT
Found at i:11542 original size:15 final size:15
Alignment explanation
Indices: 11509--11558 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
11499 TTCTTTTTTT
*
11509 CTTTTTTTTTCC-TC
1 CTTTTTTCTTCCTTC
*
11523 ATTTTTTCTTCCTTC
1 CTTTTTTCTTCCTTC
*
11538 CTTTTCTTC-TACTTC
1 CTTTT-TTCTTCCTTC
11553 CTTTTT
1 CTTTTT
11559 CTTTCTATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 11 0.37
15 16 0.53
16 3 0.10
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.68
Consensus pattern (15 bp):
CTTTTTTCTTCCTTC
Found at i:11825 original size:14 final size:14
Alignment explanation
Indices: 11806--11868 Score: 69
Period size: 14 Copynumber: 4.6 Consensus size: 14
11796 ACTTAAAACC
11806 TTTTTGAAAACTCA-
1 TTTTTGAAAA-TCAT
11820 TTTTTGAAAATCAT
1 TTTTTGAAAATCAT
*
11834 TTTTTG-AAAGCAGT
1 TTTTTGAAAATCA-T
*
11848 TTCTTGAAAATC-T
1 TTTTTGAAAATCAT
11861 TTTTTGAA
1 TTTTTGAA
11869 GAAATGTCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
13 16 0.38
14 22 0.52
15 4 0.10
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.48
Consensus pattern (14 bp):
TTTTTGAAAATCAT
Found at i:11841 original size:28 final size:28
Alignment explanation
Indices: 11806--11868 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
11796 ACTTAAAACC
*
11806 TTTTTGAAAACTCA-TTT-TTGAAAATCAT
1 TTTTTGAAAA-GCAGTTTCTTGAAAATC-T
11834 TTTTTG-AAAGCAGTTTCTTGAAAATCT
1 TTTTTGAAAAGCAGTTTCTTGAAAATCT
11861 TTTTTGAA
1 TTTTTGAA
11869 GAAATGTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 2 0.06
27 13 0.42
28 16 0.52
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.48
Consensus pattern (28 bp):
TTTTTGAAAAGCAGTTTCTTGAAAATCT
Found at i:11948 original size:13 final size:13
Alignment explanation
Indices: 11926--11969 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
11916 ATATTGCAAT
11926 TTTTTCTTTTGTTC
1 TTTTT-TTTTGTTC
11940 TTTTTTTTTGTTC
1 TTTTTTTTTGTTC
11953 --TTTTTTTGTTC
1 TTTTTTTTTGTTC
11964 TTTTTT
1 TTTTTT
11970 GCCATTTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.39
13 12 0.43
14 5 0.18
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (13 bp):
TTTTTTTTTGTTC
Found at i:11956 original size:11 final size:11
Alignment explanation
Indices: 11932--11969 Score: 58
Period size: 11 Copynumber: 3.3 Consensus size: 11
11922 CAATTTTTTC
11932 TTTTGTTCTTTTT
1 TTTTGTTC--TTT
11945 TTTTGTTCTTT
1 TTTTGTTCTTT
11956 TTTTGTTCTTT
1 TTTTGTTCTTT
11967 TTT
1 TTT
11970 GCCATTTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 17 0.68
13 8 0.32
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (11 bp):
TTTTGTTCTTT
Found at i:19877 original size:4 final size:4
Alignment explanation
Indices: 19868--19914 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
19858 GGAGCCAAAA
19868 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
19915 TATAAATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:20610 original size:15 final size:15
Alignment explanation
Indices: 20592--20620 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20582 AAACTTGAAA
20592 TTATTATGATTATTT
1 TTATTATGATTATTT
20607 TTATTATGATTATT
1 TTATTATGATTATT
20621 ATGAAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (15 bp):
TTATTATGATTATTT
Found at i:20636 original size:62 final size:62
Alignment explanation
Indices: 20534--20819 Score: 538
Period size: 62 Copynumber: 4.6 Consensus size: 62
20524 TTATATATTG
*
20534 TTATG-TTATTTTTATTATGATTATTATGAAGTAATTATTATGATTATCAAACTTGAAATTA
1 TTATGATTATTTTTATTATGATTATTATGAAGTTATTATTATGATTATCAAACTTGAAATTA
*
20595 TTATGATTATTTTTATTATGATTATTATGAAGTAATTATTATGATTATCAAACTTGAAATTA
1 TTATGATTATTTTTATTATGATTATTATGAAGTTATTATTATGATTATCAAACTTGAAATTA
20657 TTATGATTATTTTTATTATGATTATTATGAAGTTATTATTATGATTATCAAACTTGAAATTA
1 TTATGATTATTTTTATTATGATTATTATGAAGTTATTATTATGATTATCAAACTTGAAATTA
20719 TTATGATTATTTTTATTATGATTATTATGAAGTTATTATTATGATTATCAAACTTGAAATTA
1 TTATGATTATTTTTATTATGATTATTATGAAGTTATTATTATGATTATCAAACTTGAAATTA
*
20781 TTATGATTATTTTTATTATGATTATCATGAAGTTATTAT
1 TTATGATTATTTTTATTATGATTATTATGAAGTTATTAT
20820 ACGATATCTA
Statistics
Matches: 222, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
61 5 0.02
62 217 0.98
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (62 bp):
TTATGATTATTTTTATTATGATTATTATGAAGTTATTATTATGATTATCAAACTTGAAATTA
Found at i:20672 original size:15 final size:15
Alignment explanation
Indices: 20654--20682 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20644 AAACTTGAAA
20654 TTATTATGATTATTT
1 TTATTATGATTATTT
20669 TTATTATGATTATT
1 TTATTATGATTATT
20683 ATGAAGTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (15 bp):
TTATTATGATTATTT
Found at i:20734 original size:15 final size:15
Alignment explanation
Indices: 20716--20744 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20706 AAACTTGAAA
20716 TTATTATGATTATTT
1 TTATTATGATTATTT
20731 TTATTATGATTATT
1 TTATTATGATTATT
20745 ATGAAGTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (15 bp):
TTATTATGATTATTT
Found at i:20766 original size:9 final size:9
Alignment explanation
Indices: 20591--20748 Score: 58
Period size: 9 Copynumber: 18.1 Consensus size: 9
20581 CAAACTTGAA
20591 ATTATTATG
1 ATTATTATG
20600 ATTATT-T-
1 ATTATTATG
20607 -TTATTATG
1 ATTATTATG
20615 ATTATTATG
1 ATTATTATG
*
20624 A--AGTA--
1 ATTATTATG
20629 ATTATTATG
1 ATTATTATG
*
20638 ATTATCAAACTTG
1 ATTAT--TA--TG
20651 AAATTATTATG
1 --ATTATTATG
20662 ATTATT-T-
1 ATTATTATG
20669 -TTATTATG
1 ATTATTATG
20677 ATTATTATG
1 ATTATTATG
*
20686 AAGTTATTATT
1 -A-TTATTATG
* *
20697 ATGATTATC
1 ATTATTATG
* *
20706 A-AACTTGA-A
1 ATTA-TT-ATG
20715 ATTATTATG
1 ATTATTATG
20724 ATTATT-T-
1 ATTATTATG
20731 -TTATTATG
1 ATTATTATG
20739 ATTATTATG
1 ATTATTATG
20748 A
1 A
20749 AGTTATTATT
Statistics
Matches: 113, Mismatches: 11, Indels: 50
0.65 0.06 0.29
Matches are distributed among these distances:
5 1 0.01
6 15 0.13
7 9 0.08
8 5 0.04
9 61 0.54
10 4 0.04
11 10 0.09
13 3 0.03
15 5 0.04
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (9 bp):
ATTATTATG
Done.