Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008855.1 Corchorus capsularis cultivar CVL-1 contig08876, 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: 11633
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2685 original size:135 final size:135
Alignment explanation
Indices: 2443--2979 Score: 966
Period size: 135 Copynumber: 4.0 Consensus size: 135
2433 ATGCTTAAAG
*
2443 AACAAGAAGAAGAGCAAACATGACAGTGGCTCGTTTGTCATATCAAAGGTGCAAAAACAAAGTAG
1 AACAAGAAGAAGAGCAAACATGACAGTGGCTCATTTGTCATATCAAAGGTGCAAAAACAAAGTAG
* *
2508 GCCCTTGCTTAAACCCCCCGAGGATCTTGCAAAAGATGAGACACTTGGAAGGAAAGATGAGACAT
66 CCCCTTGCTTAAACCCCCCGAGGATCTTGCAAAAGATGAGACACTTGGAAGGAAAGATGAGACGT
2573 TGAAC
131 TGAAC
2578 AACAAGAAGAAGAGCAAACATGACAGTGGCTCATTTGTCATATCAAAGGTGCAAAAACAAAGTAG
1 AACAAGAAGAAGAGCAAACATGACAGTGGCTCATTTGTCATATCAAAGGTGCAAAAACAAAGTAG
* *
2643 CCCCTTGCTTAAACCCCCTGAGGATGTTGCAAAAGATGAGACACTTGGAAGGAAAGATGAGACGT
66 CCCCTTGCTTAAACCCCCCGAGGATCTTGCAAAAGATGAGACACTTGGAAGGAAAGATGAGACGT
2708 TGAAC
131 TGAAC
* * *
2713 AACAAGAAGAATAGTAAACATGACAGCGGCTCATTTGTCATATCAAAGGTGCAAAAACAAAGTAG
1 AACAAGAAGAAGAGCAAACATGACAGTGGCTCATTTGTCATATCAAAGGTGCAAAAACAAAGTAG
* *
2778 CCCCTTGCTTAAACCCCCTGAGGATCTTGCAGAAGATGAGACACTTGGAAGGAAAGATGAGACGT
66 CCCCTTGCTTAAACCCCCCGAGGATCTTGCAAAAGATGAGACACTTGGAAGGAAAGATGAGACGT
2843 TGAAC
131 TGAAC
*
2848 AACAACAAGAAGAGCAAACATGACAGTGGCTCATTTGTCATATCAAAGGTGCAAAAACAAAGTAG
1 AACAAGAAGAAGAGCAAACATGACAGTGGCTCATTTGTCATATCAAAGGTGCAAAAACAAAGTAG
*
2913 CCCATTGCTTAAACCCCCCGAGGATCTTGCAAAAGATGAGACACTTGGAAGGAAAGATGAGACGT
66 CCCCTTGCTTAAACCCCCCGAGGATCTTGCAAAAGATGAGACACTTGGAAGGAAAGATGAGACGT
2978 TG
131 TG
2980 GGAAGACCAG
Statistics
Matches: 385, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
135 385 1.00
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.18
Consensus pattern (135 bp):
AACAAGAAGAAGAGCAAACATGACAGTGGCTCATTTGTCATATCAAAGGTGCAAAAACAAAGTAG
CCCCTTGCTTAAACCCCCCGAGGATCTTGCAAAAGATGAGACACTTGGAAGGAAAGATGAGACGT
TGAAC
Found at i:6981 original size:7 final size:7
Alignment explanation
Indices: 6969--7019 Score: 81
Period size: 7 Copynumber: 7.7 Consensus size: 7
6959 AAACGTAATT
6969 TAAAAAA
1 TAAAAAA
6976 TAAAAAA
1 TAAAAAA
6983 TAAAAAA
1 TAAAAAA
6990 TAAAAAA
1 TAAAAAA
6997 T-AAAAA
1 TAAAAAA
7003 T-AAAAA
1 TAAAAAA
7009 T-AAAAA
1 TAAAAAA
7015 TAAAA
1 TAAAA
7020 GCACGTATAC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.42
7 25 0.58
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:6987 original size:6 final size:6
Alignment explanation
Indices: 6971--7019 Score: 71
Period size: 6 Copynumber: 7.7 Consensus size: 6
6961 ACGTAATTTA
6971 AAAAAT AAAAAAT AAAAAAT AAAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT -AAAAAT -AAAAAT -AAAAAT AAAAAT AAAAAT AAAAAT AAAA
7020 GCACGTATAC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 22 0.52
7 20 0.48
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:7584 original size:9 final size:9
Alignment explanation
Indices: 7570--7598 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
7560 CTTGAAGACA
7570 AGCATGAAG
1 AGCATGAAG
7579 AGCATGAAG
1 AGCATGAAG
7588 AGCATGAAG
1 AGCATGAAG
7597 AG
1 AG
7599 GATGTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.34, T:0.10
Consensus pattern (9 bp):
AGCATGAAG
Found at i:7784 original size:16 final size:16
Alignment explanation
Indices: 7726--7850 Score: 87
Period size: 16 Copynumber: 7.9 Consensus size: 16
7716 CATTCGGGAT
* *
7726 TTCGGGTTTAGGGTCA
1 TTCGGGTCTCGGGTCA
*
7742 -TCTGGGT-TCGGGTTA
1 TTC-GGGTCTCGGGTCA
* *
7757 TTCGGATTTCGGGTCA
1 TTCGGGTCTCGGGTCA
*
7773 TTCGGGTCTCGGATCA
1 TTCGGGTCTCGGGTCA
* * * *
7789 TACGGGTTTCAGGTAA
1 TTCGGGTCTCGGGTCA
* *
7805 TTCGGGTCCCAGGTCA
1 TTCGGGTCTCGGGTCA
*
7821 TACGGGT-TCCGGGTCA
1 TTCGGGTCT-CGGGTCA
7837 TTC-GGTCTCGGGTC
1 TTCGGGTCTCGGGTC
7851 TACCGAGTTT
Statistics
Matches: 84, Mismatches: 20, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
15 20 0.24
16 64 0.76
ACGTcount: A:0.12, C:0.21, G:0.34, T:0.33
Consensus pattern (16 bp):
TTCGGGTCTCGGGTCA
Found at i:7840 original size:32 final size:32
Alignment explanation
Indices: 7766--7841 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
7756 ATTCGGATTT
* *
7766 CGGGTCATTCGGGTCTCGGATCATACGGGTTT
1 CGGGTCATTCGGGTCCCGGATCATACGGGTTC
* *
7798 CAGGTAATTCGGGTCCCAGG-TCATACGGGTTC
1 CGGGTCATTCGGGTCCC-GGATCATACGGGTTC
7830 CGGGTCATTCGG
1 CGGGTCATTCGG
7842 TCTCGGGTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
32 35 0.95
33 2 0.05
ACGTcount: A:0.14, C:0.24, G:0.34, T:0.28
Consensus pattern (32 bp):
CGGGTCATTCGGGTCCCGGATCATACGGGTTC
Found at i:10682 original size:13 final size:13
Alignment explanation
Indices: 10637--10683 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
10627 ATCATTTTTA
10637 CTCTTTTCTTACT
1 CTCTTTTCTTACT
* *
10650 CT-TTTTACTAATT
1 CTCTTTT-CTTACT
10663 ACTCTTTTCTTACT
1 -CTCTTTTCTTACT
10677 CTCTTTT
1 CTCTTTT
10684 ATTTATTTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.62
Consensus pattern (13 bp):
CTCTTTTCTTACT
Found at i:10768 original size:21 final size:21
Alignment explanation
Indices: 10744--11214 Score: 217
Period size: 21 Copynumber: 22.1 Consensus size: 21
10734 ACTCTTTGAA
*
10744 TTACTGATCACCTTTTACTCT
1 TTACTGATTACCTTTTACTCT
*
10765 TTACTGATTACTATTTTACTC-
1 TTACTGATTAC-CTTTTACTCT
* * *
10786 TTACTAATTACCACTTTGCT-T
1 TTACTGATTACC-TTTTACTCT
*
10807 TTACTGATTACTGTTTTACTC-
1 TTACTGATTAC-CTTTTACTCT
**
10828 TTACTGATTACCTTTTACTGA
1 TTACTGATTACCTTTTACTCT
*
10849 TTACT-ATTTTACTCTTTACTGATTACCT
1 TTACTGA--TTAC-CTTT--T-ACT--CT
*
10877 TCTACTGATTACTATTTTACTC-
1 T-TACTGATTAC-CTTTTACTCT
* **
10899 TTACTGATTACCTTTTGCTGA
1 TTACTGATTACCTTTTACTCT
**
10920 TTACT-ATTTTA-CTCTTTACTGA
1 TTACTGA--TTACCT-TTTACTCT
* *
10942 TTAC--CTT--C--TTACTTT
1 TTACTGATTACCTTTTACTCT
* *
10957 TTATTGATTACTATTTTACTCT
1 TTACTGATTAC-CTTTTACTCT
*
10979 TTACTGATTACCATTTTACTTT
1 TTACTGATTACC-TTTTACTCT
* * * *
11001 TTAATGACTACC-ATTGCT-T
1 TTACTGATTACCTTTTACTCT
* *
11020 CTTACTGATTA-CTATTACTTTT
1 -TTACTGATTACCTTTTAC-TCT
*
11042 TTACTGATTACTGTTTTACTC-
1 TTACTGATTAC-CTTTTACTCT
*
11063 TTACTGATTACCTTTTTCTTCT
1 TTACTGATTACCTTTTAC-TCT
* * *
11085 TTACTAATTACTCTCTTAC-CC
1 TTACTGATTAC-CTTTTACTCT
* *
11106 TTACTGACTACCTTTTACTTT
1 TTACTGATTACCTTTTACTCT
* *
11127 TTACTTATTACTATTTTACTC-
1 TTACTGATTAC-CTTTTACTCT
*
11148 TTACTGATTACCTTATACTTCT
1 TTACTGATTACCTTTTAC-TCT
* *
11170 TTACTAATTACTCTCTTACTC-
1 TTACTGATTAC-CTTTTACTCT
11191 TTACTGATTACCTTTTACTTCT
1 TTACTGATTACCTTTTAC-TCT
11213 TT
1 TT
11215 TCCTTAATTA
Statistics
Matches: 342, Mismatches: 64, Indels: 87
0.69 0.13 0.18
Matches are distributed among these distances:
15 8 0.02
17 2 0.01
18 1 0.00
19 4 0.01
20 53 0.15
21 140 0.41
22 94 0.27
23 20 0.06
25 3 0.01
26 3 0.01
28 9 0.03
29 4 0.01
30 1 0.00
ACGTcount: A:0.21, C:0.22, G:0.05, T:0.52
Consensus pattern (21 bp):
TTACTGATTACCTTTTACTCT
Found at i:10811 original size:35 final size:35
Alignment explanation
Indices: 10758--10946 Score: 227
Period size: 35 Copynumber: 5.1 Consensus size: 35
10748 TGATCACCTT
* *
10758 TTACTCTTTACTGATTACTATTTTACTCTTACTAA
1 TTACCCTTTACTGATTACTATTTTACTCTTACTGA
*
10793 TTACCACTTTGCTTTTACTGATTACTGTTTTACTCTTACTGA
1 TTA-C-C----C-TTTACTGATTACTATTTTACTCTTACTGA
*
10835 TTACCTTTTACTGATTACTATTTTACTCTTTACTGA
1 TTACCCTTTACTGATTACTATTTTACTC-TTACTGA
10871 TTA-CCTTCTACTGATTACTATTTTACTCTTACTGA
1 TTACCCTT-TACTGATTACTATTTTACTCTTACTGA
* *
10906 TTACCTTTTGCTGATTACTATTTTACTCTTTACTGA
1 TTACCCTTTACTGATTACTATTTTACTC-TTACTGA
10942 TTACC
1 TTACC
10947 TTCTTACTTT
Statistics
Matches: 135, Mismatches: 8, Indels: 21
0.82 0.05 0.13
Matches are distributed among these distances:
35 56 0.41
36 46 0.34
40 1 0.01
41 2 0.01
42 30 0.22
ACGTcount: A:0.22, C:0.21, G:0.06, T:0.51
Consensus pattern (35 bp):
TTACCCTTTACTGATTACTATTTTACTCTTACTGA
Found at i:10875 original size:36 final size:36
Alignment explanation
Indices: 10804--10998 Score: 268
Period size: 35 Copynumber: 5.2 Consensus size: 36
10794 TACCACTTTG
*
10804 CTTTTACTGATTACTGTTTTACTC-TTACTGATTAC
1 CTTTTACTGATTACTATTTTACTCTTTACTGATTAC
10839 CTTTTACTGATTACTATTTTACTCTTTACTGATTAC
1 CTTTTACTGATTACTATTTTACTCTTTACTGATTAC
*
10875 CTTCTACTGATTACTATTTTACTC-TTACTGATTAC
1 CTTTTACTGATTACTATTTTACTCTTTACTGATTAC
*
10910 CTTTTGCTGATTACTATTTTACTCTTTACTGATTAC
1 CTTTTACTGATTACTATTTTACTCTTTACTGATTAC
10946 CTTCTTACTTTTTATTGATTACTATTTTACTCTTTACTGATTAC
1 CTT-TTAC-------TGATTACTATTTTACTCTTTACTGATTAC
10990 CATTTTACT
1 C-TTTTACT
10999 TTTTAATGAC
Statistics
Matches: 144, Mismatches: 5, Indels: 20
0.85 0.03 0.12
Matches are distributed among these distances:
35 56 0.39
36 48 0.33
37 4 0.03
44 34 0.24
45 2 0.01
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.53
Consensus pattern (36 bp):
CTTTTACTGATTACTATTTTACTCTTTACTGATTAC
Found at i:10898 original size:71 final size:72
Alignment explanation
Indices: 10807--10998 Score: 278
Period size: 71 Copynumber: 2.6 Consensus size: 72
10797 CACTTTGCTT
*
10807 TTACTGATTACTGTTTTACTCTTACTGATTACCTTTTACTGATTACTATTTTACTCTTTACTGAT
1 TTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTGATTACTATTTTACTCTTTACTGAT
10872 TACCTTC
66 TACCTTC
*
10879 -TACTGATTACTATTTTACTCTTACTGATTACCTTTTGCTGATTACTATTTTACTCTTTACTGAT
1 TTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTGATTACTATTTTACTCTTTACTGAT
10943 TACCTTC
66 TACCTTC
10950 TTACTTTTTATTGATTACTATTTTACTCTTTACTGATTACCATTTTACT
1 TTAC-------TGATTACTATTTTACTC-TTACTGATTACC-TTTTACT
10999 TTTTAATGAC
Statistics
Matches: 107, Mismatches: 3, Indels: 11
0.88 0.02 0.09
Matches are distributed among these distances:
71 69 0.64
72 3 0.03
79 17 0.16
80 12 0.11
81 6 0.06
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.53
Consensus pattern (72 bp):
TTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTGATTACTATTTTACTCTTTACTGAT
TACCTTC
Found at i:11053 original size:15 final size:14
Alignment explanation
Indices: 11028--11068 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
11018 TTCTTACTGA
*
11028 TTACTATTACTTTT
1 TTACTATTACTGTT
11042 TTACTGATTACTGTT
1 TTACT-ATTACTGTT
*
11057 TTACTCTTACTG
1 TTACTATTACTG
11069 ATTACCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.56
Consensus pattern (14 bp):
TTACTATTACTGTT
Found at i:11059 original size:85 final size:85
Alignment explanation
Indices: 10935--11210 Score: 308
Period size: 85 Copynumber: 3.2 Consensus size: 85
10925 ATTTTACTCT
* *
10935 TTACTGATTACCTTCTTACTTTTTATTGATTACTATTTTACTCTTTACTGATTACCATTTTACTT
1 TTACTGATTACC-TATTACTTTTTACTGATTACTATTTTACTC-TTACTGATTACC-TTTTACTT
* * *
11000 -TTTAATGACTAC-C-ATTGCTTC
63 CTTTAATAACTACTCTATTAC-CC
* *
11021 TTACTGATTA-CTATTACTTTTTTACTGATTACTGTTTTACTCTTACTGATTACCTTTTTCTTCT
1 TTACTGATTACCTATTAC-TTTTTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTTCT
* * *
11085 TTACTAATTACTCTCTTACCC
65 TTAATAACTACTCTATTACCC
* * * *
11106 TTACTGACTACCTTTTACTTTTTACTTATTACTATTTTACTCTTACTGATTACCTTATACTTCTT
1 TTACTGATTACCTATTACTTTTTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTTCTT
* * * *
11171 TACTAATTACTCTCTTACTC
66 TAATAACTACTCTATTACCC
*
11191 TTACTGATTACCTTTTACTT
1 TTACTGATTACCTATTACTT
11211 CTTTTCCTTA
Statistics
Matches: 167, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
83 7 0.04
84 26 0.16
85 115 0.69
86 19 0.11
ACGTcount: A:0.21, C:0.22, G:0.04, T:0.53
Consensus pattern (85 bp):
TTACTGATTACCTATTACTTTTTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTTCTT
TAATAACTACTCTATTACCC
Found at i:11096 original size:128 final size:127
Alignment explanation
Indices: 10911--11214 Score: 355
Period size: 128 Copynumber: 2.4 Consensus size: 127
10901 ACTGATTACC
* * * *
10911 TTTTGCTGATTACTATTTTACTCTTTACTGATTACCTTCTTACTT-TTTATTGATTACTATTTTA
1 TTTTACTGATTACTATTTTACTC-TTACTGATTACCTT-TTACTTCTTTACTAATTACTATCTTA
* *
10975 CTCTTTACTGATTACCATTTTACTTTTTAATGACTACCATTGCT-TCTTACTGATTA-C-TATTA
64 C-CCTTACTGACTACC-TTTTACTTTTTAATGACTACCATT-CTATCTTACTGATTACCTTA-TA
11037 CTT
125 CTT
* * *
11040 TTTTACTGATTACTGTTTTACTCTTACTGATTACCTTTTTCTTCTTTACTAATTACTCTCTTACC
1 TTTTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTTCTTTACTAATTACTATCTTACC
* * * * *
11105 CTTACTGACTACCTTTTACTTTTTACTTATTACTATTTTACTCTTACTGATTACCTTATACTT
66 CTTACTGACTACCTTTTACTTTTTAATGACTACCATTCTA-TCTTACTGATTACCTTATACTT
* * * *
11168 CTTTACTAATTACTCTCTTACTCTTACTGATTACCTTTTACTTCTTT
1 TTTTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTTCTTT
11215 TCCTTAATTA
Statistics
Matches: 151, Mismatches: 19, Indels: 11
0.83 0.10 0.06
Matches are distributed among these distances:
125 1 0.01
126 20 0.13
127 29 0.19
128 78 0.52
129 23 0.15
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (127 bp):
TTTTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTTCTTTACTAATTACTATCTTACC
CTTACTGACTACCTTTTACTTTTTAATGACTACCATTCTATCTTACTGATTACCTTATACTT
Found at i:11195 original size:106 final size:107
Alignment explanation
Indices: 10744--11202 Score: 312
Period size: 106 Copynumber: 4.3 Consensus size: 107
10734 ACTCTTTGAA
* * * * * * *
10744 TTACTGATCAC-CTTTTACTCTTTACTGATTACTATTTTACT-CTTACTAATTACCACTTTGCTT
1 TTACTGATTACTCTTTTACTCTTTACTGATTACCATCTTACTCCTTAATGACTACCA--TTACTT
* **
10807 -TTACTGATTACTGTTTTACTCTTACTGATTACCTTTTAC-TGA
64 CTTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTTCT
* * * * *
10849 TTACT-ATTTTACTCTTTACTGATTACCTTCTACTGATTACTATTTTACT-CTTACTGATTA-C-
1 TTACTGA--TTACTCTTT--T-ACT--CTT-TACTGATTACCATCTTACTCCTTAATGACTACCA
*
10910 ---CTT-TTGCTGATTACTATTTTACTCTTTACTGATTACCTTCTTACTT-T
58 TTACTTCTTACTGATTACTATTTTACTC-TTACTGATTACCTT-TTACTTCT
* * * ** *
10957 TTATTGATTACTATTTTACTCTTTACTGATTACCATTTTACTTTTTAATGACTACCATTGCTTCT
1 TTACTGATTACTCTTTTACTCTTTACTGATTACCATCTTACTCCTTAATGACTACCATTACTTCT
* *
11022 TACTGATTACTA--TTACTTTTTTACTGATTACTGTTTTAC-TC-
66 TACTGATTACTATTTTAC--TCTTACTGATTAC-CTTTTACTTCT
* * * *
11063 TTACTGATTAC-CTTTTTCTTCTTTACTAATTACTC-TCTTAC-CCTTACTGACTACCTTTTACT
1 TTACTGATTACTCTTTTAC-TCTTTACTGATTAC-CATCTTACTCCTTAATGACTACC-ATTACT
* * *
11125 TTTTACTTATTACTATTTTACTCTTACTGATTACCTTATACTTCT
63 TCTTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTTCT
* *
11170 TTACTAATTACTCTCTTACTC-TTACTGATTACC
1 TTACTGATTACTCTTTTACTCTTTACTGATTACC
11203 TTTTACTTCT
Statistics
Matches: 287, Mismatches: 35, Indels: 64
0.74 0.09 0.17
Matches are distributed among these distances:
101 18 0.06
102 11 0.04
103 1 0.00
104 3 0.01
105 28 0.10
106 99 0.34
107 57 0.20
108 32 0.11
109 3 0.01
110 2 0.01
112 4 0.01
113 29 0.10
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.51
Consensus pattern (107 bp):
TTACTGATTACTCTTTTACTCTTTACTGATTACCATCTTACTCCTTAATGACTACCATTACTTCT
TACTGATTACTATTTTACTCTTACTGATTACCTTTTACTTCT
Found at i:11214 original size:43 final size:42
Alignment explanation
Indices: 10906--11210 Score: 337
Period size: 43 Copynumber: 7.1 Consensus size: 42
10896 CTCTTACTGA
* *
10906 TTACCTTTTGCTGATTACTATTTTACTCTTTACTGATTACCTT
1 TTACTTTTTACTGATTACTATTTTACTC-TTACTGATTACCTT
*
10949 CTTACTTTTTATTGATTACTATTTTACTCTTTACTGATTACCATT
1 -TTACTTTTTACTGATTACTATTTTACTC-TTACTGATTACC-TT
* * * * *
10994 TTACTTTTTAATGACTACCA--TTGCTTCTTACTGATTA-CTA
1 TTACTTTTTACTGATTACTATTTTAC-TCTTACTGATTACCTT
*
11034 TTACTTTTTTACTGATTACTGTTTTACTCTTACTGATTACCTT
1 TTAC-TTTTTACTGATTACTATTTTACTCTTACTGATTACCTT
* * * * * *
11077 TTTCTTCTTTACTAATTACTCTCTTACCCTTACTGACTACCTT
1 TTACTT-TTTACTGATTACTATTTTACTCTTACTGATTACCTT
*
11120 TTACTTTTTACTTATTACTATTTTACTCTTACTGATTACCTT
1 TTACTTTTTACTGATTACTATTTTACTCTTACTGATTACCTT
* * * *
11162 ATACTTCTTTACTAATTACTCTCTTACTCTTACTGATTACCTT
1 TTACTT-TTTACTGATTACTATTTTACTCTTACTGATTACCTT
11205 TTACTT
1 TTACTT
11211 CTTTTCCTTA
Statistics
Matches: 222, Mismatches: 31, Indels: 17
0.82 0.11 0.06
Matches are distributed among these distances:
40 5 0.02
41 13 0.06
42 63 0.28
43 84 0.38
44 55 0.25
45 2 0.01
ACGTcount: A:0.21, C:0.22, G:0.05, T:0.53
Consensus pattern (42 bp):
TTACTTTTTACTGATTACTATTTTACTCTTACTGATTACCTT
Found at i:11369 original size:38 final size:38
Alignment explanation
Indices: 11312--11519 Score: 303
Period size: 38 Copynumber: 5.5 Consensus size: 38
11302 ATTACTATTT
* *
11312 TTACCTTGACTCTTAATTATCAATTTTAATGGTTACTA
1 TTACTTTGACTCTTAATTATCAATTTTACTGGTTACTA
*
11350 TTACTTTGACTCTTGATTATCAATTTTACTGGTTACTA
1 TTACTTTGACTCTTAATTATCAATTTTACTGGTTACTA
*
11388 TTACTTTGACTCTTAATTATCAATTTTACTGATTACTA
1 TTACTTTGACTCTTAATTATCAATTTTACTGGTTACTA
* *
11426 TTATTTTGACTCTTAATTATCAATTTTACTGATTACTA
1 TTACTTTGACTCTTAATTATCAATTTTACTGGTTACTA
* * *
11464 TTACTTTGACACTTAATTACTTAA-TTCACTGGTTACTA
1 TTACTTTGACTCTTAATTA-TCAATTTTACTGGTTACTA
11502 TTA-TCTTGACTCTTAATT
1 TTACT-TTGACTCTTAATT
11520 TATCGGGGTA
Statistics
Matches: 156, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
37 1 0.01
38 152 0.97
39 3 0.02
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.50
Consensus pattern (38 bp):
TTACTTTGACTCTTAATTATCAATTTTACTGGTTACTA
Found at i:11401 original size:76 final size:75
Alignment explanation
Indices: 11277--11519 Score: 303
Period size: 76 Copynumber: 3.2 Consensus size: 75
11267 GATTAATCTC
* * *
11277 TTGACTCTTAATTA-CTGA-TTTATTGATTACTATTTTTACCTTGACTCTTAATTATCAATTTTA
1 TTGACTCTTAATTATC-AATTTTACTGATTACTA---TTACTTTGACTCTTAATTATCAATTTTA
*
11340 ATGGTTACTATTACT
62 CTGGTTACTATTA-T
* * *
11355 TTGACTCTTGATTATCAATTTTACTGGTTACTATTACTTTGACTCTTAATTATCAATTTTACTGA
1 TTGACTCTTAATTATCAATTTTACTGATTACTATTACTTTGACTCTTAATTATCAATTTTACTGG
11420 TTACTATTATT
66 TTACTATTA-T
* * *
11431 TTGACTCTTAATTATCAATTTTACTGATTACTATTACTTTGACACTTAATTACTTAA-TTCACTG
1 TTGACTCTTAATTATCAATTTTACTGATTACTATTACTTTGACTCTTAATTA-TCAATTTTACTG
11495 GTTACTATTAT
65 GTTACTATTAT
11506 CTTGACTCTTAATT
1 -TTGACTCTTAATT
11520 TATCGGGGTA
Statistics
Matches: 147, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
75 1 0.01
76 116 0.79
77 3 0.02
78 14 0.10
79 13 0.09
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.50
Consensus pattern (75 bp):
TTGACTCTTAATTATCAATTTTACTGATTACTATTACTTTGACTCTTAATTATCAATTTTACTGG
TTACTATTAT
Found at i:11446 original size:114 final size:114
Alignment explanation
Indices: 11275--11519 Score: 327
Period size: 114 Copynumber: 2.1 Consensus size: 114
11265 CTGATTAATC
* * *
11275 TCTTGACTCTTAATTACTGATTTATTGATTACTATTTTTACCTTGACTCTTAATTATCAATTTTA
1 TCTTGACTCTTAATTACTAATTTACTGATTACTATTATT--CTTGACTCTTAATTATCAATTTTA
* * * *
11340 ATGGTTACTATTACTTTGACTCTTGATTA-TCAATTTTACTGGTTACTATTA
64 ATGATTACTATTACTTTGACACTTAATTACTCAA-TTCACTGGTTACTATTA
11391 -CTTTGACTCTTAATTA-TCAATTTTACTGATTACTATTATT-TTGACTCTTAATTATCAATTTT
1 TC-TTGACTCTTAATTACT-AA-TTTACTGATTACTATTATTCTTGACTCTTAATTATCAATTTT
* *
11453 ACTGATTACTATTACTTTGACACTTAATTACTTAATTCACTGGTTACTATTA
63 AATGATTACTATTACTTTGACACTTAATTACTCAATTCACTGGTTACTATTA
11505 TCTTGACTCTTAATT
1 TCTTGACTCTTAATT
11520 TATCGGGGTA
Statistics
Matches: 115, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
114 77 0.67
115 6 0.05
116 15 0.13
117 17 0.15
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.50
Consensus pattern (114 bp):
TCTTGACTCTTAATTACTAATTTACTGATTACTATTATTCTTGACTCTTAATTATCAATTTTAAT
GATTACTATTACTTTGACACTTAATTACTCAATTCACTGGTTACTATTA
Done.