Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009801.1 Corchorus capsularis cultivar CVL-1 contig09822, 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: 24434
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:212 original size:30 final size:31
Alignment explanation
Indices: 152--217 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
142 TTATTTGAGC
*
152 ATTTAGCCTTTTTCAAGAGTTAACGGGACTT
1 ATTTGGCCTTTTTCAAGAGTTAACGGGACTT
183 ATTTGGCCTTTTTCAAGAGTTAA-GGGACTT
1 ATTTGGCCTTTTTCAAGAGTTAACGGGACTT
213 ATTTG
1 ATTTG
218 ACCAAAATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 12 0.35
31 22 0.65
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (31 bp):
ATTTGGCCTTTTTCAAGAGTTAACGGGACTT
Found at i:948 original size:66 final size:66
Alignment explanation
Indices: 854--982 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
844 GCAAGTAAAC
854 ACTTGCTCTACAAAAGTCAGGCCTAGAAGACCCAACAGAGAAACAATACAA-AGGAAAGCAACAT
1 ACTTGCTCTACAAAAGTCAGGCCTAGAAGACCCAACAGAGAAACAATA-AAGAGGAAAGCAACAT
918 TT
65 TT
*
920 ACTTGCTCTACAAAAGTCAGGCCTAGAAGATCCAACAGAGAAACAATAAAGAGGAAAGCAACA
1 ACTTGCTCTACAAAAGTCAGGCCTAGAAGACCCAACAGAGAAACAATAAAGAGGAAAGCAACA
983 AAACAAACCA
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
65 2 0.03
66 59 0.97
ACGTcount: A:0.47, C:0.22, G:0.18, T:0.14
Consensus pattern (66 bp):
ACTTGCTCTACAAAAGTCAGGCCTAGAAGACCCAACAGAGAAACAATAAAGAGGAAAGCAACATT
T
Found at i:1873 original size:31 final size:31
Alignment explanation
Indices: 1838--1900 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
1828 GAATCCAATG
*
1838 ACTCCTGTCTTAACAAAACACTCCAATCTTC
1 ACTCCTATCTTAACAAAACACTCCAATCTTC
*
1869 ACTCCTATCTTAGCAAAACACTCCAATCTTC
1 ACTCCTATCTTAACAAAACACTCCAATCTTC
1900 A
1 A
1901 TAATCGACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (31 bp):
ACTCCTATCTTAACAAAACACTCCAATCTTC
Found at i:6013 original size:33 final size:33
Alignment explanation
Indices: 5952--6098 Score: 138
Period size: 33 Copynumber: 4.5 Consensus size: 33
5942 GGGCTTATTT
5952 AGCCGCCCCA-TGAGGGCGG-TTTGCCGTGG-TG
1 AGCCGCCCCAGTG-GGGCGGCTTTGCCGTGGTTG
5983 AAGCCGCCCCAGTGGGGCGGCTTTGCCGTGGTTG
1 -AGCCGCCCCAGTGGGGCGGCTTTGCCGTGGTTG
* * **
6017 AGCCTCCCCAGTGGGGAGGCTCCGCCGTGGTTG
1 AGCCGCCCCAGTGGGGCGGCTTTGCCGTGGTTG
* * ** ** *
6050 AGCCTCCCTAGTGGGAAGGCTCCGCCGTGGCTG
1 AGCCGCCCCAGTGGGGCGGCTTTGCCGTGGTTG
* *
6083 AGCCGTCCTAGTGGGG
1 AGCCGCCCCAGTGGGG
6099 AGACTAGTGT
Statistics
Matches: 102, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
32 16 0.16
33 84 0.82
34 2 0.02
ACGTcount: A:0.10, C:0.31, G:0.40, T:0.19
Consensus pattern (33 bp):
AGCCGCCCCAGTGGGGCGGCTTTGCCGTGGTTG
Found at i:15341 original size:43 final size:41
Alignment explanation
Indices: 15269--15566 Score: 211
Period size: 43 Copynumber: 6.8 Consensus size: 41
15259 CATCACTATT
* *
15269 TTACTGATTA-TTCTTTACTTTGTACTGATTACTATTTTACTC
1 TTACTGATTACCT-TTTACTTTTTACTGATTACT-TTTTACTC
** *
15311 TTGTTGATTACCTTCTTACTTTTTACTGATTACCATTTTACTC
1 TTACTGATTACCTT-TTACTTTTTACTGATTA-CTTTTTACTC
* * * *
15354 TTTCACTGATTACTATTTTCTGCTCCTTTTTTTACTGATTACTCTTTTATTTT
1 -TT-ACTGATTAC---CTT-T--TAC--TTTTTACTGATTACT-TTTTA-CTC
* *
15407 TTACTGATTGCCTTTTGCTTTTTACTGATTACCTTTTTACTTC
1 TTACTGATTACCTTTTACTTTTTACTGATTA-CTTTTTAC-TC
* * *
15450 TTGCTGATTAGCCTTTTACTCTTTACTGATCACCTTTTTACTC
1 TTACTGATTA-CCTTTTACTTTTTACTGATTA-CTTTTTACTC
* * *
15493 TTACTGATTTCCTTTTACTTCTTACTTATTACTTTTTTACTC
1 TTACTGATTACCTTTTACTTTTTACTGATTAC-TTTTTACTC
* * *
15535 TTACTGATTACTATTTTACCTTTAACTGATTA
1 TTACTGATTAC-CTTTTACTTTTTACTGATTA
15567 TCATTACTTT
Statistics
Matches: 203, Mismatches: 34, Indels: 37
0.74 0.12 0.14
Matches are distributed among these distances:
41 1 0.00
42 45 0.22
43 77 0.38
44 32 0.16
45 9 0.04
47 1 0.00
48 6 0.03
50 2 0.01
51 9 0.04
52 20 0.10
53 1 0.00
ACGTcount: A:0.18, C:0.20, G:0.07, T:0.55
Consensus pattern (41 bp):
TTACTGATTACCTTTTACTTTTTACTGATTACTTTTTACTC
Found at i:15342 original size:22 final size:21
Alignment explanation
Indices: 15267--15366 Score: 80
Period size: 21 Copynumber: 4.6 Consensus size: 21
15257 AGCATCACTA
*
15267 TTTTACTGATTA-TTCTTTACT
1 TTTTACTGATTACCT-TTTACT
* *
15288 TTGTACTGATTACTATTTTACT
1 TTTTACTGATTAC-CTTTTACT
*
15310 CTTGT--TGATTACCTTCTTACT
1 -TTTTACTGATTACCTT-TTACT
15331 TTTTACTGATTACCATTTTACT
1 TTTTACTGATTACC-TTTTACT
*
15353 CTTTCACTGATTAC
1 -TTTTACTGATTAC
15367 TATTTTCTGC
Statistics
Matches: 66, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
20 5 0.08
21 23 0.35
22 19 0.29
23 19 0.29
ACGTcount: A:0.20, C:0.19, G:0.07, T:0.54
Consensus pattern (21 bp):
TTTTACTGATTACCTTTTACT
Found at i:15421 original size:21 final size:21
Alignment explanation
Indices: 15382--15598 Score: 161
Period size: 22 Copynumber: 10.0 Consensus size: 21
15372 TCTGCTCCTT
*
15382 TTTTTACTGATTACTCTTTTAT
1 TTTTTACTGATTAC-CTTTTAC
* *
15404 TTTTTACTGATTGCCTTTTGC
1 TTTTTACTGATTACCTTTTAC
15425 TTTTTACTGATTACCTTTTTAC
1 TTTTTACTGATTACC-TTTTAC
* *
15447 TTCTTGCTGATTAGCCTTTTAC
1 TTTTTACTGATTA-CCTTTTAC
* *
15469 TCTTTACTGATCACCTTTTTAC
1 TTTTTACTGATTACC-TTTTAC
* *
15491 -TCTTACTGATTTCCTTTTAC
1 TTTTTACTGATTACCTTTTAC
* * *
15511 TTCTTACTTATTACTTTTTTAC
1 TTTTTACTGATTAC-CTTTTAC
* *
15533 -TCTTACTGATTACTATTTTAC
1 TTTTTACTGATTAC-CTTTTAC
* * * *
15554 CTTTAACTGATTATCATTACTT-T
1 TTTTTACTGATTA-CCTT--TTAC
*
15577 TTTTTATTGATTACCTTTTAC
1 TTTTTACTGATTACCTTTTAC
15598 T
1 T
15599 ATTTCATTCT
Statistics
Matches: 157, Mismatches: 28, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
20 8 0.05
21 62 0.39
22 72 0.46
23 13 0.08
24 2 0.01
ACGTcount: A:0.18, C:0.19, G:0.06, T:0.57
Consensus pattern (21 bp):
TTTTTACTGATTACCTTTTAC
Found at i:15457 original size:65 final size:64
Alignment explanation
Indices: 15385--15542 Score: 178
Period size: 65 Copynumber: 2.5 Consensus size: 64
15375 GCTCCTTTTT
* * ** * *
15385 TTACTGATTACTCTTTTATTTTTTACTGATTGCC-TTTTGCTTTTTACTGATTACCTTTTTACTT
1 TTACTGATTACTCTTTTACTCTTTACTGATCACCTTTTTAC-TCTTACTGATTACC-TTTTACTT
15449 C
64 C
* *
15450 TTGCTGATTAGC-CTTTTACTCTTTACTGATCACCTTTTTACTCTTACTGATTTCCTTTTACTTC
1 TTACTGATTA-CTCTTTTACTCTTTACTGATCACCTTTTTACTCTTACTGATTACCTTTTACTTC
* *
15514 TTACTTATTACTTTTTTACTC-TTACTGAT
1 TTACTGATTACTCTTTTACTCTTTACTGAT
15543 TACTATTTTA
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
63 9 0.11
64 25 0.32
65 39 0.49
66 6 0.08
ACGTcount: A:0.16, C:0.21, G:0.07, T:0.56
Consensus pattern (64 bp):
TTACTGATTACTCTTTTACTCTTTACTGATCACCTTTTTACTCTTACTGATTACCTTTTACTTC
Found at i:15647 original size:22 final size:21
Alignment explanation
Indices: 15606--15655 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
15596 ACTATTTCAT
* *
15606 TCTTTACTGATTATCTTTTTAC
1 TCTTTACTGATTACCCTTTT-C
*
15628 TTTTTACTGATTACCCTTTTC
1 TCTTTACTGATTACCCTTTTC
15649 TCTTTAC
1 TCTTTAC
15656 CATTCTCCCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.16, C:0.22, G:0.04, T:0.58
Consensus pattern (21 bp):
TCTTTACTGATTACCCTTTTC
Found at i:15704 original size:21 final size:21
Alignment explanation
Indices: 15679--15743 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
15669 CTGATTACTC
15679 TTTACTTTTTACCATTCTTCT
1 TTTACTTTTTACCATTCTTCT
**
15700 TTTACTGATTA-C-TT-TT-T
1 TTTACTTTTTACCATTCTTCT
15717 TTT-CTTTTTTACCATTCTTCT
1 TTTAC-TTTTTACCATTCTTCT
15738 TTTACT
1 TTTACT
15744 GATTACTCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
16 1 0.03
17 8 0.24
18 3 0.09
19 4 0.12
20 3 0.09
21 14 0.41
22 1 0.03
ACGTcount: A:0.14, C:0.20, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTACTTTTTACCATTCTTCT
Found at i:15731 original size:38 final size:36
Alignment explanation
Indices: 15629--15824 Score: 220
Period size: 35 Copynumber: 5.4 Consensus size: 36
15619 TCTTTTTACT
* * * *
15629 TTTTACTGATTACCCTTTTC-TCTTTACCATTCTCC
1 TTTTACTGATTACTCTTTACTTTTTTACCATTCTTC
* *
15664 CTTAACTGATTACTCTTTAC-TTTTTACCATTCTTC
1 TTTTACTGATTACTCTTTACTTTTTTACCATTCTTC
* *
15699 TTTTACTGATTACTTTTTTTTCTTTTTTACCATTCTTC
1 TTTTACTGATTAC--TCTTTACTTTTTTACCATTCTTC
15737 TTTTACTGATTACTCTTTACTTTTTTACCATTCTTC
1 TTTTACTGATTACTCTTTACTTTTTTACCATTCTTC
* *
15773 TTTTGCTGATTACTCTTTACTTCTTTT--CATTTTTAC
1 TTTTACTGATTACTCTTTACTT-TTTTACCATTCTT-C
*
15809 TCTTTACTAATTACTC
1 T-TTTACTGATTACTC
15825 CTGATTACTG
Statistics
Matches: 139, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
35 46 0.33
36 44 0.32
37 21 0.15
38 28 0.20
ACGTcount: A:0.16, C:0.23, G:0.03, T:0.57
Consensus pattern (36 bp):
TTTTACTGATTACTCTTTACTTTTTTACCATTCTTC
Found at i:15796 original size:23 final size:23
Alignment explanation
Indices: 15769--15816 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
15759 TTTTACCATT
15769 CTTCTTTTGC-TGATTACTCTTTA
1 CTTCTTTT-CATGATTACTCTTTA
**
15792 CTTCTTTTCATTTTTACTCTTTA
1 CTTCTTTTCATGATTACTCTTTA
15815 CT
1 CT
15817 AATTACTCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.12, C:0.23, G:0.04, T:0.60
Consensus pattern (23 bp):
CTTCTTTTCATGATTACTCTTTA
Found at i:15815 original size:73 final size:71
Alignment explanation
Indices: 15629--15824 Score: 202
Period size: 73 Copynumber: 2.7 Consensus size: 71
15619 TCTTTTTACT
** * * * *
15629 TTTTACTGATTACCCTT--TTCTCTTTACCATTCTCCCTTAACTGATTACTCTTTACTTTTTACC
1 TTTTACTGATTACTTTTACTTCTTTTTA-CATTCTTCTTTTACTGATTACTCTTTACTTTTTACC
15692 ATTCTTC
65 ATTCTTC
**
15699 TTTTACTGATTACTTTTTTTTCTTTTTTACCATTCTTCTTTTACTGATTACTCTTTACTTTTTTA
1 TTTTACTGATTACTTTTACTTC-TTTTTA-CATTCTTCTTTTACTGATTACTCTTTAC-TTTTTA
15764 CCATTCTTC
63 CCATTCTTC
* * *
15773 TTTTGCTGATTACTCTTTACTTC-TTTT-CATTTTTACTCTTTACTAATTACTC
1 TTTTACTGATTACT-TTTACTTCTTTTTACATTCTT-CT-TTTACTGATTACTC
15825 CTGATTACTG
Statistics
Matches: 108, Mismatches: 11, Indels: 11
0.83 0.08 0.08
Matches are distributed among these distances:
70 15 0.14
71 6 0.06
72 5 0.05
73 48 0.44
74 28 0.26
75 6 0.06
ACGTcount: A:0.16, C:0.23, G:0.03, T:0.57
Consensus pattern (71 bp):
TTTTACTGATTACTTTTACTTCTTTTTACATTCTTCTTTTACTGATTACTCTTTACTTTTTACCA
TTCTTC
Found at i:15889 original size:55 final size:55
Alignment explanation
Indices: 15828--16174 Score: 555
Period size: 55 Copynumber: 6.4 Consensus size: 55
15818 ATTACTCCTG
*
15828 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTTTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
* *
15883 ACTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTGTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
* *
15938 ATTACTGATTTACTGATTACTATTACCTTGACTATGATTAATCTGTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
*
15993 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCACTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
16048 ATTACTGATTTACT-ATTAC----A--TTGACTCTGATTAATCTCTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
* * *
16096 ATTACTGATTTACTGATTACTATTATCTTAACTCTGATTAACCTCTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
*
16151 ATTACTGACTTACTGATTACTATT
1 ATTACTGATTTACTGATTACTATT
16175 CTGACTGATC
Statistics
Matches: 274, Mismatches: 11, Indels: 14
0.92 0.04 0.05
Matches are distributed among these distances:
48 41 0.15
49 5 0.02
50 1 0.00
53 1 0.00
54 5 0.02
55 221 0.81
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.49
Consensus pattern (55 bp):
ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
Found at i:16072 original size:48 final size:49
Alignment explanation
Indices: 16002--16170 Score: 218
Period size: 48 Copynumber: 3.4 Consensus size: 49
15992 AATTACTGAT
* *
16002 TTACTGA-TTACT-ATTACCTTGACTCTGATTAATCACTTTTTACTTAA
1 TTACTGATTTACTGATTACATTGACTCTGATTAATCTCTTTTTACTTAA
16049 TTACTGATTTACT-ATTACATTGACTCTGATTAATCTCTTTTTACTTAA
1 TTACTGATTTACTGATTACATTGACTCTGATTAATCTCTTTTTACTTAA
* *
16097 TTACTGATTTACTGATTACTATTATCTTAACTCTGATTAACCTCTTTTTACTTAA
1 TTACTGATTTACTGATTAC----A--TTGACTCTGATTAATCTCTTTTTACTTAA
*
16152 TTACTGACTTACTGATTAC
1 TTACTGATTTACTGATTAC
16171 TATTCTGACT
Statistics
Matches: 109, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
47 7 0.06
48 51 0.47
49 5 0.05
53 1 0.01
55 45 0.41
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (49 bp):
TTACTGATTTACTGATTACATTGACTCTGATTAATCTCTTTTTACTTAA
Found at i:16094 original size:103 final size:102
Alignment explanation
Indices: 15947--16170 Score: 358
Period size: 103 Copynumber: 2.2 Consensus size: 102
15937 AATTACTGAT
* *
15947 TTACTGATTACTATTACCTTGACTATGATTAATCTGTTTTTACTTAATTACTGATTTACTGATTA
1 TTACTGATTACTATTACATTGACTATGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTA
* *
16012 CTATTACCTTGACTCTGATTAATCACTTTTTACTTAA
66 CTATTACCTTAACTCTGATTAACCACTTTTTACTTAA
*
16049 TTACTGATTTACTATTACATTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATT
1 TTACTGA-TTACTATTACATTGACTATGATTAATCTCTTTTTACTTAATTACTGATTTACTGATT
* *
16114 ACTATTATCTTAACTCTGATTAACCTCTTTTTACTTAA
65 ACTATTACCTTAACTCTGATTAACCACTTTTTACTTAA
16152 TTACTGACTTACTGATTAC
1 TTACTGA-TTACT-ATTAC
16171 TATTCTGACT
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
102 7 0.06
103 100 0.89
104 5 0.04
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.48
Consensus pattern (102 bp):
TTACTGATTACTATTACATTGACTATGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTA
CTATTACCTTAACTCTGATTAACCACTTTTTACTTAA
Found at i:16119 original size:158 final size:161
Alignment explanation
Indices: 15828--16174 Score: 547
Period size: 158 Copynumber: 2.1 Consensus size: 161
15818 ATTACTCCTG
**
15828 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTTTTTTTACTTAACTACTGATT
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCACTTTTTACTTAACTACTGATT
*
15893 TACTGATTACTATTACCTTGACTCTGATTAATCTGTTTTTACTTAATTACTGATTTACTGATTAC
66 TACTGATTAC---TA-CTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTAC
* * *
15958 TATTACCTTGACTATGATTAATCTGTTTTTACTTA
127 TATTACCTTAACTATGATTAACCTCTTTTTACTTA
*
15993 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCACTTTTTACTTAATTACTGATT
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCACTTTTTACTTAACTACTGATT
16058 TACT-ATTAC-A-TTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATT
66 TACTGATTACTACTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATT
* *
16120 ATCTTAACTCTGATTAACCTCTTTTTACTTA
131 ACCTTAACTATGATTAACCTCTTTTTACTTA
*
16151 ATTACTGACTTACTGATTACTATT
1 ATTACTGATTTACTGATTACTATT
16175 CTGACTGATC
Statistics
Matches: 172, Mismatches: 10, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
158 100 0.58
160 1 0.01
164 5 0.03
165 66 0.38
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.49
Consensus pattern (161 bp):
ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCACTTTTTACTTAACTACTGATT
TACTGATTACTACTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATT
ACCTTAACTATGATTAACCTCTTTTTACTTA
Found at i:18265 original size:1 final size:1
Alignment explanation
Indices: 18259--18294 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
18249 ATGTGTACTG
**
18259 TTTTTTTTTTTAATTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
18295 GTAACTTCTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.06, C:0.00, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:21003 original size:26 final size:27
Alignment explanation
Indices: 20973--21043 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 27
20963 CTAAATATGC
20973 AAATGACCAAAATACCCT-T-A-GTGCA
1 AAATGACCAAAATACCCTATGATGTG-A
*
20998 AGAATGACCAAAATGCCCCTATGATGTGA
1 A-AATGACCAAAAT-ACCCTATGATGTGA
21027 AAATGACCAAAATACCC
1 AAATGACCAAAATACCC
21044 CTGGATGACC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
25 1 0.03
26 12 0.31
27 7 0.18
28 13 0.33
29 3 0.08
30 3 0.08
ACGTcount: A:0.44, C:0.24, G:0.14, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATACCCTATGATGTGA
Found at i:21807 original size:13 final size:15
Alignment explanation
Indices: 21744--21809 Score: 59
Period size: 15 Copynumber: 4.4 Consensus size: 15
21734 ATATATCATG
21744 TTTATTAGTTAGAAT
1 TTTATTAGTTAGAAT
*
21759 TTTGATGTTGTATAG--T
1 TTT-AT-TAGT-TAGAAT
21775 GTTTATTAGTTAGAAT
1 -TTTATTAGTTAGAAT
21791 TTTATT-GTTAG-AT
1 TTTATTAGTTAGAAT
21804 TTTATT
1 TTTATT
21810 TTTTGCTGGG
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
13 8 0.19
14 8 0.19
15 12 0.28
16 6 0.14
17 6 0.14
18 3 0.07
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.58
Consensus pattern (15 bp):
TTTATTAGTTAGAAT
Found at i:24190 original size:9 final size:8
Alignment explanation
Indices: 24163--24228 Score: 55
Period size: 8 Copynumber: 7.9 Consensus size: 8
24153 ATACTTATGT
24163 GTGA-TTA
1 GTGATTTA
*
24170 GTGATATA
1 GTGATTTA
24178 GTGATTTTA
1 GTGA-TTTA
24187 GTGATTTA
1 GTGATTTA
*
24195 GTGACTTATT
1 GTGA-TT-TA
24205 GTCTGA-TTA
1 G--TGATTTA
24214 GTGATTTA
1 GTGATTTA
24222 GTGATTT
1 GTGATTT
24229 TATTTAATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
7 7 0.15
8 24 0.50
9 11 0.23
10 3 0.06
12 3 0.06
ACGTcount: A:0.24, C:0.03, G:0.24, T:0.48
Consensus pattern (8 bp):
GTGATTTA
Found at i:24242 original size:2 final size:2
Alignment explanation
Indices: 24235--24268 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
24225 ATTTTATTTA
24235 AT AT 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
24269 GAATATTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24391 original size:32 final size:32
Alignment explanation
Indices: 24346--24406 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
24336 GACGGGGAAT
* *
24346 GGAAAACAATCCCCATCCCCGTCCCCGTTCCC
1 GGAAAACAATCCCCATACCCGCCCCCGTTCCC
* *
24378 GGAAAATACTCCCCATACCCGCCCCCGTT
1 GGAAAACAATCCCCATACCCGCCCCCGTT
24407 GGGGCGGGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.23, C:0.48, G:0.13, T:0.16
Consensus pattern (32 bp):
GGAAAACAATCCCCATACCCGCCCCCGTTCCC
Done.