Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012947.1 Corchorus olitorius cultivar O-4 contig12980, 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: 21455
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3654 original size:34 final size:34
Alignment explanation
Indices: 3611--3677 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
3601 TCCTCCTCTT
3611 CTTCTTGTTCCAGGCCGCCCCATACACACGTGAC
1 CTTCTTGTTCCAGGCCGCCCCATACACACGTGAC
* *
3645 CTTCTTGTTCTAGGCCGCCCCATACACATGTGA
1 CTTCTTGTTCCAGGCCGCCCCATACACACGTGA
3678 ATTTGATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.18, C:0.37, G:0.18, T:0.27
Consensus pattern (34 bp):
CTTCTTGTTCCAGGCCGCCCCATACACACGTGAC
Found at i:4955 original size:27 final size:26
Alignment explanation
Indices: 4920--4977 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
4910 ATTTTATTTC
4920 AAATATATTTCTAA-ATTGTCATTATT-
1 AAATATATTT-TAATATT-TCATTATTG
4946 AAATAATATTTTAATTATTTCATTATTG
1 AAAT-ATATTTTAA-TATTTCATTATTG
4974 AAAT
1 AAAT
4978 CATGGAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
26 7 0.25
27 14 0.50
28 7 0.25
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.50
Consensus pattern (26 bp):
AAATATATTTTAATATTTCATTATTG
Found at i:5650 original size:3 final size:3
Alignment explanation
Indices: 5637--5717 Score: 153
Period size: 3 Copynumber: 26.7 Consensus size: 3
5627 TAAAACTATG
5637 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5683 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5718 GGCCAATCCA
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 74 0.96
4 3 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:7136 original size:26 final size:26
Alignment explanation
Indices: 7117--7169 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
7107 TTTTATTTCT
7117 TGATTACTGATTACCATTTTTTACTC
1 TGATTACTGATTACCATTTTTTACTC
* *
7143 TGTTTACTTATTACCATTTTTTACTC
1 TGATTACTGATTACCATTTTTTACTC
7169 T
1 T
7170 ATCTAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.06, T:0.55
Consensus pattern (26 bp):
TGATTACTGATTACCATTTTTTACTC
Found at i:7184 original size:28 final size:26
Alignment explanation
Indices: 7126--7178 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
7116 TTGATTACTG
* * *
7126 ATTACCATTTTTTACTCTGTTTACTT
1 ATTACCATTTTTTACTCTATCTAATT
7152 ATTACCATTTTTTACTCTATCTAATT
1 ATTACCATTTTTTACTCTATCTAATT
7178 A
1 A
7179 AATTACTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.19, G:0.02, T:0.55
Consensus pattern (26 bp):
ATTACCATTTTTTACTCTATCTAATT
Found at i:7290 original size:34 final size:34
Alignment explanation
Indices: 7252--7361 Score: 87
Period size: 34 Copynumber: 3.1 Consensus size: 34
7242 TTTTTTTTAC
7252 TGATTTCATTTTCTACTCTTTTTAACTAAGTTAT
1 TGATTTCATTTTCTACTCTTTTTAACTAAGTTAT
* * * * * *** *
7286 TGATTACCCTTTTGTTTACTCTTCTCT-CCTTTTTTAC
1 TGATT--TCATTT-TCTACTCTT-TTTAACTAAGTTAT
*
7323 TGATTTCATTTTCTAATCTTTTTAACTAAGTTAT
1 TGATTTCATTTTCTACTCTTTTTAACTAAGTTAT
7357 TGATT
1 TGATT
7362 ACCCTTACTC
Statistics
Matches: 52, Mismatches: 19, Indels: 10
0.64 0.23 0.12
Matches are distributed among these distances:
33 2 0.04
34 22 0.42
35 4 0.08
36 4 0.08
37 18 0.35
38 2 0.04
ACGTcount: A:0.20, C:0.17, G:0.06, T:0.56
Consensus pattern (34 bp):
TGATTTCATTTTCTACTCTTTTTAACTAAGTTAT
Found at i:7319 original size:71 final size:71
Alignment explanation
Indices: 7226--7367 Score: 257
Period size: 71 Copynumber: 2.0 Consensus size: 71
7216 GTGATTACCA
** *
7226 TTGTTTACTCTTCTCTTTTTTTTTACTGATTTCATTTTCTACTCTTTTTAACTAAGTTATTGATT
1 TTGTTTACTCTTCTCTCCTTTTTTACTGATTTCATTTTCTAATCTTTTTAACTAAGTTATTGATT
7291 ACCCTT
66 ACCCTT
7297 TTGTTTACTCTTCTCTCCTTTTTTACTGATTTCATTTTCTAATCTTTTTAACTAAGTTATTGATT
1 TTGTTTACTCTTCTCTCCTTTTTTACTGATTTCATTTTCTAATCTTTTTAACTAAGTTATTGATT
7362 ACCCTT
66 ACCCTT
7368 ACTCTTTTTT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.18, C:0.19, G:0.06, T:0.58
Consensus pattern (71 bp):
TTGTTTACTCTTCTCTCCTTTTTTACTGATTTCATTTTCTAATCTTTTTAACTAAGTTATTGATT
ACCCTT
Found at i:7502 original size:34 final size:34
Alignment explanation
Indices: 7464--7552 Score: 133
Period size: 34 Copynumber: 2.6 Consensus size: 34
7454 TTGCCTGTTG
* **
7464 TACTTTAATTCCTGAATACCATTTTTACCTTTTT
1 TACTTTAATTACTGAATACCATTTTTACAATTTT
**
7498 TACTTTAATTACTGAATACCATTTTTTTAATTTT
1 TACTTTAATTACTGAATACCATTTTTACAATTTT
7532 TACTTTAATTACTGAATACCA
1 TACTTTAATTACTGAATACCA
7553 CTTCATTTTC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.29, C:0.17, G:0.03, T:0.51
Consensus pattern (34 bp):
TACTTTAATTACTGAATACCATTTTTACAATTTT
Found at i:7632 original size:21 final size:21
Alignment explanation
Indices: 7606--7670 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
7596 TTTTAATTAA
7606 TGATTATTATTACCATTTTAC
1 TGATTATTATTACCATTTTAC
7627 TGATTACTCT-TTA-C-TCTTTAC
1 TGATTA-T-TATTACCAT-TTTAC
* * *
7648 GGATTACTATGACCATTTTAC
1 TGATTATTATTACCATTTTAC
7669 TG
1 TG
7671 TTTACTGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
19 1 0.03
20 3 0.09
21 24 0.71
22 5 0.15
23 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.48
Consensus pattern (21 bp):
TGATTATTATTACCATTTTAC
Found at i:7663 original size:42 final size:42
Alignment explanation
Indices: 7607--7687 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
7597 TTTAATTAAT
* *
7607 GATTATTATTACCATTTTACTGATTACTCTTTACTCTTTACG
1 GATTACTATGACCATTTTACTGATTACTCTTTACTCTTTACG
* *
7649 GATTACTATGACCATTTTACTGTTTACTGTTTACTCTTT
1 GATTACTATGACCATTTTACTGATTACTCTTTACTCTTT
7688 TATTGATTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.22, C:0.19, G:0.09, T:0.51
Consensus pattern (42 bp):
GATTACTATGACCATTTTACTGATTACTCTTTACTCTTTACG
Found at i:7726 original size:7 final size:7
Alignment explanation
Indices: 7664--7804 Score: 51
Period size: 7 Copynumber: 20.3 Consensus size: 7
7654 CTATGACCAT
*
7664 TTTACTG
1 TTTACTC
*
7671 TTTACTG
1 TTTACTC
7678 TTTACTC
1 TTTACTC
* *
7685 TTTTATTG
1 -TTTACTC
*
7693 ATTACT-
1 TTTACTC
*
7699 TTTGCTC
1 TTTACTC
*
7706 TTT-CTT
1 TTTACTC
7712 TATTACTC
1 T-TTACTC
7720 TTTACTC
1 TTTACTC
*
7727 TTTACTA
1 TTTACTC
** *
7734 ACTA-TT
1 TTTACTC
7740 TTTACTC
1 TTTACTC
*
7747 TTTCCT-
1 TTTACTC
7753 TATTACTC
1 T-TTACTC
*
7761 ATTACTC
1 TTTACTC
*
7768 TTTACTG
1 TTTACTC
**
7775 ACTA-T-
1 TTTACTC
7780 TATTACTC
1 T-TTACTC
7788 TTTCACTC
1 TTT-ACTC
7796 TTTACTC
1 TTTACTC
7803 TT
1 TT
7805 ACCATTTACT
Statistics
Matches: 98, Mismatches: 25, Indels: 22
0.68 0.17 0.15
Matches are distributed among these distances:
6 14 0.14
7 68 0.69
8 16 0.16
ACGTcount: A:0.18, C:0.22, G:0.04, T:0.57
Consensus pattern (7 bp):
TTTACTC
Found at i:7745 original size:20 final size:20
Alignment explanation
Indices: 7721--7790 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
7711 TTATTACTCT
*
7721 TTACTCTTTACTAACTATTT
1 TTACTCTTTACTAACTATTA
* * * *
7741 TTACTCTTTCCTTATTACTCA
1 TTACTCTTTACTAACTA-TTA
*
7762 TTACTCTTTACTGACTATTA
1 TTACTCTTTACTAACTATTA
7782 TTACTCTTT
1 TTACTCTTT
7791 CACTCTTTAC
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 25 0.62
21 15 0.38
ACGTcount: A:0.21, C:0.23, G:0.01, T:0.54
Consensus pattern (20 bp):
TTACTCTTTACTAACTATTA
Found at i:7813 original size:41 final size:41
Alignment explanation
Indices: 7703--7816 Score: 144
Period size: 41 Copynumber: 2.8 Consensus size: 41
7693 ATTACTTTTG
* * * *
7703 CTCTTTCTTTATTACTCTTTACTCTTTACTAACTATTTTTA
1 CTCTTTCCTTATTACTCATTACTCTTTACTGACTATTATTA
7744 CTCTTTCCTTATTACTCATTACTCTTTACTGACTATTATTA
1 CTCTTTCCTTATTACTCATTACTCTTTACTGACTATTATTA
7785 CTCTTTCACTCT-TTACTC-TTAC-CATTTACTGA
1 CTCTTTC-CT-TATTACTCATTACTC-TTTACTGA
7817 TTGCTCTTTA
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
40 1 0.02
41 56 0.85
42 8 0.12
43 1 0.02
ACGTcount: A:0.20, C:0.25, G:0.02, T:0.53
Consensus pattern (41 bp):
CTCTTTCCTTATTACTCATTACTCTTTACTGACTATTATTA
Found at i:7831 original size:56 final size:56
Alignment explanation
Indices: 7740--7860 Score: 145
Period size: 56 Copynumber: 2.2 Consensus size: 56
7730 ACTAACTATT
* * *
7740 TTTACTCTTTCCTTATTACTCATTACTCTTTACTGACTATTATTACTCTTTCACTC
1 TTTACTCTTACCATATTACTCATTACTCTTTACTGACTACTATTACTCTTTCACTC
* * * * *
7796 TTTACTCTTACCAT-TTACTGATTGCTCTTTAACTGATTACTATTACTCTTTTACTG
1 TTTACTCTTACCATATTACTCATTACTCTTT-ACTGACTACTATTACTCTTTCACTC
*
7852 ATTACTCTT
1 TTTACTCTT
7861 TCATTCTGTA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
55 14 0.25
56 41 0.75
ACGTcount: A:0.21, C:0.24, G:0.04, T:0.51
Consensus pattern (56 bp):
TTTACTCTTACCATATTACTCATTACTCTTTACTGACTACTATTACTCTTTCACTC
Found at i:7845 original size:21 final size:20
Alignment explanation
Indices: 7622--8233 Score: 194
Period size: 21 Copynumber: 30.9 Consensus size: 20
7612 TTATTACCAT
*
7622 TTTACTGATTACTCTTTACTC
1 TTTACTGATTACT-ATTACTC
* *
7643 TTTACGGATTACTATGAC-C
1 TTTACTGATTACTATTACTC
* *
7662 ATTTTACTGTTTACTGTTTACTC
1 --TTTACTGATTACT-ATTACTC
* * *
7685 TTTTATTGATTACTTTTGCTC
1 -TTTACTGATTACTATTACTC
* *
7706 TTT-CTTTATTACTCTTTACTC
1 TTTAC-TGATTACT-ATTACTC
* * * *
7727 TTTACTAACTATTTTTACTC
1 TTTACTGATTACTATTACTC
* *
7747 TTTCCTTATTACTCATTACTC
1 TTTACTGATTACT-ATTACTC
* *
7768 TTTACTGACTATTATTACTC
1 TTTACTGATTACTATTACTC
*
7788 TTT-C--ACT-CT-TTACTC
1 TTTACTGATTACTATTACTC
* *
7803 -TTAC-CATTTACTGATTGCTC
1 TTTACTGA-TTACT-ATTACTC
7823 TTTAACTGATTACTATTACTC
1 TTT-ACTGATTACTATTACTC
*
7844 TTTTACTGATTACTCTT--TC
1 -TTTACTGATTACTATTACTC
*
7863 ATT-CTG--TACTGATTACTC
1 TTTACTGATTACT-ATTACTC
* *
7881 -TGA---ATTACCCTTTTACTC
1 TTTACTGATTA--CTATTACTC
* * *
7899 TATACTGACTATTATTACTC
1 TTTACTGATTACTATTACTC
*
7919 TTT--T-ACT-C-ATTACTC
1 TTTACTGATTACTATTACTC
*
7934 TTTTACTGATTACTCTTTACTC
1 -TTTACTGATTACT-ATTACTC
*
7956 TTTACTGGTTACTATTACTC
1 TTTACTGATTACTATTACTC
*
7976 TTT--T--CT-CT-TTACTC
1 TTTACTGATTACTATTACTC
* * *
7990 GTTACT-ATTACTCTTTTATTC
1 TTTACTGATTA--CTATTACTC
8011 TTTACTGATTACTATTAC-C
1 TTTACTGATTACTATTACTC
*
8030 ATTATGA-TGATTACTCTTTACTC
1 -TT-T-ACTGATTACT-ATTACTC
8053 TTTTACTGATTACTATTAC-C
1 -TTTACTGATTACTATTACTC
* *
8073 ATTT--T-ACT-CT-TTACTG
1 -TTTACTGATTACTATTACTC
* *
8089 ATTACT-ATTACCATTTTACTC
1 TTTACTGATTA-C-TATTACTC
8110 TTTACTGATTACTATTAC-C
1 TTTACTGATTACTATTACTC
*
8129 ATTTTACTGATTACTCTTTACTC
1 --TTTACTGATTACT-ATTACTC
*
8152 TTTTACTGAATACTATTAC-C
1 -TTTACTGATTACTATTACTC
*
8172 ATTTTACTGATTACTCTTAC-C
1 --TTTACTGATTACTATTACTC
* *
8193 AATT-CTTGATTACTCTTTACTC
1 -TTTAC-TGATTACT-ATTACTC
8215 TTTACTGATTACTATTACT
1 TTTACTGATTACTATTACT
8234 GAATTGCTAC
Statistics
Matches: 449, Mismatches: 74, Indels: 137
0.68 0.11 0.21
Matches are distributed among these distances:
14 10 0.02
15 26 0.06
16 11 0.02
17 19 0.04
18 16 0.04
19 13 0.03
20 98 0.22
21 174 0.39
22 76 0.17
23 6 0.01
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.51
Consensus pattern (20 bp):
TTTACTGATTACTATTACTC
Found at i:7857 original size:15 final size:14
Alignment explanation
Indices: 7832--7861 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
7822 CTTTAACTGA
7832 TTACTATTACTCTT
1 TTACTATTACTCTT
7846 TTACTGATTACTCTT
1 TTACT-ATTACTCTT
7861 T
1 T
7862 CATTCTGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.57
Consensus pattern (14 bp):
TTACTATTACTCTT
Found at i:7932 original size:15 final size:15
Alignment explanation
Indices: 7912--8007 Score: 96
Period size: 14 Copynumber: 6.8 Consensus size: 15
7902 ACTGACTATT
7912 ATTACTCTTTTACTC
1 ATTACTCTTTTACTC
*
7927 ATTACTCTTTTACTG
1 ATTACTCTTTTACTC
7942 ATTACTC-TTTACTC
1 ATTACTCTTTTACTC
* **
7956 TTTACT-GGTTACT-
1 ATTACTCTTTTACTC
7969 ATTACTCTTTT-CTC
1 ATTACTCTTTTACTC
* *
7983 TTTACTC-GTTACT-
1 ATTACTCTTTTACTC
7996 ATTACTCTTTTA
1 ATTACTCTTTTA
8008 TTCTTTACTG
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
13 15 0.23
14 29 0.45
15 21 0.32
ACGTcount: A:0.19, C:0.23, G:0.04, T:0.54
Consensus pattern (15 bp):
ATTACTCTTTTACTC
Found at i:7933 original size:7 final size:7
Alignment explanation
Indices: 7921--8233 Score: 73
Period size: 7 Copynumber: 44.7 Consensus size: 7
7911 TATTACTCTT
7921 TTACTCA
1 TTACTCA
*
7928 TTACTCTT
1 TTACTC-A
*
7936 TTACTGA
1 TTACTCA
*
7943 TTACTCT
1 TTACTCA
*
7950 TTACTCT
1 TTACTCA
**
7957 TTACTGG
1 TTACTCA
7964 TTACT-A
1 TTACTCA
*
7970 TTACTCT
1 TTACTCA
* *
7977 TTTCTCT
1 TTACTCA
*
7984 TTACTCG
1 TTACTCA
7991 TTACT-A
1 TTACTCA
*
7997 TTACTCTT
1 TTACTC-A
* *
8005 TTATTCT
1 TTACTCA
*
8012 TTACTGA
1 TTACTCA
8019 TTACT-A
1 TTACTCA
8025 TTAC-CA
1 TTACTCA
* *
8031 TTATGATGA
1 TTA--CTCA
*
8040 TTACTCT
1 TTACTCA
*
8047 TTACTCTT
1 TTACTC-A
*
8055 TTACTGA
1 TTACTCA
8062 TTACT-A
1 TTACTCA
8068 TTAC-CA
1 TTACTCA
*
8074 TTTTACTCT
1 --TTACTCA
*
8083 TTACTGA
1 TTACTCA
8090 TTACT-A
1 TTACTCA
8096 TTAC-CA
1 TTACTCA
*
8102 TTTTACTCT
1 --TTACTCA
*
8111 TTACTGA
1 TTACTCA
8118 TTACT-A
1 TTACTCA
8124 TTAC-CA
1 TTACTCA
*
8130 TTTTACTGA
1 --TTACTCA
*
8139 TTACTCT
1 TTACTCA
*
8146 TTACTCTT
1 TTACTC-A
*
8154 TTACTGA
1 TTACTCA
*
8161 ATACT-A
1 TTACTCA
8167 TTAC-CA
1 TTACTCA
*
8173 TTTTACTGA
1 --TTACTCA
8182 TTACTC-
1 TTACTCA
8188 TTAC-CAA
1 TTACTC-A
*
8195 TT-CTTGA
1 TTAC-TCA
*
8202 TTACTCT
1 TTACTCA
*
8209 TTACTCT
1 TTACTCA
*
8216 TTACTGA
1 TTACTCA
8223 TTACT-A
1 TTACTCA
8229 TTACT
1 TTACT
8234 GAATTGCTAC
Statistics
Matches: 230, Mismatches: 45, Indels: 63
0.68 0.13 0.19
Matches are distributed among these distances:
5 1 0.00
6 53 0.23
7 129 0.56
8 39 0.17
9 8 0.03
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (7 bp):
TTACTCA
Found at i:7983 original size:27 final size:28
Alignment explanation
Indices: 7846--8233 Score: 189
Period size: 28 Copynumber: 13.4 Consensus size: 28
7836 TATTACTCTT
* * *
7846 TTACTGATTACTCTTTCATTCTGTACTGA
1 TTACT-ATTACTCTTTTACTCTTTACTGA
* *
7875 TTACTCTGAATTACCCTTTTACTCTATACTGA
1 TTA--CT--ATTACTCTTTTACTCTTTACTGA
* * * **
7907 CTATTATTACTCTTTTACTCATTACTCTT
1 TTACTATTACTCTTTTACTCTTTACT-GA
*
7936 TTACTGATTACTC-TTTACTCTTTACTGG
1 TTACT-ATTACTCTTTTACTCTTTACTGA
7964 TTACTATTACTCTTTT-CTCTTTACTCG-
1 TTACTATTACTCTTTTACTCTTTACT-GA
*
7991 TTACTATTACTCTTTTATTCTTTACTGA
1 TTACTATTACTCTTTTACTCTTTACTGA
*
8019 TTACTATTACCATTATGATGATTACTCTTTACTCTTTTACTGA
1 TTACTATTA-C--TCT--T--TTACTC--T------TTACTGA
8062 TTACTATTAC-CATTTTACTCTTTACTGA
1 TTACTATTACTC-TTTTACTCTTTACTGA
8090 TTACTATTAC-CATTTTACTCTTTACTGA
1 TTACTATTACTC-TTTTACTCTTTACTGA
8118 TTACTATTAC-C----A-T-TTTACTGA
1 TTACTATTACTCTTTTACTCTTTACTGA
* ***
8139 TTACTCTTTACTCTTTTACTGAATACT-A
1 TTACT-ATTACTCTTTTACTCTTTACTGA
* ** **
8167 TTACCATTTTACT-GATTACTC-TTACCAA
1 TTA-C-TATTACTCTTTTACTCTTTACTGA
8195 TT-CTTGATTACTC-TTTACTCTTTACTGA
1 TTAC-T-ATTACTCTTTTACTCTTTACTGA
8223 TTACTATTACT
1 TTACTATTACT
8234 GAATTGCTAC
Statistics
Matches: 285, Mismatches: 34, Indels: 82
0.71 0.08 0.20
Matches are distributed among these distances:
21 13 0.05
22 5 0.02
23 2 0.01
26 2 0.01
27 54 0.19
28 111 0.39
29 31 0.11
30 9 0.03
31 4 0.01
32 21 0.07
33 1 0.00
34 1 0.00
35 5 0.02
36 6 0.02
37 1 0.00
38 1 0.00
40 1 0.00
42 1 0.00
43 16 0.06
ACGTcount: A:0.23, C:0.22, G:0.05, T:0.50
Consensus pattern (28 bp):
TTACTATTACTCTTTTACTCTTTACTGA
Found at i:8078 original size:71 final size:70
Alignment explanation
Indices: 7969--8232 Score: 216
Period size: 71 Copynumber: 3.9 Consensus size: 70
7959 ACTGGTTACT
* *
7969 ATTACTCTTTTCTCTTTACTCGTTACTATTACTCTTTTATTCTTTACTGATTACTATTACCATTA
1 ATTACTCTTTACTCTTTACTCGTTACTATTACTCTTTTACTCTTTACTGATTACTATTACCATTA
8034 TGATG
66 TGATG
8039 ATTACTCTTTACTCTTTTACT-GATTACTATTAC-CATTTTACTCTTTACTGATTACTATTACCA
1 ATTACTCTTTACTC-TTTACTCG-TTACTATTACTC-TTTTACTCTTTACTGATTACTATTACCA
* *
8102 TT-TTACTC
63 TTATGA-TG
* ** * * *
8110 TTTACTGATTACT-ATTAC-CATTTTACTGATTACTC-TTTACTCTTTTACTGAATACTATTACC
1 ATTACTCTTTACTCTTTACTC--GTTACT-ATTACTCTTTTACTC-TTTACTGATTACTATTACC
*
8172 ATT-TTACTG
62 ATTATGA-TG
* * *
8181 ATTACTC-TTAC-C--AATTC-TT--GATTACTC-TTTACTCTTTACTGATTACTATTAC
1 ATTACTCTTTACTCTTTACTCGTTACTATTACTCTTTTACTCTTTACTGATTACTATTAC
8233 TGAATTGCTA
Statistics
Matches: 165, Mismatches: 17, Indels: 32
0.77 0.08 0.15
Matches are distributed among these distances:
62 17 0.10
63 14 0.08
66 2 0.01
68 1 0.01
69 5 0.03
70 33 0.20
71 92 0.56
72 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.05, T:0.50
Consensus pattern (70 bp):
ATTACTCTTTACTCTTTACTCGTTACTATTACTCTTTTACTCTTTACTGATTACTATTACCATTA
TGATG
Found at i:8087 original size:43 final size:43
Alignment explanation
Indices: 7991--8189 Score: 197
Period size: 43 Copynumber: 4.3 Consensus size: 43
7981 TCTTTACTCG
*
7991 TTACT-ATTACTCTTTTATTC-TTTACTGATTACTATTACCATT
1 TTACTGATTACTC-TTTACTCTTTTACTGATTACTATTACCATT
*
8033 ATGA-TGATTACTCTTTACTCTTTTACTGATTACTATTACCATT
1 -TTACTGATTACTCTTTACTCTTTTACTGATTACTATTACCATT
**
8076 TTACTCTTTACTGATTACTATTACCATTTTACTCTTTACTGATTACTATTACCATT
1 TTACTGATTAC----T-CT-TTA-C----T-CT-TTTACTGATTACTATTACCATT
*
8132 TTACTGATTACTCTTTACTCTTTTACTGAATACTATTACCATT
1 TTACTGATTACTCTTTACTCTTTTACTGATTACTATTACCATT
8175 TTACTGATTACTCTT
1 TTACTGATTACTCTT
8190 ACCAATTCTT
Statistics
Matches: 132, Mismatches: 8, Indels: 32
0.77 0.05 0.19
Matches are distributed among these distances:
42 9 0.07
43 72 0.55
44 2 0.02
45 1 0.01
47 1 0.01
48 2 0.02
49 4 0.03
50 4 0.03
51 2 0.02
52 1 0.01
54 1 0.01
55 2 0.02
56 31 0.23
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.51
Consensus pattern (43 bp):
TTACTGATTACTCTTTACTCTTTTACTGATTACTATTACCATT
Found at i:8186 original size:99 final size:99
Alignment explanation
Indices: 7921--8232 Score: 381
Period size: 99 Copynumber: 3.1 Consensus size: 99
7911 TATTACTCTT
*
7921 TTACTCATTACTC-TTTTACTGATTACTCTTTACTC-TTTACTGGTTACTATTACTC-TTTT-CT
1 TTACT-ATTAC-CATTTTACTGATTACTCTTTACTCTTTTACTGATTACTATTAC-CATTTTACT
*
7982 CTTTACTCGTTACTATTACTCTTTTATTCTTTACTGA
63 CTTTACTCGTTACTATTACTCTTTTACTCTTTACTGA
*
8019 TTACTATTACCATTATGA-TGATTACTCTTTACTCTTTTACTGATTACTATTACCATTTTACTCT
1 TTACTATTACCATT-TTACTGATTACTCTTTACTCTTTTACTGATTACTATTACCATTTTACTCT
8083 TTACT-GATTACTATTAC-CATTTTACTCTTTACTGA
65 TTACTCG-TTACTATTACTC-TTTTACTCTTTACTGA
* **
8118 TTACTATTACCATTTTACTGATTACTCTTTACTCTTTTACTGAATACTATTACCATTTTACTGAT
1 TTACTATTACCATTTTACTGATTACTCTTTACTCTTTTACTGATTACTATTACCATTTTACTCTT
8183 TACTC-TTACCAATTCTTGATTACTC-TTTACTCTTTACTGA
66 TACTCGTT----A--C-T-ATTACTCTTTTACTCTTTACTGA
8223 TTACTATTAC
1 TTACTATTAC
8233 TGAATTGCTA
Statistics
Matches: 189, Mismatches: 7, Indels: 29
0.84 0.03 0.13
Matches are distributed among these distances:
96 1 0.01
97 24 0.13
98 34 0.18
99 96 0.51
102 1 0.01
104 1 0.01
105 26 0.14
106 5 0.03
107 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (99 bp):
TTACTATTACCATTTTACTGATTACTCTTTACTCTTTTACTGATTACTATTACCATTTTACTCTT
TACTCGTTACTATTACTCTTTTACTCTTTACTGA
Found at i:11117 original size:1 final size:1
Alignment explanation
Indices: 11111--11135 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
11101 ATAGGTGCTC
11111 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
11136 CTTTGTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:11917 original size:76 final size:76
Alignment explanation
Indices: 11827--11983 Score: 314
Period size: 76 Copynumber: 2.1 Consensus size: 76
11817 GAAGGGAAAA
11827 GGTAATCCAAAGCAACAAAGACCCAAACTGAAGATTAATAATTGATGTACTAAGTTAATGAAGCA
1 GGTAATCCAAAGCAACAAAGACCCAAACTGAAGATTAATAATTGATGTACTAAGTTAATGAAGCA
11892 AGATTTAACTT
66 AGATTTAACTT
11903 GGTAATCCAAAGCAACAAAGACCCAAACTGAAGATTAATAATTGATGTACTAAGTTAATGAAGCA
1 GGTAATCCAAAGCAACAAAGACCCAAACTGAAGATTAATAATTGATGTACTAAGTTAATGAAGCA
11968 AGATTTAACTT
66 AGATTTAACTT
11979 GGTAA
1 GGTAA
11984 AGTGATTGAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 81 1.00
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.25
Consensus pattern (76 bp):
GGTAATCCAAAGCAACAAAGACCCAAACTGAAGATTAATAATTGATGTACTAAGTTAATGAAGCA
AGATTTAACTT
Found at i:12138 original size:16 final size:16
Alignment explanation
Indices: 12119--12149 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12109 TTTTCCCATT
*
12119 TTCTTTCTTTTTTTTC
1 TTCTCTCTTTTTTTTC
12135 TTCTCTCTTTTTTTT
1 TTCTCTCTTTTTTTT
12150 TGCTTTTCGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTCTCTCTTTTTTTTC
Found at i:12363 original size:26 final size:24
Alignment explanation
Indices: 12327--12375 Score: 80
Period size: 26 Copynumber: 2.0 Consensus size: 24
12317 GGTGTCTACA
12327 TGGAGATAATGAACATTTACCTTATT
1 TGGAGATAATGAACA--TACCTTATT
12353 TGGAGATAATGAACATACCTTAT
1 TGGAGATAATGAACATACCTTAT
12376 ATATATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 8 0.35
26 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (24 bp):
TGGAGATAATGAACATACCTTATT
Found at i:13462 original size:22 final size:22
Alignment explanation
Indices: 13382--13531 Score: 130
Period size: 22 Copynumber: 6.9 Consensus size: 22
13372 TCTCTCAGGG
*
13382 AGGTTATCAAAA-ATCATAGGA
1 AGGTTATCAAAATTTCATAGGA
13403 AGGTTA-CAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGA
* **
13424 AGGTTTATTAAAATTTCATAGTT
1 AGG-TTATCAAAATTTCATAGGA
*
13447 AGGTTATCAAAGTTTCATATGG-
1 AGGTTATCAAAATTTCATA-GGA
* *
13469 AGTTTATCACAATTTCATAGGTA
1 AGGTTATCAAAATTTCATAGG-A
* * * *
13492 A-ATCATCAAAATTTAATATGGT
1 AGGTTATCAAAATTTCATA-GGA
13514 A-GTTATCAAAATTTCATA
1 AGGTTATCAAAATTTCATA
13532 AAAATATTCA
Statistics
Matches: 104, Mismatches: 18, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
20 5 0.05
21 19 0.18
22 61 0.59
23 19 0.18
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:13474 original size:44 final size:45
Alignment explanation
Indices: 13385--13531 Score: 151
Period size: 44 Copynumber: 3.4 Consensus size: 45
13375 CTCAGGGAGG
* *
13385 TTATCAAAA-ATCATAGGAAGGTTA-CAAAATTTCATA-GGAAGGT
1 TTATCAAAATTTCATAGGTAGGTTATCAAAATTTCATATGGAA-GT
* * *
13428 TTATTAAAATTTCATAGTTAGGTTATCAAAGTTTCATATGG-AGT
1 TTATCAAAATTTCATAGGTAGGTTATCAAAATTTCATATGGAAGT
* ** * * *
13472 TTATCACAATTTCATAGGTAAATCATCAAAATTTAATATGGTAG-
1 TTATCAAAATTTCATAGGTAGGTTATCAAAATTTCATATGGAAGT
13516 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
13532 AAAATATTCA
Statistics
Matches: 86, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
43 8 0.09
44 62 0.72
45 14 0.16
46 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.37
Consensus pattern (45 bp):
TTATCAAAATTTCATAGGTAGGTTATCAAAATTTCATATGGAAGT
Found at i:13710 original size:15 final size:15
Alignment explanation
Indices: 13692--13740 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
13682 ATTTTATTAT
13692 TAATTATTAAAATAA
1 TAATTATTAAAATAA
* * *
13707 TAA-TATTTTAATTAT
1 TAATTA-TTAAAATAA
13722 TAATTATTAAAATAA
1 TAATTATTAAAATAA
13737 TAAT
1 TAAT
13741 ATTTTAATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 2 0.08
15 22 0.85
16 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTATTAAAATAA
Found at i:13723 original size:30 final size:30
Alignment explanation
Indices: 13676--13765 Score: 155
Period size: 30 Copynumber: 3.0 Consensus size: 30
13666 GCCATTACCA
13676 AATAATATTTT-ATTATTAATTATTAAAAT
1 AATAATATTTTAATTATTAATTATTAAAAT
13705 AATAATATTTTAATTATTAATTATTAAAAT
1 AATAATATTTTAATTATTAATTATTAAAAT
*
13735 AATAATATTTTAATTATTTTATTATTAAAAT
1 AATAATATTTTAATTA-TTAATTATTAAAAT
13766 TATGGAAATT
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 11 0.19
30 34 0.59
31 13 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
AATAATATTTTAATTATTAATTATTAAAAT
Found at i:17719 original size:31 final size:30
Alignment explanation
Indices: 17673--17814 Score: 126
Period size: 31 Copynumber: 4.7 Consensus size: 30
17663 TAGAGGATAA
* * *
17673 GCAAGTAATTTAGGATATAACGTTTTC-TGCC
1 GCAAGCAATTAAGGATATAACGTTTTCAT--T
* **
17704 GCAAGCAATTAAGGATATAACG-TTACAAA
1 GCAAGCAATTAAGGATATAACGTTTTCATT
* *
17733 ACAAGCAATTAAGGATATAACGTTTTTTATT
1 GCAAGCAATTAAGGATATAACG-TTTTCATT
* * *
17764 TCAAGCAATTAGGGATATGACGTTTTCGATT
1 GCAAGCAATTAAGGATATAACGTTTTC-ATT
*
17795 TCAAGCAATTAAGGATATAA
1 GCAAGCAATTAAGGATATAA
17815 TCAGTTAGGG
Statistics
Matches: 91, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
29 21 0.23
30 7 0.08
31 63 0.69
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.32
Consensus pattern (30 bp):
GCAAGCAATTAAGGATATAACGTTTTCATT
Found at i:18008 original size:29 final size:31
Alignment explanation
Indices: 17946--18010 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
17936 TAACGGACTG
*
17946 TATCCTTAATTACTCGCTTTTCGTAACGTTA
1 TATCCTTAATTACTCGCTTTTCGTAACATTA
* *
17977 TATCCTTAATTGCTTG-TTTT-GTAACATTA
1 TATCCTTAATTACTCGCTTTTCGTAACATTA
18006 TATCC
1 TATCC
18011 CAAATTGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 13 0.42
30 4 0.13
31 14 0.45
ACGTcount: A:0.23, C:0.20, G:0.09, T:0.48
Consensus pattern (31 bp):
TATCCTTAATTACTCGCTTTTCGTAACATTA
Found at i:18267 original size:17 final size:17
Alignment explanation
Indices: 18245--18278 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
18235 ACATGTTCAC
18245 ATTTATTATT-TTATTAT
1 ATTTA-TATTATTATTAT
18262 ATTTATATTATTATTAT
1 ATTTATATTATTATTAT
18279 TTATAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTATATTATTATTAT
Found at i:18272 original size:14 final size:15
Alignment explanation
Indices: 18250--18283 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
18240 TTCACATTTA
*
18250 TTATTTTATTA-TAT
1 TTATATTATTATTAT
18264 TTATATTATTATTAT
1 TTATATTATTATTAT
18279 TTATA
1 TTATA
18284 AAATTATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATATTATTATTAT
Done.