Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016556.1 Corchorus olitorius cultivar O-4 contig16589, 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: 48931
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4970 original size:23 final size:23
Alignment explanation
Indices: 4944--4992 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
4934 AGAATTTTAG
* *
4944 CTTTATAGAGT-TGATTGTTTAAA
1 CTTTATAGA-TATGACTATTTAAA
4967 CTTTATAGATATGACTATTTAAA
1 CTTTATAGATATGACTATTTAAA
4990 CTT
1 CTT
4993 AGAAAATTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (23 bp):
CTTTATAGATATGACTATTTAAA
Found at i:6879 original size:29 final size:31
Alignment explanation
Indices: 6832--6903 Score: 96
Period size: 29 Copynumber: 2.4 Consensus size: 31
6822 CCAATCTTGC
* *
6832 AAGTTGAGGGACTAGATTGATCATTTTT-T-T
1 AAGTAGAGGGACTAAATTGAT-ATTTTTGTGT
6862 -AGTAGAGGGACTAAATTGATATTTTTGTGT
1 AAGTAGAGGGACTAAATTGATATTTTTGTGT
6892 AAGTAGAGGGAC
1 AAGTAGAGGGAC
6904 GTCCTGTCGG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
28 6 0.16
29 19 0.51
30 1 0.03
31 11 0.30
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.36
Consensus pattern (31 bp):
AAGTAGAGGGACTAAATTGATATTTTTGTGT
Found at i:7230 original size:42 final size:44
Alignment explanation
Indices: 7179--7272 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 44
7169 AGTGCATTAC
* *
7179 CTAA-ATTCTACT-T-CATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAA
*
7220 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAGAATAAAA
1 CTAATATTCTACT-CTCCATCTCTAGATAATTCATCAAAATAAAA
7265 CTAATATT
1 CTAATATT
7273 AATTGTTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
44 1 0.02
45 33 0.72
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.35
Consensus pattern (44 bp):
CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:8250 original size:12 final size:12
Alignment explanation
Indices: 8233--8267 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
8223 AATCAGTAAG
*
8233 TATATACTATAA
1 TATATAATATAA
8245 TATATAATATAA
1 TATATAATATAA
8257 TATATAATATA
1 TATATAATATA
8268 TAGAATGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:14648 original size:14 final size:16
Alignment explanation
Indices: 14619--14653 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
14609 AACCCATTGT
14619 TCTTTCCTCTTCTCTC
1 TCTTTCCTCTTCTCTC
14635 TCTTT-CTC-TCTCTC
1 TCTTTCCTCTTCTCTC
14649 TCTTT
1 TCTTT
14654 TTTTTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.58
15 3 0.16
16 5 0.26
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (16 bp):
TCTTTCCTCTTCTCTC
Found at i:14837 original size:70 final size:70
Alignment explanation
Indices: 14707--14845 Score: 194
Period size: 70 Copynumber: 2.0 Consensus size: 70
14697 AAATAGACAA
* * * *
14707 GTCTTTACACATTCAAAATAACATAACAGAAACATATAAAAGTCTTTACACGAGTTCCTCTCAAA
1 GTCTTCACACATTCAAAATAACATAACAGAAACATAAAAAAGTCTATACACGAGTGCCTCTCAAA
14772 AGATG
66 AGATG
14777 GTCTTCACACATTCAAAATAACATAACAGAAACATACAAAACAGTAC-ATA-A-GAGTGCCTCTC
1 GTCTTCACACATTCAAAATAACATAACAGAAACATA-AAAA-AGT-CTATACACGAGTGCCTCTC
14839 AAAAGAT
63 AAAAGAT
14846 AATCTTTACA
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
70 52 0.84
71 4 0.06
72 5 0.08
73 1 0.02
ACGTcount: A:0.45, C:0.21, G:0.10, T:0.24
Consensus pattern (70 bp):
GTCTTCACACATTCAAAATAACATAACAGAAACATAAAAAAGTCTATACACGAGTGCCTCTCAAA
AGATG
Found at i:17044 original size:14 final size:14
Alignment explanation
Indices: 17025--17052 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17015 TGTTCTCATG
17025 TCGTCTGGTAAGGA
1 TCGTCTGGTAAGGA
17039 TCGTCTGGTAAGGA
1 TCGTCTGGTAAGGA
17053 ACAACAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.36, T:0.29
Consensus pattern (14 bp):
TCGTCTGGTAAGGA
Found at i:18337 original size:31 final size:30
Alignment explanation
Indices: 18296--18376 Score: 103
Period size: 28 Copynumber: 2.7 Consensus size: 30
18286 GCTAAATACC
*
18296 CAAAAAAATCCCTTATGTTTCACTTTCGGGA
1 CAAAATAATCCCTTATGTTTCA-TTTCGGGA
*
18327 CAAAATAATCCCTTATGTTT--TTTTGGGA
1 CAAAATAATCCCTTATGTTTCATTTCGGGA
* *
18355 CAAATTAATCCCTTACGTTTCA
1 CAAAATAATCCCTTATGTTTCA
18377 AAAGTGAGCC
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
28 25 0.57
31 19 0.43
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTCATTTCGGGA
Found at i:20222 original size:27 final size:28
Alignment explanation
Indices: 20166--20232 Score: 84
Period size: 30 Copynumber: 2.4 Consensus size: 28
20156 AGCTAGCTTT
*
20166 GAGAAAGATGATGAGCAAGATTTGGCAGAA
1 GAGAAAGATGATGAGCAAGATCT-G-AGAA
20196 GAGAAAGATGATGAGCAAGATCT-AGAA
1 GAGAAAGATGATGAGCAAGATCTGAGAA
20223 GA-AATAGATG
1 GAGAA-AGATG
20233 CTGCAGAAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
26 2 0.06
27 11 0.31
30 22 0.63
ACGTcount: A:0.46, C:0.06, G:0.31, T:0.16
Consensus pattern (28 bp):
GAGAAAGATGATGAGCAAGATCTGAGAA
Found at i:23855 original size:29 final size:31
Alignment explanation
Indices: 23813--23886 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 31
23803 CTCACTTTTG
* *
23813 AAACGTAAGGGATTAATTTGTCTC-AAA-AA
1 AAACATAAGGGATTAATTTGTCCCGAAAGAA
* **
23842 AAACATAAGGGATTATTTTGTCCCGAAAGTG
1 AAACATAAGGGATTAATTTGTCCCGAAAGAA
23873 AAACATAAGGGATT
1 AAACATAAGGGATT
23887 TTTTTGGGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 21 0.55
30 3 0.08
31 14 0.37
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (31 bp):
AAACATAAGGGATTAATTTGTCCCGAAAGAA
Found at i:26161 original size:17 final size:17
Alignment explanation
Indices: 26141--26191 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
26131 TGACTGAATG
26141 GAGAAGAAGACTATTTT
1 GAGAAGAAGACTATTTT
* *
26158 GAGAAGAAGACTGA-ATG
1 GAGAAGAAGACT-ATTTT
*
26175 GAGAAGAAAACTATTTT
1 GAGAAGAAGACTATTTT
26192 AAATAAGTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
16 1 0.04
17 25 0.93
18 1 0.04
ACGTcount: A:0.45, C:0.06, G:0.25, T:0.24
Consensus pattern (17 bp):
GAGAAGAAGACTATTTT
Found at i:29163 original size:56 final size:56
Alignment explanation
Indices: 29072--29206 Score: 261
Period size: 56 Copynumber: 2.4 Consensus size: 56
29062 AAACTCTAAA
29072 CTACAGCAAGCAGATGAGGCAAACAAGATAATTAATGAGCTTAAGCCTATCATTAG
1 CTACAGCAAGCAGATGAGGCAAACAAGATAATTAATGAGCTTAAGCCTATCATTAG
*
29128 CTACAGCAAGCAGATGAGGCAAACAAGATATTTAATGAGCTTAAGCCTATCATTAG
1 CTACAGCAAGCAGATGAGGCAAACAAGATAATTAATGAGCTTAAGCCTATCATTAG
29184 CTACAGCAAGCAGATGAGGCAAA
1 CTACAGCAAGCAGATGAGGCAAA
29207 AGCTTCTGGT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 78 1.00
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.20
Consensus pattern (56 bp):
CTACAGCAAGCAGATGAGGCAAACAAGATAATTAATGAGCTTAAGCCTATCATTAG
Found at i:30617 original size:20 final size:19
Alignment explanation
Indices: 30579--30618 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
30569 AATGATAGTG
*
30579 ATACTTTAGTTGAAAATTA
1 ATACTTTAGTTAAAAATTA
*
30598 ATACTTTATTTAAGAAATTA
1 ATACTTTAGTTAA-AAATTA
30618 A
1 A
30619 AGCCCTGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (19 bp):
ATACTTTAGTTAAAAATTA
Found at i:33160 original size:15 final size:15
Alignment explanation
Indices: 33140--33170 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33130 AGAAACGACA
33140 AGGGGGGGGGGGGGT
1 AGGGGGGGGGGGGGT
*
33155 AGGGGGGGGGTGGGT
1 AGGGGGGGGGGGGGT
33170 A
1 A
33171 AGGATTATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.00, G:0.81, T:0.10
Consensus pattern (15 bp):
AGGGGGGGGGGGGGT
Found at i:39344 original size:31 final size:31
Alignment explanation
Indices: 39309--39386 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
39299 TAAATTATAT
*
39309 TTTAGGCTCAAATTGAGCAAATTTTGAAAGG
1 TTTAGGCTCAAATTGAGCAAATTTTGAAAGA
*
39340 TTTAGGCTCAAATTGAGTAAATTTTGAAAGA
1 TTTAGGCTCAAATTGAGCAAATTTTGAAAGA
*
39371 TTTAGACTCAAATTGA
1 TTTAGGCTCAAATTGA
39387 TCAACTTGTC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (31 bp):
TTTAGGCTCAAATTGAGCAAATTTTGAAAGA
Found at i:39505 original size:29 final size:29
Alignment explanation
Indices: 39472--39530 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
39462 CAATGAATGC
*
39472 TTGAGAATATCATAAAATTACCATAGAAA
1 TTGAGAATACCATAAAATTACCATAGAAA
39501 TTGAGAATACCATAAAATTACCATAGAAA
1 TTGAGAATACCATAAAATTACCATAGAAA
39530 T
1 T
39531 GGTTATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (29 bp):
TTGAGAATACCATAAAATTACCATAGAAA
Found at i:40155 original size:30 final size:30
Alignment explanation
Indices: 40095--40159 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
40085 ATTCAAATTT
**
40095 TATTAGAAATATTTATTAATATGTAATAAA
1 TATTAGAAATATTTATTAATATACAATAAA
*
40125 TATTAG-AATATTTATTTAATATACAGTAAA
1 TATTAGAAATATTTA-TTAATATACAATAAA
40155 TATTA
1 TATTA
40160 TTAAAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 8 0.26
30 23 0.74
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.45
Consensus pattern (30 bp):
TATTAGAAATATTTATTAATATACAATAAA
Found at i:40162 original size:33 final size:30
Alignment explanation
Indices: 40081--40168 Score: 74
Period size: 30 Copynumber: 2.8 Consensus size: 30
40071 TTATTTCAAA
*
40081 TAATAT-TCAAATTTTATTAGAAATATTTAT
1 TAATATGT-AAATATTATTAGAAATATTTAT
*
40111 TAATATGT-AATAAATATTAG-AATATTTATT
1 TAATATGTAAAT-ATTATTAGAAATATTTA-T
*
40141 TAATATACAGTAAATATTATTAAAAATA
1 TAATAT---GTAAATATTATTAGAAATA
40169 ATATGTAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
29 11 0.24
30 19 0.41
31 1 0.02
33 8 0.17
34 7 0.15
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (30 bp):
TAATATGTAAATATTATTAGAAATATTTAT
Found at i:40198 original size:21 final size:20
Alignment explanation
Indices: 40156--40198 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
40146 TACAGTAAAT
*
40156 ATTATTAAAAATAATATGTA
1 ATTATTAAAAATAATATCTA
* *
40176 ATTATTAGAAATTAATTTCTA
1 ATTATTA-AAAATAATATCTA
40197 AT
1 AT
40199 GAAATATTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (20 bp):
ATTATTAAAAATAATATCTA
Found at i:40876 original size:6 final size:6
Alignment explanation
Indices: 40867--40900 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
40857 CTATTCCCCT
*
40867 TTTTCC TTTTCT TTCTTCC TTTTCC TTTTCC TTT
1 TTTTCC TTTTCC TT-TTCC TTTTCC TTTTCC TTT
40901 CTTTCTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTCC
Found at i:40887 original size:13 final size:13
Alignment explanation
Indices: 40865--40923 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
40855 TCCTATTCCC
40865 CTTT-TTCCTTTT
1 CTTTCTTCCTTTT
40877 CTTTCTTCCTTTT
1 CTTTCTTCCTTTT
*
40890 CCTT-TTCC-TTT
1 CTTTCTTCCTTTT
**
40901 CTTTCTTTTTTTT
1 CTTTCTTCCTTTT
40914 CTTTC-TCCTT
1 CTTTCTTCCTT
40924 GGGCCTGGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
11 6 0.16
12 13 0.34
13 19 0.50
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
CTTTCTTCCTTTT
Found at i:40889 original size:20 final size:21
Alignment explanation
Indices: 40864--40910 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
40854 TTCCTATTCC
40864 CCTTTTTCCTTTT-CTTTCTT
1 CCTTTTTCCTTTTCCTTTCTT
40884 CC-TTTTCCTTTTCCTTTCTT
1 CCTTTTTCCTTTTCCTTTCTT
*
40904 TCTTTTT
1 CCTTTTT
40911 TTTCTTTCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 10 0.42
20 10 0.42
21 4 0.17
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (21 bp):
CCTTTTTCCTTTTCCTTTCTT
Found at i:40913 original size:24 final size:23
Alignment explanation
Indices: 40867--40923 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 23
40857 CTATTCCCCT
40867 TTTTCCTTTTCTTTCTTCCTTTTCC
1 TTTTCC-TTTCTTTCTTCCTTTT-C
**
40892 TTTTCCTTTCTTTCTTTTTTTTC
1 TTTTCCTTTCTTTCTTCCTTTTC
40915 TTTCTCCTT
1 TTT-TCCTT
40924 GGGCCTGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 4 0.14
24 19 0.66
25 6 0.21
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTTCCTTTCTTTCTTCCTTTTC
Found at i:41802 original size:16 final size:16
Alignment explanation
Indices: 41781--41812 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41771 ACCACCTACC
41781 GTGTAAATTGATTCAT
1 GTGTAAATTGATTCAT
41797 GTGTAAATTGATTCAT
1 GTGTAAATTGATTCAT
41813 ACAGTGTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (16 bp):
GTGTAAATTGATTCAT
Found at i:46963 original size:13 final size:13
Alignment explanation
Indices: 46945--46969 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46935 TTTGCCAAAA
46945 AATAATTTTAAGC
1 AATAATTTTAAGC
46958 AATAATTTTAAG
1 AATAATTTTAAG
46970 GTGGTAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (13 bp):
AATAATTTTAAGC
Done.