Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013958.1 Corchorus olitorius cultivar O-4 contig13991, 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: 35299
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:8177 original size:19 final size:21
Alignment explanation
Indices: 8153--8193 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
8143 AGTTAGTAAC
8153 TAATTACT-ATTTT-CATAAT
1 TAATTACTAATTTTCCATAAT
*
8172 TAATTAGTAATTTTCCATAAT
1 TAATTACTAATTTTCCATAAT
8193 T
1 T
8194 GATTTGGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 5 0.26
21 7 0.37
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (21 bp):
TAATTACTAATTTTCCATAAT
Found at i:10807 original size:141 final size:136
Alignment explanation
Indices: 10666--11003 Score: 398
Period size: 141 Copynumber: 2.5 Consensus size: 136
10656 CATCAGTTCT
*
10666 TTTTTTCCCAAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCTTTTTACATTTAAGTTTAGTAT
1 TTTTTTCCCAAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCTTTTTACATTCAAGTTTAGTAT
** * * *
10731 TTTCTTTTTCCCAAAATAATACCCTTTCGGTCGAAGGG-TCGTTTCCGTCTTTTTGCATTTAAGT
66 TTT-GATTT--CAAAA-AATACCCTTTCGGTCAAAGGGTTCGTTT-CGTCTTTTTGCATTCAAAT
10795 TTAGTATTTTC
126 TTAGTATTTTC
* *
10806 TTTTTTCCAGAAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCTTTTTGCATTCAAGTTTAGTA
1 TTTTTTCC-CAAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCTTTTTACATTCAAGTTTAGTA
* * * *
10871 TTTTGATTTCTAGAAATACCCTTTCGGTCAAAGGGTTGGTTTTGTCTTTTTGCATTCAAATTTAG
65 TTTTGATTTCAAAAAATACCCTTTCGGTCAAAGGGTTCGTTTCGTCTTTTTGCATTCAAATTTAG
10936 TATTTTC
130 TATTTTC
* * * * * * *
10943 --GTCT-CCAGAGATACCCTTTCGGTCGAAGGGTCAGTTT-CATCTTTTTGCAATCAGGTTTAGT
1 TTTTTTCCCA-AAATACCCTTTCGGTCGAAGGGTCA-TTTCCGTCTTTTTACATTCAAGTTTAGT
11004 TTTACTTTCC
Statistics
Matches: 175, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
133 1 0.01
134 46 0.26
135 5 0.03
137 47 0.27
138 8 0.05
140 11 0.06
141 57 0.33
ACGTcount: A:0.20, C:0.19, G:0.17, T:0.44
Consensus pattern (136 bp):
TTTTTTCCCAAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCTTTTTACATTCAAGTTTAGTAT
TTTGATTTCAAAAAATACCCTTTCGGTCAAAGGGTTCGTTTCGTCTTTTTGCATTCAAATTTAGT
ATTTTC
Found at i:10923 original size:67 final size:68
Alignment explanation
Indices: 10668--11045 Score: 405
Period size: 67 Copynumber: 5.5 Consensus size: 68
10658 TCAGTTCTTT
* * *
10668 TTTTCCCA-AAATACCCTTTCGGTCGAAGGGTCATTTCCGTCTTTTTACATTTAAGTTTAGTATT
1 TTTT-CCAGAAATACCCTTTCGGTCGAAGGGTCGTTTCCGTCTTTTTGCATTCAAGTTTAGTATT
*
10732 TTCT
65 TTCG
* *
10736 TTTTCCCAAAATAATACCCTTTCGGTCGAAGGGTCGTTTCCGTCTTTTTGCATTTAAGTTTAGTA
1 TTTT-CC-AGA-AATACCCTTTCGGTCGAAGGGTCGTTTCCGTCTTTTTGCATTCAAGTTTAGTA
*
10801 TTTTCTT
63 TTTTC-G
*
10808 TTTTCCAGAAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCTTTTTGCATTCAAGTTTAGTATT
1 TTTTCCAG-AAATACCCTTTCGGTCGAAGGGTCGTTTCCGTCTTTTTGCATTCAAGTTTAGTATT
10873 TT-G
65 TTCG
* * * * * *
10876 ATTTCTAGAAATACCCTTTCGGTCAAAGGGTTGGTTT-TGTCTTTTTGCATTCAAATTTAGTATT
1 TTTTCCAGAAATACCCTTTCGGTCGAAGGG-TCGTTTCCGTCTTTTTGCATTCAAGTTTAGTATT
10940 TTCG
65 TTCG
* * * * *
10944 -TCTCCAGAGATACCCTTTCGGTCGAAGGGTCAGTTT-CATCTTTTTGCAATCAGGTTTAGT-TT
1 TTTTCCAGAAATACCCTTTCGGTCGAAGGGTC-GTTTCCGTCTTTTTGCATTCAAGTTTAGTATT
*
11006 TAC-
65 TTCG
* *
11009 -TTTCCA-AAAGTATCCTTCCGGTCGAAGGGTCAGTTTC
1 TTTTCCAGAAA-TACCCTTTCGGTCGAAGGGTC-GTTTC
11046 ATCAGGTTGT
Statistics
Matches: 272, Mismatches: 28, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
64 2 0.01
65 29 0.11
66 5 0.02
67 96 0.35
68 18 0.07
69 1 0.00
70 57 0.21
71 59 0.22
72 5 0.02
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.43
Consensus pattern (68 bp):
TTTTCCAGAAATACCCTTTCGGTCGAAGGGTCGTTTCCGTCTTTTTGCATTCAAGTTTAGTATTT
TCG
Found at i:11185 original size:66 final size:65
Alignment explanation
Indices: 11076--11231 Score: 165
Period size: 66 Copynumber: 2.4 Consensus size: 65
11066 TCTAGGCTTT
* * * **
11076 CTTTCCAAAGAATACCCTTTCGGTCAAAGGGTTAATTCGGTCA-TTCTTGCATTTGAGTTTACTT
1 CTTTCCAAA-AATACCCTTTCGGTCAAAAGGTCAATTCGGTCATTTC-CGCATTCCAGTTTA-TT
*
11140 TTGA
63 CT-A
* *
11144 -TTTCCAAAAATACCCTTTCGGTGAAAAGGTCAGTTTC-GTCATTTCCGCATTCCAGTTTATTCT
1 CTTTCCAAAAATACCCTTTCGGTCAAAAGGTCA-ATTCGGTCATTTCCGCATTCCAGTTTATTCT
11207 A
65 A
*
11208 CTTTCCAAAAATGCCCTTTCGGTC
1 CTTTCCAAAAATACCCTTTCGGTC
11232 GAAGGGCGAA
Statistics
Matches: 75, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
64 1 0.01
65 24 0.32
66 36 0.48
67 14 0.19
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (65 bp):
CTTTCCAAAAATACCCTTTCGGTCAAAAGGTCAATTCGGTCATTTCCGCATTCCAGTTTATTCTA
Found at i:18884 original size:18 final size:15
Alignment explanation
Indices: 18845--18898 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 15
18835 GTTTAATCAA
18845 TTTTTG-TTATAAAG
1 TTTTTGTTTATAAAG
18859 TTGTTTGTCTTGATAAAG
1 TT-TTTGT-TT-ATAAAG
18877 TTTATTGTTTATAACAG
1 TTT-TTGTTTATAA-AG
18894 TTTTT
1 TTTTT
18899 AGAAACTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 2 0.06
15 4 0.12
16 6 0.18
17 10 0.29
18 12 0.35
ACGTcount: A:0.24, C:0.04, G:0.15, T:0.57
Consensus pattern (15 bp):
TTTTTGTTTATAAAG
Found at i:28399 original size:15 final size:16
Alignment explanation
Indices: 28375--28414 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
28365 AGAGGTTGAA
*
28375 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
28390 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
28406 AGAAAACAA
1 AGAAAACAA
28415 AGCAAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:31566 original size:16 final size:16
Alignment explanation
Indices: 31545--31575 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
31535 AGGAATAGGC
31545 AATCAATCAAAGCAAT
1 AATCAATCAAAGCAAT
31561 AATCAATCAAAGCAA
1 AATCAATCAAAGCAA
31576 CAATGCAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.19, G:0.06, T:0.16
Consensus pattern (16 bp):
AATCAATCAAAGCAAT
Found at i:33709 original size:15 final size:16
Alignment explanation
Indices: 33685--33724 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
33675 AGAGGTTGAA
*
33685 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
33700 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
33716 AGAAAACAA
1 AGAAAACAA
33725 AGCAAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:34244 original size:19 final size:18
Alignment explanation
Indices: 34220--34255 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
34210 TGAAGAATTA
34220 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
34239 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
34256 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:35116 original size:14 final size:16
Alignment explanation
Indices: 35089--35122 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
35079 ATCTTTTTAA
35089 TTTTCCTTGCATTAT-
1 TTTTCCTTGCATTATG
35104 TTTTCCTTG-ATTATG
1 TTTTCCTTGCATTATG
35119 TTTT
1 TTTT
35123 AATTGCTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.12, C:0.15, G:0.09, T:0.65
Consensus pattern (16 bp):
TTTTCCTTGCATTATG
Done.