Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021255.1 Corchorus olitorius cultivar O-4 contig21288, 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: 5889
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Found at i:2840 original size:41 final size:41
Alignment explanation
Indices: 2733--3003 Score: 224
Period size: 41 Copynumber: 6.4 Consensus size: 41
2723 TCTCTCTCCC
* * * * ** *
2733 CAAAGTTCCCAAGCACATATATAACACAGGGGCAACTCCCTTT
1 CAAAGTCCCCAAACACATTTATAACACAGAGGC-A-TCTATAT
*
2776 CTAAAGTCCTCAAGA-ACATTTATAACACAGAGGCATCTATAT
1 C-AAAGTCCCCAA-ACACATTTATAACACAGAGGCATCTATAT
* *
2818 CAAAGTCCCCAAACACAATTATAACACAG-GGTCAATCCT-TCCT
1 CAAAGTCCCCAAACACATTTATAACACAGAGG-C-AT-CTAT-AT
* * *
2861 AAAAGTCCTCAAACACATTTATAACACAGAGGCATCCATAT
1 CAAAGTCCCCAAACACATTTATAACACAGAGGCATCTATAT
* * * * *
2902 CAAAGTCCCCAAGCACAATTATAACACAGTGGCATCACTCTCT
1 CAAAGTCCCCAAACACATTTATAACACAGAGGCAT--CTATAT
* * *
2945 CAAAGTCCTCAAGCACATTTATAACATAGAGGCATCTATAT
1 CAAAGTCCCCAAACACATTTATAACACAGAGGCATCTATAT
* *
2986 CTAAGTCCCTAAACACAT
1 CAAAGTCCCCAAACACAT
3004 GTAACACAAG
Statistics
Matches: 183, Mismatches: 34, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
40 3 0.02
41 75 0.41
42 11 0.06
43 66 0.36
44 28 0.15
ACGTcount: A:0.38, C:0.28, G:0.11, T:0.23
Consensus pattern (41 bp):
CAAAGTCCCCAAACACATTTATAACACAGAGGCATCTATAT
Found at i:2874 original size:43 final size:41
Alignment explanation
Indices: 2733--2980 Score: 218
Period size: 43 Copynumber: 5.9 Consensus size: 41
2723 TCTCTCTCCC
* * *
2733 CAAAGTTCC-CAAGCACATATATAACACAGGGGCAACTCCCTT-T
1 CAAAG-TCCTCAAACACATTTATAACACAGAGGC-A-T-CCTTCT
*
2776 CTAAAGTCCTCAAGA-ACATTTATAACACAGAGGCAT-CTATAT
1 C-AAAGTCCTCAA-ACACATTTATAACACAGAGGCATCCT-TCT
* *
2818 CAAAGTCCCCAAACACAATTATAACACAG-GGTCAATCCTTCCT
1 CAAAGTCCTCAAACACATTTATAACACAGAGG-C-ATCCTT-CT
* * *
2861 AAAAGTCCTCAAACACATTTATAACACAGAGGCATCCATAT
1 CAAAGTCCTCAAACACATTTATAACACAGAGGCATCCTTCT
* * * *
2902 CAAAGTCCCCAAGCACAATTATAACACAGTGGCATCACTCTCT
1 CAAAGTCCTCAAACACATTTATAACACAGAGGCATC-CT-TCT
* *
2945 CAAAGTCCTCAAGCACATTTATAACATAGAGGCATC
1 CAAAGTCCTCAAACACATTTATAACACAGAGGCATC
2981 TATATCTAAG
Statistics
Matches: 170, Mismatches: 22, Indels: 26
0.78 0.10 0.12
Matches are distributed among these distances:
40 5 0.03
41 58 0.34
42 12 0.07
43 69 0.41
44 26 0.15
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.22
Consensus pattern (41 bp):
CAAAGTCCTCAAACACATTTATAACACAGAGGCATCCTTCT
Found at i:2886 original size:84 final size:82
Alignment explanation
Indices: 2733--3019 Score: 334
Period size: 84 Copynumber: 3.4 Consensus size: 82
2723 TCTCTCTCCC
* * *
2733 CAAAGTTCCCAAGCAC-ATATATAACACAGGGGCAACTCCCTTTCTAAAGTCCTCAAGA-ACATT
1 CAAAGTCCCCAAACACAAT-TATAACACA-GGGCAA-T-CCTTCCTAAAGTCCTCAA-ACACATT
2796 TATAACACAGAGGCATCTATAT
61 TATAACACAGAGGCATCTATAT
2818 CAAAGTCCCCAAACACAATTATAACACAGGGTCAATCCTTCCTAAAAGTCCTCAAACACATTTAT
1 CAAAGTCCCCAAACACAATTATAACACAGGG-CAATCCTTCCT-AAAGTCCTCAAACACATTTAT
*
2883 AACACAGAGGCATCCATAT
64 AACACAGAGGCATCTATAT
* *
2902 CAAAGTCCCCAAGCACAATTATAACACAGTGGC-ATCAC-TCTCTCAAAGTCCTCAAGCACATTT
1 CAAAGTCCCCAAACACAATTATAACACAG-GGCAATC-CTTC-CT-AAAGTCCTCAAACACATTT
*
2965 ATAACATAGAGGCATCTATAT
62 ATAACACAGAGGCATCTATAT
* * *
2986 CTAAGTCCCTAAACAC-A-TGTAACACAAGGGCAAT
1 CAAAGTCCCCAAACACAATTATAACAC-AGGGCAAT
3020 TTTCTCTACA
Statistics
Matches: 180, Mismatches: 13, Indels: 20
0.85 0.06 0.09
Matches are distributed among these distances:
82 10 0.06
83 17 0.09
84 123 0.68
85 28 0.16
86 2 0.01
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.22
Consensus pattern (82 bp):
CAAAGTCCCCAAACACAATTATAACACAGGGCAATCCTTCCTAAAGTCCTCAAACACATTTATAA
CACAGAGGCATCTATAT
Found at i:5097 original size:20 final size:20
Alignment explanation
Indices: 5072--5116 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
5062 AGGGAAGGGC
5072 AAAACGGGAATAAAACATTG
1 AAAACGGGAATAAAACATTG
* *
5092 AAAACGGGAATGAAATATTG
1 AAAACGGGAATAAAACATTG
5112 AAAAC
1 AAAAC
5117 AACACCTTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.56, C:0.09, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAACGGGAATAAAACATTG
Found at i:5155 original size:68 final size:68
Alignment explanation
Indices: 5046--5234 Score: 279
Period size: 68 Copynumber: 2.8 Consensus size: 68
5036 AGAGAATAGG
* ** ** * *
5046 AACAACTCCTTCCGATAGGGAAGGGCAAAACGGGAATAAAACATTGAAAACGGGAATGAAATATT
1 AACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAAAACATTGAAAACAAGAATAAAACATT
5111 GAA
66 GAA
* *
5114 AACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAACATTGAATACAAGAATAAAACATT
1 AACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAAAACATTGAAAACAAGAATAAAACATT
5179 GAA
66 GAA
* *
5182 AACAACACCTTCCGACCAGGAAGGGCAAAACGGGAATAAAACATTGAACACAA
1 AACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAAAACATTGAAAACAA
5235 CACCTCTCGA
Statistics
Matches: 109, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 109 1.00
ACGTcount: A:0.48, C:0.19, G:0.20, T:0.13
Consensus pattern (68 bp):
AACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAAAACATTGAAAACAAGAATAAAACATT
GAA
Found at i:5172 original size:20 final size:20
Alignment explanation
Indices: 5140--5186 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
5130 CGGGAAGGGC
*
5140 AAAACAGGAATAAAACATTG
1 AAAACAAGAATAAAACATTG
*
5160 AATACAAGAATAAAACATTG
1 AAAACAAGAATAAAACATTG
5180 AAAACAA
1 AAAACAA
5187 CACCTTCCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.15
Consensus pattern (20 bp):
AAAACAAGAATAAAACATTG
Found at i:5238 original size:48 final size:48
Alignment explanation
Indices: 5167--5354 Score: 288
Period size: 48 Copynumber: 3.9 Consensus size: 48
5157 TTGAATACAA
5167 GAATAAAACATTGAAAACAACACCTTCCGACCAGGAAGGGCAAAACGG
1 GAATAAAACATTGAAAACAACACCTTCCGACCAGGAAGGGCAAAACGG
* *
5215 GAATAAAACATTGAACACAACACC-TCTCGACCGGGAAGGGCAAAACGG
1 GAATAAAACATTGAAAACAACACCTTC-CGACCAGGAAGGGCAAAACGG
* * **
5263 GAATAAAATATTGAAAACAACACCATCCGACTGGGAAGGGCAAAACGG
1 GAATAAAACATTGAAAACAACACCTTCCGACCAGGAAGGGCAAAACGG
* *
5311 GAATAAAATATTGAAACCAACACCTTCCGACCAGGAAGGGCAAA
1 GAATAAAACATTGAAAACAACACCTTCCGACCAGGAAGGGCAAA
5355 TTGGGGATAT
Statistics
Matches: 129, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
47 2 0.02
48 125 0.97
49 2 0.02
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (48 bp):
GAATAAAACATTGAAAACAACACCTTCCGACCAGGAAGGGCAAAACGG
Found at i:5506 original size:41 final size:40
Alignment explanation
Indices: 5369--5637 Score: 271
Period size: 40 Copynumber: 6.7 Consensus size: 40
5359 GGATATGCTG
* *
5369 ACAACACCTTCC-GATGAGGAAGGGCAAATTGGTAAAGGCA
1 ACAACACC-TCCTAATGAGGAAGGGCAAATTGGCAAAGGCA
* * * *
5409 ACAACACCTCCTGAT-AGGGAAGGGCAAATTGG-TAATGCTG
1 ACAACACCTCCTAATGA-GGAAGGGCAAATTGGCAAAGGC-A
* *
5449 ACAACGCCTTCTAATGAGGAAGGGCAAATTGGACAAAGGCA
1 ACAACACCTCCTAATGAGGAAGGGCAAATTGG-CAAAGGCA
* * * *
5490 ACAACACCTCCTAATGAGGAAGGGCAAACTGG-TAATGCTG
1 ACAACACCTCCTAATGAGGAAGGGCAAATTGGCAAAGGC-A
*
5530 ACAACACCTTCTAATGAGGAAGGGCAAATTGGACAAAGGCA
1 ACAACACCTCCTAATGAGGAAGGGCAAATTGG-CAAAGGCA
* *
5571 ACAACACCTCCCAATGAGGAAGGGCAAATTGGCAAATG-A
1 ACAACACCTCCTAATGAGGAAGGGCAAATTGGCAAAGGCA
*
5610 TGACAACACCTTCC-GATGAGGAAGGGCA
1 --ACAACACC-TCCTAATGAGGAAGGGCA
5638 GACTAGTAAA
Statistics
Matches: 193, Mismatches: 24, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
39 13 0.07
40 88 0.46
41 81 0.42
42 11 0.06
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (40 bp):
ACAACACCTCCTAATGAGGAAGGGCAAATTGGCAAAGGCA
Found at i:5523 original size:81 final size:81
Alignment explanation
Indices: 5343--5637 Score: 432
Period size: 81 Copynumber: 3.6 Consensus size: 81
5333 CCTTCCGACC
* * *
5343 AGGAAGGGCAAATTGGGGATATGCTGACAACACCTTCCGATGAGGAAGGGCAAATTGG-TAAAGG
1 AGGAAGGGCAAATT-GGTA-ATGCTGACAACACCTTCCAATGAGGAAGGGCAAATTGGACAAAGG
*
5407 CAACAACACCTCCTGAT-
64 CAACAACACCTCCTAATG
* *
5424 AGGGAAGGGCAAATTGGTAATGCTGACAACGCCTTCTAATGAGGAAGGGCAAATTGGACAAAGGC
1 A-GGAAGGGCAAATTGGTAATGCTGACAACACCTTCCAATGAGGAAGGGCAAATTGGACAAAGGC
5489 AACAACACCTCCTAATG
65 AACAACACCTCCTAATG
* *
5506 AGGAAGGGCAAACTGGTAATGCTGACAACACCTTCTAATGAGGAAGGGCAAATTGGACAAAGGCA
1 AGGAAGGGCAAATTGGTAATGCTGACAACACCTTCCAATGAGGAAGGGCAAATTGGACAAAGGCA
*
5571 ACAACACCTCCCAATG
66 ACAACACCTCCTAATG
* * *
5587 AGGAAGGGCAAATTGGCAAATGATGACAACACCTTCCGATGAGGAAGGGCA
1 AGGAAGGGCAAATTGG-TAATGCTGACAACACCTTCCAATGAGGAAGGGCA
5638 GACTAGTAAA
Statistics
Matches: 196, Mismatches: 14, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
80 35 0.18
81 117 0.60
82 44 0.22
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.16
Consensus pattern (81 bp):
AGGAAGGGCAAATTGGTAATGCTGACAACACCTTCCAATGAGGAAGGGCAAATTGGACAAAGGCA
ACAACACCTCCTAATG
Found at i:5688 original size:31 final size:31
Alignment explanation
Indices: 5653--5714 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
5643 GTAAACTTTA
5653 ACAACACCTTCCAAAGAGGAAGGGAAAACTG
1 ACAACACCTTCCAAAGAGGAAGGGAAAACTG
* * * *
5684 ACAACACCTTTCGATGAGGAAGGGCAAACTG
1 ACAACACCTTCCAAAGAGGAAGGGAAAACTG
5715 GGAAAAGTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.23, G:0.24, T:0.13
Consensus pattern (31 bp):
ACAACACCTTCCAAAGAGGAAGGGAAAACTG
Found at i:5794 original size:46 final size:46
Alignment explanation
Indices: 5738--5888 Score: 202
Period size: 46 Copynumber: 3.4 Consensus size: 46
5728 TAGACAACAT
* * *
5738 CTTCCGACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACAGGGGC
1 CTTCCAACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACAGAGAC
* * *
5784 CTTCCAACCAGGAAGGGGCATTTTTGGAAAGAAAGAAAACTGTGAC
1 CTTCCAACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACAGAGAC
* *
5830 CTTCCGACCGGGAAGGGGCATTTTTGGAAT---A-AAAACAGAGAC
1 CTTCCAACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACAGAGAC
5872 CTTCCAACCAGGAAGGG
1 CTTCCAACCAGGAAGGG
5889 C
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
42 24 0.26
43 1 0.01
46 68 0.73
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (46 bp):
CTTCCAACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACAGAGAC
Done.