Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020709.1 Corchorus olitorius cultivar O-4 contig20742, 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: 9516
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Found at i:723 original size:124 final size:125
Alignment explanation
Indices: 562--792 Score: 419
Period size: 124 Copynumber: 1.9 Consensus size: 125
552 CGAAACGCCA
* *
562 CTATATATAATCTTCTACAAAGAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATG
1 CTATATATAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATATGTTATG
627 AATAGCGGCG-CTTTCATGACAGACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCTG
66 AATAGCGGCGTCTTTCATGACAGACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCTG
*
686 CTATATTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATATGTTATG
1 CTATATATAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATATGTTATG
*
751 AATAGCGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCG
66 AATAGCGGCGTCTTTCATGACAGACGCCGCTAAATAGTGGCG
793 TTTTTCATGA
Statistics
Matches: 102, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
124 72 0.71
125 30 0.29
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (125 bp):
CTATATATAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATATGTTATG
AATAGCGGCGTCTTTCATGACAGACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCTG
Found at i:829 original size:160 final size:157
Alignment explanation
Indices: 638--946 Score: 530
Period size: 160 Copynumber: 1.9 Consensus size: 157
628 ATAGCGGCGC
*
638 TTTCATGACAGACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCTGCTATATTTAATCTTCTA
1 TTTCATGACAGACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTATATTTAATCTTCTA
*
703 CAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATATGTTATGAATAGCGGCGTTTTTCA
66 CAAACAATAGAAATTCGGTGAAACTAAAAACACCATTTATATGTTATGAATAGCGGCGTTTTTCA
768 TGACAGACGCCGCTAAATAGTGGCGTT
131 TGACAGACGCCGCTAAATAGTGGCGTT
795 TTTCATGACAGACTGTCCATGC-AAATAGTGGCGCTTCTAAAGTAAACGCCGCTATATTTAATCT
1 TTTCATGACAGAC-G-CC--GCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTATATTTAATCT
* * *
859 TCTACAAACAATAGAAATTCGGTGAAACTGAACACACCATTTATTTGTTATGAATAGCGGCGTTT
62 TCTACAAACAATAGAAATTCGGTGAAACTAAAAACACCATTTATATGTTATGAATAGCGGCGTTT
924 TTCATGACAGACGCCGCTAAATA
127 TTCATGACAGACGCCGCTAAATA
947 TTTAATCTTC
Statistics
Matches: 143, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
157 13 0.09
158 1 0.01
159 2 0.01
160 125 0.87
161 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (157 bp):
TTTCATGACAGACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTATATTTAATCTTCTA
CAAACAATAGAAATTCGGTGAAACTAAAAACACCATTTATATGTTATGAATAGCGGCGTTTTTCA
TGACAGACGCCGCTAAATAGTGGCGTT
Found at i:1016 original size:96 final size:96
Alignment explanation
Indices: 840--1042 Score: 356
Period size: 96 Copynumber: 2.1 Consensus size: 96
830 TCTAAAGTAA
* *
840 ACGCCGCT--ATATTTAATCTTCTACAAACAATAGAAATTCGGTGAAACTGAACACACCATTTAT
1 ACGCCGCTAAATATTTAATCTTCTACAAACAATAGAAATTCGGTGAAACTAAAAACACCATTTAT
*
903 TTGTTATGAATAGCGGCGTTTTTCATGACAG
66 TTGTTATGAATAACGGCGTTTTTCATGACAG
*
934 ACGCCGCTAAATATTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTAT
1 ACGCCGCTAAATATTTAATCTTCTACAAACAATAGAAATTCGGTGAAACTAAAAACACCATTTAT
999 TTGTTATGAATAACGGCGTTTTTCATGACAG
66 TTGTTATGAATAACGGCGTTTTTCATGACAG
1030 ACGCCGCTAAATA
1 ACGCCGCTAAATA
1043 GTGGCGCTTT
Statistics
Matches: 103, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
94 8 0.08
96 95 0.92
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (96 bp):
ACGCCGCTAAATATTTAATCTTCTACAAACAATAGAAATTCGGTGAAACTAAAAACACCATTTAT
TTGTTATGAATAACGGCGTTTTTCATGACAG
Found at i:3164 original size:126 final size:125
Alignment explanation
Indices: 2822--3152 Score: 612
Period size: 127 Copynumber: 2.6 Consensus size: 125
2812 TTTTCATAAG
*
2822 CAATAGAAATTTGGTGAAACTGAAAACACCATTTATTTG-TATGAATAGCGGCGTTTTTCATGAC
1 CAATAGAAATTCGGTGAAACTGAAAACACCATTTATTTGTTATGAATAGCGGCGTTTTTCATGAC
2886 AGACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTATATTTAATCTTCTACAAA
66 AGACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTATATTTAATCTTCTACAAA
2946 CAATAGAAATTCGGTGAAACTGAAAACACCATTTATTTGTTATGAATAGCGGCGTTTTTTCA-GA
1 CAATAGAAATTCGGTGAAACTGAAAACACCATTTATTTGTTATGAATAGCGGCG-TTTTTCATGA
3010 CAGACGCCGCTAAATAGTGGCGCTTTCTAAAGTAAACGCCGCTATATTTAATCTTCTACAAA
65 CAGACGCCGCTAAATAGTGGCGC-TTCTAAAGTAAACGCCGCTATATTTAATCTTCTACAAA
3072 CAATAGAAAGTTCGGTGAAACTGAAAACACCATTTATTTGTTATGAATAGCGGCGTTTTTCATGA
1 CAATAGAAA-TTCGGTGAAACTGAAAACACCATTTATTTGTTATGAATAGCGGCGTTTTTCATGA
3137 CAGACGCCGCTAAATA
65 CAGACGCCGCTAAATA
3153 TTTAATCTTC
Statistics
Matches: 201, Mismatches: 1, Indels: 7
0.96 0.00 0.03
Matches are distributed among these distances:
124 38 0.19
125 39 0.19
126 61 0.30
127 63 0.31
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (125 bp):
CAATAGAAATTCGGTGAAACTGAAAACACCATTTATTTGTTATGAATAGCGGCGTTTTTCATGAC
AGACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTATATTTAATCTTCTACAAA
Found at i:3209 original size:96 final size:97
Alignment explanation
Indices: 3045--3248 Score: 351
Period size: 96 Copynumber: 2.1 Consensus size: 97
3035 TCTAAAGTAA
*
3045 ACGCCGCT--ATATTTAATCTTCTACAAACAATAGAAAGTTCGGTGAAACTGAAAACACCATTTA
1 ACGCCGCTAAATATTTAATCTTCTACAAACAATAGAAAGTTCGGTGAAACTAAAAACACCATTTA
3108 TTTGTTATGAATAGCGGCGTTTTTCATGACAG
66 TTTGTTATGAATAGCGGCGTTTTTCATGACAG
*
3140 ACGCCGCTAAATATTTAATCTTCTACAAACAATAGAAA-TTTGGTGAAACTAAAAACACCATTTA
1 ACGCCGCTAAATATTTAATCTTCTACAAACAATAGAAAGTTCGGTGAAACTAAAAACACCATTTA
*
3204 TTTGTTATGAATAGCGGCGTTTTTCATGATAG
66 TTTGTTATGAATAGCGGCGTTTTTCATGACAG
*
3236 ACGCTGCTAAATA
1 ACGCCGCTAAATA
3249 GTGGCGCTTT
Statistics
Matches: 103, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
95 8 0.08
96 67 0.65
97 28 0.27
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (97 bp):
ACGCCGCTAAATATTTAATCTTCTACAAACAATAGAAAGTTCGGTGAAACTAAAAACACCATTTA
TTTGTTATGAATAGCGGCGTTTTTCATGACAG
Found at i:5982 original size:23 final size:23
Alignment explanation
Indices: 5952--5999 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
5942 ATTAACTAAT
5952 AGAAACCGTTTGGTTTATTTGAG
1 AGAAACCGTTTGGTTTATTTGAG
5975 AGAAACCGTTTGGTTTATTTGAG
1 AGAAACCGTTTGGTTTATTTGAG
5998 AG
1 AG
6000 GTTTGTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.38
Consensus pattern (23 bp):
AGAAACCGTTTGGTTTATTTGAG
Found at i:7956 original size:31 final size:30
Alignment explanation
Indices: 7913--8082 Score: 121
Period size: 31 Copynumber: 5.6 Consensus size: 30
7903 TAGGGCTAAT
*
7913 TGCTTAAATAAGGGCCTAATGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAATGTTTG-CAAAA
** * * **
7944 TGCTCAAATAAGGGCCCGATCTTT-TAATT
1 TGCTCAAATAAGGGCCTAATGTTTGCAAAA
* * *
7973 TGGTTAAATAAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAATGTTTG-CAAAA
** * * **
8004 TGCTCAAATAAGGGCCCGATCTTT-TAATT
1 TGCTCAAATAAGGGCCTAATGTTTGCAAAA
* *
8033 TGGC-CAAATAAGGGGCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAATGTTTG-CAAAA
8064 TGCTCAAATAAGGGCCTAA
1 TGCTCAAATAAGGGCCTAA
8083 CATCAGTTTT
Statistics
Matches: 99, Mismatches: 34, Indels: 12
0.68 0.23 0.08
Matches are distributed among these distances:
29 38 0.38
30 4 0.04
31 57 0.58
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAATGTTTGCAAAA
Found at i:7988 original size:29 final size:29
Alignment explanation
Indices: 7947--8046 Score: 103
Period size: 29 Copynumber: 3.4 Consensus size: 29
7937 GCCAAAATGC
7947 TCAAATAAGGGCCCGATCTTTTAATTTGG
1 TCAAATAAGGGCCCGATCTTTTAATTTGG
* * * ** *
7976 TTAAATAAGGG-CCTAACGTTTGTCAAAATGC
1 TCAAATAAGGGCCCGATC-TTT-T-AATTTGG
8007 TCAAATAAGGGCCCGATCTTTTAATTTGG
1 TCAAATAAGGGCCCGATCTTTTAATTTGG
*
8036 CCAAATAAGGG
1 TCAAATAAGGG
8047 GCTAACGTTT
Statistics
Matches: 54, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
28 4 0.07
29 27 0.50
30 2 0.04
31 17 0.31
32 4 0.07
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (29 bp):
TCAAATAAGGGCCCGATCTTTTAATTTGG
Found at i:8009 original size:60 final size:60
Alignment explanation
Indices: 7916--8079 Score: 283
Period size: 60 Copynumber: 2.7 Consensus size: 60
7906 GGCTAATTGC
*
7916 TTAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGG
1 TTAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGG
*
7976 TTAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGG
1 TTAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGG
** *
8036 CCAAATAAGGGGCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
1 TTAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
8080 TAACATCAGT
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 98 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (60 bp):
TTAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGG
Found at i:8154 original size:31 final size:30
Alignment explanation
Indices: 8119--8286 Score: 132
Period size: 31 Copynumber: 5.6 Consensus size: 30
8109 TTTCGATGCC
8119 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGG-AAACGTT
** * *
8150 AGGCCCTTATTTG-GCCAAATT--AAAAGAT
1 AGGCCCTTATTTGAG-CATTTTGGAAACGTT
*
8178 CGAGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AG-GCCCTTATTTGAGCATTTTGG-AAACGTT
** * *
8210 AGGCCCTTATTTG-GCCAAATT--AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGGAAACG-TT
* *
8239 ATGCCCTTATTTGAGTATTTTGGGAAACGTT
1 AGGCCCTTATTTGAGCATTTT-GGAAACGTT
8270 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
8287 ATTAGCCATT
Statistics
Matches: 103, Mismatches: 22, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
28 10 0.10
29 31 0.30
30 4 0.04
31 48 0.47
32 10 0.10
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (30 bp):
AGGCCCTTATTTGAGCATTTTGGAAACGTT
Found at i:8214 original size:60 final size:60
Alignment explanation
Indices: 8121--8282 Score: 290
Period size: 60 Copynumber: 2.7 Consensus size: 60
8111 TCGATGCCAG
8121 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGA-
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC-AT
8181 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAT
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAT
* *
8241 GCCCTTATTTGAGTATTTTGGGAAACGTTAGGCCCTTATTTG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
8283 AGCAATTAGC
Statistics
Matches: 99, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
59 1 0.01
60 98 0.99
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (60 bp):
GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAT
Found at i:8251 original size:29 final size:28
Alignment explanation
Indices: 8152--8251 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 28
8142 CAAACGTTAG
8152 GCCCTTATTTGGCCAAATTAAAAGATCGA
1 GCCCTTATTTGGCCAAATTAAAAGATC-A
** * *
8181 GCCCTTATTTGAG-CATTTTGGCAAACG-TTA
1 GCCCTTATTTG-GCCAAATT---AAAAGATCA
8211 GGCCCTTATTTGGCCAAATTAAAAGATCA
1 -GCCCTTATTTGGCCAAATTAAAAGATCA
8240 TGCCCTTATTTG
1 -GCCCTTATTTG
8252 AGTATTTTGG
Statistics
Matches: 55, Mismatches: 9, Indels: 14
0.71 0.12 0.18
Matches are distributed among these distances:
28 4 0.07
29 28 0.51
30 3 0.05
31 16 0.29
32 4 0.07
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (28 bp):
GCCCTTATTTGGCCAAATTAAAAGATCA
Found at i:9144 original size:23 final size:23
Alignment explanation
Indices: 9111--9158 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
9101 ATTAACTAAT
9111 AGAAACCGTTTGGTTTATTTGAG
1 AGAAACCGTTTGGTTTATTTGAG
*
9134 AGAAACTGTTTGGTTTATTTGAG
1 AGAAACCGTTTGGTTTATTTGAG
9157 AG
1 AG
9159 GTTTGTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.06, G:0.27, T:0.40
Consensus pattern (23 bp):
AGAAACCGTTTGGTTTATTTGAG
Done.