Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011538.1 Corchorus olitorius cultivar O-4 contig11571, 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: 3479
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Found at i:797 original size:21 final size:21
Alignment explanation
Indices: 768--807 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
758 ATCTTAGGCA
768 ACTCCGATGAGCTTGAAACCG
1 ACTCCGATGAGCTTGAAACCG
*
789 ACTCTGATGAGCTTGAAAC
1 ACTCCGATGAGCTTGAAAC
808 TTTTTCCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (21 bp):
ACTCCGATGAGCTTGAAACCG
Found at i:1962 original size:154 final size:153
Alignment explanation
Indices: 1682--2954 Score: 1942
Period size: 154 Copynumber: 8.3 Consensus size: 153
1672 TGATACTTGA
* * * * **
1682 TCATTTTGAACACTTGTTATTTTGAGCCTATTGGGGCCCAATAGTGACGTTTTGAATCGTCTTCG
1 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
* * *
1747 ATTTGCAACCCTCAATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGAT
66 ATTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGAT
* *
1812 TAGTCCACTGTGAAGTTTTAAAC
131 TAGTCCACTGTGAAGTTTTTAGC
* *
1835 TCATTTGGAACACTTTTTATTTTGGGCCTATCTGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
1 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
*
1900 ATTAGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATAGCCTAACTATAATCATTTTGGTGAGA
66 ATT-GGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
1965 TTAGTCCACTGTGAAGTTTTTAGC
130 TTAGTCCACTGTGAAGTTTTTAGC
*
1989 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCATCTTCG
1 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
*
2054 ATTTGGCAAACGTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
66 A-TTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
2119 TTAGTCCACTGTGAAGTTTTTAGC
130 TTAGTCCACTGTGAAGTTTTTAGC
* * * ** *
2143 TAATTTAGAACACTTGTTATTTT-GGCATATCGTAGCCCATTAGTTCAGTTTTGAATCGTCTTCG
1 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
* * * * *
2207 ATGTGGCAAACCTCAAAGCTTTTCTTTCCATTATATATGGACTAACTATAAACATTTTGGTGAGA
66 AT-TGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
2272 TTTAGTCCCACTGTGAAGTTTTTTAGC
130 -TTAGT-CCACTGTGAAG-TTTTTAGC
2299 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAG-TCCGTTTTGAATCGTCTTCG
1 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
* ** *
2363 ATTAGGCAAAACCTCAAAGCTTTTCTTTAAATTGTTTATGGCCTAACTATAATCATTTTGATGAG
66 ATT-GGC-AAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
2428 ATTAGTCCACTGTGAAGTTTTTAGC
129 ATTAGTCCACTGTGAAGTTTTTAGC
**
2453 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCG
1 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
* *
2518 ATTTGGCAAACCTCAATGCTTTTCTTTCCTATTGTTCATGGCCTAACTATAATCGTTTTGGTGAG
66 A-TTGGCAAACCTCAATGCTTTTCTTTCC-ATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
2583 ATTAGTCCACTGTGAAGTTTTT-GC
129 ATTAGTCCACTGTGAAGTTTTTAGC
* * * * *
2607 TAATTTAGAACACTTGTTATTTTGGGCCTGTCGGGGCACATTAGTTCCATTTTGAATCGTCTTCG
1 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
2672 ATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
66 A-TTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
* *
2737 TTAGTCCACTGTGAAGATTTTATC
130 TTAGTCCACTGTGAAGTTTTTAGC
** * *
2761 TCATTTGGAACACTTGTTATTTTAAGCCTATC-GGGCCCATTAGTGCTGTTTTGAATCGTCTTCG
1 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
* * *
2825 ATTTGCAACCCTCAATGCATTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGAT
66 ATTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGAT
2890 TAGTCCACTGTGAAGTTTTTAGC
131 TAGTCCACTGTGAAGTTTTTAGC
* * * *
2913 TCATTTGGAACACTTGTTATTTCGAGTCAATCGGGGCCCATT
1 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATT
2955 GTTTATGGCC
Statistics
Matches: 1024, Mismatches: 82, Indels: 28
0.90 0.07 0.02
Matches are distributed among these distances:
152 111 0.11
153 245 0.24
154 439 0.43
155 101 0.10
156 60 0.06
157 68 0.07
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.40
Consensus pattern (153 bp):
TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
ATTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGAT
TAGTCCACTGTGAAGTTTTTAGC
Found at i:3022 original size:99 final size:99
Alignment explanation
Indices: 2851--3053 Score: 352
Period size: 99 Copynumber: 2.1 Consensus size: 99
2841 GCATTTCTTT
* *
2851 CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA
1 CCATTGTTTATGGCCTAACTATAATCATTTTGGTCAGATTAGTCCACTGTGAAGTTTTTAGCACA
* *
2916 TTTGGAACACTTGTTATTTCGAGTCAATCGGGGC
66 TTTGGAACACTTGTTATTTCAAGCCAATCGGGGC
2950 CCATTGTTTATGGCCTAACTATAATCATTTTGGTCAGATTAGTCCACTGTGAAGTTTTTAGCACA
1 CCATTGTTTATGGCCTAACTATAATCATTTTGGTCAGATTAGTCCACTGTGAAGTTTTTAGCACA
* *
3015 TTTGGAACACTTGTTATTTTAAGCCTATCGGGGC
66 TTTGGAACACTTGTTATTTCAAGCCAATCGGGGC
3049 CCATT
1 CCATT
3054 AGTGCTGTTT
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 98 1.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (99 bp):
CCATTGTTTATGGCCTAACTATAATCATTTTGGTCAGATTAGTCCACTGTGAAGTTTTTAGCACA
TTTGGAACACTTGTTATTTCAAGCCAATCGGGGC
Found at i:3115 original size:252 final size:251
Alignment explanation
Indices: 2699--3186 Score: 888
Period size: 252 Copynumber: 1.9 Consensus size: 251
2689 GCTTTTCTTT
* * *
2699 CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGATTTTATCTCA
1 CCATTGTTTATGGCCTAACTATAATCATTTTGGTCAGATTAGTCCACTGTGAAGATTTTAGCACA
2764 TTTGGAACACTTGTTATTTTAAGCCTATCGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTT
66 TTTGGAACACTTGTTATTTTAAGCCTATCGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTT
2829 GCAACCCTCAATGCATTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGT
131 GCAACCCTCAATGCATTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGT
* *
2894 CCACTGTGAAGTTTTTAGCTCATTTGGAACAC-TTGTTATTTCGAGTCAATCGGGGC
196 CCACTGTGAAGTTTTTAACTCATATGGAACACATT-TTATTTCGAGTCAATCGGGGC
*
2950 CCATTGTTTATGGCCTAACTATAATCATTTTGGTCAGATTAGTCCACTGTGAAGTTTTTAGCACA
1 CCATTGTTTATGGCCTAACTATAATCATTTTGGTCAGATTAGTCCACTGTGAAGATTTTAGCACA
3015 TTTGGAACACTTGTTATTTTAAGCCTATCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATT
66 TTTGGAACACTTGTTATTTTAAGCCTATC-GGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATT
3080 TGCAACCCTCAATGCATTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
130 TGCAACCCTCAATGCATTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
*
3145 TCCACTGTGAAGTTTTTAACTCATATGGAGCACATTTTATTT
195 TCCACTGTGAAGTTTTTAACTCATATGGAACACATTTTATTT
3187 TGGGCCTATC
Statistics
Matches: 228, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
251 90 0.39
252 136 0.60
253 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (251 bp):
CCATTGTTTATGGCCTAACTATAATCATTTTGGTCAGATTAGTCCACTGTGAAGATTTTAGCACA
TTTGGAACACTTGTTATTTTAAGCCTATCGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTT
GCAACCCTCAATGCATTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGT
CCACTGTGAAGTTTTTAACTCATATGGAACACATTTTATTTCGAGTCAATCGGGGC
Found at i:3303 original size:154 final size:153
Alignment explanation
Indices: 2950--3479 Score: 828
Period size: 154 Copynumber: 3.4 Consensus size: 153
2940 CAATCGGGGC
* *
2950 CCATTGTTTATGGCCTAACTATAATCATTTTGGTCAGATTAGTCCACTGTGAAGTTTTTAGCACA
1 CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA
** * *
3015 TTTGGAACACTTGTTATTTTAAGCCTATCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATT
66 TTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATT
* * *
3080 TGCAACCCTCAATGCATTTCTTT
131 GGCAAACCTCAATGCTTTTCTTT
*
3103 CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCA
1 CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA
* * ** * *
3168 TATGGAGCACATT-TTATTTTGGGCCTATCTTGGCCCATTAGTTCCGTTTAGAATCGTCTTCAAT
66 TTTGGAACAC-TTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGAT
3232 TAGGCAAACCTCAATGCTTTTCTTT
130 T-GGCAAACCTCAATGCTTTTCTTT
* *
3257 CCATTGTTTATAGCCTAACTATGATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA
1 CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA
3322 TTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATT
66 TTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGA-T
*
3387 TGGCAAGCCTCAATGCTTTTCTTT
130 TGGCAAACCTCAATGCTTTTCTTT
* *
3411 CCATTGTTTATGGACCTAACTATAATCGTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTA
1 CCATTGTTTATGG-CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
3476 ATTT
65 ATTT
Statistics
Matches: 342, Mismatches: 30, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
153 116 0.34
154 172 0.50
155 54 0.16
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (153 bp):
CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA
TTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATT
GGCAAACCTCAATGCTTTTCTTT
Done.