Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010949.1 Corchorus olitorius cultivar O-4 contig10981, 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, 606
Length: 1011
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Found at i:320 original size:154 final size:154
Alignment explanation
Indices: 1--767 Score: 1211
Period size: 154 Copynumber: 5.0 Consensus size: 154
* * *
1 TCAATGC-TTTCTTTCCA-TGTTTATGGCCTAAGTATAATCATTTTGGTGAGATTGGTCCACTTT
1 TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
* * **
64 GAAGTTTTTAGCTCATTTAGAACTACTTG-TATTTT-GGCCTATGGGGGTCCATTAGTTCCGTTT
66 GAAGTTTTTAGCTCATTTGGAAC-ACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTGACGTTT
127 TGAATCGTCTTCGATTTGGCAAACC
130 TGAATCGTCTTCGATTTGGCAAACC
* *
152 TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCAACTTT
1 TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
* * ** *
217 GAAGTTTCTAGCTTATTTGGAACACTTGTTATTTTGTACCTATCGGGGTCCATTTGTGACGTTTT
66 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTGACGTTTT
*
282 GAATCATCTTCGATTTGGCAAACC
131 GAATCGTCTTCGATTTGGCAAACC
306 TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
1 TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
* * **
371 GAAGTTTTTAACTCATTTGGAACACTTGTTATTTTTGGCCTATCGGGGTCCATTAGTTCCGTTTT
66 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTGACGTTTT
436 GAATCGTCTTCGATTTGGCAAACC
131 GAATCGTCTTCGATTTGGCAAACC
* *
460 TCAATGTTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTGGTCCACTGT
1 TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
** * *
525 GAAGTTTTTAGCTCATTTACAACACTTGTTATTTTGGGTCTATCGGGGTCCATTAGTGACGTTTC
66 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTGACGTTTT
*
590 GAATCTTCTTCGATTTGGCAAACC
131 GAATCGTCTTCGATTTGGCAAACC
*
614 TCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
1 TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
* *
679 GAAGTTTTTAGCTCATTTGGAACCCTTGTTATTTTGGGCCTATCGGGG-CCTATTAGTAACGTTT
66 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGTCC-ATTAGTGACGTTT
*
743 TGAATCGTCTTCGATTTGGAAAACC
130 TGAATCGTCTTCGATTTGGCAAACC
768 ACTCATTTGG
Statistics
Matches: 564, Mismatches: 47, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
151 7 0.01
152 15 0.03
153 71 0.13
154 471 0.84
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (154 bp):
TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTGACGTTTT
GAATCGTCTTCGATTTGGCAAACC
Found at i:821 original size:79 final size:79
Alignment explanation
Indices: 690--846 Score: 262
Period size: 79 Copynumber: 2.0 Consensus size: 79
680 AAGTTTTTAG
*
690 CTCATTTGGAACCCTTGTTATTTTGGGCCTATCGGGGCCTATTAGTAACGTTTTGAATCGTCTTC
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCTATTAGTAACGTTTTGAATCGTCTTC
755 GATTTGGAAAACCA
66 GATTTGGAAAACCA
* *
769 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGTCC-ATTAGTGACGTTTTGAATCTTCTT
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGG-CCTATTAGTAACGTTTTGAATCGTCTT
*
833 CGATTTGGCAAACC
65 CGATTTGGAAAACC
847 TCAATGCTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
79 71 0.97
80 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (79 bp):
CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCTATTAGTAACGTTTTGAATCGTCTTC
GATTTGGAAAACCA
Found at i:944 original size:233 final size:233
Alignment explanation
Indices: 536--992 Score: 779
Period size: 233 Copynumber: 2.0 Consensus size: 233
526 AAGTTTTTAG
*
536 CTCATTTACAACACTTGTTATTTTGGGTCTATCGGGGTCCATTAGTGACGTTTCGAATCTTCTTC
1 CTCATTTACAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTGACGTTTCGAATCTTCTTC
* *
601 GATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAG
66 GATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATCGACTAACTATAATCATTCTGGTGAG
* * * *
666 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACCCTTGTTATTTTGGGCCTATCGGGGCCTA
131 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACATGTTATTTTGGACCTATCGGGGCCCA
731 TTAGTAACGTTTTGAATCGTCTTCGATTTGGAAAACCA
196 TTAGTAACGTTTTGAATCGTCTTCGATTTGGAAAACCA
** *
769 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTGACGTTTTGAATCTTCTTC
1 CTCATTTACAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTGACGTTTCGAATCTTCTTC
834 GATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATCGACTAACTATAATCATTCTGGTGAG
66 GATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATCGACTAACTATAATCATTCTGGTGAG
* **
899 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACAGATGTTATTTTGGACCTATCTTGGCCCA
131 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACATGTTATTTTGGACCTATCGGGGCCCA
* *
964 TTGGTGACGTTTTGAATCGTCTTCGATTT
196 TTAGTAACGTTTTGAATCGTCTTCGATTT
993 TACAAACCTC
Statistics
Matches: 209, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
233 209 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (233 bp):
CTCATTTACAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTGACGTTTCGAATCTTCTTC
GATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATCGACTAACTATAATCATTCTGGTGAG
ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACATGTTATTTTGGACCTATCGGGGCCCA
TTAGTAACGTTTTGAATCGTCTTCGATTTGGAAAACCA
Done.