Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011352.1 Corchorus olitorius cultivar O-4 contig11385, 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: 1773
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Found at i:1510 original size:153 final size:154
Alignment explanation
Indices: 806--1773 Score: 1444
Period size: 154 Copynumber: 6.3 Consensus size: 154
796 ATACATATCA
806 AATCGTCTTCGATTTGG-AAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
1 AATCGTCTTCGATTTGGCAAA-CCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
* *
870 ATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAATACTTGTTATTTTGGACCT
65 ATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* * ***
935 ATTAAGGCCCTTTAGTTTTGTTTTG
130 ATTCAGGCCCATTAGTGACGTTTTG
* *
960 AATCGTCTTCGATTTGGAAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
1 AATCGTCTTCGATTTGGCAAACCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
*
1025 TTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTCGAACACTTGTTATTTTGGGCCT-
66 TTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTA
*
1089 TTCGGGGCCCATTAGTGACGTTTTG
131 TTC-AGGCCCATTAGTGACGTTTTG
*
1114 AATCGTCTTCGATTTGCCAATACCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
1 AATCGTCTTCGATTTGGCAA-ACCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
* **
1179 ATTTT-GCTGAGATTAGTCCACTGTAAAGTTTTTAGCTC-TTTTTAACACTTGTTATTTTGGGCC
65 ATTTTAG-TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
1242 TA-TCAGGGCCCATTAGTGACGTTTTG
129 TATTCA-GGCCCATTAGTGACGTTTTG
1268 AATCGTCTTCGATTTGGCAAA-----ATGCTTTTCTTTCCATTGTTTATGG-CTAACTATAATCA
1 AATCGTCTTCGATTTGGCAAACCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
1327 TTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTA
66 TTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTA
1392 TT-AGGCCCATTAGTGACGTTTTG
131 TTCAGGCCCATTAGTGACGTTTTG
* * * *
1415 AATCGTCTTCGATTTGGCAACCCACCATGCTTTTCTTTCCATTATTTATGGCCTAACTATAATCA
1 AATCGTCTTCGATTTGGCAAACCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
* * *
1480 TTTTAGTGAGATTAGTCCACTGTAAAGTTTTTAGCTCTTTTGGAACACTTGTTATTTTGGACCTA
66 TTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTA
* *** *
1545 -TCAGGGCCCTTTAGTTTTGCTTTG
131 TTCA-GGCCCATTAGTGACGTTTTG
* *
1569 AATCGTCTTCGATTTGGCAAACCTCCATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCC
1 AATCGTCTTCGATTTGGCAAACCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
* * *
1634 TTTTAGTGAGATTAGTCCACTATGAAGTTTTT-GCTCATTTCGAACACTTGTTATTTTGTGCC-A
66 TTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTA
* **
1697 TTCGGGGCCCATTAGTTCCGTTTTG
131 TTC-AGGCCCATTAGTGACGTTTTG
*
1722 AATCGTCTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGC
1 AATCGTCTTCGATTTGGCAAACCTCGATGCTTTTCTTTCCATTGTTTATGGC
Statistics
Matches: 747, Mismatches: 48, Indels: 39
0.90 0.06 0.05
Matches are distributed among these distances:
147 87 0.12
148 52 0.07
149 1 0.00
152 26 0.03
153 173 0.23
154 327 0.44
155 81 0.11
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (154 bp):
AATCGTCTTCGATTTGGCAAACCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
TTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTA
TTCAGGCCCATTAGTGACGTTTTG
Done.