Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011558.1 Corchorus olitorius cultivar O-4 contig11591, 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: 3226
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Found at i:841 original size:154 final size:154
Alignment explanation
Indices: 557--3226 Score: 3830
Period size: 154 Copynumber: 17.4 Consensus size: 154
547 CCCCGTATCA
* *
557 CCCATTAGTTCCGTTTTGAATCGACTTAGATTTGGCAAACCTCAAAGCTTTTCTATCCATTGTTT
1 CCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTT
* * **
622 ATGGCCTAACTATAATAATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTAATTTATAACA
66 ATGGCCTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
* **
687 CATGTTATTTTGCACCTTTCGGGG
131 CTTGTTATTTTGGGCCTTTCGGGG
* *
711 ACCATTAGTTCCGTTTTGAATCGAATTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTT
1 CCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTT
* * * *
776 ATGGCCTAACTATAATCATTTTGCTGAGAT-TAGTCCACTGTGAAATTTTTCGCTGATTTGGAAC
66 ATGGCCTAACTATAATCATTTTGGTGAGATAT-GTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
*
840 ACTTGTTATGTTGGGCCTTTCGGGG
130 ACTTGTTATTTTGGGCCTTTCGGGG
* * * * *
865 CTCAATAGTACCGTTTTGAATCTACTTCGATTTGGCAAACCTCAAAGCTTTTCTATCCATTGTTT
1 CCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTT
*
930 ATGGCCTAACTATAATCATTTTGGTGAGATATGTCCACTGGGAAGTTTTTAGCTCATTTGGAACA
66 ATGGCCTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
* * *
995 CTTATAATTTTGGGCGTTTCGGGG
131 CTTGTTATTTTGGGCCTTTCGGGG
* * * * * *
1019 CCCATTAGATCCGTTTTGAATCGACATCGTTTTGGCAAACCTAAAAGCTTTTCTTTCTATTTTTT
1 CCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTT
* *
1084 ATGGACTAACTATAATAATTTTGGTGAGAT-TAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
66 ATGGCCTAACTATAATCATTTTGGTGAGATAT-GTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
1148 ACTTGTTATTTTGGGCCTTTCGGGG
130 ACTTGTTATTTTGGGCCTTTCGGGG
* * * * *
1173 CCCATTAGTTCCATTTTGAATAGATTTCGATTTGGCAAACCTAAAAGCTTTTCTTTCCATTATTT
1 CCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTT
* *
1238 ATGGCCTAACTATAATCATTTT-TTAGAGATATGTCCACTGTGAAATTTTTAGCTCATTTGGAAC
66 ATGGCCTAACTATAATCATTTTGGT-GAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
*
1302 ACTTGTTATTTTGGGCCTTTCCGGG
130 ACTTGTTATTTTGGGCCTTTCGGGG
* * * *
1327 CCCATTAGTACCGTTTTGAATAGATTTCGATTTGGCAAACCTAAAAGCTTTTCTTTCCATTGTTT
1 CCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTT
* ** *
1392 ATGGCCTAAATATAATCATTTTGGAAAAATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
66 ATGGCCTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
*
1457 CTTGTCATTTTGGGCCTTTCGGGG
131 CTTGTTATTTTGGGCCTTTCGGGG
* * * *
1481 CCCATTAGATCCGTTTTGAATCGACTTCGATTTAGCAAACCTCAAAGCCTTTCTATCCATTGTTT
1 CCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTT
1546 ATGGCCTAACTATAATCA-TTTGGTGAGATATGTCCACTGTGAAG-TTTTAGCTCATTTGGAACA
66 ATGGCCTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
1609 CTTGTTA-TTTGGGCCTTTC-GGG
131 CTTGTTATTTTGGGCCTTTCGGGG
*
1631 CCCATTA-TATCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAACTTTTCTTTCCATTGTT
1 CCCATTAGT-TCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTT
** *
1695 TATGAACTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTAGAAC
65 TATGGCCTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
1760 ACTTGTTATTTTGGGCCTTTCGGGG
130 ACTTGTTATTTTGGGCCTTTCGGGG
* * *
1785 CCCATTAGTACCGTTTTGAATCGACTTCGATTTAGCAAACCTAAAAGCTTTTCTTTCCATTGTTT
1 CCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTT
* * *
1850 ATGGCCTAACTATAATCATTTTTGTTGAGAT-TAGTCCACTGTGAAATTTTTAGCTGATTTGGAA
66 ATGGCCTAACTATAATCA-TTTTGGTGAGATAT-GTCCACTGTGAAGTTTTTAGCTCATTTGGAA
*
1914 CACTTGTTATTTTAGGCCTTTCGGGG
129 CACTTGTTATTTTGGGCCTTTCGGGG
* * * * *
1940 CTCATTAGTACCGTTTTGAATCGACCTCGATTTGGCAAACCTCAAAGCTTTTCTTT-AAGTTGAT
1 CCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCA-TTGTT
* * * *
2004 TATGGCCTAACAATAATCATTTTGGTGAG--ATGTCTAATGTGAAGTTTTTATCTCATTTGGAAC
65 TATGGCCTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
*
2067 ACTTGTTATTTTGGGTCTTTCGGGG
130 ACTTGTTATTTTGGGCCTTTCGGGG
* * *
2092 -CCATTAGTTCCGTTTTGAATCGACATCGATTTGGCAAACCTCAATGCTTTTCTATCCATTGTTT
1 CCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTT
* * * *
2156 ATGGCCTAACTATAATCATTTTGGTGAGCTATGTCAACT-TCGAAGTTTTTAGCTCATTGGGAAT
66 ATGGCCTAACTATAATCATTTTGGTGAGATATGTCCACTGT-GAAGTTTTTAGCTCATTTGGAAC
*
2220 ACTTCTTATTTTGGGCCTTTCGGGG
130 ACTTGTTATTTTGGGCCTTTCGGGG
* * *
2245 CACATTAGATCCGTTTTGAATCGACTTCGATCTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTT
1 CCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTT
* *
2310 ATGGCCTAACTATAATCATTTTGGTGTGATATGTCCATTGTGAAGTTTTTAGCTCATTTGGAACA
66 ATGGCCTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
*
2375 CTTCTTATTTTGGGCCTTTCGGGG
131 CTTGTTATTTTGGGCCTTTCGGGG
* * * *
2399 CACATGAGTTCCATTTTGAAACGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTT
1 CCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTT
* * * * *
2464 GTGGCCTAACTATAATCATTTTCGTGAGATATGTCCACTGCGAAGTTTTTAACTCTTTTGGAACA
66 ATGGCCTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
* * * *
2529 ATTGTAATTTTGGGTCTTTCGGAG
131 CTTGTTATTTTGGGCCTTTCGGGG
** *
2553 CCCATTAAATCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAACTTTTCTTTCCATTGTTT
1 CCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTT
* * * * *
2618 ATGGCCTAACTATAATCATTTTGCTGAGATACGTCCAATGTGAAGTTTTTATCTCATTTCGAACA
66 ATGGCCTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
* *
2683 ATTGTAATTTTGGGCCTTTCGGGG
131 CTTGTTATTTTGGGCCTTTCGGGG
*
2707 CCCATTAGATCCGTTTTGAATCGACTTCGATTTGGCAAACC-CTAAAGCTTTTCTTTCCATTGTT
1 CCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTC-AAAGCTTTTCTTTCCATTGTT
* * * *
2771 TATGAACC-AACTATAATCATTTTGGTGAGGTATGTCCACTATGAATTTTTTAGCTCATTTGGAA
65 TATG-GCCTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
2835 CACTTGTTATTTTGGGCCTTTCGGGG
129 CACTTGTTATTTTGGGCCTTTCGGGG
* * *
2861 CCCATTAGTTCCGTTTTGAATAGATTTCGATTTGGCAAACCTAAAAG-TTTTCTTTCCATTGTTT
1 CCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTT
** *
2925 ATGAACTAACTATAACCATTTTGGTGAGAT-TAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
66 ATGGCCTAACTATAATCATTTTGGTGAGATAT-GTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
* * *
2989 ACTTCTAATTTTGGGCGTTTCGGGG
130 ACTTGTTATTTTGGGCCTTTCGGGG
* * * * *
3014 TCCATTGGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTT-AAGTTGAT
1 CCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCA-TTGTT
* * * *
3078 TATGGCCTAACAATAATCATTTTGGAGAGATATGTCCATTGTGAAATTTTTAGCTCATTTGGAAC
65 TATGGCCTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
*
3143 ACTTGTTATTTTGGGCCTTTCTGGG
130 ACTTGTTATTTTGGGCCTTTCGGGG
* * * * *
3168 CCCGTTAGTTCCGTTTTGAATCGACATCGATTTGGCAAACCTCAATGCTATTCTATCCA
1 CCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCA
Statistics
Matches: 2251, Mismatches: 234, Indels: 61
0.88 0.09 0.02
Matches are distributed among these distances:
150 78 0.03
151 120 0.05
152 105 0.05
153 225 0.10
154 1577 0.70
155 146 0.06
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.40
Consensus pattern (154 bp):
CCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTT
ATGGCCTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
CTTGTTATTTTGGGCCTTTCGGGG
Done.