Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011899.1 Corchorus olitorius cultivar O-4 contig11932, 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: 3144
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Found at i:645 original size:154 final size:153
Alignment explanation
Indices: 44--727 Score: 1033
Period size: 154 Copynumber: 4.5 Consensus size: 153
34 AATTTTTTAT
44 GGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACTCAATGCTTTTCTTTCCATTGTT
1 GGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACTCAATGCTTTTCTTTCCATTGTT
*
109 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGACTTTGAAGTTTTTAGCTCATTTGGAAC
66 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGACTGTGAAGTTTTTAGCTCATTTGGAAC
* *
174 ACTTGTTATTTTGGGCCTATAGG
131 ACTTGTTATTTTGGGCCTATCGA
* *
197 GGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTAGCAAACCTCAATGCTTTTCCTTCCATTGT
1 GGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAA-CTCAATGCTTTTCTTTCCATTGT
* *
262 TAATGGCCTAACTATAATCATTTTGGTGAAATTAGTCGACTGTGAAG-TTTTAGCTCATTTGGAA
65 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGACTGTGAAGTTTTTAGCTCATTTGGAA
*
326 CACTTGTTATTTTGGGTCTATC-A
130 CACTTGTTATTTTGGGCCTATCGA
* *
349 GTGCCCATTAGTTCCGTTTTGAA-CTGTCTTCAATTTGGCAAATCTCAATG-TTTCTCTTTGCA-
1 G-GCCCATTAGTTCCGTTTTGAATC-GTCTTCGATTTGGCAAA-CTCAATGCTTT-TCTTTCCAT
*
411 T-TTTATGGCCTAACTATAATAATTTTGGTGAGATTAGTCGACTGTGAAGTTTTTAGCTCATTTG
62 TGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGACTGTGAAGTTTTTAGCTCATTTG
475 GAACACTTGTTATTTTGGGCCTATCGA
127 GAACACTTGTTATTTTGGGCCTATCGA
* *
502 GACCCATTAGTTCCGTTTAGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
1 GGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAA-CTCAATGCTTTTCTTTCCATTGT
* * * *
567 TTATGGCCTAACTATAATCATCTTGGTGACATT-TTGCGACTGTGAAGTTTTTAGCTCACTTGGA
65 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGT-CGACTGTGAAGTTTTTAGCTCATTTGGA
* *
631 ACATTTGTTATTTTGGGCTTATCTG-
129 ACACTTGTTATTTTGGGCCTATC-GA
* * * *
656 GGCTCATTAGTTACGGTTTGAATCGTCTTCGATTTGGCAAACTCAATGCTTTTCTTTCAATTGTT
1 GGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACTCAATGCTTTTCTTTCCATTGTT
721 TATGGCC
66 TATGGCC
728 CATTAGTTCC
Statistics
Matches: 484, Mismatches: 35, Indels: 24
0.89 0.06 0.04
Matches are distributed among these distances:
151 45 0.09
152 93 0.19
153 164 0.34
154 181 0.37
155 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.41
Consensus pattern (153 bp):
GGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACTCAATGCTTTTCTTTCCATTGTT
TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGACTGTGAAGTTTTTAGCTCATTTGGAAC
ACTTGTTATTTTGGGCCTATCGA
Found at i:769 original size:68 final size:68
Alignment explanation
Indices: 660--863 Score: 381
Period size: 68 Copynumber: 3.0 Consensus size: 68
650 TATCTGGGCT
* * *
660 CATTAGTTACGGTTTGAATCGTCTTCGATTTGGCAAACTCAATGCTTTTCTTTCAATTGTTTATG
1 CATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACTCAATGCTTTTCTTTCCATTGTTTATG
725 GCC
66 GCC
728 CATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACTCAATGCTTTTCTTTCCATTGTTTATG
1 CATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACTCAATGCTTTTCTTTCCATTGTTTATG
793 GCC
66 GCC
796 CATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACTCAATGCTTTTCTTTCCATTGTTTATG
1 CATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACTCAATGCTTTTCTTTCCATTGTTTATG
861 GCC
66 GCC
864 TAACTATAAT
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 133 1.00
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.44
Consensus pattern (68 bp):
CATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACTCAATGCTTTTCTTTCCATTGTTTATG
GCC
Found at i:1034 original size:154 final size:154
Alignment explanation
Indices: 792--3144 Score: 3534
Period size: 154 Copynumber: 15.2 Consensus size: 154
782 CATTGTTTAT
**
792 GGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAA-CTCAATGCTTTTCTTTCCATTGT
1 GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
*
856 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGACT-TGAAGTTTTTAGCTCATTTGGAA
66 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
920 CACTTGTTATTTTGGGCCTATACGG
131 CACTTGTTATTTTGGGCCTAT-CGG
* * * *
945 GGCCCATTTGT-CCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTTTTTCCTATTG
1 GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC-ATTG
* * *
1009 TTTTTGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGCGAAGTTTTTAGCTCACTTGGA
65 TTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
* *
1074 ACACTTGTTATTTTGGGTCATATCGA
130 ACACTTGTTATTTTGGG-CCTATCGG
* * ** * *
1100 GGACCACTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAATGT
1 GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
* * *
1165 TTATGGCCTAACTATAATCATTTTTGTAAGATTAGTCCACCTTTGAACCGTTTTTAGCTCACTTT
66 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCA-CTGTGAA--GTTTTTAGCTCA-TTT
*
1230 GGGAACACTTGTTA-TTTGGGCCTATCGA
127 -GGAACACTTGTTATTTTGGGCCTATCGG
* ** *
1258 GACCCATTAGTTCCGTTTTGAATCGTTTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
1 GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
* * *
1323 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGACTCTGAAGTTTTTAGCTCATTTGAAA
66 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
*
1388 TACTTGTTATTTTGGGCCTATCGG
131 CACTTGTTATTTTGGGCCTATCGG
** * *
1412 GGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCGCAATGCTTTTCTTTCCATTTT
1 GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
* * * * * *
1477 TTATGGCCTAACCATAATCAATTTGGTCAGATTAGTCCATTGTGAAATTTTTAGCTTATTTGGAA
66 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
*
1542 AACTTGTTATTTTGGGCCTATCGG
131 CACTTGTTATTTTGGGCCTATCGG
* * * *
1566 GGCCCATTAGCGACGTATTGAATCTTCTTCGATTTGGCAAACCTCAATACTTTTCTTTCCATTGT
1 GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
* * * * * * *
1631 TTATGGCCTAACCATAATCAATTTGGTCAGATTAGTCCATTGTTAACTTTTTAGCTTATTTGGAA
66 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
* * *
1696 AACTTGTTATTTTGGACCTATCAG
131 CACTTGTTATTTTGGGCCTATCGG
* * * * *
1720 GGCCCATTAGTAACGTATTGAATCTTCTTCGATTTGGCAAACCTCAGTGCTTTTATTTCCATTGT
1 GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
* * * *
1785 TTATGGCCTAATTGTAATCATTTTGGTGAGATTAGTCCACTATGAAGTTTTTAGCTCATTTAGAA
66 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
*
1850 CACTTGTTATTTTGGGCCTATCGA
131 CACTTGTTATTTTGGGCCTATCGG
* *
1874 GGCCCATTAGT-TCTATTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
1 GGCCCATTAGTGAC-GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
* *
1938 TTTATGGCCTAACTATAATCAATTTGGTGAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGA
65 TTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
* * *
2003 TCACTTGTTATTTTGGGCTTATCTG
130 ACACTTGTTATTTTGGGCCTATCGG
* * * *
2028 GGCCCATTAGTGACGTTTTGAATCGTTTTCGATTTCGCAAACCTCAAAGCTTTTCTTT-AAGTTG
1 GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCA-TTG
* * *
2092 TTTATGGCCTAACTATAATCATTTTGATGAGATTAGTCCACTGTGCAGTTCTTAGCTCATTTGGA
65 TTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
2157 ACACTTGTTATTTTGGGCCTATCGG
130 ACACTTGTTATTTTGGGCCTATCGG
* * *
2182 GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGTTTTTCTTTTCATTGT
1 GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
* *
2247 TTATGGCCTAACTATAATCAATTTGGTGAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAA
66 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
*
2312 CACTTGTTATTTTGGGCCTATCGC
131 CACTTGTTATTTTGGGCCTATCGG
* * * * *
2336 GACCGATTAGTGACGTTTTGAATCGTATTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTTT
1 GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
2401 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
66 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
2466 CACTTGTTATTTTGGGCCTATCGG
131 CACTTGTTATTTTGGGCCTATCGG
* *
2490 GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCAATTGT
1 GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
*
2555 TTATGGCCTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
66 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
2620 CACTTGTTATTTTGGGCCTATCGG
131 CACTTGTTATTTTGGGCCTATCGG
* *
2644 GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGCCAAA-CTCAAAGCTTTTCTTTCCATTGT
1 GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
*
2708 TTATGGCCTAACTATAATCA-TTTGGTGAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAA
66 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
* *
2772 CAATTGTTATTTTGGGCCTATCGC
131 CACTTGTTATTTTGGGCCTATCGG
* ** * * * *
2796 GACCCATTAGTGACGTTTTGAAGAGTATACAATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGT
1 GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
* *
2861 TTATGGACTAACTATAATCATTTAGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
66 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
2926 CACTTGTTATTTTGGGCCTAGTCGG
131 CACTTGTTATTTTGGGCCTA-TCGG
2951 GGTCCCATTAGTGTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAATGCTTTTACTTTCCA
1 GG-CCCATTAGTG-ACGTTTTGAATCGTCTTCGATTTGGCAAACCTC-AATGCTTTT-CTTTCCA
*
3016 TTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
62 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
*
3081 GGAACACTTGTTATTTTGGGCCTATCAG
127 GGAACACTTGTTATTTTGGGCCTATCGG
3109 GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTG
1 GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTG
Statistics
Matches: 2018, Mismatches: 160, Indels: 41
0.91 0.07 0.02
Matches are distributed among these distances:
152 126 0.06
153 124 0.06
154 1288 0.64
155 105 0.05
156 90 0.04
157 44 0.02
158 127 0.06
159 101 0.05
160 13 0.01
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (154 bp):
GGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
CACTTGTTATTTTGGGCCTATCGG
Done.