Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016806.1 Corchorus olitorius cultivar O-4 contig16839, 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: 9226
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Found at i:4298 original size:25 final size:24
Alignment explanation
Indices: 4261--4307 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
4251 CTAGAAAATT
4261 TGAAAAACATTGATGGATGAGATGGA
1 TGAAAAACATTGAT-GAT-AGATGGA
4287 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACATTGATGATAGATG
4308 AATAGAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.43, C:0.04, G:0.28, T:0.26
Consensus pattern (24 bp):
TGAAAAACATTGATGATAGATGGA
Found at i:5164 original size:21 final size:21
Alignment explanation
Indices: 5140--5231 Score: 159
Period size: 21 Copynumber: 4.4 Consensus size: 21
5130 CTTAGGCAAT
*
5140 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
5161 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
5182 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
5203 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
5224 TCCAATGA
1 TCCAATGA
5232 TCTCCAAGCA
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
20 3 0.04
21 66 0.96
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:8388 original size:154 final size:154
Alignment explanation
Indices: 8106--9073 Score: 1419
Period size: 154 Copynumber: 6.3 Consensus size: 154
8096 TGGCGCATCA
* * * * *
8106 AGTCCACCGTGAAGTTTTTAGCTCATTTGGAACACTTGTCACTTTGGGCCTATCGGGGACCATTC
1 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
* * * * *
8171 GTGACGTTTTGAATCGTCTTCGATTTGGCAATCTTCGATGCCTTTCTTTCCTTTGTTTATGGCCT
66 GTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
8236 AACTATAATCAATTTGGTGAGATT
131 AACTATAATCAATTTGGTGAGATT
* *
8260 ATTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
1 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
** *
8325 GTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCT
66 GTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
*
8390 AACTATAATCAATTTGGTGAAATT
131 AACTATAATCAATTTGGTGAGATT
* *
8414 AGTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTT-GGCCTATCGGTGCCCATTA
1 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
* * * * * ***
8478 GTGACATTTTGAATCGTCGTCGATTTGGTAAACCTTAAAG-TTTTCTTTATGTTGTTTATGGCCT
66 GTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
*
8542 AACTATAATCATTTTGAGT-AGATT
131 AACTATAATCAATTTG-GTGAGATT
* *
8566 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGACCCATTA
1 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
** * *
8631 GTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCCTTTC-TTCCATTGTTTATGGCCT
66 GTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
*
8695 AACTATAATC-ATTTGGTGAGGTT
131 AACTATAATCAATTTGGTGAGATT
*
8718 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGCTACTTTT-GGCCTATCGGGGCCCATT
1 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA-TTTTGGGCCTATCGGGGCCCATT
** * * *
8782 AGTTCCGTTTTGAATCGTCTTCGATTTGACAAACCCCAATGTTTTTCTTTCCATTGTTTATGGCC
65 AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCC
*
8847 TAACTATAATCATTTTGGTGAGATT
130 TAACTATAATCAATTTGGTGAGATT
* * *
8872 AGTCCACCGTGAAGTTTTTAGTTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATCA
1 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
* * * *
8937 GTGACGTTTTGAATCGTGTTCGATTTGGCAAACCTTAATGCTTTTCATTCCATTGTTTATGACCT
66 GTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
9002 AACTATAAT-AATTTTGGTGAGATT
131 AACTATAATCAA-TTTGGTGAGATT
*
9026 AGTCCACTGTGAAGTTTTTGGCTCATTTGGAACACTTGTTATTTTGGG
1 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
9074 TGAATAACCT
Statistics
Matches: 731, Mismatches: 74, Indels: 18
0.89 0.09 0.02
Matches are distributed among these distances:
151 2 0.00
152 190 0.26
153 164 0.22
154 375 0.51
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (154 bp):
AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
GTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
AACTATAATCAATTTGGTGAGATT
Found at i:8661 original size:306 final size:305
Alignment explanation
Indices: 8106--9072 Score: 1424
Period size: 306 Copynumber: 3.2 Consensus size: 305
8096 TGGCGCATCA
* * * * *
8106 AGTCCACCGTGAAGTTTTTAGCTCATTTGGAACACTTGTCACTTTGGGCCTATCGGGGACCATTC
1 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTACTTTTGGCCTATCGGGGCCCATTA
* * * *
8171 GTGACGTTTTGAATCGTCTTCGATTTGGCAATCTTCGATGCCTTTCTTTCCTTTGTTTATGGCCT
66 GTGACGTTTTGAATCGTCTTCGATTTGGAAACCTT-AATGCTTTTCTTT-CTTTGTTTATGGCCT
* * *
8236 AACTATAATCAATTTGGTGAGATTATTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTA
129 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
*
8301 TTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGC
194 TTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGC
*
8366 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCAATTTGGTGAAATT
259 TTTTC-TTCCATTGTTTATGGCCTAACTATAATCAATTTGGTGAGATT
* *
8414 AGTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTA-TTTTGGCCTATCGGTGCCCATTA
1 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTACTTTTGGCCTATCGGGGCCCATTA
* * * *
8478 GTGACATTTTGAATCGTCGTCGATTTGGTAAACCTTAAAG-TTTTCTTTATGTTGTTTATGGCCT
66 GTGACGTTTTGAATCGTCTTCGATTTGG-AAACCTTAATGCTTTTCTTTCT-TTGTTTATGGCCT
8542 AACTATAATCATTTTGAGT-AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT
129 AACTATAATCATTTTG-GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT
* * *
8606 ATTTTGGGCCTATCGAGACCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATG
193 ATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
* *
8671 CCTTTCTTCCATTGTTTATGGCCTAACTATAATC-ATTTGGTGAGGTT
258 CTTTTCTTCCATTGTTTATGGCCTAACTATAATCAATTTGGTGAGATT
*
8718 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGCTACTTTTGGCCTATCGGGGCCCATTA
1 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTACTTTTGGCCTATCGGGGCCCATTA
** * ** * *
8783 GTTCCGTTTTGAATCGTCTTCGATTTGACAAACCCCAATGTTTTTCTTTCCATTGTTTATGGCCT
66 GTGACGTTTTGAATCGTCTTCGATTTG-GAAACCTTAATGCTTTTCTTT-CTTTGTTTATGGCCT
* *
8848 AACTATAATCATTTTGGTGAGATTAGTCCACCGTGAAGTTTTTAGTTCATTTGGAACACTTGTTA
129 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
* ** * *
8913 TTTTGGGCCTATCGGGGCCCATCAGTGACGTTTTGAATCGTGTTCGATTTGGCAAACCTTAATGC
194 TTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGC
*
8978 TTTTCATTCCATTGTTTATGACCTAACTATAAT-AATTTTGGTGAGATT
259 TTTTC-TTCCATTGTTTATGGCCTAACTATAATCAA-TTTGGTGAGATT
*
9026 AGTCCACTGTGAAGTTTTTGGCTCATTTGGAACACTTGTTA-TTTTGG
1 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTACTTTTGG
9073 GTGAATAACC
Statistics
Matches: 595, Mismatches: 53, Indels: 23
0.89 0.08 0.03
Matches are distributed among these distances:
304 50 0.08
305 84 0.14
306 286 0.48
307 82 0.14
308 93 0.16
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (305 bp):
AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTACTTTTGGCCTATCGGGGCCCATTA
GTGACGTTTTGAATCGTCTTCGATTTGGAAACCTTAATGCTTTTCTTTCTTTGTTTATGGCCTAA
CTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATT
TTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTT
TTCTTCCATTGTTTATGGCCTAACTATAATCAATTTGGTGAGATT
Done.