Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019971.1 Corchorus olitorius cultivar O-4 contig20004, 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: 4149
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Found at i:3045 original size:154 final size:154
Alignment explanation
Indices: 2627--3792 Score: 1833
Period size: 154 Copynumber: 7.6 Consensus size: 154
2617 CACAGTTAAA
*
2627 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACT
1 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACT
* ** *
2692 TGTTATCTTGGGCCTTTCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTCGCAAACCTC
66 TGTTATTTTGGGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTC
*
2757 AATGCTTTTCTTTCCATTGTTTAG
131 AATGCTTTTCTTTCCATTGTTTAT
* **
2781 GGCCTACCTATAATCATTTT-GTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACTGT
1 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACT
* * ** * *
2845 TGTTATTTTGGGCATATCGGGGAACATTAGTTTCGTTTTGAATCGTCTTTGATTTGGCAAACCTC
66 TGTTATTTTGGGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTC
2910 AATGCTTTTCTTTCCATTGTTTAT
131 AATGCTTTTCTTTCCATTGTTTAT
* * *
2934 GGCCTAAGTATAATAATTTTGGTGATATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACT
1 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACT
* *
2999 TGTTATTTTGGGTCTTTCAGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTC
66 TGTTATTTTGGGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTC
3064 AATGCTTTTCTTTCCATTGTTTAT
131 AATGCTTTTCTTTCCATTGTTTAT
* * *
3088 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTAAAGTTCTTAGA-ACATTTGGAACAC
1 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA-ACTCATTTGGAACAC
* *
3152 TTGTTATTTTGGGCCTTTCGAGGCCCATTCGTTCCGTTTT---TCGTCTTCGATTTGGCAAACCT
65 TTGTTATTTTGGGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCT
*
3214 CAATGCTTTTCTTT-AAGTTGTTTAT
130 CAATGCTTTTCTTTCCA-TTGTTTAT
3239 GGCCTAACTATAA-CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACT
1 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACT
* *** * *
3303 TGTAATTTTGGGCCTTTTACGGCCCATTTGTTCTGTTTTGAATCGTCTTCGATTTGGCAAACCTC
66 TGTTATTTTGGGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTC
3368 AATGCTTTTCTTTCCATTGTTTAT
131 AATGCTTTTCTTTCCATTGTTTAT
* * * *
3392 GGCCTAAATATAATCATTTTGGTGAGATTAGTCCACTATGAGGTTTTTAACTCATTTGGAACTCT
1 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACT
* **
3457 TGTTATTTTGGGCCTTTCGGGACCCATTAGTTCCGTTTTGAATCGTCTTCGATTTTCCAAACCTC
66 TGTTATTTTGGGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTC
*
3522 AATTCTTTTCTTTCCATTGTTTAT
131 AATGCTTTTCTTTCCATTGTTTAT
* *
3546 GGCCTAACTATAATCATTTTGGTGAGAATAGTCCACTGTGAAGTTTTTAACTCATTTGGAACAGT
1 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACT
* * * *
3611 TGCTATTTTGGGCATATCGGGGCACATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTC
66 TGTTATTTTGGGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTC
3676 AATGCTTTTCTTTCCATTGTTTAT
131 AATGCTTTTCTTTCCATTGTTTAT
* *
3700 GGCCTAAGTATAATAATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACT
1 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACT
3765 TGTTATTTTGGGCCTTTCGGGGCCCATT
66 TGTTATTTTGGGCCTTTCGGGGCCCATT
3793 GACACGGGAG
Statistics
Matches: 918, Mismatches: 85, Indels: 18
0.90 0.08 0.02
Matches are distributed among these distances:
149 1 0.00
150 80 0.09
151 57 0.06
153 193 0.21
154 586 0.64
155 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (154 bp):
GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACT
TGTTATTTTGGGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTC
AATGCTTTTCTTTCCATTGTTTAT
Found at i:3487 original size:458 final size:460
Alignment explanation
Indices: 2627--3782 Score: 1804
Period size: 458 Copynumber: 2.5 Consensus size: 460
2617 CACAGTTAAA
*
2627 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACT
1 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGATCATTTGGAACACT
* ** *
2692 TGTTATCTTGGGCCTTTCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTCGCAAACCTC
66 TGTTATTTTGGGCCTTTCGGGGCCCATTAGTTCCGTTTT--ATCGTCTTCGATTTGGCAAACCTC
* *
2757 AATGCTTTTCTTTCCATTGTTTAGGGCCTACCTATAATCATTTT-GTGAGATTAGTCCACTGTGA
129 AATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGA
** * * **
2821 AGTTTTTAACTCATTTGGAACTGTTGTTATTTTGGGCATATCGGGGAACATTAGTTTCGTTTTGA
194 AGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTTTCACGGAACATTAGTTTCGTTTTGA
* *
2886 ATCGTCTTTGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAGTATAATAAT
259 ATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAATATAATAAT
* * *
2951 TTTGGTGATATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGTCTTT
324 TTTGGTGAGATTAGTCCACTATGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTTT
*
3016 CAGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAT
389 CAGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGCCAAACCTCAATGCTTTTCTTTCCAT
3081 TGTTTAT
454 TGTTTAT
* * *
3088 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTAAAGTTCTTAGAACATTTGGAACACT
1 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGATCATTTGGAACACT
* *
3153 TGTTATTTTGGGCCTTTCGAGGCCCATTCGTTCCGTTTT-TCGTCTTCGATTTGGCAAACCTCAA
66 TGTTATTTTGGGCCTTTCGGGGCCCATTAGTTCCGTTTTATCGTCTTCGATTTGGCAAACCTCAA
*
3217 TGCTTTTCTTT-AAGTTGTTTATGGCCTAACTATAA-CATTTTGGTGAGATTAGTCCACTGTGAA
131 TGCTTTTCTTTCCA-TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA
* * ** *
3280 GTTTTTAACTCATTTGGAACACTTGTAATTTTGGGCCTTTTACGGCCCATTTG-TTCTGTTTTGA
195 GTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTTTCACGGAACATTAGTTTC-GTTTTGA
*
3344 ATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAATATAATCAT
259 ATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAATATAATAAT
* *
3409 TTTGGTGAGATTAGTCCACTATGAGGTTTTTAACTCATTTGGAACTCTTGTTATTTTGGGCCTTT
324 TTTGGTGAGATTAGTCCACTATGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTTT
* *
3474 C-GGGACCCATTAGTTCCGTTTTGAATCGTCTTCGATTTTCCAAACCTCAATTCTTTTCTTTCCA
389 CAGGG-CCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGCCAAACCTCAATGCTTTTCTTTCCA
3538 TTGTTTAT
453 TTGTTTAT
* *
3546 GGCCTAACTATAATCATTTTGGTGAGAATAGTCCACTGTGAAGTTTTTA-ACTCATTTGGAACAG
1 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGA-TCATTTGGAACAC
* * * *
3610 TTGCTATTTTGGGCATATCGGGGCACATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCT
65 TTGTTATTTTGGGCCTTTCGGGGCCCATTAGTTCCGTTTT--ATCGTCTTCGATTTGGCAAACCT
* *
3675 CAATGCTTTTCTTTCCATTGTTTATGGCCTAAGTATAATAATTTTGGTGAGATTAGTCCACTGTG
128 CAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTG
3740 AAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTTTC
193 AAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTTTC
3783 GGGGCCCATT
Statistics
Matches: 634, Mismatches: 51, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
457 14 0.02
458 402 0.63
461 151 0.24
462 67 0.11
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (460 bp):
GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGATCATTTGGAACACT
TGTTATTTTGGGCCTTTCGGGGCCCATTAGTTCCGTTTTATCGTCTTCGATTTGGCAAACCTCAA
TGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
TTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTTTCACGGAACATTAGTTTCGTTTTGAAT
CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAATATAATAATTT
TGGTGAGATTAGTCCACTATGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTTTCA
GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGCCAAACCTCAATGCTTTTCTTTCCATTG
TTTAT
Found at i:3791 original size:612 final size:612
Alignment explanation
Indices: 2627--3792 Score: 1910
Period size: 612 Copynumber: 1.9 Consensus size: 612
2617 CACAGTTAAA
*
2627 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACT
1 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACT
* **
2692 TGTTATCTTGGGCCTTTCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTCGCAAACCTC
66 TGTAATCTTGGGCCTTTCACGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTCGCAAACCTC
** *
2757 AATGCTTTTCTTTCCATTGTTTAGGGCCTACCTATAATCATTTTGTGAGATTAGTCCACTGTGAA
131 AATGCTTTTCTTTCCATTGTTTAGGGCCTAAATATAATCATTTTGTGAGATTAGTCCACTATGAA
* *
2822 GTTTTTAACTCATTTGGAACTGTTGTTATTTTGGGCATATCGGGGAACATTAGTTTCGTTTTGAA
196 GTTTTTAACTCATTTGGAACTCTTGTTATTTTGGGCATATCGGGGAACATTAGTTCCGTTTTGAA
* * *
2887 TCGTCTTTGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAGTATAATAATT
261 TCGTCTTCGATTTGCCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATAATT
* * * *
2952 TTGGTGATATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGTCTTTC
326 TTGGTGAGAATAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGCTATTTTGGGTCTATC
*
3017 AGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT
391 AGGGCACATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT
*
3082 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTAAAGTTCTTAGAACATTTGG
456 GTTTATGGCCTAACTATAATAATTTTGGTGAGATTAGTCCACTGTAAAGTTCTTAGAACATTTGG
3147 AACACTTGTTATTTTGGGCCTTTCGAGGCCCATTCGTTCCGTTTTTCGTCTTCGATTTGGCAAAC
521 AACACTTGTTATTTTGGGCCTTTCGAGGCCCATTCGTTCCGTTTTTCGTCTTCGATTTGGCAAAC
3212 CTCAATGCTTTTCTTTAAGTTGTTTAT
586 CTCAATGCTTTTCTTTAAGTTGTTTAT
3239 GGCCTAACTATAA-CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACT
1 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACT
* * * * *
3303 TGTAATTTTGGGCCTTTTACGGCCCATTTGT-TCTGTTTTGAATCGTCTTCGATTTGGCAAACCT
66 TGTAATCTTGGGCCTTTCACGGCCCATTAGTGAC-GTTTTGAATCGTCTTCGATTTCGCAAACCT
*
3367 CAATGCTTTTCTTTCCATTGTTTATGGCCTAAATATAATCATTTTGGTGAGATTAGTCCACTATG
130 CAATGCTTTTCTTTCCATTGTTTAGGGCCTAAATATAATCATTTT-GTGAGATTAGTCCACTATG
* * * *
3432 AGGTTTTTAACTCATTTGGAACTCTTGTTATTTTGGGCCTTTC-GGGACCCATTAGTTCCGTTTT
194 AAGTTTTTAACTCATTTGGAACTCTTGTTATTTTGGGCATATCGGGGA-ACATTAGTTCCGTTTT
* * *
3496 GAATCGTCTTCGATTTTCCAAACCTCAATTCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
258 GAATCGTCTTCGATTTGCCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATA
*
3561 ATTTTGGTGAGAATAGTCCACTGTGAAGTTTTTAACTCATTTGGAACAGTTGCTATTTTGGG-CA
323 ATTTTGGTGAGAATAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGCTATTTTGGGTC-
*
3625 TATCGGGGCACATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTC
387 TATCAGGGCACATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTC
* * * *
3690 CATTGTTTATGGCCTAAGTATAATAATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA-ACTCA
452 CATTGTTTATGGCCTAACTATAATAATTTTGGTGAGATTAGTCCACTGTAAAGTTCTTAGA-ACA
*
3754 TTTGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATT
516 TTTGGAACACTTGTTATTTTGGGCCTTTCGAGGCCCATT
3793 GACACGGGAG
Statistics
Matches: 511, Mismatches: 38, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
610 1 0.00
611 152 0.30
612 358 0.70
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (612 bp):
GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACT
TGTAATCTTGGGCCTTTCACGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTCGCAAACCTC
AATGCTTTTCTTTCCATTGTTTAGGGCCTAAATATAATCATTTTGTGAGATTAGTCCACTATGAA
GTTTTTAACTCATTTGGAACTCTTGTTATTTTGGGCATATCGGGGAACATTAGTTCCGTTTTGAA
TCGTCTTCGATTTGCCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATAATT
TTGGTGAGAATAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGCTATTTTGGGTCTATC
AGGGCACATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT
GTTTATGGCCTAACTATAATAATTTTGGTGAGATTAGTCCACTGTAAAGTTCTTAGAACATTTGG
AACACTTGTTATTTTGGGCCTTTCGAGGCCCATTCGTTCCGTTTTTCGTCTTCGATTTGGCAAAC
CTCAATGCTTTTCTTTAAGTTGTTTAT
Done.