Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009499.1 Corchorus olitorius cultivar O-4 contig09531, 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: 5421
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Found at i:893 original size:5 final size:5
Alignment explanation
Indices: 877--906 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
867 TAATAATAGG
877 AAGGA GAAGGA AAGGA AAGGA AAGGA AAGG
1 AAGGA -AAGGA AAGGA AAGGA AAGGA AAGG
907 GGAGGGAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (5 bp):
AAGGA
Found at i:936 original size:5 final size:5
Alignment explanation
Indices: 926--970 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
916 TTTTTTAAAG
* * *
926 GAAAA GAAAA GAAAA GAAAA TGAAAG GAAAA GAAAG GAAAG GAAA
1 GAAAA GAAAA GAAAA GAAAA -GAAAA GAAAA GAAAA GAAAA GAAA
971 GGGGAGGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
5 32 0.89
6 4 0.11
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (5 bp):
GAAAA
Found at i:955 original size:21 final size:21
Alignment explanation
Indices: 926--965 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
916 TTTTTTAAAG
926 GAAAAGAAAAGAAAAGAAAAT
1 GAAAAGAAAAGAAAAGAAAAT
* *
947 GAAAGGAAAAGAAAGGAAA
1 GAAAAGAAAAGAAAAGAAA
966 GGAAAGGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (21 bp):
GAAAAGAAAAGAAAAGAAAAT
Found at i:987 original size:66 final size:65
Alignment explanation
Indices: 883--1062 Score: 296
Period size: 66 Copynumber: 2.8 Consensus size: 65
873 TAGGAAGGAG
883 AAGGAAAGGAAAGGAAAGGAAAGGGGAGGGAAGTTTTTTAAAGGAAAAGAAAAGAAAAGAAAATG
1 AAGGAAA-GAAAGGAAAGGAAAGGGGAGGGAAGTTTTTTAAAGGAAAAGAAAAGAAAAGAAAATG
948 A
65 A
949 AAGGAAAAGAAAGGAAAGGAAAGGGGAGGGAAGTTTTTTAAAGGAAAAGAAAAGAAAAGAAAATG
1 AAGG-AAAGAAAGGAAAGGAAAGGGGAGGGAAGTTTTTTAAAGGAAAAGAAAAGAAAAGAAAATG
1014 A
65 A
*
1015 AA-G---GAACGGAAAGGAAAGGGGAGGGAAGTTTTTTTAAAGGAAAAGAAA
1 AAGGAAAGAAAGGAAAGGAAAGGGGAGGGAAG-TTTTTTAAAGGAAAAGAAA
1063 GGATATAGGT
Statistics
Matches: 111, Mismatches: 1, Indels: 8
0.93 0.01 0.07
Matches are distributed among these distances:
61 24 0.22
62 19 0.17
65 1 0.01
66 64 0.58
67 3 0.03
ACGTcount: A:0.54, C:0.01, G:0.33, T:0.12
Consensus pattern (65 bp):
AAGGAAAGAAAGGAAAGGAAAGGGGAGGGAAGTTTTTTAAAGGAAAAGAAAAGAAAAGAAAATGA
Found at i:4677 original size:328 final size:320
Alignment explanation
Indices: 3866--5385 Score: 1122
Period size: 328 Copynumber: 4.7 Consensus size: 320
3856 TTTGACAAAA
* * * *
3866 ATACTCATAAAATATATATAATTAAACGCCAAAAATATTGGAGGACTTTTCACGCTTTTAATATC
1 ATACTCATAAAAAATATATAATTCAACGACAAAAA-AAT-GA-GACTTTTCACGCTTTTAATATC
* * ** * * *
3931 ATTTTTC-ATTTTTTTCTGAATTAATTTCTAATTAAATCGATACAAGA-TCA-AATGCACATAAA
63 GTTTTCCTATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGAA-ACTCATAAA
* ** * * *
3993 AACAAATCCTTAAATCCAATGTGGCTGAA-ATTTTATTAAATGAATAAAGATATTTCAAGGAGTC
127 AACAAATCCTTAAAT-CAATGTGACT-AAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTC
* * * * * ** * **
4057 -TCGGCGCCAAAAATCATGCAAAACAGAGCTGTGGCCTTGGAACGCGTTTTTAGTTAAAAACTGT
190 AT-GGCACCAAAAATCATGCAAAACTGAGCCGAGACC-CCGAACGCATTTTTAGCAAAAAACTGT
* * * * * * * *
4121 GATGGTTTGTACACGATTTTGGCTAAAACTTTGCAGAAATGGACCCGAAAGATGTTTTCTCGATT
253 GATGG-TAGTACAAGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATAT-TTTTCTCAATT
4186 TT---
316 TTAGC
** * * * * * * *
4188 -T-GGC-TAAAAAAT-TCATGATTCGA-TATCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATA
1 ATACTCATAAAAAATAT-ATAATTCAACGA-CAAAAA-AATG-A-GACTTTTCACGCTTTTAATA
* ** * * *
4248 TTGTTTTTCCTA------TCCGGATTAATTTCTAATTAAATCGAACCAAGATTCAGATACTCGTA
61 TCG-TTTTCCTATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGAAACTCATA
* * * *
4307 AAAATAAATCCTTAAATCTAATGTAACTAAGATTTGGTTAGATAAATATAGATATTTCAAGGAGT
125 AAAACAAATCCTTAAATC-AATGTGACTAAGATTTGGTTAGATGAATATAGATATTTCAAGAAGT
* **
4372 CATGGCACCAAAAATCATGCAAAACTGAGCC-AGACCCCGTAAGGCATTTTTAGCTGAAAACTGT
189 CATGGCACCAAAAATCATGCAAAACTGAGCCGAGACCCCG-AACGCATTTTTAGCAAAAAACTGT
* * *
4436 GATGGTTAGTACAAGATTTCAGCTAAACTTTTCCAAAAATTGACCCGAAATATTTTTCCTCAATT
253 GATGG-TAGTACAAGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTT-CTCAATT
4501 TCTAG-
316 T-TAGC
*
4506 ATACTCATAAAAAATATATAATTCAACGACAAAAAAATGAAAGCCTTTTTCACGCTTTTAATATC
1 ATACTCATAAAAAATATATAATTCAACGACAAAAAAATG--AGAC-TTTTCACGCTTTTAATATC
* * * * *
4571 GTTTTCCCTATTTTATTTCCAAATTAATTTCTGATTAAATCAAAACAAGATTTAGAAATTCGTAA
63 GTTTT-CCTATTTT-TTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGAAACTCATAA
* * * * * *
4636 AAACAAATCTTTAAATACAATGTGGCTGAGACTTCGTTAGATGAATATAGATATATTTTAAGAAG
126 AAACAAATCCTTAAAT-CAATGTGACTAAGATTTGGTTAGATGAATATAG--ATATTTCAAGAAG
* * * * * *
4701 TCTTGGCGCCAAAAAT-ATGCAAAACTGA-CCTAGGACCCCAGAACGTATTTTTAGCCAAAAACA
188 TCATGGCACCAAAAATCATGCAAAACTGAGCCGA-GACCCC-GAACGCATTTTTAGCAAAAAACT
* * * *
4764 ATGATGGTA-CAC-A-ATTTCGGCTAAAATTTTGCAAAAATTAACCCAAAATATTTTTCTCAATT
251 GTGATGGTAGTACAAGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCTCAA-T
4826 TTTAGCCAC
315 TTTAG---C
* * * * * * *
4835 AATACTAATTAAAAATATATAATTCAACGCCAAAAAAAGTG-GGCTTCTCACGCTTTCAATATAA
1 -ATACTCATAAAAAATATATAATTCAACGACAAAAAAA-TGAGACTTTTCACGCTTTTAATAT-C
* * * * * *
4899 TTTTTCCTA-TTTTTT-CAAATTAATTTTTAATTAAATTGAAACATGATTCA-AATGCTCACAAA
63 GTTTTCCTATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGAA-ACTCATAAA
* * **
4961 AACAAATCCTTAAATCAAGTGTGACTAAGATTTGGTTAGATGAATATAGATATTTCAAGGATTTT
127 AACAAATCCTTAAATCAA-TGTGACTAAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCA
* * * * * *
5026 TGCCACAAAAAATCATGCAAAACTGATCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAAAAAAAC
191 TGGCACCAAAAATCATGCAAAACTGAGCCGAGACCCC-GAACGCATTTTTAG-C----AAAAAAC
*
5091 TGTGAT-G--GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTGTCTCAA
250 TGTGATGGTAGTACAAGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTT-TCTCAA
5153 TTTTAGGCCAC
314 TTTTA-G---C
* * * * * *
5164 AACACTCATAAAATATATATAATTTAA-TACCAAAAAGACTGGAGGACTTTTCACACTTTTAATA
1 -ATACTCATAAAAAATATATAATTCAACGA-CAAAAA-AAT-GA-GACTTTTCACGCTTTTAATA
* ** *
5228 TCGTTTT-C-ATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGAGACTCATAA
61 TCGTTTTCCTATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGAAACTCATAA
* * * *
5291 AAACAAATCCTTAGATTCAATGTGGCTGAA-ATTTGATTAGATGAATATAGATATTTAAAGAAGT
126 AAACAAATCCTTA-AATCAATGTGACT-AAGATTTGGTTAGATGAATATAGATATTTCAAGAAG-
*
5355 CTCAAT-GCA--AAAAATCATGCAAAACTAAGCC
188 -TC-ATGGCACCAAAAATCATGCAAAACTGAGCC
5386 AGGGCCTCAA
Statistics
Matches: 955, Mismatches: 172, Indels: 133
0.76 0.14 0.11
Matches are distributed among these distances:
314 5 0.01
315 105 0.11
316 86 0.09
317 2 0.00
318 2 0.00
319 43 0.05
320 16 0.02
321 46 0.05
322 24 0.03
323 34 0.04
324 77 0.08
325 11 0.01
326 45 0.05
327 22 0.02
328 144 0.15
329 57 0.06
330 96 0.10
331 111 0.12
332 25 0.03
333 3 0.00
334 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.32
Consensus pattern (320 bp):
ATACTCATAAAAAATATATAATTCAACGACAAAAAAATGAGACTTTTCACGCTTTTAATATCGTT
TTCCTATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGAAACTCATAAAAACA
AATCCTTAAATCAATGTGACTAAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCATGGCA
CCAAAAATCATGCAAAACTGAGCCGAGACCCCGAACGCATTTTTAGCAAAAAACTGTGATGGTAG
TACAAGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCTCAATTTTAGC
Found at i:5368 original size:331 final size:326
Alignment explanation
Indices: 3827--5415 Score: 1181
Period size: 331 Copynumber: 4.9 Consensus size: 326
3817 CCATAATGGT
* * * *
3827 AAAAA-TGACCCGAAAGATTTTT-TCCAATTTTTGACAAAAATACTCATAAAATATATATAATTA
1 AAAAATTGACCCGAAATATTTTTCT-CAATTTTAGGC--AAATACTCATAAAA-ATATATAATTC
* * * *
3890 AACGCCAAAAATATTGGAGGACTTTTCACGCTTTTAATATCATTTTTCATTTTTTTCTGAATTAA
62 AACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATC-GTTTTCATATTTTTCTGAATTAA
* * * *
3955 TTTCTAATTAAATCGATACAAGA-TCAAATG-CACATAAAAACAAATCCTTAAATCCAATGTGGC
126 TTTCTAATTAAATCGAAACAAGATTCAGA-GACTCATAAAAACAAATCCTT-AATTCAATGTGGC
* * * * * * * *
4018 TGAAATTTTATTAAATGAATAAAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACAG
189 TGAAATTTGATTAGATGAATATAGATATTTAAAGAAGTCTCGACGCAAAAAATCATGCAAAACTG
* ** ** *
4083 AG-CTGTGGCCTTGGAACGCGTTTTTAG---TTAAAAACTGTGATGGTTTGTACACGATTTTGGC
254 AGCCAG-GGCCCCGGAACGCGTTTTTAGCCAAAAAAAACTGTGATGG--TGTACACGATTTCGGC
*
4144 TAAAACTTTGC
316 TAAAATTTTGC
* * * * * * *
4155 AGAAATGGACCCGAAAGATGTTTTCTCGATTTTTGG------CT-A-AAAAAT-TCATGATTCGA
1 AAAAATTGACCCGAAATAT-TTTTCTCAATTTTAGGCAAATACTCATAAAAATAT-ATAATTCAA
* * * * * * * * * *
4211 TATCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCTA----TCCGGATTAATT
64 CACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCG-TTTTCATATTTTTCTGAATTAATT
* * * * * **
4272 TCTAATTAAATCGAACCAAGATTCAGATACTCGTAAAAATAAATCCTTAAATCTAATGTAACT-A
128 TCTAATTAAATCGAAACAAGATTCAGAGACTCATAAAAACAAATCCTTAATTC-AATGTGGCTGA
* * * * *
4336 AGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCATGGCAC-C-AAAAATCATGCAAAACTG
192 A-ATTTGATTAGATGAATATAGATATTTAAAGAAGTC-TCG-ACGCAAAAAATCATGCAAAACTG
* * * * ** * *
4399 AGCCA-GACCCCGTAAGGCATTTTTAG-C--TGAAAACTGTGATGGTTAGTACAAGATTTCAGCT
254 AGCCAGGGCCCCGGAACGCGTTTTTAGCCAAAAAAAACTGTGATGG-T-GTACACGATTTCGGCT
* *
4460 AAACTTTTCC
317 AAAATTTTGC
4470 AAAAATTGACCCGAAATATTTTTCCTCAATTTCTA-G---ATACTCATAAAAAATATATAATTCA
1 AAAAATTGACCCGAAATATTTTT-CTCAATTT-TAGGCAAATACTCAT-AAAAATATATAATTCA
* * * * * **
4531 ACGA-CAAAAA-AATGAAAGCCTTTTTCACGCTTTTAATATCGTTTTCCCTATTTTATTTCCAAA
63 AC-ACCAAAAAGATTGGAGGAC-TTTTCACGCTTTTAATATCGTTTT--C-ATATT-TTTCTGAA
* * * * * * * *
4594 TTAATTTCTGATTAAATCAAAACAAGATTTAGAAATTCGTAAAAACAAATCTTTAAATACAATGT
122 TTAATTTCTAATTAAATCGAAACAAGATTCAGAGACTCATAAAAACAAATCCTT-AATTCAATGT
* * * * * *
4659 GGCTGAGACTTCG-TTAGATGAATATAGATATATTTTAAGAAGTCTTGGCGCCAAAAAT-ATGCA
186 GGCTGA-AATTTGATTAGATGAATATAG--ATATTTAAAGAAGTCTCGACGCAAAAAATCATGCA
* * ** * *
4722 AAACTGA-CCTAGGACCCCAGAACGTATTTTTAGCCAAAAACAA---TGAT-G-GTACACAATTT
248 AAACTGAGCC-AGGGCCCCGGAACGCGTTTTTAGCCAAAAAAAACTGTGATGGTGTACACGATTT
4781 CGGCTAAAATTTTGC
312 CGGCTAAAATTTTGC
* * * *
4796 AAAAATTAACCCAAAATATTTTTCTCAATTTTTAGCCACAATACTAATTAAAAATATATAATTCA
1 AAAAATTGACCCGAAATATTTTTCTCAA-TTTTAGGCA-AATACTCA-TAAAAATATATAATTCA
* * * * * ** * *
4861 ACGCCAAAAAAAGT-G-GG-CTTCTCACGCTTTCAATATAATTTTTCCTATTTTT-TCAAATTAA
63 ACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATAT-CGTTTTCATATTTTTCT-GAATTAA
* * * * * * *
4922 TTTTTAATTAAATTGAAACATGATTCAAATG-CTCACAAAAACAAATCCTTAAATCAAGTGTGAC
126 TTTCTAATTAAATCGAAACAAGATTCAGA-GACTCATAAAAACAAATCCTTAATTCAA-TGTGGC
* * * * * * * *
4986 T-AAGATTTGGTTAGATGAATATAGATATTTCAAGGATTTTTGCCACAAAAAATCATGCAAAACT
189 TGAA-ATTTGATTAGATGAATATAGATATTTAAAGAAGTCTCGACGCAAAAAATCATGCAAAACT
* *
5050 GATCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAAAAAAACTGTGAT-G-GTACACGATTTCGGC
253 GAGCCAGGGCCCCGGAACGCGTTTTTAGCC--AAAAAAAACTGTGATGGTGTACACGATTTCGGC
5113 TAAAATTTTGC
316 TAAAATTTTGC
* *
5124 AAAAATTGACCCGAAATATTTTGTCTCAATTTTAGGCCACAACACTCATAAAATATATATAATTT
1 AAAAATTGACCCGAAATATTTT-TCTCAATTTTAGG-CA-AATACTCATAAAA-ATATATAATTC
* * *
5189 AATACCAAAAAGACTGGAGGACTTTTCACACTTTTAATATCGTTTTCATATTTTTCTGAATTAAT
62 AACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTCATATTTTTCTGAATTAAT
5254 TTCTAATTAAATCGAAACAAGATTCAGAGACTCATAAAAACAAATCCTTAGATTCAATGTGGCTG
127 TTCTAATTAAATCGAAACAAGATTCAGAGACTCATAAAAACAAATCCTTA-ATTCAATGTGGCTG
* * *
5319 AAATTTGATTAGATGAATATAGATATTTAAAGAAGTCTCAATGCAAAAAATCATGCAAAACTAAG
191 AAATTTGATTAGATGAATATAGATATTTAAAGAAGTCTCGACGCAAAAAATCATGCAAAACTGAG
* ** *
5384 CCAGGGCCTCAAAACGCGTTTTTAACCAAAAA
256 CCAGGGCCCCGGAACGCGTTTTTAGCCAAAAA
5416 CCGTGA
Statistics
Matches: 994, Mismatches: 190, Indels: 153
0.74 0.14 0.11
Matches are distributed among these distances:
314 6 0.01
315 107 0.11
316 77 0.08
317 4 0.00
318 4 0.00
319 45 0.05
320 15 0.02
321 37 0.04
322 28 0.03
323 42 0.04
324 69 0.07
325 17 0.02
326 46 0.05
327 16 0.02
328 143 0.14
329 78 0.08
330 85 0.09
331 148 0.15
332 24 0.02
333 3 0.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.32
Consensus pattern (326 bp):
AAAAATTGACCCGAAATATTTTTCTCAATTTTAGGCAAATACTCATAAAAATATATAATTCAACA
CCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTCATATTTTTCTGAATTAATTTCT
AATTAAATCGAAACAAGATTCAGAGACTCATAAAAACAAATCCTTAATTCAATGTGGCTGAAATT
TGATTAGATGAATATAGATATTTAAAGAAGTCTCGACGCAAAAAATCATGCAAAACTGAGCCAGG
GCCCCGGAACGCGTTTTTAGCCAAAAAAAACTGTGATGGTGTACACGATTTCGGCTAAAATTTTG
C
Done.