Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019066.1 Corchorus olitorius cultivar O-4 contig19099, 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: 41117
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2112 original size:335 final size:332
Alignment explanation
Indices: 971--2768 Score: 1565
Period size: 335 Copynumber: 5.4 Consensus size: 332
961 ATTTTCGGTA
* * * *
971 TTTT-GCTAAAAACGCGTTTCGGGGTCCCGATTCAGTTTTGCATGATTTTTGGCGTCAAGACTCC
1 TTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC
* * * *
1035 TTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCATTTAAAAATTTGTTTTTACTA
66 TTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAATTT-AAGATTTATTTTTACGA
* * * *
1100 GCATCTGAATCTTGTTTTGATTTAAATAGAATTTAATTCAGAAAGTATGAAAAACGATATTAAAA
130 GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAATATGAAAAACGATATTAAAA
* ** * * * *
1165 GCGTGAAAAGTCCTCCAATCTTGTTT-TAGTTGAATTATATATATTTTATGTGTATTTTAGACAA
195 GCGTGAAAAGTCCTCCAATATT-TTTGGCGTTGAATTATATATTTTTTATGAGTATTATAGCCAA
* * * * * * *
1229 AAATTGAGGAAAAATATTTCTAG-TTAACTTTTGCAAAATATTAGCCGAAATCGTGTACATTA-G
259 AAATTGAGGAAAAAAATTTCT-GCTCAAATTTTGCAAAATTTTAGCTGAAATCGTGTAC-TAACA
* *
1292 TCGA-AATCATGGT
322 TC-ACAGT--TGTT
* * * *
1305 TTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAATGTTCCATG-TTTTTGGCGCCGAGACTCC
1 TTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC
* ** * * * *** *
1369 TTGAAATATTTATATTCATCTAACCAAATCTCAGGTACAATGGATTTAAGGATTT-GTAAAACAA
66 TTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAATTTAA-GATTTATTTTTACGA
* *
1433 GCATCTGAATATTGTTTCGATTTAATTAAAAATTAATTCAGAAAATAATAGGAAAAACGATATTA
130 GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAT-AT--GAAAAACGATATTA
* * * * * * *
1498 GAAGCATGAAAAGCCCTTCAATATTTTTAGCGTTAAATTATATAATTTTTATGAGTATTA-AGGC
192 AAAGCGTGAAAAGTCCTCCAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTATA-GC
* * * * * *
1562 TAAAAATTGAGGAAATAACTTTCGGCTCAAATTTTGCAAAATTTTAGCTGAAATCGTGTAATGAT
256 CAAAAATTGAGGAAAAAAATTTCTGCTCAAATTTTGCAAAATTTTAGCTGAAATCGTGTACT-AA
1627 CATCAC-G--GTT
320 CATCACAGTTGTT
* * * *
1637 TTTTGGCTAAAAACGCGTTCCGAGGCCCCGGCTAAGTTTTGCATGATTTTTGGCGCCAAGACTCT
1 TTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC
* * * * * * ** * *
1702 TTGAGATATCCATATTCATCTAATCAAATTTCAACTACATTTTATTTAAGAATTAGATTTTACGA
66 TTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAGATTTA-TTTTTACGA
1767 GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATTG-AAAACGATATTAA
130 GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAATA-TGAAAAACGATATTAA
* *
1831 AAGCGTAAAAAGTCCTCCAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTATATCCA
193 AAGCGTGAAAAGTCCTCCAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTATAGCCA
* * ** * *
1896 AAAATTGAGAAAAAAAATTTATGCTCATTTTTTACAAAATTTTAACTGAAATCGTGTACTAACCA
258 AAAATTGAGGAAAAAAATTTCTGCTCAAATTTTGCAAAATTTTAGCTGAAATCGTGTACTAA-CA
*
1961 TCACAGTTTTT
322 TCACAGTTGTT
* ** * * *
1972 TTTTGGCTAAAAACGCGTTTCGGGGCTTCGGCTCAGTTTTGCATGGTTTTTGGCGCCGAGACTCC
1 TTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC
* * * * *
2037 TTAAAATTTTTATATTCATCTAATCAAATCTCATCCACATTGAATTTAAGTATTTATTTTTACGA
66 TTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAG-ATTTATTTTTACGA
*
2102 GTATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAA
130 GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAATATGAAAAACGATATTAAA
* *
2167 AGCGTGAAAAGTCCTCCAAT-CTTTTGGTGTTGATATATATATATATATATATATATATATAAAT
194 AGCGTGAAAAGTCCTCCAATATTTTTGGCGTTG--------------A-AT-TATATAT-T---T
* * * * * * *
2231 TTTATGAGTATTGTGGCAAAAAATTGTA-GAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAG
239 TTTATGAGTATTATAGCCAAAAATTG-AGGAAAAAAATTTCTGCTCAAATTTTGCAAAATTTTA-
*
2295 GC-GAAATCGTGTAC---CAT--CA--TGGT
302 GCTGAAATCGTGTACTAACATCACAGTTGTT
* * * * * * *
2318 TTTTGGCTAAAAAAGAGTTCCGGGGCCCC-AGGTCAAG-TTTGCATGATTTTTTGTGGCAAAACT
1 TTTTGGCTAAAAACGCGTTCCGGGGCCCCGA-CTC-AGTTTTGCATGATTTTTGGCGCCAAGACT
* * * * * * *
2381 CATTGAATTATCTATATTCATCTAGCCAAATCTTAACCACATTGGATTTAAGGATTTGTTTTTAC
64 CCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAATTTAA-GATTTATTTTTAC
* * ** * * *
2446 GAGCATTTGAATCATGTTTTAATTTAATTAGAAATTAATTTGAAAAAAATTAGGAAAAACGATAT
128 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TT-CAGAAAA-TATGAAAAACGATAT
* * * * * * * * *
2511 TAGAAGCGTGAGAAGCCCTTCAATTTTTTTGACGTTGAATTATATATATTTTTATTAGTATTGTG
190 TAAAAGCGTGAAAAGTCCTCCAATATTTTTGGCGTTGAATTATATAT-TTTTTATGAGTATTATA
* * * * * *
2576 GCTAAAAGTTGA-GAAAAATATTTCGGAT-AAATTTTTGCAAAATTTTAGCCGAAATCGTG-A--
254 GCCAAAAATTGAGGAAAAAAATTTCTGCTCAAA-TTTTGCAAAATTTTAGCTGAAATCGTGTACT
*
2636 ACCATCAC-G--GTT
318 AACATCACAGTTGTT
* * * * * *
2648 TTTTGGGCTAAAAACGGGTTCCAGGGCCCCGAGTCAGTTCTGCATGATTTTTGGCACCAAGACTT
1 TTTT-GGCTAAAAACGCGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTC
* * *
2713 CTTAAAATACATCTATATTCATCTAACCAAATCTCAACCACATTGTATTTAA-ATTT
65 CTTGAAAT--ATCTATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAGATTT
2769 TTGCAAAATT
Statistics
Matches: 1200, Mismatches: 200, Indels: 131
0.78 0.13 0.09
Matches are distributed among these distances:
328 5 0.00
329 43 0.04
330 32 0.03
331 56 0.05
332 168 0.14
333 153 0.13
334 127 0.11
335 234 0.19
336 113 0.09
337 2 0.00
346 133 0.11
347 9 0.01
348 38 0.03
349 11 0.01
350 10 0.01
351 1 0.00
354 63 0.05
355 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (332 bp):
TTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC
TTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAGATTTATTTTTACGAG
CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAATATGAAAAACGATATTAAAAG
CGTGAAAAGTCCTCCAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTATAGCCAAAA
ATTGAGGAAAAAAATTTCTGCTCAAATTTTGCAAAATTTTAGCTGAAATCGTGTACTAACATCAC
AGTTGTT
Found at i:2206 original size:2 final size:2
Alignment explanation
Indices: 2199--2227 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2189 TTTGGTGTTG
2199 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2228 AATTTTATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2921 original size:158 final size:157
Alignment explanation
Indices: 2603--2922 Score: 407
Period size: 158 Copynumber: 2.0 Consensus size: 157
2593 ATATTTCGGA
*
2603 TAAATTTTTGCAAAATTTTAGCCGAAATCGTGAACCATCACGGTTTTTTGGGCTAAAAACGGGTT
1 TAAATTTTTGCAAAATTTTAGCCGAAATCGTGAACCATCACGG-TTTTTCGGCTAAAAACGGGTT
* *
2668 CCAGGGCCCCGAGTCAGTTCTGCATGATTTTTGGCACCAAGACTTCTTAAAATACATCTATATTC
65 CCAGGGCCCCGACTCAGTTCTGCATGATTTTTGGCACCAAGACTCCTTAAAATA-ATCTATATTC
*
2733 ATCTAACCAAATCTCAACCACATTGTATT
129 ATCTAACCAAATCTCAACCACATTGGATT
*
2762 TAAATTTTTGCAAAATTTTAGCCGTAATCGTGTATTAACCATCACGG-TTTTCGGCTAAAAA-GG
1 TAAATTTTTGCAAAATTTTAGCCGAAATCGTG----AACCATCACGGTTTTTCGGCTAAAAACGG
* * * * ** * *
2825 CGTTTC-GGGGCCCG-CTCAGTTTTTGTATGATTTTTGGTGCCAATACTCCTTGAAAT-ATCTAT
62 -GTTCCAGGGCCCCGACTCAG-TTCTGCATGATTTTTGGCACCAAGACTCCTTAAAATAATCTAT
*
2887 ATTCATCTAATCAAATCTCAACCACATTGGATT
125 ATTCATCTAACCAAATCTCAACCACATTGGATT
2920 TAA
1 TAA
2923 GGATTTGTTT
Statistics
Matches: 141, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
158 40 0.28
159 35 0.25
160 38 0.27
161 17 0.12
163 11 0.08
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (157 bp):
TAAATTTTTGCAAAATTTTAGCCGAAATCGTGAACCATCACGGTTTTTCGGCTAAAAACGGGTTC
CAGGGCCCCGACTCAGTTCTGCATGATTTTTGGCACCAAGACTCCTTAAAATAATCTATATTCAT
CTAACCAAATCTCAACCACATTGGATT
Found at i:8667 original size:30 final size:29
Alignment explanation
Indices: 8629--8715 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 29
8619 ACTTTTCAGA
*
8629 AAAAAGGATTGGCAAAAAG-GGTTCTGAGG
1 AAAAAGGATTGGCAAAAAGAAGTT-TGAGG
* *
8658 AAGAAAGGATTGGCAGAAAGAAGTTTGGGG
1 AA-AAAGGATTGGCAAAAAGAAGTTTGAGG
* *
8688 AAATAAGAATTGGCAAAAAGAAGATTGA
1 AAA-AAGGATTGGCAAAAAGAAGTTTGA
8716 CAAAAATTCG
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
29 3 0.06
30 42 0.88
31 3 0.06
ACGTcount: A:0.46, C:0.05, G:0.32, T:0.17
Consensus pattern (29 bp):
AAAAAGGATTGGCAAAAAGAAGTTTGAGG
Found at i:11003 original size:3 final size:3
Alignment explanation
Indices: 10995--11024 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
10985 GTATTAATAC
10995 AAT AAT AAT AAT AAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA
11025 GGAATTATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:13608 original size:66 final size:66
Alignment explanation
Indices: 13502--13633 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
13492 AGTCTCACGG
13502 GATGTGAATTAAATTTATTTATTTGTTTGTTGTTTGTTGTTTGTTCTGGTAGTTTGTTGAGTAGG
1 GATGTGAATTAAATTTATTTATTTGTTTGTTGTTTGTTGTTTGTTCTGGTAGTTTGTTGAGTAGG
13567 T
66 T
13568 GATGTGAATTAAATTTATTTATTTGTTTGTTGTTTGTTGTTTGTTCTGGTAGTTTGTTGAGTAGG
1 GATGTGAATTAAATTTATTTATTTGTTTGTTGTTTGTTGTTTGTTCTGGTAGTTTGTTGAGTAGG
13633 T
66 T
13634 TATTTAAGCT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.17, C:0.02, G:0.26, T:0.56
Consensus pattern (66 bp):
GATGTGAATTAAATTTATTTATTTGTTTGTTGTTTGTTGTTTGTTCTGGTAGTTTGTTGAGTAGG
T
Found at i:13787 original size:11 final size:11
Alignment explanation
Indices: 13771--13795 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13761 ATTATTGTCC
13771 AAAAAAAAACA
1 AAAAAAAAACA
13782 AAAAAAAAACA
1 AAAAAAAAACA
13793 AAA
1 AAA
13796 TCCGAAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:23226 original size:38 final size:37
Alignment explanation
Indices: 23184--23261 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 37
23174 CAAAGAGTTA
*
23184 AATTCCTTTTTATT-CATTCGAAATCAAAATGTTTAGAG
1 AATTCCTTTTTATTCCAGT-GAAATCAAAATGTTTA-AG
*
23222 AATTCCTTTTTATTCCAGTGAAATCGAAATGTTTAAG
1 AATTCCTTTTTATTCCAGTGAAATCAAAATGTTTAAG
23259 AAT
1 AAT
23262 AAATAAGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
37 5 0.14
38 29 0.78
39 3 0.08
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41
Consensus pattern (37 bp):
AATTCCTTTTTATTCCAGTGAAATCAAAATGTTTAAG
Found at i:28691 original size:1 final size:1
Alignment explanation
Indices: 28685--28712 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
28675 TTATGTTCTC
28685 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
28713 CCCGGAAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:40488 original size:12 final size:12
Alignment explanation
Indices: 40471--40497 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40461 AAATAGAAAA
40471 TAATTATAAATT
1 TAATTATAAATT
40483 TAATTATAAATT
1 TAATTATAAATT
40495 TAA
1 TAA
40498 AGTCTTGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAATTATAAATT
Found at i:40791 original size:22 final size:22
Alignment explanation
Indices: 40763--40951 Score: 132
Period size: 22 Copynumber: 8.5 Consensus size: 22
40753 TAGATTATTG
*
40763 AAATTTCATAGTGTGGCTATCA
1 AAATTTCATAGTGTGGTTATCA
*
40785 AAATTTCATAATGTGGTTA-CAA
1 AAATTTCATAGTGTGGTTATC-A
** *
40807 AAATTTCATAG-AAGGTAATCA
1 AAATTTCATAGTGTGGTTATCA
* * *
40828 AAGTTTCATATTGTGTTTATCA
1 AAATTTCATAGTGTGGTTATCA
* * * *
40850 AAATTTCATAATGAGATTAACA
1 AAATTTCATAGTGTGGTTATCA
* **
40872 CTAAA-TTCTATAGGGAAGTTATCA
1 --AAATTTC-ATAGTGTGGTTATCA
* * *
40896 ACATTTCATAGGGAGGTTATCA
1 AAATTTCATAGTGTGGTTATCA
* * *
40918 AAATTTCATAGTTTGATTATCC
1 AAATTTCATAGTGTGGTTATCA
40940 AAATTTCATAGT
1 AAATTTCATAGT
40952 CTACCAAATC
Statistics
Matches: 130, Mismatches: 30, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
21 15 0.12
22 96 0.74
23 6 0.05
24 13 0.10
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (22 bp):
AAATTTCATAGTGTGGTTATCA
Found at i:41077 original size:22 final size:22
Alignment explanation
Indices: 41020--41117 Score: 94
Period size: 22 Copynumber: 4.5 Consensus size: 22
41010 CATCAAAATT
*
41020 AATTTCATA-TAGAGGTTATCACA
1 AATTTCATAGT-GTGGTTATCA-A
*
41043 AATTT-ATACTGTGGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
* * *
41064 AATTTCAGAGTGTGGTGACCAA
1 AATTTCATAGTGTGGTTATCAA
*
41086 AATTTCATAG-GATGGTTATCAG
1 AATTTCATAGTG-TGGTTATCAA
41108 AATTTCATAG
1 AATTTCATAG
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
21 7 0.11
22 50 0.79
23 6 0.10
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (22 bp):
AATTTCATAGTGTGGTTATCAA
Done.