Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017145.1 Corchorus olitorius cultivar O-4 contig17178, 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: 17563
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Found at i:1084 original size:32 final size:32
Alignment explanation
Indices: 1028--1099 Score: 110
Period size: 32 Copynumber: 2.2 Consensus size: 32
1018 AATTGGTGTA
1028 AAGTTAATAAAAAAATAGAAGGATAAATTGGAG
1 AAGTTAATAAAAAAATAG-AGGATAAATTGGAG
1061 AAGTTAATAAAAAATATAG-GGATAAATTGGAG
1 AAGTTAATAAAAAA-ATAGAGGATAAATTGGAG
*
1093 AAATTAA
1 AAGTTAA
1100 GTGTGAATAG
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
32 19 0.51
33 14 0.38
34 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.19, T:0.24
Consensus pattern (32 bp):
AAGTTAATAAAAAAATAGAGGATAAATTGGAG
Found at i:2270 original size:338 final size:331
Alignment explanation
Indices: 1531--2543 Score: 1094
Period size: 338 Copynumber: 3.0 Consensus size: 331
1521 CAATAGCTGG
* * * * ** * * * *
1531 GATTTGGTTAGATGAATATAGATATTTCAAGGAGTATCGGCGCCAAAAATCATTCAAAATTGAAC
1 GATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGC-ATAAAAACCATGCAAAACTGAGC
* * ** * * * *
1596 CGGGTCCCGC--AACGCGTTTTTAG-ACAAAAACCCTAATGATTATTACATGATTTCGGCTAAAA
65 CGGGGCCC-CAAAACACGTTTTTAGCA-AAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAA
* * * * * * *
1658 TTTTGTAAAAATTGACCCGAAAGATATTTC-CTCAATTTTTAG-TCATAATACTCATAAAAAATA
128 TTTTGCAAAAAATAACACGAAAGATATTTCGCCCAATTTTTGGAT-AAAATACTCATAAAAAATA
* * * *
1721 CATAAATCAATGCCAAAAATA-TTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTT
192 TATAATTCAACGCCAAAAATATTTG-AGGGCTTTTCATGCTTTTAATATCGTTTTTCATA-TTTT
* *
1785 TTCTAAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACATATCCTTAAAT
255 TTCT-AATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGTAAAAACATATTCTTAAAT
* *
1850 GCAATGTGG-TAA
319 CCAATGTGGTTGA
* * * *
1862 GATTTTATTAGATGAATATAGATTTTTCAAGGAGTGTTGGCATAAAAACCATGCAAAACTGAGCC
1 GATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGCATAAAAACCATGCAAAACTGAGCC
* *
1927 GGGGCCCCAAAATACGTTTTTAGCCAAAAAAATTAACTGTGATGGGTTAGTACACGATTTTGGCT
66 GGGGCCCCAAAACACGTTTTTAG-C---AAAA--AACTGTGAT-GGTTAGTACACGATTTCGGCT
* * * ** * *
1992 AAAATTTTGCAAAAAATAATATGAAA-ATTTTTTTCCCATTTTTTGGATAAAATACTCATAAAAT
124 AAAATTTTGCAAAAAATAACACGAAAGATATTTCGCCCAATTTTTGGATAAAATACTCATAAAAA
* * * *
2056 ATATATAATTTAACGCCAAAAAGATTTGAGGACTTTTCATGCTTTTAATATCGTTTTTCATA-TG
189 ATATATAATTCAACGCCAAAAATATTTGAGGGCTTTTCATGCTTTTAATATCGTTTTTCATATTT
*
2120 TTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGTAAAAACAAATTCTTAAA
254 TTTCT-AATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGTAAAAACATATTCTTAAA
2185 TCCAATGTGGTTGA
318 TCCAATGTGGTTGA
* * * * *
2199 GATTTGATTCGATGAATATGGATATCTCAAGGAGTCTTGGCGTCAAAAATCATGCAAAACTGAGT
1 GATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGCAT-AAAAACCATGCAAAACTGAGC
* * * * * * *
2264 CGGGGCCCTAGAACGCTTTTTTAGCTAAAAACTGTGATGGTTATTACACGATTTCGGTTAAAATT
65 CGGGGCCCCAAAACACGTTTTTAGCAAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATT
* * * * *
2329 TTGTAAAAATTAACCCGAAAGATATTTCGCTCAATTTTTGGCTAAAATACTCATAAAAAATATAT
130 TTGCAAAAAATAACACGAAAGATATTTCGCCCAATTTTTGGATAAAATACTCATAAAAAATATAT
* * * *
2394 AATTCAACGCCAAAAATATTGGAGGGCTTATT-ACT-CTTTTAATATTGTATTTCTTATTTTTTC
195 AATTCAACGCCAAAAATATTTGAGGGCTT-TTCA-TGCTTTTAATATCGTTTTTCATATTTTTTC
* *
2457 TATATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAGCATATTCTTAAATCCA
258 TA-ATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGTAAAAACATATTCTTAAATCCA
*
2522 ATGTTGTTGA
322 ATGTGGTTGA
*
2532 GATTTGGTTAGA
1 GATTTGATTAGA
2544 GATGTAAAGT
Statistics
Matches: 570, Mismatches: 92, Indels: 38
0.81 0.13 0.05
Matches are distributed among these distances:
329 1 0.00
330 24 0.04
331 86 0.15
332 91 0.16
333 87 0.15
334 3 0.01
335 3 0.01
336 72 0.13
337 50 0.09
338 149 0.26
339 4 0.01
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (331 bp):
GATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGCATAAAAACCATGCAAAACTGAGCC
GGGGCCCCAAAACACGTTTTTAGCAAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTT
TGCAAAAAATAACACGAAAGATATTTCGCCCAATTTTTGGATAAAATACTCATAAAAAATATATA
ATTCAACGCCAAAAATATTTGAGGGCTTTTCATGCTTTTAATATCGTTTTTCATATTTTTTCTAA
TTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGTAAAAACATATTCTTAAATCCAATGT
GGTTGA
Found at i:2918 original size:15 final size:16
Alignment explanation
Indices: 2894--2923 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2884 ATAAATAATA
2894 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
2909 ATATTATAATCTAAA
1 ATATTATAATCTAAA
2924 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:3308 original size:26 final size:28
Alignment explanation
Indices: 3279--3341 Score: 85
Period size: 26 Copynumber: 2.3 Consensus size: 28
3269 ATCCATACTC
3279 AATTATATAATTCTAT-CGGCC-AAAAA
1 AATTATATAATTCTATGCGGCCAAAAAA
* * *
3305 AATTATATAGTTCTGTGTGGCCAAAAAA
1 AATTATATAATTCTATGCGGCCAAAAAA
3333 AATTATATA
1 AATTATATA
3342 TTTTTTGCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 14 0.44
27 4 0.12
28 14 0.44
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (28 bp):
AATTATATAATTCTATGCGGCCAAAAAA
Found at i:4338 original size:5 final size:5
Alignment explanation
Indices: 4328--4359 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
4318 TTAAAGATTA
4328 TTATC TTATC TTATC TTATC TTA-C -TATC TTAT
1 TTATC TTATC TTATC TTATC TTATC TTATC TTAT
4360 TTTACTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
3 2 0.08
4 2 0.08
5 21 0.84
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATC
Found at i:4355 original size:13 final size:13
Alignment explanation
Indices: 4328--4367 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
4318 TTAAAGATTA
4328 TTATCTTATCTTATC
1 TTATCTTA-C-TATC
4343 TTATCTTACTATC
1 TTATCTTACTATC
*
4356 TTATTTTACTAT
1 TTATCTTACTAT
4368 TATATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 15 0.62
14 1 0.04
15 8 0.33
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATCTTACTATC
Found at i:11756 original size:20 final size:21
Alignment explanation
Indices: 11728--11767 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
11718 ACAATTAATG
11728 TTAGATTTATTTTGA-GAATA
1 TTAGATTTATTTTGATGAATA
*
11748 TTAGTTTTATTTTGATGAAT
1 TTAGATTTATTTTGATGAAT
11768 TACCTAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (21 bp):
TTAGATTTATTTTGATGAATA
Found at i:13181 original size:331 final size:325
Alignment explanation
Indices: 12337--13345 Score: 963
Period size: 329 Copynumber: 3.1 Consensus size: 325
12327 ATACTTTACA
** * * * ***
12337 TCATCTAACCAAATCTCAGCAATATTGGATTTAAGAATTTGCTTTTATGAGCATCTGAATCTTGT
1 TCATCTAATAAAATCTCAGCCACATTGCATTTAAGAATTTG-TTTTATGAGCATAAAAATCTTGT
* * * * *
12402 TTCGATTTAATTAGAAATTAATTTAGAAAAATAAGAAATACGATATTAAAAGAGTAAAAAGCACT
65 TTCGATTTAATTAGAAATTAATTTAGAAAAATAA-AAAAAAGATATTAAAAGCGTGAAAA-CGCT
12467 CCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAGAAAT
128 CCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGA-AAAT
* * *
12531 CTTTTGTGTCAACTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACAAATCC-TCACGATTTTT
192 TTTTTG-GTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTACT----AATCCATCACGA---TT
* * * * *
12595 TTTTGGCTAAAAACGTGTTCCAGGGACCTGACTCA--TT--TGG---CT--C-CGAGACTACTTG
249 TTTTGGCTAAAAACGTGTTTCAGGGACCCGGCTCATTTTGATGGTTTTTGGCGCGAGACTCCTTG
12650 AAATATGC-ATAT
314 AAATAT-CTATAT
* * ** * ** *
12662 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACAAACATCTGAATCTAGC
1 TCATCTAATAAAATCTCAGCCACATTGCATTTAAGAATTTG-TTTTATGAGCA--T-AA-AAATC
* *
12727 TTGTTTCGATTTAATTAGCAATTAATTCAGAAAAATAAAAAAAACGATATTAAAAGCGTGAAAA-
61 TTGTTTCGATTTAATTAGAAATTAATTTAGAAAAATAAAAAAAA-GATATTAAAAGCGTGAAAAC
* * * *
12791 GTCCTCCAATCTTTTTGGCGGTAAATTATATATTTTTTATGAGTATTTTATCCAAAAATTGGGGA
125 G--CTCCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGA
* * *
12856 AAATTTTTTGGATTATGTTTTTGCAAAATTTTAGCCAAAATTGTGTACTAATCCATCACGATTTT
188 AAATTTTTTGG-TCA-ATTTTTGCAAAATTTTAGCCAAAATCGTGTACTAATCCATCACGATTTT
* * *
12921 TTGGCTAAAAATGTGTTTCAGGGCCCCGGCTCAGTTTTGCATGGTTTTTGGCGTCGACACTCCTT
251 TTGGCTAAAAACGTGTTTCAGGGACCCGGCTCA-TTTTG-ATGGTTTTTGGCG-CGAGACTCCTT
12986 GAAATATCTATAT
313 GAAATATCTATAT
* * * *
12999 TCATCTTATAAAATCTTAGCCACTTTGCATTTAAGGATTTGTTTTAATGAGCATAAAAATCTTGT
1 TCATCTAATAAAATCTCAGCCACATTGCATTTAAGAATTTGTTTT-ATGAGCATAAAAATCTTGT
* *
13064 TTCGATTTAATTAG-AATTAATTTAGAAAAATACTAAAAAAGATATTAAAATCGTGAAAACGCTC
65 TTCGATTTAATTAGAAATTAATTTAGAAAAATA-AAAAAAAGATATTAAAAGCGTGAAAACGCTC
* * * * * *
13128 CAATTTTTTTGACATTGAATTATATATTTTTTATGAGTATTATGGCTAAAAATTGAGGAAATATC
129 CAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAA-AT-
* * * * **
13193 TTTTAGGTCAATTTTTGCAAAGTTTTAGCCAAAATCGTGTAATAAT-CATTA-GGGTTTTTGGCT
192 TTTTTGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTACTAATCCATCACGATTTTTTGGCT
**** * * * * * *
13256 AAAAACGCAAATCCGGGGCCCAGTTCAATTTTGAATGATTTTTGGCGCTGAGACACCTTGAAATA
257 AAAAACGTGTTTCAGGGACCCGGCTC-ATTTTG-ATGGTTTTTGGCGC-GAGACTCCTTGAAATA
13321 TCTATAT
319 TCTATAT
**
13328 TCATCTAACCAAATCTCA
1 TCATCTAATAAAATCTCA
13346 TCCATTATTT
Statistics
Matches: 564, Mismatches: 88, Indels: 60
0.79 0.12 0.08
Matches are distributed among these distances:
324 32 0.06
325 46 0.08
326 5 0.01
327 9 0.02
328 6 0.01
329 172 0.30
330 67 0.12
331 86 0.15
332 39 0.07
333 34 0.06
334 2 0.00
335 2 0.00
336 5 0.01
337 59 0.10
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (325 bp):
TCATCTAATAAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTATGAGCATAAAAATCTTGTT
TCGATTTAATTAGAAATTAATTTAGAAAAATAAAAAAAAGATATTAAAAGCGTGAAAACGCTCCA
ATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAATTTTT
TGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTACTAATCCATCACGATTTTTTGGCTAAAA
ACGTGTTTCAGGGACCCGGCTCATTTTGATGGTTTTTGGCGCGAGACTCCTTGAAATATCTATAT
Done.