Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008326.1 Corchorus olitorius cultivar O-4 contig08353, 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: 11450
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:2074 original size:329 final size:328
Alignment explanation
Indices: 651--2449 Score: 1722
Period size: 331 Copynumber: 5.5 Consensus size: 328
641 AAGTCCTCAA
* * * * * * *
651 ATCACGGTTTTTGGCTAAAAACGCGTTCCTGGGCCCAGGTTC-AATGTTCCATGATTTTTTGTGC
1 ATCACGGTTTTTGGCTAAAAACGCGTTCCAGGGCCC-GGCTCTAGTTTTGCATGATTTTTGGCGC
* ** * * * * *
715 TGAGACTCCTTGAAATATCTGCATTCATCTAACCAAATTTCAGCCAAATTGGATTTAAGAATTTG
65 CGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGACACATTGGATTTAAGGATTTG
*** * * * ** *
780 TAAAT-CAAGCATCTGAATCATGTTTCAATTTAATTAGAAATTAATTCAGAAAATAATA-GAATA
130 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAA-AATATGAAAA
* * * * * * *
843 ACGATATTAGAAGCATGAAAAGTCCTTTAATCATTTTGGCGTTGTATTATATAATTTTTATGAGT
194 ACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGT
* * ** * *
908 ATTGTGGTTAAAAATTGAGAAAATAACTTT-GGAGTCAATTTTTGCAAAATTCTAGCCGATCGAA
259 ATTTTAGCCAAAAATTGAGGAAATATCTTTCGG-GTCAATTTTTGCAAAATT-TAG-C---CGAA
972 ATCGTGTAATAATC
318 ATCGTG---TAATC
* * *
986 ATCACGGTTTTTGG-TAAAAACGCGTTCCGGGGTCCCGGCT-AAGTTTTGCATGATTTTTGGTGC
1 ATCACGGTTTTTGGCTAAAAACGCGTTCCAGGG-CCCGGCTCTAGTTTTGCATGATTTTTGGCGC
* * * * * * ** *
1049 CAAGACTCTTTGAGATATCCATATTCATTTAATCAAATATCAGTTA-AGTTGGATTTAAGAATTT
65 CGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGACACA-TTGGATTTAAGGATTT
* * **
1113 GTTTTTACAAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATCCGG-AAAAATATGAAAA
129 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATATGAAAA
* * *
1177 ACGATATTAAAAGCGTGAAAAGCCCTCCAATTTTTTTGGCGTTGAATTATATATATTTTATGAGT
194 ACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGT
* * * * *
1242 ATTTTA-CGCAAAAATTAACGG-AATAATTTTTCAGGTCATTTTTTTGCAAAATTTTAGCCCAAA
259 ATTTTAGC-CAAAAATTGA-GGAAAT-ATCTTTCGGGTCA-ATTTTTGCAAAA-TTTAGCCGAAA
* * *
1305 TCATATAAACC
319 TCGTGT-AATC
* *
1316 ATCACGGTTTTCGGCTAAAAACGCGTTCCGGGGCCCCGGCT-TAGTTTTGCATGATTTTTGGCGC
1 ATCACGGTTTTTGGCTAAAAACGCGTTCCAGGG-CCCGGCTCTAGTTTTGCATGATTTTTGGCGC
* * * * * * *
1380 CTAGACTCCTTGAAGTATCTATATTCATTTAATCAAATCTTAGCCACATTGAATTTAAGGATTTA
65 CGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGACACATTGGATTTAAGGATTTG
* *
1445 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTTA-TT-CACAAAAATATGAAAA
130 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGGA-AAAAATATGAAAA
* * * *
1508 ACGATATTAAAAGCGTGAAAAAGGCTTTCAAT-TTTTTGGCATTGAATTATATGTTTTTTATGAG
194 ACGATATTAAAAGCGTG-AAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAG
* ** * * *
1572 TATTTTCGTTAGAAATTGAGGAAAAATCTTTCGGATCAATTTTTGCAAAATTTTAGCCGAAATCG
258 TATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAA-TTTAGCCGAAATCG
1637 TGCACTAATC
322 TG---TAATC
* * * ** *
1647 ATCACGGTTTTCGGCTAAAAATGCGTTCTAGGGCCCGGCTC-AGTTTTATATGATTTTTGGTG-C
1 ATCACGGTTTTTGGCTAAAAACGCGTTCCAGGGCCCGGCTCTAGTTTTGCATGATTTTTGGCGCC
* *
1710 -A-A-TCCTTGAAATATCTATATTCATCTAACCAAATCTCAGACACATTAGATTTAAGGATTTGT
66 GAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGACACATTGGATTTAAGGATTTGT
1772 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAT-TGGAAAAA
131 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAT-GAAAAA
* * **
1836 CGATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTGATGTTGAATTATATATTTTTCTATGAGT
195 CGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTT-TATGAGT
1901 ATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAAGTTTTTGCAAAAGTTTAGCCGAAATCG
259 ATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAA-TTTTTGCAAAA-TTTAGCCGAAATCG
1966 TGT-A-C
322 TGTAATC
* * * * *
1971 GTTACGGTTTTTGGCTAAAAACGCGTTCCAGGACCACAGCTCTA-TTTTGCATGATTTTTGACGC
1 ATCACGGTTTTTGGCTAAAAACGCGTTCCAGGGCC-CGGCTCTAGTTTTGCATGATTTTTGGCGC
* * *
2035 CGAGACTCCTTGAAATATATTTATTCATCTAATCAAATCTCAGGCACATTGGATTTAAGGATTTG
65 CGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGACACATTGGATTTAAGGATTTG
* * * * ** *
2100 TATTTACGTGCATCTGAATCTTTTTTCGATTTAATTAGAATTTAA-TTCAAAAAGAATATGAATA
130 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAA-AATATGAAAA
* ** * *
2164 ATGATATTAAAAGCGTGAAAATTCGTTCAATCTTTTTGGCGTTGAATTATATA-TATTTATGAGT
194 ACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGT
* * *
2228 AGTTGT-GCCGAAAAAATGAGGAAAAATCTTTCGGGTC-A---TT------TTTA-CC---A---
259 A-TTTTAGCC-AAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTAGCCGAAATCG
2275 --T--T-
322 TGTAATC
* * ** *
2277 AT--GGGTTTTTGGCTAAAAACGCATTCCGAGTCCCCGGCTCT-GTTTTGCATGATTTTTAGCGC
1 ATCACGGTTTTTGGCTAAAAACGCGTTCC-AGGGCCCGGCTCTAGTTTTGCATGATTTTTGGCGC
* * * **
2339 CGAGACTCCTTAAAATATCTATATT-ATCTAATCAAATATCAGACATATTCTATTTAAGGATTTG
65 CGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGACACATTGGATTTAAGGATTTG
* * *
2403 TTTTTACGAGTATTTAAATCTTGTTTCGATTTAATTAGAAATTAATT
130 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT
2450 CCAAAAAAAT
Statistics
Matches: 1239, Mismatches: 182, Indels: 117
0.81 0.12 0.08
Matches are distributed among these distances:
303 72 0.06
304 70 0.06
305 4 0.00
306 1 0.00
307 1 0.00
312 1 0.00
315 2 0.00
316 4 0.00
323 2 0.00
324 30 0.02
325 21 0.02
326 111 0.09
327 64 0.05
328 79 0.06
329 201 0.16
330 54 0.04
331 246 0.20
332 20 0.02
333 5 0.00
334 168 0.14
335 66 0.05
336 15 0.01
337 2 0.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (328 bp):
ATCACGGTTTTTGGCTAAAAACGCGTTCCAGGGCCCGGCTCTAGTTTTGCATGATTTTTGGCGCC
GAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGACACATTGGATTTAAGGATTTGT
TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATATGAAAAAC
GATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTAT
TTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTAGCCGAAATCGTGTA
ATC
Found at i:7521 original size:6 final size:6
Alignment explanation
Indices: 7504--7533 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
7494 TGATATGCTC
*
7504 ATGGTA AGGGTA ATGGTA ATGGTA ATGGTA
1 ATGGTA ATGGTA ATGGTA ATGGTA ATGGTA
7534 TTTTATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (6 bp):
ATGGTA
Found at i:8094 original size:5 final size:5
Alignment explanation
Indices: 8086--8177 Score: 105
Period size: 5 Copynumber: 20.4 Consensus size: 5
8076 AATTCTAATC
*
8086 TATCT TATCT TATTT TATCT TATCT TA-C- TATCT TATCT TATCT TA-C-
1 TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT
8132 TATCT TA-C- TATCT TATCT TATCT TATCT TA-C- TATCT TA-C- TATCT
1 TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT
8176 TA
1 TA
8178 CTACTATAAT
Statistics
Matches: 75, Mismatches: 2, Indels: 20
0.77 0.02 0.21
Matches are distributed among these distances:
3 10 0.13
4 10 0.13
5 55 0.73
ACGTcount: A:0.23, C:0.21, G:0.00, T:0.57
Consensus pattern (5 bp):
TATCT
Found at i:8105 original size:10 final size:10
Alignment explanation
Indices: 8086--8177 Score: 105
Period size: 8 Copynumber: 10.2 Consensus size: 10
8076 AATTCTAATC
8086 TATCTTATCT
1 TATCTTATCT
*
8096 TATTTTATCT
1 TATCTTATCT
8106 TATCTTA-C-
1 TATCTTATCT
8114 TATCTTATCT
1 TATCTTATCT
8124 TATCTTA-C-
1 TATCTTATCT
8132 TATCTTA-C-
1 TATCTTATCT
8140 TATCTTATCT
1 TATCTTATCT
8150 TATCTTATCT
1 TATCTTATCT
8160 TA-C-TATCT
1 TATCTTATCT
8168 TA-C-TATCT
1 TATCTTATCT
8176 TA
1 TA
8178 CTACTATAAT
Statistics
Matches: 76, Mismatches: 2, Indels: 10
0.86 0.02 0.11
Matches are distributed among these distances:
8 37 0.49
9 5 0.07
10 34 0.45
ACGTcount: A:0.23, C:0.21, G:0.00, T:0.57
Consensus pattern (10 bp):
TATCTTATCT
Found at i:8149 original size:31 final size:31
Alignment explanation
Indices: 8086--8177 Score: 122
Period size: 31 Copynumber: 3.1 Consensus size: 31
8076 AATTCTAATC
*
8086 TATCTTATCTTATTTTATCTTATCTTACTATCT
1 TATCTTATCTTATCTTA-C-TATCTTACTATCT
8119 TATCTTA--T---CTTACTATCTTACTATCT
1 TATCTTATCTTATCTTACTATCTTACTATCT
8145 TATCTTATCTTATCTTACTATCTTACTATCT
1 TATCTTATCTTATCTTACTATCTTACTATCT
8176 TA
1 TA
8178 CTACTATAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
26 20 0.38
27 1 0.02
28 4 0.08
31 21 0.40
33 7 0.13
ACGTcount: A:0.23, C:0.21, G:0.00, T:0.57
Consensus pattern (31 bp):
TATCTTATCTTATCTTACTATCTTACTATCT
Found at i:11303 original size:10 final size:10
Alignment explanation
Indices: 11288--11313 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
11278 GTATGTTTTT
11288 AAAAAAAAGA
1 AAAAAAAAGA
11298 AAAAAAAAGA
1 AAAAAAAAGA
11308 AAAAAA
1 AAAAAA
11314 TTGTCTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Done.