Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009801.1 Corchorus olitorius cultivar O-4 contig09833, 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: 3358
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1029 original size:214 final size:214
Alignment explanation
Indices: 658--1316 Score: 937
Period size: 214 Copynumber: 3.1 Consensus size: 214
648 GGGGCGTGAC
* * * * *
658 AAAACGTCTCTACAAACGTCGCAAAATTATAAATAAGAGCGACGCTATTAAAAAACATCATTCAA
1 AAAACGTCTCTACAAACATCGCAAAAGTATAAACAAGAGCAACGCTATTAAAAAACGTCATTCAA
* *
723 TTTTTAAAAAAAAGTCGCAAGATTTTGCGACGTTTATTAAAATGTCATTTATTAAACAACGTTTC
66 -TTTTAAAAAAGAGTCGCAAGA-TTTGCGACGTTTATTAAAATGTCATTTATTAAACGACGTTTC
*
788 CGAAACACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTAAAAAATGTCGC
129 CGAAAAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTAAAAAATGTCGC
*
853 ATAATTGAACGACGTTTGAGA
194 ATGATTGAACGACGTTTGAGA
* * * * *
874 AAAACGTCTTTACAAACATCGCAAAAGCATAAACAAGAGCAACGTTACTAAAAAACGTCACTCAA
1 AAAACGTCTCTACAAACATCGCAAAAGTATAAACAAGAGCAACGCTATTAAAAAACGTCATTCAA
* * *
939 -TTTAAAAAAGAGTCGCAAGATACTGCGACGTTTATTAAAATGTCATATATTAAACGACGTTTCT
66 TTTTAAAAAAGAGTCGCAAGAT-TTGCGACGTTTATTAAAATGTCATTTATTAAACGACGTTTCC
* * * *
1003 GAAAAACATTGTTATAAATTTCGGAAAAGTCTATATTAAAGCGATGTTTGTTAAAAAATGTCGCA
130 GAAAAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTAAAAAATGTCGCA
1068 TGATTGAACGACGTTTGAG-
195 TGATTGAACGACGTTTGAGA
* * * *
1087 AATACATCTCTACAAACATCGCAACAGTATAAACAAGAGCAACGCAATTAAAAAACGTCATTCAA
1 AAAACGTCTCTACAAACATCGCAAAAGTATAAACAAGAGCAACGCTATTAAAAAACGTCATTCAA
*
1152 TTTTAAAAAAGAGTCGCAAGCATTTACGACGTTTATTAAAATGTCATTTATTAAACGACGTTTCC
66 TTTTAAAAAAGAGTCGCAAG-ATTTGCGACGTTTATTAAAATGTCATTTATTAAACGACGTTTCC
** * * * *
1217 CTAAAACGTTGTCAAAAATGTCGGAAAAGTCTATCTTAAAGCGAGGTTTG-TCAAAAATGTCGCA
130 GAAAAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTAAAAAATGTCGCA
* * *
1281 TGATTAAACGACGTTAGACA
195 TGATTGAACGACGTTTGAGA
*
1301 AAAATGTCTCTACAAA
1 AAAACGTCTCTACAAA
1317 TGTCGTAAAA
Statistics
Matches: 390, Mismatches: 49, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
213 86 0.22
214 247 0.63
215 2 0.01
216 55 0.14
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (214 bp):
AAAACGTCTCTACAAACATCGCAAAAGTATAAACAAGAGCAACGCTATTAAAAAACGTCATTCAA
TTTTAAAAAAGAGTCGCAAGATTTGCGACGTTTATTAAAATGTCATTTATTAAACGACGTTTCCG
AAAAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTAAAAAATGTCGCAT
GATTGAACGACGTTTGAGA
Found at i:1842 original size:17 final size:16
Alignment explanation
Indices: 1788--1838 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
1778 GATCACCCCC
*
1788 AGATCACTAGTGATCTA
1 AGATCACCAGTGATC-A
1805 AGATCACCAGTGATGCA
1 AGATCACCAGTGAT-CA
*
1822 AGATCACCGGTGATCA
1 AGATCACCAGTGATCA
1838 A
1 A
1839 AGATTACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Found at i:2540 original size:51 final size:51
Alignment explanation
Indices: 2464--2568 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
2454 TTAATCCTCA
*
2464 ATTTGGCCTTTAAGTAATTTCCATAGCTACTAAAAATAATATATAGTATAT
1 ATTTGGCCTTTAAGTAATTTCCATAGCTACTAAAAATAATATACAGTATAT
2515 ATTTGGCCTTTAAGTAATTTCCATAGCTACTAAAAATAATATACAGTATAT
1 ATTTGGCCTTTAAGTAATTTCCATAGCTACTAAAAATAATATACAGTATAT
2566 ATT
1 ATT
2569 ATCCACAAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (51 bp):
ATTTGGCCTTTAAGTAATTTCCATAGCTACTAAAAATAATATACAGTATAT
Found at i:3228 original size:24 final size:23
Alignment explanation
Indices: 3196--3252 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 23
3186 GCCTTATACA
* **
3196 CAAAGTAATGATATGTTTAGGATT
1 CAAACTAATGATATGTACA-GATT
3220 CAAACTAATG---TGTACAGATT
1 CAAACTAATGATATGTACAGATT
3240 CAAACTAATGATA
1 CAAACTAATGATA
3253 AACAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
20 14 0.52
21 4 0.15
24 9 0.33
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (23 bp):
CAAACTAATGATATGTACAGATT
Done.