Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005552.1 Corchorus capsularis cultivar CVL-1 contig05570, 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: 2327
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:206 original size:117 final size:113
Alignment explanation
Indices: 51--261 Score: 343
Period size: 117 Copynumber: 1.8 Consensus size: 113
41 TTTTTGGCTG
* *
51 AAAATTAAGGAAAAAATTTTTGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTACTAACCA
1 AAAATTAAAGAAAAAATTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTACTAA-C-
116 TCATCACAGTTTTGTAGCTAAAATCGTGATTCGAGGCCCCGACTTGTGGCAA
64 -CATCACAGTTTT-TAGCTAAAATCGTGATTCGAGGCCCCGACTTGTGGCAA
168 AAAATTAAAG-AAAAATATTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTACTAACC
1 AAAATTAAAGAAAAAAT-TTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTACTAACC
*
232 ATCACAGTTTTTGGCTAAAATCGTGATTCG
65 ATCACAGTTTTTAGCTAAAATCGTGATTCG
262 GGGTATCGAC
Statistics
Matches: 90, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
113 18 0.20
114 12 0.13
116 7 0.08
117 53 0.59
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Consensus pattern (113 bp):
AAAATTAAAGAAAAAATTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTACTAACCA
TCACAGTTTTTAGCTAAAATCGTGATTCGAGGCCCCGACTTGTGGCAA
Found at i:905 original size:332 final size:331
Alignment explanation
Indices: 159--2327 Score: 3105
Period size: 332 Copynumber: 6.5 Consensus size: 331
149 AGGCCCCGAC
* * *
159 TTGTGGCAAAAAATTAAAGAAAAATATTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTG
1 TTGTGGCAAAAAATTAAGGAAAAATATTTCGGGTCAATTTTCACAAAATTTTAGCCGAAATCGTT
* * * ** *
224 TACTAACCATCACAGTTTTTGGCTAAAATCGTGATTCGGGGTATCGACTCAGTGTTGCATGATTT
66 TAC-AACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGACTCAGTTTTGCATGATTT
* *
289 TTGGCGCCAAGACTCGTTGAAATATCTGTGTTCATCAAACCAAATCTCAGCCACATGAGATTTAA
130 TTGGCGCCAAGACTCGTTGAAATATCTGTATTCATCAAACCAAATCTCAGCCACATGGGATTTAA
*
354 GGATTTCATTTTATAAGCATCAGAATCTTGTTTCGATTTAATTAGAAAATTAATTCAGAAAAAAT
195 GGATTTCATTTTATAAGCATCAGAATCTTGTTTCGATTTAATTAG-AAATTAATTCGGAAAAAAT
419 AGGATAAATGATATTAGAAACGTGAAATGCCCATCAATCTTTTTGGCATTGAATTCTATATTTTT
259 AGGATAAATGATATTAGAAACGTGAAATGCCCATCAATCTTTTTGGCATTGAATTCTATATTTTT
* *
484 TAAGAGTC
324 TATGAGTA
* *
492 TTGTGGCAAAAAATTAAGGAAAAATGTTTCGGGCCAATTTTCACAAAATTTTAGCCGAAATCGTT
1 TTGTGGCAAAAAATTAAGGAAAAATATTTCGGGTCAATTTTCACAAAATTTTAGCCGAAATCGTT
* * * * * *
557 TACTACCATAACAGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGGCTTAGCTTTGCATGATTCT
66 TACAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGACTCAGTTTTGCATGATTTT
*
622 TGGCGCCAAGACTCATTGAAATATCTGTATTCATCAAACCAAATCTCAGCCACATGGGATTTAAG
131 TGGCGCCAAGACTCGTTGAAATATCTGTATTCATCAAACCAAATCTCAGCCACATGGGATTTAAG
* * *
687 GATCTCCTTTTATAAGCTTCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAG
196 GATTTCATTTTATAAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAG
* * *
752 GATAAATGATATTAGAAACGTGAAATGCCCATCAATCTTTTCGGCAGTGAATTCAATATTTTTTA
261 GATAAATGATATTAGAAACGTGAAATGCCCATCAATCTTTTTGGCATTGAATTCTATATTTTTTA
817 TGAGTA
326 TGAGTA
* * * * *
823 TTGTGGCAAATAATTAAGGAAAAACATTTCGTGCCAATTTTCACAAAATTTTAGCCGCAATCGTT
1 TTGTGGCAAAAAATTAAGGAAAAATATTTCGGGTCAATTTTCACAAAATTTTAGCCGAAATCGTT
*
888 TACAAGCCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGACTCAGTTTTGAATGATTT
66 TACAA-CCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGACTCAGTTTTGCATGATTT
** * *
953 CAGGCACCAAGACTCGTTGAAATATCTGTATTCATCTAACCAAATCTCAGCCACATGGGATTTAA
130 TTGGCGCCAAGACTCGTTGAAATATCTGTATTCATCAAACCAAATCTCAGCCACATGGGATTTAA
* * *
1018 GGATGTCATTTTATAAGCATCAGAATCATGTTTTGATTTAATTAGAAATTAATTCGGAAAAAATA
195 GGATTTCATTTTATAAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATA
*
1083 GGATAAATGATATTAGAAACGTGAAATGCCCATCAACCTTTTTGGCATTGAATTCTATATTTTTT
260 GGATAAATGATATTAGAAACGTGAAATGCCCATCAATCTTTTTGGCATTGAATTCTATATTTTTT
*
1148 ATTAGTA
325 ATGAGTA
* * *
1155 TTGTGGCAAAAAATTAAGGAGAAATATTTCGGGTCAATTTTCGCAAAATTTTAGCCAAAATC-TT
1 TTGTGGCAAAAAATTAAGGAAAAATATTTCGGGTCAATTTTCACAAAATTTTAGCCGAAATCGTT
* * * * * * * * * *
1219 GTACTAACCTTTATAGTTTTTTGCTAAAATCGTGATTCGGGGTCACGACTTAGTTTTACATGATT
66 -TAC-AACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGACTCAGTTTTGCATGATT
* *
1284 TTTGGCACCAAGACTCGTTGAAATATCTGTATTCATCAAACCAAATCCCAGCCACATGGGATTTA
129 TTTGGCGCCAAGACTCGTTGAAATATCTGTATTCATCAAACCAAATCTCAGCCACATGGGATTTA
* * *
1349 AGGATCTCCTTTTATAAGCATCAGAATCTTGTATCGATTTAATTAGAAATTAATTCGG-AAAAAT
194 AGGATTTCATTTTATAAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAT
* * * * * *
1413 AGGAAAAATGATATTAGTAACGTGAAATACCTATCAATCTTTTTGGCACTGAATTCTATAATTTT
259 AGGATAAATGATATTAGAAACGTGAAATGCCCATCAATCTTTTTGGCATTGAATTCTATATTTTT
1478 TATGAGTA
324 TATGAGTA
* *
1486 TTGTGGCAAAAAATTAAGGAAAAATATTTCGGGTCAATTTTCACAAAATTTTAGCCAAAATCATT
1 TTGTGGCAAAAAATTAAGGAAAAATATTTCGGGTCAATTTTCACAAAATTTTAGCCGAAATCGTT
* * * * * *
1551 AATTAACCATCACAGTTTTTGGCTAAAAACGTGTTTCGAGGTCCCGGCTCAGTTTTGCTTGATTT
66 TA-CAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGACTCAGTTTTGCATGATTT
* * * * * *
1616 TTGGCGTCAAGACTCATTAAAATATCTGTATTCATCTAGCGAAATCTCAGCCACATGGGATTTAA
130 TTGGCGCCAAGACTCGTTGAAATATCTGTATTCATCAAACCAAATCTCAGCCACATGGGATTTAA
* * **
1681 GGATTTCATTTTATAAGCATCAAAATCATGTTTTTATTTAATTAGAAATTAATTCGGAAAAAATA
195 GGATTTCATTTTATAAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATA
*
1746 GGATAAATGATATTAGAAACGTGAAATGCCCATCAATCATTTTTGGCATTGAATTCTATATTGTT
260 GGATAAATGATATTAGAAACGTGAAATGCCCATCAATC-TTTTTGGCATTGAATTCTATATTTTT
1811 TATGAGTA
324 TATGAGTA
*
1819 TTGTGGCAAAAAATTAAAGG-AAAATATTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGT
1 TTGTGGCAAAAAATT-AAGGAAAAATATTTCGGGTCAATTTTCACAAAATTTTAGCCGAAATCGT
* * * * *
1883 GTACTAACCATCACAGTTTTTGGC-AAAAATCACGATTCGGGGTCCCGACTCAGTTTTGAATAAT
65 TTAC-AACCATCACAGTTTTTGGCTAAAAA-CGCGTTTCGGGGTCCCGACTCAGTTTTGCATGAT
* * * *
1947 TTCTGGCACCAAAACTCGTTGAAATATCTGTATTCATCTAAACC-AATTTCAGCCACATGGGATT
128 TTTTGGCGCCAAGACTCGTTGAAATATCTGTATTCATC-AAACCAAATCTCAGCCACATGGGATT
* * *
2011 TAAGGATTTCATTTTATAAGCATCACAATCTTGTTTTGATTTAATTAGAAACTAATTCGGAAAAA
192 TAAGGATTTCATTTTATAAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAA
* * * *
2076 ATAGGATAAATGATATTCGAAACGTGAAATGGCCAGCAATCATTTTGGCATTGAATTCTAT-TTT
257 ATAGGATAAATGATATTAGAAACGTGAAATGCCCATCAATCTTTTTGGCATTGAATTCTATATTT
* * *
2140 TTGAAGAGTC
322 TTTATGAGTA
* * *
2150 TT-TGGCAAAAAATTAAGGAGAAATATTTCGTGCCAATTTTCAC--AATTTTAGCCGAAATCGTT
1 TTGTGGCAAAAAATTAAGGAAAAATATTTCGGGTCAATTTTCACAAAATTTTAGCCGAAATCGTT
** * ** *
2212 TACAAGCCATCACAGTTTTTTACTAAAAACACGTTTCGGAATCCCGACTCAATTTTGCATGATTT
66 TACAA-CCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGACTCAGTTTTGCATGATTT
*
2277 TTGGCGCCAAGACTCGTTGAAATATCTGTGTTCATCAAACCAAAATCTCAG
130 TTGGCGCCAAGACTCGTTGAAATATCTGTATTCATCAAACC-AAATCTCAG
Statistics
Matches: 1636, Mismatches: 184, Indels: 36
0.88 0.10 0.02
Matches are distributed among these distances:
327 7 0.00
328 98 0.06
329 16 0.01
330 32 0.02
331 451 0.28
332 678 0.41
333 348 0.21
334 6 0.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (331 bp):
TTGTGGCAAAAAATTAAGGAAAAATATTTCGGGTCAATTTTCACAAAATTTTAGCCGAAATCGTT
TACAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGACTCAGTTTTGCATGATTTT
TGGCGCCAAGACTCGTTGAAATATCTGTATTCATCAAACCAAATCTCAGCCACATGGGATTTAAG
GATTTCATTTTATAAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAG
GATAAATGATATTAGAAACGTGAAATGCCCATCAATCTTTTTGGCATTGAATTCTATATTTTTTA
TGAGTA
Done.