Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011056.1 Corchorus olitorius cultivar O-4 contig11089, 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, 987
Length: 1645
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.40
Found at i:287 original size:154 final size:153
Alignment explanation
Indices: 2--1645 Score: 2384
Period size: 154 Copynumber: 10.7 Consensus size: 153
1 T
*
2 TGAAGTTTTTAGTCTCATTTTGGAACACTTGTATTTTGGGCCTATCGGGG-CCATTAGTGACATT
1 TGAAGTTTTTAG-CTCA-TTTGGAACACTTGTATTTTGGGCCTATCGGGGCCCATTAGTGACGTT
* *
66 TTGAATCGTCTTCCATTTGGCAAA-CTCAATGCTTTTCTTTACATTGTTTATGGTACTAACTATA
64 TTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGG-ACTAACTATA
* * *
130 ATCATTTTCGTGAAATTAGACCACTG
128 ATCATTTTGGTGAGATTAGTCCACTG
* *
156 TGAAGTTCTTAGCTCATTTGGAACACTTGTATTTTGGGCCTATCGGGGCCCATTAGTGACATTTT
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTT
** * *
221 GAATTCGTCTTCGATTTTCCAAACCTCAAGGCTTTTCTTTCCATTTTTTATGGACTAACTATAAT
66 GAA-TCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAAT
*
286 CATTTTGGTGAGATTAGTCCACTA
130 CATTTTGGTGAGATTAGTCCACTG
* * *
310 TTAAGTTTTTAGCTCATTTGGAACACTTGTTATATTGGGCCTATCGGGGCTCATTAGTGACGTTT
1 TGAAGTTTTTAGCTCATTTGGAACACTTG-TATTTTGGGCCTATCGGGGCCCATTAGTGACGTTT
* * * *
375 TGAATCGTCTTCGATTTGGCAAACCTCAAGGCTTTTCCTTCCATTGTTTATGGCCTAAGTATAAT
65 TGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAAT
440 CATTTTGGTGAGATTAGTCCACTG
130 CATTTTGGTGAGATTAGTCCACTG
* ** * *
464 TGAAATTTTTAGCTCATTTACAACACTTGTTATATTGGGCCTATCGGGGCCCATTAGTGACATTT
1 TGAAGTTTTTAGCTCATTTGGAACACTTG-TATTTTGGGCCTATCGGGGCCCATTAGTGACGTTT
* * * * *
529 TGAATCGTCTTCGATTTGTCAAACCTTAAGGCTTTTCTTTCCATTGGTTATGGCCTAACTATAAT
65 TGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAAT
594 CATTTTGGTGAGATTAGTCCACTG
130 CATTTTGGTGAGATTAGTCCACTG
* *
618 TGAAG---TT---T--TTT--AACACTTGTTATTTTGGGCCTATCGCGGCCCATTAGTGTCGTTT
1 TGAAGTTTTTAGCTCATTTGGAACACTTG-TATTTTGGGCCTATCGGGGCCCATTAGTGACGTTT
* * *
673 TGAATCGTCTTCGATTTTGCAAACCTCAAGGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
65 TGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAAT
*
738 CATTTTGGTGAGATTAGTCTACTG
130 CATTTTGGTGAGATTAGTCCACTG
* **
762 TGAAGTATTTAGCTCATTTGGAACACTTGTACTTTTGGGCCTATCGGGGCCCATTAGTTCCGTTT
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTA-TTTTGGGCCTATCGGGGCCCATTAGTGACGTTT
*
827 TGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATAGTTTATGGACTAACTATAAT
65 TGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAAT
*
892 CATTTTGGTGAGATTAGTCTACTG
130 CATTTTGGTGAGATTAGTCCACTG
* * **
916 TAAAGTATTTAGCTCATTTGGAACACTTGTACTTTTGGGCCTATCGGGGCCCATTAGTTCCGTTT
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTA-TTTTGGGCCTATCGGGGCCCATTAGTGACGTTT
* * * * *
981 TGAATCGTCTTCAATTTGGCAAACCTCAAAGCTATTCTTT-AAGTTGTTTATGGCCTAACTATAA
65 TGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCA-TTGTTTATGGACTAACTATAA
* *
1045 TTATTTTGATGAGATTAGTCCACTG
129 TCATTTTGGTGAGATTAGTCCACTG
* *
1070 TGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGGCCTATCGTGGCCCATTAGTGACGTT
1 TGAAGTTTTTAGCTCATTTGGAACACTTG-TATTTT-GGGCCTATCGGGGCCCATTAGTGACGTT
*
1135 TTGAATCGTCTTCAATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAA
64 TTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAA
*
1200 TCATTTTGGTGAGATTAATCCACTG
129 TCATTTTGGTGAGATTAGTCCACTG
* **
1225 TGAAATTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTT
1 TGAAGTTTTTAGCTCATTTGGAACACTTG-TATTTTGGGCCTATCGGGGCCCATTAGTGACGTTT
*
1290 TGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTGTGGACTAACTATAAT
65 TGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAAT
1355 CATTTTGGTGAGATTAGTCCACTG
130 CATTTTGGTGAGATTAGTCCACTG
* * * * **
1379 TGAAGTTTTTTCGCTCATTTGGAACACTTATTATTTTAGGG-CTATCAGGGCCCATTAAT-TTGT
1 TGAAG-TTTTTAGCTCATTTGGAACACTT-GTATTTT-GGGCCTATCGGGGCCCATTAGTGACGT
*** *
1442 TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCACAATATATGGACTAACTATA
63 TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATA
1507 ATCATTTTGGTGAGATTAGTCCACTG
128 ATCATTTTGGTGAGATTAGTCCACTG
**
1533 TGAAGTTTTTAGCTCATTTGGAACACTTGTATTTTGGGCCTATCGCAGCCCATTAGTGACGTTTT
1 TGAAGTTTTTAGCTCATTTGGAACACTTGTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTT
1598 GAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT-TTTA
66 GAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTA
Statistics
Matches: 1361, Mismatches: 105, Indels: 50
0.90 0.07 0.03
Matches are distributed among these distances:
144 129 0.09
146 3 0.00
147 2 0.00
148 1 0.00
150 1 0.00
151 5 0.00
152 58 0.04
153 95 0.07
154 815 0.60
155 248 0.18
156 4 0.00
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (153 bp):
TGAAGTTTTTAGCTCATTTGGAACACTTGTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTT
GAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATC
ATTTTGGTGAGATTAGTCCACTG
Found at i:1307 original size:463 final size:460
Alignment explanation
Indices: 4--1645 Score: 2404
Period size: 463 Copynumber: 3.6 Consensus size: 460
1 TTG
4 AAGTTTTTAGTCTCATTTTGGAACACTTGTATTTTGGGCCTATCGGGG-CCATTAGTGACATTTT
1 AAGTTTTTAG-CTCA-TTTGGAACACTTGTATTTTGGGCCTATCGGGGCCCATTAGTGACATTTT
*
68 GAATCGTCTTCCATTTGGCAAA-CTCAATGCTTTTCTTT-ACATTGTTTATGGTACTAACTATAA
64 GAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCA-ATTGTTTATGG-ACTAACTATAA
* * *
131 TCATTTTCGTGAAATTAGACCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGTATTTTGGGCC
127 TCATTTTGGTGAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGTATTTTGGGCC
* * **
196 TATCGGGGCCCATTAGTGACATTTTGAATTCGTCTTCGATTTTCCAAACCTCAAGGCTTTTCTTT
192 TATCGCGGCCCATTAGTGACGTTTTGAA-TCGTCTTCGATTTGGCAAACCTCAAGGCTTTTCTTT
* * *
261 CCATTTTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTATTAAGTTTTTAGCTCA
256 CCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA
* * **
326 TTTGGAACACTTGTTATATTGGGCCTATCGGGGCTCATTAGTGACGTTTTGAATCGTCTTCGATT
321 TTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATT
* * * *
391 TGGCAAACCTCAAGGCTTTTCCTTCCATTGTTTATGGCCTAAGTATAATCATTTTGGTGAGATTA
386 TGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTA
456 GTCCACTGTGA
451 GTCCACTGT-A
** *
467 AA-TTTTTAGCTCATTTACAACACTTGTTATATTGGGCCTATCGGGGCCCATTAGTGACATTTTG
1 AAGTTTTTAGCTCATTTGGAACACTTG-TATTTTGGGCCTATCGGGGCCCATTAGTGACATTTTG
* * * * * *
531 AATCGTCTTCGATTTGTCAAACCTTAAGGCTTTTCTTTCCATTGGTTATGGCCTAACTATAATCA
65 AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCAATTGTTTATGGACTAACTATAATCA
596 TTTTGGTGAGATTAGTCCACTGTGAAG---TT---T--TTT--AACACTTGTTATTTTGGGCCTA
130 TTTTGGTGAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTG-TATTTTGGGCCTA
* *
651 TCGCGGCCCATTAGTGTCGTTTTGAATCGTCTTCGATTTTGCAAACCTCAAGGCTTTTCTTTCCA
194 TCGCGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAGGCTTTTCTTTCCA
* * *
716 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCTACTGTGAAGTATTTAGCTCATTT
259 TTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
781 GGAACACTTG-TACTTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
324 GGAACACTTGTTA-TTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
*
845 GCAAACCTCAATGCTTTTCTTTCCATAGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGT
388 GCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGT
*
910 CTACTGTA
453 CCACTGTA
* ** *
918 AAGTATTTAGCTCATTTGGAACACTTGTACTTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTG
1 AAGTTTTTAGCTCATTTGGAACACTTGTA-TTTTGGGCCTATCGGGGCCCATTAGTGACATTTTG
* * * * *
983 AATCGTCTTCAATTTGGCAAACCTCAAAGCTATTCTTT-AAGTTGTTTATGGCCTAACTATAATT
65 AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCAA-TTGTTTATGGACTAACTATAATC
*
1047 ATTTTGATGAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGGCC
129 ATTTTGGTGAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTG-TATTTT-GGGCC
* * *
1112 TATCGTGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGGCAAACCTCAATGCTTTTCTTTC
192 TATCGCGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAGGCTTTTCTTTC
* *
1177 CATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAATCCACTGTGAAATTTTTAGCTCAT
257 CATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCAT
1242 TTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTT
322 TTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTT
*
1307 GGCAAACCTCAATGCTTTTCTTTCCATTGTTTGTGGACTAACTATAATCATTTTGGTGAGATTAG
387 GGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAG
*
1372 TCCACTGTG
452 TCCACTGTA
* * * * ***
1381 AAGTTTTTTCGCTCATTTGGAACACTTATTATTTTAGGG-CTATCAGGGCCCATTAAT-TTGTTT
1 AAG-TTTTTAGCTCATTTGGAACACTT-GTATTTT-GGGCCTATCGGGGCCCATTAGTGACATTT
* *** *
1444 TGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCACAATATATGGACTAACTATAAT
63 TGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCAATTGTTTATGGACTAACTATAAT
*
1509 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTATTTTGGGCCT
128 CATTTTGGTGAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGTATTTTGGGCCT
* *
1574 ATCGCAGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
193 ATCGCGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAGGCTTTTCTTTCC
1639 ATT-TTTA
258 ATTGTTTA
Statistics
Matches: 1069, Mismatches: 85, Indels: 53
0.89 0.07 0.04
Matches are distributed among these distances:
451 8 0.01
452 361 0.34
453 36 0.03
454 3 0.00
455 2 0.00
456 1 0.00
458 1 0.00
459 2 0.00
460 18 0.02
461 93 0.09
462 101 0.09
463 394 0.37
464 44 0.04
465 5 0.00
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (460 bp):
AAGTTTTTAGCTCATTTGGAACACTTGTATTTTGGGCCTATCGGGGCCCATTAGTGACATTTTGA
ATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCAATTGTTTATGGACTAACTATAATCAT
TTTGGTGAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGTATTTTGGGCCTATC
GCGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAGGCTTTTCTTTCCATT
GTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
AACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCA
AACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCA
CTGTA
Done.