Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011066.1 Corchorus olitorius cultivar O-4 contig11099, 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: 2289
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Found at i:516 original size:24 final size:24
Alignment explanation
Indices: 489--535 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
479 TGACCAAAGA
*
489 AACCAAGCCAAGAAATGGGCTTCG
1 AACCAAGCAAAGAAATGGGCTTCG
*
513 AACCAAGCAAAGTAATGGGCTTC
1 AACCAAGCAAAGAAATGGGCTTC
536 TAAAATGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (24 bp):
AACCAAGCAAAGAAATGGGCTTCG
Found at i:546 original size:30 final size:30
Alignment explanation
Indices: 512--574 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
502 AATGGGCTTC
* * *
512 GAACCAAGCAAAGTAATGGGCTTCTAAAAT
1 GAACCAAGCAAAGGAAAGGGCTGCTAAAAT
* *
542 GAACCAAGTAAAGGAAAGGGCTGCTGAAAT
1 GAACCAAGCAAAGGAAAGGGCTGCTAAAAT
572 GAA
1 GAA
575 AATGGTAAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.44, C:0.14, G:0.25, T:0.16
Consensus pattern (30 bp):
GAACCAAGCAAAGGAAAGGGCTGCTAAAAT
Found at i:1044 original size:154 final size:154
Alignment explanation
Indices: 770--2287 Score: 2233
Period size: 154 Copynumber: 9.9 Consensus size: 154
760 TACACCTAGT
* * * * * *
770 TATAATCATTTTGATGAGATTAGTCTACTATGAAGTTCTTAGCTCATTTGGAACACTTATTATTT
1 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTT
* * *
835 TGGGCATATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCAATTTGG-AAACCTCAAAGTG-T
66 GGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTC-AA-TGCT
* * * **
898 GTTCTTT-AAGTTGTTTATGGCCTAGT
129 TTTCTTTCCA-TTGTTTATGGACTAAC
* * * * *
924 TATAATCATTTTGATGAGATTAGTCTACTATGAAGTTCTTAGCTCATTTGGAACACTTGTTATTT
1 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTT
989 -GGGCCTATCGGGGCCCATTAGTTCCGTTTCT-AATCGTCTTCGATTTGGCAAACCTCAATGCTT
66 GGGGCCTATCGGGGCCCATTAGTTCCGTTT-TGAATCGTCTTCGATTTGGCAAACCTCAATGCTT
*
1052 TTCTTTCCATTGTTTATGGCCTAAC
130 TTCTTTCCATTGTTTATGGACTAAC
* * * *
1077 TATAATCATTTTGTTAAGATTAGACCACTTTGAAGTTTTTAGCTCAA-TTGGAACACTTGTTATT
1 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT-AATTTGGAACACTTGTTATT
* *
1141 TTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGATTCGTCTTCGATTTGGCAAACCTCAATGCTT
65 TGGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTT
*
1206 TTCTTTCCATT-TTTCATAGACTAAC
130 TTCTTTCCATTGTTT-ATGGACTAAC
* *
1231 TATAATCATTTTGGTAAGATTAGTTCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTT
1 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTT
* * **
1296 GGGGCCTATCGAGGCTCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTT
66 GGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTT
1361 TCTTTCCATTGTTTATGGACTAAC
131 TCTTTCCATTGTTTATGGACTAAC
* * *
1385 TATAATCATTTTGGTGAGATTAGTCCACAGTAAAGTTTTTAACTAATTTGGAACACTTGTTATTT
1 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTT
* * * * * * *
1450 GGGGCCTATCGAGGCCCATTAGTTCTGTCTCGAATCGTCTTCAATTTTGCAAACCTCAGTGCTTT
66 GGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTT
*
1515 TCTTTCCATTGTTTAGGGACTAAC
131 TCTTTCCATTGTTTATGGACTAAC
* * *
1539 TATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
1 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTT
** * *
1604 TAGGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGTCGTCGATTTGGCAAACCTCAATGC-TT
66 GGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTT
1668 TCTTTCCATTGTTTATGGACTAAC
131 TCTTTCCATTGTTTATGGACTAAC
1692 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTT
1 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTT
* **
1757 GGGGCCTATCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAAACTT
66 GGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTC-AATGCTT
*
1822 TTCTTTCCAATGGTTTATGGACTAAC
130 TTCTTTCC-ATTGTTTATGGACTAAC
* * *
1848 TATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTTTTTTAGATAATTTGGAACACTTGTTATT
1 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTTTTAGCTAATTTGGAACACTTGTTATT
* * **
1913 TTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTT
65 TGGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTT
*
1978 TTCTTTCCAATGTTTATGGACTAAC
130 TTCTTTCCATTGTTTATGGACTAAC
2003 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTT
1 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTT
* *
2068 GGGGCCTATCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTT
66 GGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTT
* * *
2133 TCTTTCAATTTTTTATAGACTAAC
131 TCTTTCCATTGTTTATGGACTAAC
* *
2157 TATAATCACTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTT
1 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTT
* * **
2222 GGGGCCTATCGAGGCTCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTT
66 GGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTT
2287 T
131 T
2288 TC
Statistics
Matches: 1245, Mismatches: 105, Indels: 28
0.90 0.08 0.02
Matches are distributed among these distances:
152 2 0.00
153 268 0.22
154 772 0.62
155 60 0.05
156 62 0.05
157 81 0.07
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (154 bp):
TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTT
GGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTT
TCTTTCCATTGTTTATGGACTAAC
Found at i:2122 original size:618 final size:615
Alignment explanation
Indices: 770--2286 Score: 2346
Period size: 618 Copynumber: 2.5 Consensus size: 615
760 TACACCTAGT
* * * * * *
770 TATAATCATTTTGATGAGATTAGTCTACTATGAAGTTCTTAGCTCATTTGGAACACTTATTATTT
1 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTT
* * *
835 TGGGCATATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCAATTTGG-AAACCTCAAAGTG-T
66 GGGGCCTATCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCAATTTGGCAAACCTC--AGTGCT
* * ** * * *
898 GTTCTTT-AAGTTGTTTATGGCCTAGTTATAATCATTTTGATGAGATTAGTCTACTATGAAGTTC
129 TTTCTTTCAA-TTGTTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTT
962 TTAGCTCATTTGGAACACTTGTTA-TTTGGGCCTATCGGGGCCCATTAGTTCCGTTTCT-AATCG
193 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTT-TGAATCG
*
1025 TCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
257 TCTTCGATTTGGCAAACCTCAATGC-TTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTG
* * *
1090 TTAAGATTAGACCACTTTGAAGTTTTTAGCTCAATTGGAACACTTGTTATTTTGGGCCTATCGGG
321 GTAAGATTAGACCACTGTGAAGTTTTTAGCTCAATTGGAACACTTGTTATTTGGGGCCTATCGGG
* ** *
1155 GCCCATTAGTTCCGTTTTGATTCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTTTT
386 GCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAACTTTTCTTTCCATGTTT
* *
1220 CATAGACTAACTATAATCATTTTGGTAAGATTAGTTCACTGTGAAGTTTTTAGCTAATTTGGAAC
451 CATAGACTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGATAATTTGGAAC
*
1285 ACTTGTTATTTGGGGCCTATCGAGGCTCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAAC
516 ACTTGTTATTTGGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAAC
*
1350 CTCAATGCTTTTCTTTCCATTGTTTATGGACTAAC
581 CTCAATGCTTTTCTTTCCAATGTTTATGGACTAAC
* * *
1385 TATAATCATTTTGGTGAGATTAGTCCACAGTAAAGTTTTTAACTAATTTGGAACACTTGTTATTT
1 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTT
* * * *
1450 GGGGCCTATCGAGGCCCATTAGTTCTGTCTCGAATCGTCTTCAATTTTGCAAACCTCAGTGCTTT
66 GGGGCCTATCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCAATTTGGCAAACCTCAGTGCTTT
* * *
1515 TCTTTCCATTGTTTAGGGACTAACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTA
131 TCTTTCAATTGTTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTA
* * *
1580 GCTCATTTGGAACACTTGTTATTTTAGGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGTCGT
196 GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTT
*
1645 CGATTTGGCAAACCTCAATGCTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAG
261 CGATTTGGCAAACCTCAATGCTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTAAG
*
1710 ATTAGTCCACTGTGAAGTTTTTAGCT-AATTTGGAACACTTGTTATTTGGGGCCTATCGGGGCCC
326 ATTAGACCACTGTGAAGTTTTTAGCTCAA-TTGGAACACTTGTTATTTGGGGCCTATCGGGGCCC
*
1774 ATTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAAACTTTTCTTTCCAATGGTTT-
390 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTC-AAAACTTTTCTTTCC-AT-GTTTC
* *
1838 ATGGACTAACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTTTTTTAGATAATTTGGAAC
452 ATAGACTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAG-TTTTTAGATAATTTGGAAC
*
1903 ACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAAC
516 ACTTGTTATTTGGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAAC
1968 CTCAATGCTTTTCTTTCCAATGTTTATGGACTAAC
581 CTCAATGCTTTTCTTTCCAATGTTTATGGACTAAC
2003 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTT
1 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTT
* **
2068 GGGGCCTATCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTT
66 GGGGCCTATCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCAATTTGGCAAACCTCAGTGCTTT
* * * * *
2133 TCTTTCAATTTTTTATAGACTAACTATAATCACTTTGGTAAGATTAGTCCACTGTGAAGTTTTTA
131 TCTTTCAATTGTTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTA
* * * * **
2198 GCTAATTTGGAACACTTGTTATTTGGGGCCTATCGAGGCTCATTAGTGACGTTTTGAATCGTCTT
196 GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTT
2263 CGATTTGGCAAACCTCAATGCTTT
261 CGATTTGGCAAACCTCAATGCTTT
2287 TTC
Statistics
Matches: 818, Mismatches: 74, Indels: 17
0.90 0.08 0.02
Matches are distributed among these distances:
614 6 0.01
615 313 0.38
616 80 0.10
617 44 0.05
618 375 0.46
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (615 bp):
TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTT
GGGGCCTATCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCAATTTGGCAAACCTCAGTGCTTT
TCTTTCAATTGTTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTA
GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTT
CGATTTGGCAAACCTCAATGCTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTAAG
ATTAGACCACTGTGAAGTTTTTAGCTCAATTGGAACACTTGTTATTTGGGGCCTATCGGGGCCCA
TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAACTTTTCTTTCCATGTTTCATAG
ACTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGATAATTTGGAACACTTG
TTATTTGGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
TGCTTTTCTTTCCAATGTTTATGGACTAAC
Done.