Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024849.1 Corchorus olitorius cultivar O-4 contig24882, 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: 12149
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Found at i:1365 original size:41 final size:41
Alignment explanation
Indices: 1320--1429 Score: 141
Period size: 41 Copynumber: 2.7 Consensus size: 41
1310 TTTAGGCTGT
* * * *
1320 TATTTATTCATTGATTCAATTTTGTCCTTGATCTAAG-GTAA
1 TATTTATTAATTGATTCAATTTTATCCCTAAT-TAAGAGTAA
* *
1361 TATTTGTTAATTGATTCAATTTTATCCCTAATTTAGAGTAA
1 TATTTATTAATTGATTCAATTTTATCCCTAATTAAGAGTAA
*
1402 TATTTATTTATTGATTCAATTTTATCCC
1 TATTTATTAATTGATTCAATTTTATCCC
1430 GGATTTGGAA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 3 0.05
41 57 0.95
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.51
Consensus pattern (41 bp):
TATTTATTAATTGATTCAATTTTATCCCTAATTAAGAGTAA
Found at i:1447 original size:41 final size:41
Alignment explanation
Indices: 1358--1440 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
1348 TGATCTAAGG
* * *
1358 TAATATTTGTTAATTGATTCAATTTTATCCCTAATTTAGAG
1 TAATATTTATTAATTGATTCAATTTTATCCCGAATTTAGAA
* * *
1399 TAATATTTATTTATTGATTCAATTTTATCCCGGATTTGGAA
1 TAATATTTATTAATTGATTCAATTTTATCCCGAATTTAGAA
1440 T
1 T
1441 TTTATTTTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.30, C:0.10, G:0.11, T:0.49
Consensus pattern (41 bp):
TAATATTTATTAATTGATTCAATTTTATCCCGAATTTAGAA
Found at i:3905 original size:42 final size:42
Alignment explanation
Indices: 3820--3908 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
3810 ATCTTCGTTG
* * *
3820 ATATGTGTTATACATCCTTCATGCATGGTCCATGTCTTTGTAT
1 ATATATGTTATACATCCATCATGCA-GATCCATGTCTTTGTAT
3863 ATATATGTTCATACATCCATCATGC-GATCCAT-TCCTTTGTAT
1 ATATATGTT-ATACATCCATCATGCAGATCCATGT-CTTTGTAT
3905 ATAT
1 ATAT
3909 GTTCATGCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
41 1 0.02
42 18 0.44
43 8 0.20
44 14 0.34
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (42 bp):
ATATATGTTATACATCCATCATGCAGATCCATGTCTTTGTAT
Found at i:5096 original size:15 final size:14
Alignment explanation
Indices: 5075--5135 Score: 74
Period size: 14 Copynumber: 4.4 Consensus size: 14
5065 AACAAGACAT
5075 GGTTTTCAAGAAAA
1 GGTTTTCAAGAAAA
*
5089 TTGTTTTCAAGAAAA
1 -GGTTTTCAAGAAAA
5104 GGTTTTCAA-AAATA
1 GGTTTTCAAGAAA-A
5118 GGTTTTC-A-AAAA
1 GGTTTTCAAGAAAA
5130 GGTTTT
1 GGTTTT
5136 GAGTCTTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
12 7 0.16
13 7 0.16
14 16 0.37
15 13 0.30
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (14 bp):
GGTTTTCAAGAAAA
Found at i:7979 original size:67 final size:66
Alignment explanation
Indices: 7901--8289 Score: 573
Period size: 67 Copynumber: 5.8 Consensus size: 66
7891 TTTTAGAAGA
*
7901 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAGTCTCATTAAGGA
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCATTAA-GA
7966 AC
65 AC
*
7968 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTCATTAAGAA
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCATTAAGAA
8033 C
66 C
* * * *
8034 ACACCGGAAGACGGTTTGCTAGAAACAGTTTTCAAATGTTGATTGGAAGACAATCTCATCAAGGA
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCATTAA-GA
8099 AC
65 AC
* *
8101 ACACTGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTCATTAAGAA
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCATTAAGAA
8166 C
66 C
* * ** *
8167 ACACCGGAAGACGGTTTGCTAGAAACAGTTTTCAAGTGCTGATTGGAAGACAATCTCATTAAAGA
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCATT-AAGA
*
8232 AT
65 AC
* * * *
8234 ACATCGGAAGACGATTTGCTAGAAAGAGTTTTCAGAAA-TTGATTGGAAGACGATCT
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCA-AAAGTTGATTGGAAGACAATCT
8290 TGTCAAGAAG
Statistics
Matches: 291, Mismatches: 28, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
66 118 0.41
67 172 0.59
68 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (66 bp):
ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCATTAAGAA
C
Found at i:8139 original size:133 final size:133
Alignment explanation
Indices: 7901--8289 Score: 636
Period size: 133 Copynumber: 2.9 Consensus size: 133
7891 TTTTAGAAGA
* * * *
7901 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAGTCTCATTAAGGA
1 ACACCGGAAGACGGTTTGCTAGAAACAGTTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGA
*
7966 ACACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTCATTAAG
66 ACACACTGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTCATTAAG
8031 AAC
131 AAC
*
8034 ACACCGGAAGACGGTTTGCTAGAAACAGTTTTCAAATGTTGATTGGAAGACAATCTCATCAAGGA
1 ACACCGGAAGACGGTTTGCTAGAAACAGTTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGA
8099 ACACACTGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTCATTAAG
66 ACACACTGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTCATTAAG
8164 AAC
131 AAC
* * *
8167 ACACCGGAAGACGGTTTGCTAGAAACAGTTTTCAAGTGCTGATTGGAAGACAATCTCATTAAAGA
1 ACACCGGAAGACGGTTTGCTAGAAACAGTTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGA
* * * * *
8232 ATACA-TCGGAAGACGATTTGCTAGAAAGAGTTTTCAGAAATTGATTGGAAGACGATCT
66 ACACACT-GGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCT
8290 TGTCAAGAAG
Statistics
Matches: 240, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
132 1 0.00
133 239 1.00
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (133 bp):
ACACCGGAAGACGGTTTGCTAGAAACAGTTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGA
ACACACTGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTCATTAAG
AAC
Found at i:8298 original size:133 final size:134
Alignment explanation
Indices: 7895--8445 Score: 625
Period size: 133 Copynumber: 4.2 Consensus size: 134
7885 AGAGGATTTT
* * *
7895 AGAAGAACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAGTCTCAT
1 AGAAGCACACCGGAAGACGGTTTGCTAGAAACAATTTTCAAAAGTTGATTGGAAGACAATCTCAT
*
7960 TAAGGAACACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTC
66 TAAAGAACACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTC
*
8025 ATTA
131 ATCA
* *
8029 AGAA-CACACCGGAAGACGGTTTGCTAGAAACAGTTTTCAAATGTTGATTGGAAGACAATCTCAT
1 AGAAGCACACCGGAAGACGGTTTGCTAGAAACAATTTTCAAAAGTTGATTGGAAGACAATCTCAT
* * *
8093 CAAGGAACACACTGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTC
66 TAAAGAACACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTC
*
8158 ATTA
131 ATCA
* ** *
8162 AGAA-CACACCGGAAGACGGTTTGCTAGAAACAGTTTTCAAGTGCTGATTGGAAGACAATCTCAT
1 AGAAGCACACCGGAAGACGGTTTGCTAGAAACAATTTTCAAAAGTTGATTGGAAGACAATCTCAT
* * * * * * *
8226 TAAAGAATACATCGGAAGACGATTTGCTAGAAAGAGTTTTCAGAAATTGATTGGAAGACGATCTT
66 TAAAGAACACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTC
*
8291 GTCA
131 ATCA
* * * * * * * * *
8295 AGAAGTACACCAGAAGATGGTTT-CT--CAACAATTTTCAGAAGATGATCGGAAGACGATCTTAT
1 AGAAGCACACCGGAAGACGGTTTGCTAGAAACAATTTTCAAAAGTTGATTGGAAGACAATCTCAT
* * * * * * * *
8357 TAAA-AAGTACACCAGAAGATGGTTT-CT--CAAGAGTTTTCAGAAATTGATCGGAAGACGATCT
66 TAAAGAA-CACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCT
**
8418 GGTCA
130 CATCA
* * *
8423 AGAAGTACACCAGAAGATGGTTT
1 AGAAGCACACCGGAAGACGGTTT
8446 TTCAAGAATT
Statistics
Matches: 375, Mismatches: 40, Indels: 10
0.88 0.09 0.02
Matches are distributed among these distances:
128 59 0.16
130 4 0.01
131 46 0.12
133 247 0.66
134 19 0.05
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (134 bp):
AGAAGCACACCGGAAGACGGTTTGCTAGAAACAATTTTCAAAAGTTGATTGGAAGACAATCTCAT
TAAAGAACACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTC
ATCA
Found at i:8311 original size:67 final size:66
Alignment explanation
Indices: 7901--8503 Score: 550
Period size: 67 Copynumber: 9.2 Consensus size: 66
7891 TTTTAGAAGA
* *
7901 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCA-AAAGTTGATTGGAAGACAGTCTCATTAAGG
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAGAAA-TTGATTGGAAGACAATCTCATCAA-G
*
7965 AAC
64 AAT
* *
7968 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTCATTAAGAA
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAGAAATTGATTGGAAGACAATCTCATCAAGAA
*
8033 C
66 T
* * *
8034 ACACCGGAAGACGGTTTGCTAGAAACAGTTTTCA-AATGTTGATTGGAAGACAATCTCATCAAGG
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAGAA-ATTGATTGGAAGACAATCTCATCAA-G
*
8098 AAC
64 AAT
* * *
8101 ACACTGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTCATTAAGAA
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAGAAATTGATTGGAAGACAATCTCATCAAGAA
*
8166 C
66 T
* * * *
8167 ACACCGGAAGACGGTTTGCTAGAAACAGTTTTC--AAGTGCTGATTGGAAGACAATCTCATTAAA
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAGAAAT--TGATTGGAAGACAATCTCA-TCAA
8230 GAAT
63 GAAT
* * * * **
8234 ACATCGGAAGACGATTTGCTAGAAAGAGTTTTCAGAAATTGATTGGAAGACGATCTTGTCAAGAA
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAGAAATTGATTGGAAGACAATCTCATCAAGAA
8299 GT
66 -T
* * * * * * * * *
8301 ACACCAGAAGATGGTTT-CT--CAACAATTTTCAGAAGA-TGATCGGAAGACGATCTTATTAAAA
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAGAA-ATTGATTGGAAGACAATCTCATCAAGA
8362 AGT
65 A-T
* * * * * * **
8365 ACACCAGAAGATGGTTT-CT--CAAGAGTTTTCAGAAATTGATCGGAAGACGATCTGGTCAAGAA
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAGAAATTGATTGGAAGACAATCTCATCAAGAA
8427 GT
66 -T
* * ** * * **
8429 ACACCAGAAGATGGTTT--T-TCAAGAATTTTCAGAAATTGATCGGAAGACGATCTTGTCAAGAA
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAGAAATTGATTGGAAGACAATCTCATCAAGAA
8491 GT
66 -T
*
8493 ACACCAGAAGA
1 ACACCGGAAGA
8504 TGGATTCTCA
Statistics
Matches: 480, Mismatches: 43, Indels: 29
0.87 0.08 0.05
Matches are distributed among these distances:
63 2 0.00
64 166 0.35
65 3 0.01
66 120 0.25
67 181 0.38
68 5 0.01
69 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (66 bp):
ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAGAAATTGATTGGAAGACAATCTCATCAAGAA
T
Found at i:8349 original size:64 final size:64
Alignment explanation
Indices: 8257--8547 Score: 440
Period size: 64 Copynumber: 4.5 Consensus size: 64
8247 ATTTGCTAGA
* *
8257 AAGAGTTTTCAGAAATTGATTGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC
1 AAGAATTTTCAGAAATTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC
* * * *
8321 AACAATTTTCAGAAGA-TGATCGGAAGACGATCTTATTAAAAAGTACACCAGAAGATGGTTTCTC
1 AAGAATTTTCAGAA-ATTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC
* * *
8385 AAGAGTTTTCAGAAATTGATCGGAAGACGATCTGGTCAAGAAGTACACCAGAAGATGGTTTTTC
1 AAGAATTTTCAGAAATTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC
*
8449 AAGAATTTTCAGAAATTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGATTCTC
1 AAGAATTTTCAGAAATTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC
* * * *
8513 AAGAGTTTTCAGAAGTTGATCAGAGGACGATCTTG
1 AAGAATTTTCAGAAATTGATCGGAAGACGATCTTG
8548 ATACACCGGA
Statistics
Matches: 204, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
63 1 0.00
64 202 0.99
65 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (64 bp):
AAGAATTTTCAGAAATTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC
Found at i:8777 original size:35 final size:35
Alignment explanation
Indices: 8729--9050 Score: 427
Period size: 35 Copynumber: 9.2 Consensus size: 35
8719 AAATGAAATT
* *
8729 TCTTCAAAGTTAGAATCGGATGACTCAGTGTAGCA
1 TCTTCAAAGTTAGAATCAGATGACTCGGTGTAGCA
* *
8764 TCTTCAAAATTAGAATCAGATGACTCAGTGTAGCA
1 TCTTCAAAGTTAGAATCAGATGACTCGGTGTAGCA
*
8799 -CTTTCAAAGTTAGAATCAGATGACTCAGTGTAGCA
1 TC-TTCAAAGTTAGAATCAGATGACTCGGTGTAGCA
8834 TCTTCAAAGTTAGAATCAGATGACTCGGTGTAGCA
1 TCTTCAAAGTTAGAATCAGATGACTCGGTGTAGCA
* *
8869 TCTTCAAAGTTAGAATCGGATGACTCAGTGTAGCA
1 TCTTCAAAGTTAGAATCAGATGACTCGGTGTAGCA
*
8904 TCTTCAAAGTTAGAATCAGACGACTCGGTGTAGCA
1 TCTTCAAAGTTAGAATCAGATGACTCGGTGTAGCA
** * *
8939 TCTTCAAAAAT-GACTTCAGATGACTCGGTGTATCA
1 TCTTCAAAGTTAGA-ATCAGATGACTCGGTGTAGCA
** * *
8974 TCTTCAAAAAT-GATCTCGGATGACTCGGTGTAGCA
1 TCTTCAAAGTTAGA-ATCAGATGACTCGGTGTAGCA
*
9009 TCTTCAAAGAT-GAATTCAGATGACTCGGTGTAGCA
1 TCTTCAAAGTTAGAA-TCAGATGACTCGGTGTAGCA
9044 TCTTCAA
1 TCTTCAA
9051 GATGAACTCG
Statistics
Matches: 262, Mismatches: 21, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
34 3 0.01
35 258 0.98
36 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (35 bp):
TCTTCAAAGTTAGAATCAGATGACTCGGTGTAGCA
Found at i:10101 original size:39 final size:39
Alignment explanation
Indices: 10048--10125 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 39
10038 AGTATTAGCC
10048 CATCTTTATTTACAA-TCCTTTTGCCTTGCATAGTACCT
1 CATCTTTATTTACAATTCCTTTTGCCTTGCATAGTACCT
*
10086 CATCTTTTATTTACAATTCCTTTTGCCTTTCATAGTACCT
1 CATC-TTTATTTACAATTCCTTTTGCCTTGCATAGTACCT
10126 TGAATCGCCC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
38 4 0.11
39 11 0.30
40 22 0.59
ACGTcount: A:0.21, C:0.26, G:0.06, T:0.47
Consensus pattern (39 bp):
CATCTTTATTTACAATTCCTTTTGCCTTGCATAGTACCT
Done.