Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016305.1 Corchorus capsularis cultivar CVL-1 contig16326, 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: 140645
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:776 original size:3 final size:3
Alignment explanation
Indices: 768--847 Score: 54
Period size: 3 Copynumber: 27.0 Consensus size: 3
758 GGAAGTTTTC
* * * * * * *
768 ATT ATT ATT CTT AAT -TT ATT ACT ATT ATT ATT ATT GTT GTT GTT GTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
815 GTT GTT GTT GTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
848 GAGAATGATA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
2 1 0.01
3 67 0.99
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1156 original size:3 final size:3
Alignment explanation
Indices: 1148--1210 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
1138 ATTTGCTTTC
1148 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1196 ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT
1211 TTAAACAATA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4099 original size:16 final size:16
Alignment explanation
Indices: 4078--4109 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4068 CCAGTTAAAA
4078 CATCATTTTTTTTGTC
1 CATCATTTTTTTTGTC
4094 CATCATTTTTTTTGTC
1 CATCATTTTTTTTGTC
4110 ACTGTTGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.19, G:0.06, T:0.62
Consensus pattern (16 bp):
CATCATTTTTTTTGTC
Found at i:6702 original size:24 final size:24
Alignment explanation
Indices: 6669--6738 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
6659 TAAAGAAAAT
6669 TGAATCAAAACCCATTGAAGAAAC
1 TGAATCAAAACCCATTGAAGAAAC
* *
6693 TGAATAAAAACCCATTAAAGAAAC
1 TGAATCAAAACCCATTGAAGAAAC
**
6717 CAAATCAAAACCCATTG-AGAAA
1 TGAATCAAAACCCATTGAAGAAA
6739 ATAAGAAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 5 0.12
24 35 0.88
ACGTcount: A:0.54, C:0.20, G:0.10, T:0.16
Consensus pattern (24 bp):
TGAATCAAAACCCATTGAAGAAAC
Found at i:9150 original size:18 final size:18
Alignment explanation
Indices: 9101--9143 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
9091 CAAGAGCAGA
* *
9101 AAACAGGACCGAGAGGTC
1 AAACAGGACCAAAAGGTC
9119 AAACAGGACCAAAAGGTC
1 AAACAGGACCAAAAGGTC
9137 AAACAGG
1 AAACAGG
9144 CAGAAAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.47, C:0.21, G:0.28, T:0.05
Consensus pattern (18 bp):
AAACAGGACCAAAAGGTC
Found at i:9156 original size:29 final size:29
Alignment explanation
Indices: 9119--9266 Score: 154
Period size: 29 Copynumber: 5.0 Consensus size: 29
9109 CCGAGAGGTC
*
9119 AAACAGGACCAAAAGGTCAAACAGGCAGA
1 AAACAGGACCGAAAGGTCAAACAGGCAGA
* *
9148 AAATAGGACCGAAAGGTCAAACAAGCAGA
1 AAACAGGACCGAAAGGTCAAACAGGCAGA
* ** * **
9177 AAACGGGAGGGGAAGGTCAAACAGATA-A
1 AAACAGGACCGAAAGGTCAAACAGGCAGA
* *
9205 AAAAATGGGACCGAAAGTTCAAACAGGCAGA
1 AAACA--GGACCGAAAGGTCAAACAGGCAGA
*
9236 AAACAAGACCGAAAGGTCAAACAGAGCAGA
1 AAACAGGACCGAAAGGTCAAACAG-GCAGA
9266 A
1 A
9267 TACGCAAATT
Statistics
Matches: 93, Mismatches: 22, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
28 4 0.04
29 62 0.67
30 22 0.24
31 5 0.05
ACGTcount: A:0.51, C:0.17, G:0.26, T:0.06
Consensus pattern (29 bp):
AAACAGGACCGAAAGGTCAAACAGGCAGA
Found at i:9252 original size:59 final size:59
Alignment explanation
Indices: 9119--9261 Score: 171
Period size: 59 Copynumber: 2.4 Consensus size: 59
9109 CCGAGAGGTC
* * *
9119 AAACAGGACCAAAAGGTCAAACAG-GCAGAAAATAGGACCGAAAGGTCAAACAAGCAGA
1 AAACAGGACCGAAAGGTCAAACAGAGAAAAAAATAGGACCGAAAGGTCAAACAAGCAGA
* ** * * * * *
9177 AAACGGGAGGGGAAGGTCAAACAGATAAAAAAATGGGACCGAAAGTTCAAACAGGCAGA
1 AAACAGGACCGAAAGGTCAAACAGAGAAAAAAATAGGACCGAAAGGTCAAACAAGCAGA
*
9236 AAACAAGACCGAAAGGTCAAACAGAG
1 AAACAGGACCGAAAGGTCAAACAGAG
9262 CAGAATACGC
Statistics
Matches: 67, Mismatches: 17, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
58 19 0.28
59 48 0.72
ACGTcount: A:0.50, C:0.17, G:0.27, T:0.06
Consensus pattern (59 bp):
AAACAGGACCGAAAGGTCAAACAGAGAAAAAAATAGGACCGAAAGGTCAAACAAGCAGA
Found at i:10430 original size:2 final size:2
Alignment explanation
Indices: 10423--10459 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
10413 CGAATGACAT
10423 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10460 TTGGGCTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12165 original size:10 final size:10
Alignment explanation
Indices: 12150--12184 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
12140 AAAACCCCTC
12150 ATTGAAGCAA
1 ATTGAAGCAA
12160 ATTGAAGCAA
1 ATTGAAGCAA
12170 ATTGAAGCAA
1 ATTGAAGCAA
12180 ATTGA
1 ATTGA
12185 GACAATATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.49, C:0.09, G:0.20, T:0.23
Consensus pattern (10 bp):
ATTGAAGCAA
Found at i:15407 original size:3 final size:3
Alignment explanation
Indices: 15401--15430 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
15391 ATCATCATAA
*
15401 TCT TCT TCT TCT TCT TCT TCC TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
15431 GAATCAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:30231 original size:3 final size:3
Alignment explanation
Indices: 30223--30253 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
30213 CAAATTACAA
*
30223 AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
30254 GAGACGAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:34816 original size:30 final size:30
Alignment explanation
Indices: 34776--34836 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
34766 ACACCCGAAG
* *
34776 GAGGCGGAGGAATACAGGCCTCCGGCGGAA
1 GAGGAGGAGGAATACAGACCTCCGGCGGAA
* *
34806 GAGGAGGAGGAGTTCAGACCTCCGGCGGAA
1 GAGGAGGAGGAATACAGACCTCCGGCGGAA
34836 G
1 G
34837 TAATGCCAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.26, C:0.21, G:0.44, T:0.08
Consensus pattern (30 bp):
GAGGAGGAGGAATACAGACCTCCGGCGGAA
Found at i:56407 original size:38 final size:37
Alignment explanation
Indices: 56335--56426 Score: 166
Period size: 37 Copynumber: 2.5 Consensus size: 37
56325 AACAGCTGAT
*
56335 GAGTGACCTAAAAACCTTTTTTTTTTTTTTGAGAAAA
1 GAGTGACCTAAAAACTTTTTTTTTTTTTTTGAGAAAA
56372 GAGTGACCTAAAAACTTTTTTTTTTTTTTTGGAGAAAA
1 GAGTGACCTAAAAACTTTTTTTTTTTTTTT-GAGAAAA
56410 GAGTGACCTAAAAACTT
1 GAGTGACCTAAAAACTT
56427 AGATTAGTAG
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 29 0.55
38 24 0.45
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (37 bp):
GAGTGACCTAAAAACTTTTTTTTTTTTTTTGAGAAAA
Found at i:62655 original size:2 final size:2
Alignment explanation
Indices: 62648--62673 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
62638 GCCTATCTAT
62648 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
62674 CTTTGTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:72759 original size:18 final size:18
Alignment explanation
Indices: 72719--72762 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
72709 AAAATTATTA
72719 TTTTCCTTTTTTCTCTTC
1 TTTTCCTTTTTTCTCTTC
* *
72737 CTTTCCTTTTATTTTCTT-
1 TTTTCCTTTT-TTCTCTTC
72755 TTTTCCTT
1 TTTTCCTT
72763 CTCATTCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTCCTTTTTTCTCTTC
Found at i:85407 original size:28 final size:28
Alignment explanation
Indices: 85367--85426 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
85357 TGGCAGAGCC
85367 GGTGGCAAGATTTTTAGGTTATAAAAAT
1 GGTGGCAAGATTTTTAGGTTATAAAAAT
85395 GGTGGCAAGATTTTTAGGTTATAAAAAT
1 GGTGGCAAGATTTTTAGGTTATAAAAAT
85423 GGTG
1 GGTG
85427 TCGTTTCTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.35
Consensus pattern (28 bp):
GGTGGCAAGATTTTTAGGTTATAAAAAT
Found at i:91594 original size:17 final size:18
Alignment explanation
Indices: 91574--91607 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
91564 AAGGTACAGA
91574 TTTTTC-AAAAAATAATT
1 TTTTTCAAAAAAATAATT
91591 TTTTTCAAAAAAATAAT
1 TTTTTCAAAAAAATAAT
91608 CGACGGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTTTCAAAAAAATAATT
Found at i:92163 original size:167 final size:167
Alignment explanation
Indices: 91879--92183 Score: 486
Period size: 167 Copynumber: 1.8 Consensus size: 167
91869 GATTAGTTTT
* * *
91879 TTTTATTAATTCCACTACTCTATTCAAGTCCATTGAGAAATGACCAAAAAGATTACTTATTTAAT
1 TTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGACCAAAAAGATTACTTATTTAAT
*
91944 CCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGTCAAGTATGAAAAGACGAAAAAAATA
66 CACCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGTCAAGTATGAAAAGACGAAAAAAATA
92009 AGTTCTCTAACTCCAAAAGCAAGCCTTGGTAGGGATC
131 AGTTCTCTAACTCCAAAAGCAAGCCTTGGTAGGGATC
* * * *
92046 TTTTAGTAATTCCACTATTCTATTAAATTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAAT
1 TTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGACCAAAAAGATTACTTATTTAAT
* * *
92111 CACCTTAAGAATCAAAAGTTAGGGCATTTAAGTAAT-TGATCAAGTGTGAAAAGACGAAAAAAAT
66 CACCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTG-TCAAGTATGAAAAGACGAAAAAAAT
*
92175 TAGTTCTCT
130 AAGTTCTCT
92184 CGCTCCTTAT
Statistics
Matches: 125, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
166 2 0.02
167 123 0.98
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (167 bp):
TTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGACCAAAAAGATTACTTATTTAAT
CACCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGTCAAGTATGAAAAGACGAAAAAAATA
AGTTCTCTAACTCCAAAAGCAAGCCTTGGTAGGGATC
Found at i:97934 original size:12 final size:12
Alignment explanation
Indices: 97917--97941 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
97907 TTCCTCTTAT
97917 TGTTTTGTATAA
1 TGTTTTGTATAA
97929 TGTTTTGTATAA
1 TGTTTTGTATAA
97941 T
1 T
97942 ATATTTGCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (12 bp):
TGTTTTGTATAA
Found at i:103282 original size:2 final size:2
Alignment explanation
Indices: 103277--103303 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
103267 AACTTGACAC
103277 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
103304 GAGCCAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:104814 original size:15 final size:15
Alignment explanation
Indices: 104793--104836 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
104783 CGTTGTGTAG
104793 CAGAAGGTTCTGAAA
1 CAGAAGGTTCTGAAA
*
104808 TAGAAGGTTCTGAAA
1 CAGAAGGTTCTGAAA
*
104823 CAGAAGTTTCTGAA
1 CAGAAGGTTCTGAA
104837 TCAGGATAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (15 bp):
CAGAAGGTTCTGAAA
Done.