Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011155.1 Corchorus capsularis cultivar CVL-1 contig11176, 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: 93206
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3250 original size:4 final size:4
Alignment explanation
Indices: 3241--3277 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
3231 ATATGATTGG
*
3241 TAGA TAGA TAGA TAGA TAGA TAGA TTGA TAGA TAGA T
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA T
3278 TTGAGAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (4 bp):
TAGA
Found at i:16319 original size:21 final size:21
Alignment explanation
Indices: 16293--16336 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
16283 TTTTCCGAAG
*
16293 TTCAGGATCCTAATTGAGATT
1 TTCAGGACCCTAATTGAGATT
*
16314 TTCAGGGCCCTAATTGAGATT
1 TTCAGGACCCTAATTGAGATT
16335 TT
1 TT
16337 AGCCAAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (21 bp):
TTCAGGACCCTAATTGAGATT
Found at i:24763 original size:29 final size:30
Alignment explanation
Indices: 24729--24789 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
24719 AAGCATCTAC
*
24729 AATCAAAC-ATTAAACCTTCATAAAAACAG
1 AATCAAACAATAAAACCTTCATAAAAACAG
*
24758 AATCAAACAATAAAACCTTGATAAAAACAG
1 AATCAAACAATAAAACCTTCATAAAAACAG
24788 AA
1 AA
24790 ACCAGGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.59, C:0.18, G:0.05, T:0.18
Consensus pattern (30 bp):
AATCAAACAATAAAACCTTCATAAAAACAG
Found at i:26416 original size:17 final size:16
Alignment explanation
Indices: 26394--26431 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
26384 TTGGACATGG
26394 CTTTGAGACTTCTGAGA
1 CTTTGAGACTT-TGAGA
26411 CTTTGAGACTTTGAGA
1 CTTTGAGACTTTGAGA
26427 CTTTG
1 CTTTG
26432 CTGTGTTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (16 bp):
CTTTGAGACTTTGAGA
Found at i:26419 original size:8 final size:8
Alignment explanation
Indices: 26394--26431 Score: 67
Period size: 8 Copynumber: 4.6 Consensus size: 8
26384 TTGGACATGG
26394 CTTTGAGA
1 CTTTGAGA
26402 CTTCTGAGA
1 CTT-TGAGA
26411 CTTTGAGA
1 CTTTGAGA
26419 CTTTGAGA
1 CTTTGAGA
26427 CTTTG
1 CTTTG
26432 CTGTGTTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 21 0.72
9 8 0.28
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (8 bp):
CTTTGAGA
Found at i:28607 original size:6 final size:6
Alignment explanation
Indices: 28598--28624 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
28588 AAAAATCTTC
28598 TTGGCA TTGGCA TTGGCA TTGGCA TTG
1 TTGGCA TTGGCA TTGGCA TTGGCA TTG
28625 CACATCATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.33, T:0.37
Consensus pattern (6 bp):
TTGGCA
Found at i:29138 original size:16 final size:16
Alignment explanation
Indices: 29117--29150 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
29107 ACAATTCAGA
29117 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
29133 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
29149 AA
1 AA
29151 ATATTTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.12
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:31229 original size:5 final size:5
Alignment explanation
Indices: 31217--31267 Score: 68
Period size: 5 Copynumber: 10.0 Consensus size: 5
31207 CCTAAACTGC
*
31217 ACAAA A-AAA AAAAA ACAAAAA ACAAA ACAAA ACAAA ACAAA ACAAA ACAAA
1 ACAAA ACAAA ACAAA AC--AAA ACAAA ACAAA ACAAA ACAAA ACAAA ACAAA
31268 GAACTACGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
4 4 0.10
5 33 0.79
7 5 0.12
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (5 bp):
ACAAA
Found at i:31460 original size:65 final size:67
Alignment explanation
Indices: 31357--31498 Score: 243
Period size: 65 Copynumber: 2.1 Consensus size: 67
31347 CCAAACCAAA
* *
31357 AAAAAAAAAAAGAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGC
1 AAAAAAAAAAAGAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACAGCTTAGGCAAAACTTAGAGC
31422 -C
66 AC
*
31423 AAAAAAAAAAAG-GGCTCGCTAAGTTGAAAATCCTGCAAAGGACAGCTTAGGCAAAACTTAGAGC
1 AAAAAAAAAAAGAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACAGCTTAGGCAAAACTTAGAGC
31487 AC
66 AC
31489 AAAAAAAAAA
1 AAAAAAAAAA
31499 TGAACTACGT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
65 49 0.68
66 23 0.32
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.14
Consensus pattern (67 bp):
AAAAAAAAAAAGAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACAGCTTAGGCAAAACTTAGAGC
AC
Found at i:32280 original size:16 final size:17
Alignment explanation
Indices: 32252--32286 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
32242 ACAATTCAGA
32252 AAGCAGAAAAAGCTCTG
1 AAGCAGAAAAAGCTCTG
32269 AAGCAG-AAAAGCTCTG
1 AAGCAGAAAAAGCTCTG
32285 AA
1 AA
32287 ATATTTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (17 bp):
AAGCAGAAAAAGCTCTG
Found at i:60056 original size:19 final size:21
Alignment explanation
Indices: 60009--60056 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
59999 TGTGGCACGC
*
60009 CACATGTACCAAAAAGTCGTG
1 CACATGTACCAAAAAGTCGTA
60030 CTACATGTACCAAAAAGT-G-A
1 C-ACATGTACCAAAAAGTCGTA
60050 CACATGT
1 CACATGT
60057 CACGCCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 6 0.24
20 1 0.04
21 2 0.08
22 16 0.64
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.21
Consensus pattern (21 bp):
CACATGTACCAAAAAGTCGTA
Found at i:61498 original size:5 final size:5
Alignment explanation
Indices: 61488--61512 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
61478 ATTGTCAAGC
61488 TAGCT TAGCT TAGCT TAGCT TAGCT
1 TAGCT TAGCT TAGCT TAGCT TAGCT
61513 CTCATACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (5 bp):
TAGCT
Found at i:75402 original size:15 final size:15
Alignment explanation
Indices: 75382--75412 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
75372 TTGTTCAGTA
75382 AATACATTACATACC
1 AATACATTACATACC
75397 AATACATTACATACC
1 AATACATTACATACC
75412 A
1 A
75413 CAAGATAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (15 bp):
AATACATTACATACC
Found at i:76306 original size:1 final size:1
Alignment explanation
Indices: 76261--76295 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
76251 GCAGTTTTAG
*
76261 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
76296 AATGTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:85644 original size:13 final size:13
Alignment explanation
Indices: 85626--85653 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
85616 ATTACCATAA
85626 TAACTTCTATAGG
1 TAACTTCTATAGG
85639 TAACTTCTATAGG
1 TAACTTCTATAGG
85652 TA
1 TA
85654 GTAAATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (13 bp):
TAACTTCTATAGG
Found at i:87156 original size:2 final size:2
Alignment explanation
Indices: 87149--87199 Score: 70
Period size: 2 Copynumber: 26.0 Consensus size: 2
87139 GCTCATTTAA
*
87149 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT CA- AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
87190 AT AT AT AT AT
1 AT AT AT AT AT
87200 TTGTTTATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
1 2 0.04
2 42 0.93
3 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.