Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020661.1 Corchorus olitorius cultivar O-4 contig20694, 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: 67618
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:1036 original size:21 final size:20
Alignment explanation
Indices: 995--1037 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
985 AGGAGAAGAG
*
995 AAAAAAAAGAAAAAAATGAA
1 AAAAAAAAGAAAAAAAGGAA
*
1015 AAAAGAAAAGAAAAAAGGGAA
1 AAAA-AAAAGAAAAAAAGGAA
1036 AA
1 AA
1038 GGCTGTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (20 bp):
AAAAAAAAGAAAAAAAGGAA
Found at i:3386 original size:131 final size:131
Alignment explanation
Indices: 3152--3416 Score: 512
Period size: 131 Copynumber: 2.0 Consensus size: 131
3142 AACAAATTTA
*
3152 ATCATAATAGGTAAAATTATTACAATAATATAAATTTTATTGAATAAATGATAATTTAGAATGGT
1 ATCATAATAGGTAAAATTATAACAATAATATAAATTTTATTGAATAAATGATAATTTAGAATGGT
*
3217 TAAAATTATAACAATGTGGATTTTATTGAATAAAACATTAATTTTAGTTTATAATACTCTTTGGT
66 TAAAATTATAACAATGTGGATTTTATTGAATAAAACATTAATTTTAGTTTATAATACTCTTTAGT
3282 C
131 C
3283 ATCATAATAGGTAAAATTATAACAATAATATAAATTTTATTGAATAAATGATAATTTAGAATGGT
1 ATCATAATAGGTAAAATTATAACAATAATATAAATTTTATTGAATAAATGATAATTTAGAATGGT
3348 TAAAATTATAACAATGTGGATTTTATTGAATAAAACATTAATTTTAGTTTATAATACTCTTTAGT
66 TAAAATTATAACAATGTGGATTTTATTGAATAAAACATTAATTTTAGTTTATAATACTCTTTAGT
3413 C
131 C
3414 ATC
1 ATC
3417 GTCAGGTTAA
Statistics
Matches: 132, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
131 132 1.00
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (131 bp):
ATCATAATAGGTAAAATTATAACAATAATATAAATTTTATTGAATAAATGATAATTTAGAATGGT
TAAAATTATAACAATGTGGATTTTATTGAATAAAACATTAATTTTAGTTTATAATACTCTTTAGT
C
Found at i:10483 original size:36 final size:36
Alignment explanation
Indices: 10436--10506 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
10426 CCCGCCTCTA
* *
10436 AGGAGTCCACACGATCAAGAGGCAATCAAGATTGAG
1 AGGAGTCCACACGATCAACAGGAAATCAAGATTGAG
10472 AGGAGTCCACACGATCAACAGGAAATCAAGATTGA
1 AGGAGTCCACACGATCAACAGGAAATCAAGATTGA
10507 AGCTTGAGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.14
Consensus pattern (36 bp):
AGGAGTCCACACGATCAACAGGAAATCAAGATTGAG
Found at i:12947 original size:47 final size:48
Alignment explanation
Indices: 12893--13001 Score: 139
Period size: 49 Copynumber: 2.3 Consensus size: 48
12883 CCATAACAGG
** **
12893 ATATTCATACTTTAAAAACATA-AAATAATTTTTCTAAAAGATGATGA
1 ATATTCATACTTTAAAAACATATAAATAAACTCCCTAAAAGATGATGA
* * *
12940 ATATTCATACTTTAATAACATATTGAATAAACTCCCTAAAATATGATGA
1 ATATTCATACTTTAAAAACATA-TAAATAAACTCCCTAAAAGATGATGA
12989 ATATTCATACTTT
1 ATATTCATACTTT
13002 TCCTTTTACA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 21 0.40
49 32 0.60
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.38
Consensus pattern (48 bp):
ATATTCATACTTTAAAAACATATAAATAAACTCCCTAAAAGATGATGA
Found at i:18775 original size:2 final size:2
Alignment explanation
Indices: 18763--18799 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
18753 TGTTGGTAAT
*
18763 CA CA CA AA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
18800 TAATTGAGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:27593 original size:27 final size:27
Alignment explanation
Indices: 27545--27605 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
27535 TTACCAAAAA
* * *
27545 TACCCGTGATGGACAAATTTACTATGT
1 TACCCCTGATGGACAAAATTACGATGT
* * *
27572 TACCCCTGATTGATAAAATTACGATTT
1 TACCCCTGATGGACAAAATTACGATGT
27599 TACCCCT
1 TACCCCT
27606 ATAATGAAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (27 bp):
TACCCCTGATGGACAAAATTACGATGT
Found at i:36941 original size:16 final size:16
Alignment explanation
Indices: 36920--36950 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36910 ATAAAATACC
*
36920 CTAATTTTTTATTTTT
1 CTAATTTTTAATTTTT
36936 CTAATTTTTAATTTT
1 CTAATTTTTAATTTT
36951 ACCGTGTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (16 bp):
CTAATTTTTAATTTTT
Found at i:38372 original size:235 final size:234
Alignment explanation
Indices: 37908--38378 Score: 612
Period size: 235 Copynumber: 2.0 Consensus size: 234
37898 ATATTAGATA
37908 AATTTTACATTTTTTTAATATATAAAATACATGTTTAGAATTAGATCTGATCCATTTTCTTATTT
1 AATTTTACATTTTTTTAATATATAAAATACATGTTTAGAATTAGATCTGATCCATTTTCTTATTT
37973 TCCTGAAAAAAAAGATCTGATCCATTTTATTCATAATATATATATATAAATCAACTATATATATA
66 TCCTG---AAAAAGA--T-ATCCATTTTATTCATAATATATATATATAAATCAACTATATATATA
*
38038 TATTTAATTAAAACAGAGATTCATAAAAAGAAAAAGAGAAAGAAAAAAGAAATCAAAAGTATTTT
125 TATTTAATTAAAACAGAGATT-AT---AAGAAAAAGAAAAAGAAAAAAGAAATCAAAAGTATTTT
38103 TGCATTTAGATTTTCTTGGAAATCAAGATTCAGCTATACTTGGAAATTG
186 TGCATTTAGATTTTCTTGGAAATCAAGATTCAGCTATACTTGGAAATTG
*
38152 AATTTTACATTTTTTTCATATATAAAATACATGTTTAGAATTAGATCTGATCCATTTTCTTATTT
1 AATTTTACATTTTTTTAATATATAAAATACATGTTTAGAATTAGATCTGATCCATTTTCTTATTT
* * *
38217 TCC-G-GAAA-A-ATCCATTTTATTCATATATATATATATATATATCAACTCTCTTTCTATATAT
66 TCCTGAAAAAGATATCCATTTTATTCATA-ATATATATATATAAATCAA----C--TATATATAT
* * * * * * *
38278 TTTTTTAATTAAAACAGAGATT-T-AGAGAAAGAAAAAGAAGAAAGAAATCGAAATTATTTTTTC
124 ATATTTAATTAAAACAGAGATTATAAGAAAAAGAAAAAGAAAAAAGAAATCAAAAGTATTTTTGC
** *
38341 ATTTAGATTTTCTTGGAAATCGTGATTCAGCTTTACTT
189 ATTTAGATTTTCTTGGAAATCAAGATTCAGCTATACTT
38379 CAAAAAATCG
Statistics
Matches: 205, Mismatches: 15, Indels: 23
0.84 0.06 0.09
Matches are distributed among these distances:
234 16 0.08
235 87 0.42
238 1 0.00
239 5 0.02
241 28 0.14
243 1 0.00
244 67 0.33
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (234 bp):
AATTTTACATTTTTTTAATATATAAAATACATGTTTAGAATTAGATCTGATCCATTTTCTTATTT
TCCTGAAAAAGATATCCATTTTATTCATAATATATATATATAAATCAACTATATATATATATTTA
ATTAAAACAGAGATTATAAGAAAAAGAAAAAGAAAAAAGAAATCAAAAGTATTTTTGCATTTAGA
TTTTCTTGGAAATCAAGATTCAGCTATACTTGGAAATTG
Found at i:42217 original size:18 final size:18
Alignment explanation
Indices: 42194--42232 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
42184 ATAAAGTTTT
42194 TAATATTATTTAATCATC
1 TAATATTATTTAATCATC
42212 TAATATTATTTAATCATC
1 TAATATTATTTAATCATC
42230 TAA
1 TAA
42233 AAAAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATATTATTTAATCATC
Found at i:42240 original size:18 final size:18
Alignment explanation
Indices: 42201--42240 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42191 TTTTAATATT
* **
42201 ATTTAATCATCTAATATT
1 ATTTAATCATCTAAAAAA
42219 ATTTAATCATCTAAAAAA
1 ATTTAATCATCTAAAAAA
42237 ATTT
1 ATTT
42241 TTTGGCAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTTAATCATCTAAAAAA
Found at i:42449 original size:18 final size:18
Alignment explanation
Indices: 42428--42462 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42418 TGTATAAAAC
*
42428 ATTATTTTATTAATATAT
1 ATTATTATATTAATATAT
*
42446 ATTATTATATTATTATA
1 ATTATTATATTAATATA
42463 ATATAATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTATTATATTAATATAT
Found at i:42568 original size:15 final size:16
Alignment explanation
Indices: 42548--42577 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42538 ATATAAATAC
42548 TAAAAG-AAAAGAAAT
1 TAAAAGAAAAAGAAAT
42563 TAAAAGAAAAAGAAA
1 TAAAAGAAAAAGAAA
42578 ACCCACACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (16 bp):
TAAAAGAAAAAGAAAT
Found at i:55409 original size:14 final size:14
Alignment explanation
Indices: 55390--55416 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55380 TAAAAAAACT
55390 ATTACAATAACTGA
1 ATTACAATAACTGA
55404 ATTACAATAACTG
1 ATTACAATAACTG
55417 GGCAGGAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (14 bp):
ATTACAATAACTGA
Found at i:63118 original size:15 final size:16
Alignment explanation
Indices: 63086--63119 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
63076 TCGAAGTATG
63086 GAGATCATTCCTTCCT
1 GAGATCATTCCTTCCT
*
63102 GAGATCTTTCC-TCCT
1 GAGATCATTCCTTCCT
63117 GAG
1 GAG
63120 GCTGCTGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (16 bp):
GAGATCATTCCTTCCT
Done.