Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024669.1 Corchorus olitorius cultivar O-4 contig24702, 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: 22628
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3940 original size:15 final size:15
Alignment explanation
Indices: 3910--3951 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
3900 TTATTTTGTT
3910 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
3926 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
3941 TTGCTTTCTGT
1 TTGTTTTCTGT
3952 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:6935 original size:21 final size:21
Alignment explanation
Indices: 6893--6943 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
6883 TGGCCAGTCT
*
6893 TGGCTCGGTGGTAACCGGTGG
1 TGGCTCGGTGGTAACCGATGG
* **
6914 TGGCTCGGTTGTGGCCGATGG
1 TGGCTCGGTGGTAACCGATGG
*
6935 TGGCACGGT
1 TGGCTCGGT
6944 AGGATGCATG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.08, C:0.20, G:0.47, T:0.25
Consensus pattern (21 bp):
TGGCTCGGTGGTAACCGATGG
Found at i:7386 original size:27 final size:27
Alignment explanation
Indices: 7344--7443 Score: 173
Period size: 27 Copynumber: 3.7 Consensus size: 27
7334 AGGGTCACCT
* * *
7344 AGGGGCATTTTAGTCATTTGCACGTCC
1 AGGGGCATTTTGGTCATTTGCACATTC
7371 AGGGGCATTTTGGTCATTTGCACATTC
1 AGGGGCATTTTGGTCATTTGCACATTC
7398 AGGGGCATTTTGGTCATTTGCACATTC
1 AGGGGCATTTTGGTCATTTGCACATTC
7425 AGGGGCATTTTGGTCATTT
1 AGGGGCATTTTGGTCATTT
7444 TAAGTTCACA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 70 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGCACATTC
Found at i:8600 original size:18 final size:19
Alignment explanation
Indices: 8577--8620 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
8567 ATACACAAGA
8577 AGCATG-AAGCACAGAAGC
1 AGCATGCAAGCACAGAAGC
*
8595 AGCATGACCAAGCACATAAGC
1 AGCATG--CAAGCACAGAAGC
8616 AGCAT
1 AGCAT
8621 TGGAAAGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 6 0.27
21 16 0.73
ACGTcount: A:0.43, C:0.25, G:0.23, T:0.09
Consensus pattern (19 bp):
AGCATGCAAGCACAGAAGC
Found at i:16348 original size:27 final size:27
Alignment explanation
Indices: 16318--16369 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
16308 AGAAGATTTT
16318 TGAAGAGGGAGAGGGGCGATGAGAGTG
1 TGAAGAGGGAGAGGGGCGATGAGAGTG
*
16345 TGAAGAGTGAGAGGGGCGATGAGAG
1 TGAAGAGGGAGAGGGGCGATGAGAG
16370 AGATTGAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.04, G:0.54, T:0.12
Consensus pattern (27 bp):
TGAAGAGGGAGAGGGGCGATGAGAGTG
Found at i:18034 original size:26 final size:26
Alignment explanation
Indices: 18005--18062 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
17995 AAATAAAGGG
18005 AAGAT-GGAT-TAATCAATATGCAATGT
1 AAGATAGGATATAAT-AA-ATGCAATGT
* *
18031 AAGATATGATATACTAAATGCAATGT
1 AAGATAGGATATAATAAATGCAATGT
18057 AAGATA
1 AAGATA
18063 TGACATGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 20 0.71
27 5 0.18
28 3 0.11
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.29
Consensus pattern (26 bp):
AAGATAGGATATAATAAATGCAATGT
Found at i:18063 original size:26 final size:26
Alignment explanation
Indices: 18022--18076 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
18012 ATTAATCAAT
*
18022 ATGCAATGTAAGATATGATATACTAA
1 ATGCAATGTAAGATATGACATACTAA
*
18048 ATGCAATGTAAGATATGACATGCTAA
1 ATGCAATGTAAGATATGACATACTAA
18074 ATG
1 ATG
18077 TAACATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (26 bp):
ATGCAATGTAAGATATGACATACTAA
Found at i:18558 original size:65 final size:64
Alignment explanation
Indices: 18480--18955 Score: 562
Period size: 65 Copynumber: 7.4 Consensus size: 64
18470 CCGGTGCATC
* * *
18480 TCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTTTTCGAGAAACTATCTTCTGATGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTTTT-GAGAAACCATCTTCTGGTGTACT
* * * * * * * *
18545 TCTTGACAAGATCGTCCTCTGATCATCTTCTG-AAAGTTGTTGAGAAACCTTCTTTTGGCGTGCT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTT-TTGAGAAACCATCTTCTGGTGTACT
* * * * *
18609 TCTTTGACAAGAACGTCTTCTGACCAACTTCTGAAAACTCTTGAAAAACCATCTTCTGGTGTACT
1 TC-TTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACT
* * * * * * *
18674 TTTTGACAAGATCGTCCTCCGATCAATTTCTGAAGATTTTTGAGAAACCATCTTCTAGCGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACT
* * * * *
18738 TCTTTTGACAAGATCGTCTTCCTATCCACTTCTAAAAACTTTTGAGAAACCATCTTCTGGCGTAT
1 TC--TTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTAC
18803 T
64 T
* * *
18804 TCTTTGACAAGATCGTCTTCCGATCAACTTCTGAACACTCTTGAAAAACCATCTTCT-GTGGTAC
1 TC-TTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGT-GTAC
18868 T
64 T
* *
18869 TTTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTA-T
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACT
*
18932 TTTTGACAAGATCGTCTTCCGATC
1 TCTTGACAAGATCGTCTTCCGATC
18956 CAATATGAGA
Statistics
Matches: 348, Mismatches: 56, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
63 25 0.07
64 131 0.38
65 133 0.38
66 59 0.17
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (64 bp):
TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACT
Found at i:18717 original size:129 final size:128
Alignment explanation
Indices: 18485--18955 Score: 592
Period size: 129 Copynumber: 3.6 Consensus size: 128
18475 GCATCTCTTA
* * * *
18485 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTTTTCGAGAAACTATCTTCTGATGTACTTCTTG
1 ACAAGATCGTCTTCCGACCAACTTCTGAAAACTTTT-GAGAAACCATCTTCTGGTGTACTTTTTG
* * * * *
18550 ACAAGATCGTCCTCTGATC-ATCTTCTGAAAGTTGTTGAGAAACCTTCTTTTGGCGTGCTTCTTT
65 ACAAGATCGTCCTCCGATCAAT-TTCTGAAA-TTCTTGAGAAACCATCTTCTGGCGTACTTCTTT
18614 G
128 G
* * * *
18615 ACAAGAACGTCTTCTGACCAACTTCTGAAAACTCTTGAAAAACCATCTTCTGGTGTACTTTTTGA
1 ACAAGATCGTCTTCCGACCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACTTTTTGA
* *
18680 CAAGATCGTCCTCCGATCAATTTCTGAAGATTTTTGAGAAACCATCTTCTAGCGTACTTCTTTTG
66 CAAGATCGTCCTCCGATCAATTTCTGAA-ATTCTTGAGAAACCATCTTCTGGCGTACTTC-TTTG
* * * *
18745 ACAAGATCGTCTTCCTATCC-ACTTCTAAAAACTTTTGAGAAACCATCTTCTGGCGTATTTCTTT
1 ACAAGATCGTCTTCCGA-CCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACTT-TTT
* * * *
18809 GACAAGATCGTCTTCCGATCAACTTCTGAACACTCTTGAAAAACCATCTTCTGTG-GTACTT-TT
64 GACAAGATCGTCCTCCGATCAATTTCTGAA-ATTCTTGAGAAACCATCTTCTG-GCGTACTTCTT
18872 TG
127 TG
* *
18874 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTA-TTTTTGA
1 ACAAGATCGTCTTCCGACCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACTTTTTGA
*
18938 CAAGATCGTCTTCCGATC
66 CAAGATCGTCCTCCGATC
18956 CAATATGAGA
Statistics
Matches: 300, Mismatches: 34, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
127 23 0.08
128 3 0.01
129 128 0.43
130 88 0.29
131 57 0.19
132 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.35
Consensus pattern (128 bp):
ACAAGATCGTCTTCCGACCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACTTTTTGA
CAAGATCGTCCTCCGATCAATTTCTGAAATTCTTGAGAAACCATCTTCTGGCGTACTTCTTTG
Found at i:18823 original size:195 final size:195
Alignment explanation
Indices: 18485--18957 Score: 633
Period size: 195 Copynumber: 2.4 Consensus size: 195
18475 GCATCTCTTA
* *
18485 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTTTTCGAGAAACTATCTTCTGATGTACTTC--T
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAA-TTTTTGAGAAACCATCTTCTG-TGTACTTCTTT
* * * * * *
18548 TGACAAGATCGTCCT-CTGAT-CATCTTCTGAAAGTTGTTGAGAAACCTTCTTTTGGCGTGCTTC
64 TGACAAGATCGTCTTCCT-ATCCATCTTCTAAAACTTGTTGAGAAACCATCTTCTGGCGTACTTC
*
18611 TTTGACAAGAACGTCTTCTGACCAACTTCTGAAAACTCTTGAAAAACCATCTTCTG-GTGTACTT
128 TTTGACAAGAACGTCTTCCGACCAACTTCTGAAAACTCTTGAAAAACCATCTTCTGTG-GTACTT
18675 TTTG
192 TTTG
* * * *
18679 ACAAGATCGTCCTCCGATCAATTTCTGAAGATTTTTGAGAAACCATCTTCTAGCGTACTTCTTTT
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCT-GTGTACTTCTTTT
*
18744 GACAAGATCGTCTTCCTATCCA-CTTCTAAAAACTT-TTGAGAAACCATCTTCTGGCGTATTTCT
65 GACAAGATCGTCTTCCTATCCATCTTCT-AAAACTTGTTGAGAAACCATCTTCTGGCGTACTTCT
* * *
18807 TTGACAAGATCGTCTTCCGATCAACTTCTGAACACTCTTGAAAAACCATCTTCTGTGGTACTTTT
129 TTGACAAGAACGTCTTCCGACCAACTTCTGAAAACTCTTGAAAAACCATCTTCTGTGGTACTTTT
18872 TG
194 TG
* *
18874 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTA--T-TTTT
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCT-GTGTACTTCTTTT
*
18936 GACAAGATCGTCTTCCGATCCA
65 GACAAGATCGTCTTCCTATCCA
18958 ATATGAGATT
Statistics
Matches: 247, Mismatches: 25, Indels: 16
0.86 0.09 0.06
Matches are distributed among these distances:
192 25 0.10
193 26 0.11
194 29 0.12
195 157 0.64
196 10 0.04
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.35
Consensus pattern (195 bp):
ACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCTGTGTACTTCTTTTG
ACAAGATCGTCTTCCTATCCATCTTCTAAAACTTGTTGAGAAACCATCTTCTGGCGTACTTCTTT
GACAAGAACGTCTTCCGACCAACTTCTGAAAACTCTTGAAAAACCATCTTCTGTGGTACTTTTTG
Found at i:19047 original size:64 final size:64
Alignment explanation
Indices: 18956--19146 Score: 355
Period size: 64 Copynumber: 3.0 Consensus size: 64
18946 TCTTCCGATC
* * *
18956 CAATATGAGATTGTCTTCCAATTAATATTTGAAAACTCTTTCTAGCAAACCATCTTCCGGTGTT
1 CAATATGAGATTGTCTTCCAATCAATATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTT
19020 CAATATGAGATTGTCTTCCAATCAATATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTT
1 CAATATGAGATTGTCTTCCAATCAATATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTT
19084 CAATATGAGATTGTCTTCCAATCAATATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGT
1 CAATATGAGATTGTCTTCCAATCAATATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGT
19147 ACTTCTAAAA
Statistics
Matches: 124, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 124 1.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (64 bp):
CAATATGAGATTGTCTTCCAATCAATATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTT
Found at i:20366 original size:29 final size:28
Alignment explanation
Indices: 20304--20407 Score: 86
Period size: 29 Copynumber: 3.7 Consensus size: 28
20294 AGAATCAACT
* * *
20304 AGGGTCATTTTGGTCA-TTTTCAAAAATGC
1 AGGGGCATTTTGGTCATTTTTC--ACATCC
*
20333 AGGGGCATTTTGGTCATTTTTCACATTC
1 AGGGGCATTTTGGTCATTTTTCACATCC
* * * * *
20361 AGGGGGTATTTTAGTC-CTTTGCACGTCC
1 A-GGGGCATTTTGGTCATTTTTCACATCC
20389 AGGGGCATTTTGGTCATTT
1 AGGGGCATTTTGGTCATTT
20408 GTACTTAAAG
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
27 12 0.20
28 16 0.27
29 27 0.45
30 5 0.08
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.39
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTTCACATCC
Found at i:20419 original size:27 final size:27
Alignment explanation
Indices: 20333--20441 Score: 83
Period size: 29 Copynumber: 3.9 Consensus size: 27
20323 TCAAAAATGC
*
20333 AGGGGCATTTTGGTCATTTTTCACATTCA
1 AGGGGCATTTTGGTCATTTGT-AC-TTCA
* * * * * * *
20362 GGGGGTATTTTAGTCCTTTGCACGTCC
1 AGGGGCATTTTGGTCATTTGTACTTCA
*
20389 AGGGGCATTTTGGTCATTTGTACTTAA
1 AGGGGCATTTTGGTCATTTGTACTTCA
* *
20416 AGGGAGGCATTGTGGTCATTTCTACT
1 A-GG-GGCATTTTGGTCATTTGTACT
20442 CCATTTCTCA
Statistics
Matches: 60, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
27 22 0.37
28 4 0.07
29 34 0.57
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.39
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGTACTTCA
Done.