Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018934.1 Corchorus olitorius cultivar O-4 contig18967, 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: 100010
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:6402 original size:31 final size:29
Alignment explanation
Indices: 6367--6439 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 29
6357 ACTGATGGCT
* * *
6367 AAAAGTTCAAATAAGGGCCTGACCTTTAGGA
1 AAAAGGTCAAATAAGGGCCTAACC-TT-CGA
**
6398 AAAAGGTCATTTAAGGGCCTAACCTTCGA
1 AAAAGGTCAAATAAGGGCCTAACCTTCGA
6427 AAAAGGTCAAATA
1 AAAAGGTCAAATA
6440 GATACCTAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
29 13 0.37
30 2 0.06
31 20 0.57
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (29 bp):
AAAAGGTCAAATAAGGGCCTAACCTTCGA
Found at i:7907 original size:26 final size:24
Alignment explanation
Indices: 7864--7914 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
7854 CACTTATTTG
* *
7864 ACCTTTTCTAAAGTTCAGGCCCTT
1 ACCTTTTCTAAAGGTCAGACCCTT
7888 ACCTTTTCCCTAAAGGTCAGACCCTT
1 ACCTTTT--CTAAAGGTCAGACCCTT
7914 A
1 A
7915 TTTGAACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
26 16 0.70
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.33
Consensus pattern (24 bp):
ACCTTTTCTAAAGGTCAGACCCTT
Found at i:9055 original size:42 final size:42
Alignment explanation
Indices: 9008--9093 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
8998 ACAAGGGAGA
*
9008 AGCAGGTTTGGGTGTGGTATCAAGGGATAAACAAGGTTTGGT
1 AGCAGGTTTAGGTGTGGTATCAAGGGATAAACAAGGTTTGGT
*
9050 AGCAGGTTTAGGTGTGGTATCAAGGGATAAAGAAGGTTTGGT
1 AGCAGGTTTAGGTGTGGTATCAAGGGATAAACAAGGTTTGGT
9092 AG
1 AG
9094 TGACTTCTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.28, C:0.06, G:0.38, T:0.28
Consensus pattern (42 bp):
AGCAGGTTTAGGTGTGGTATCAAGGGATAAACAAGGTTTGGT
Found at i:11306 original size:94 final size:90
Alignment explanation
Indices: 11133--11318 Score: 318
Period size: 90 Copynumber: 2.0 Consensus size: 90
11123 GGATAAGATT
*
11133 TTTCTGCTTACTTAGTTCTTGACCAATTTACTCTAAATTGATAGCTCTATATAATTGAATTACCT
1 TTTCTGCTTACTTAGTTATTGACCAATTTACTCTAAATTGATAGCTCTATATAATTGAATTACCT
11198 CTTAATTCATCGTTAGGACTGATAA
66 CTTAATTCATCGTTAGGACTGATAA
*
11223 TTTCTGCTTACTTAGTTATTGACCTATTTACTCTAAATTGATAGCTCTATACATATATTTGAATT
1 TTTCTGCTTACTTAGTTATTGACCAATTTACTCTAAATTGATAGCTCTAT--ATA-A-TTGAATT
11288 ACCTCTTAATTCATCGTTAGGACTGATAA
62 ACCTCTTAATTCATCGTTAGGACTGATAA
11317 TT
1 TT
11319 GTTGGTTTAT
Statistics
Matches: 90, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
90 48 0.53
92 3 0.03
93 1 0.01
94 38 0.42
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (90 bp):
TTTCTGCTTACTTAGTTATTGACCAATTTACTCTAAATTGATAGCTCTATATAATTGAATTACCT
CTTAATTCATCGTTAGGACTGATAA
Found at i:15192 original size:13 final size:13
Alignment explanation
Indices: 15174--15200 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
15164 AAGGTAACAA
15174 CAAAAATCATCAC
1 CAAAAATCATCAC
15187 CAAAAATCATCAC
1 CAAAAATCATCAC
15200 C
1 C
15201 CATGCCAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:16760 original size:22 final size:22
Alignment explanation
Indices: 16711--16761 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
16701 AAATATTACC
* **
16711 ATAATTATTTTTGGCAGCCATA
1 ATAATTATTTTTGCCAGAAATA
16733 ATAATTATTTTTGCCAAGAAATA
1 ATAATTATTTTTGCC-AGAAATA
16756 A-AATTA
1 ATAATTA
16762 GGCAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (22 bp):
ATAATTATTTTTGCCAGAAATA
Found at i:30504 original size:22 final size:22
Alignment explanation
Indices: 30479--30521 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
30469 TATTTTTATG
*
30479 AAATTTTGATAATTACCCTATT
1 AAATTTTGATAACTACCCTATT
30501 AAATTTTGATAACTACCCTAT
1 AAATTTTGATAACTACCCTAT
30522 GAAGTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (22 bp):
AAATTTTGATAACTACCCTATT
Found at i:33393 original size:28 final size:27
Alignment explanation
Indices: 33361--33421 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
33351 CTAAATTTCC
33361 ATTATTTTAATAATAGAATAA-TTA-AAAT
1 ATTATTTT-ATAAT-G-ATAATTTAGAAAT
33389 ATTATTTTATAATGATAATTTAGAAAT
1 ATTATTTTATAATGATAATTTAGAAAT
33416 A-TATTT
1 ATTATTT
33422 GAAAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
25 4 0.13
26 9 0.29
27 10 0.32
28 8 0.26
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (27 bp):
ATTATTTTATAATGATAATTTAGAAAT
Found at i:34477 original size:25 final size:25
Alignment explanation
Indices: 34445--34533 Score: 108
Period size: 25 Copynumber: 3.5 Consensus size: 25
34435 ATGTGACAAT
**
34445 AAAAATCATTAACGTTTTCTA-TAAA
1 AAAAATCATTAACGTTTTC-ACCGAA
*
34470 AAAAATCATTAATGTTCTTACACCGAA
1 AAAAATCATTAACGTT-TT-CACCGAA
*
34497 AAAAATCATTAACATTTTCACCGAA
1 AAAAATCATTAACGTTTTCACCGAA
34522 AAAAATCATTAA
1 AAAAATCATTAA
34534 TGATATATTA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
25 34 0.61
26 5 0.09
27 17 0.30
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.30
Consensus pattern (25 bp):
AAAAATCATTAACGTTTTCACCGAA
Found at i:37491 original size:14 final size:13
Alignment explanation
Indices: 37472--37510 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
37462 AAATTGTAAA
37472 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
37485 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
37499 ATTTAAAAAATT
1 ATTTAAAAAATT
37511 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:37728 original size:125 final size:127
Alignment explanation
Indices: 37496--37752 Score: 387
Period size: 125 Copynumber: 2.0 Consensus size: 127
37486 ATTTAAGAAA
37496 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAAT---A
* *
37561 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
63 CA-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
37626 G
127 G
* *
37627 TATATTTAAAAAATTCTAATATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-C
1 TATATTTAAAAAATTCT-A-ATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATAC
*
37691 A-TA-AA-GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAAG
64 AGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
37752 T
1 T
37753 TTAATAATGG
Statistics
Matches: 119, Mismatches: 5, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
125 55 0.46
126 2 0.02
127 2 0.02
129 1 0.01
131 17 0.14
132 1 0.01
133 41 0.34
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATACAG
TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:81084 original size:24 final size:22
Alignment explanation
Indices: 81057--81105 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
81047 TACATATTCA
*
81057 ATTTTATTATGTATAAATATAATT
1 ATTTTAAT-TGTATAAATAT-ATT
*
81081 A-TTTAATTGTATTAATATATT
1 ATTTTAATTGTATAAATATATT
81102 ATTT
1 ATTT
81106 ATATATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 4 0.18
22 12 0.55
23 5 0.23
24 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (22 bp):
ATTTTAATTGTATAAATATATT
Found at i:81104 original size:21 final size:22
Alignment explanation
Indices: 81066--81106 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
81056 AATTTTATTA
81066 TGTATAAATATAATTATTTAAT
1 TGTATAAATATAATTATTTAAT
*
81088 TGTATTAATAT-ATTATTTA
1 TGTATAAATATAATTATTTA
81107 TATATAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (22 bp):
TGTATAAATATAATTATTTAAT
Found at i:96025 original size:40 final size:40
Alignment explanation
Indices: 95970--96046 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
95960 CCAAAACAAA
95970 TATTTACTATGATTAATTGATGATAAGTCTTTGATTCAAT
1 TATTTACTATGATTAATTGATGATAAGTCTTTGATTCAAT
96010 TATTTACTATGATTAATTGATGATAAGTCTTTGATTC
1 TATTTACTATGATTAATTGATGATAAGTCTTTGATTC
96047 TGTCCAAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.48
Consensus pattern (40 bp):
TATTTACTATGATTAATTGATGATAAGTCTTTGATTCAAT
Found at i:97632 original size:13 final size:13
Alignment explanation
Indices: 97614--97656 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
97604 ACTTGAGGTA
97614 TTCTTCCCCTTTC
1 TTCTTCCCCTTTC
97627 TTCTTCCCCTTTC
1 TTCTTCCCCTTTC
97640 TTC-T--CCTTTC
1 TTCTTCCCCTTTC
97650 TTCTTCC
1 TTCTTCC
97657 ACCAATGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.33
11 1 0.04
12 1 0.04
13 16 0.59
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (13 bp):
TTCTTCCCCTTTC
Found at i:97881 original size:4 final size:4
Alignment explanation
Indices: 97874--97908 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
97864 TATATATATA
97874 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
97909 AAATGCTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Done.