Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022070.1 Corchorus olitorius cultivar O-4 contig22103, 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: 59545
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:2161 original size:29 final size:29
Alignment explanation
Indices: 2119--2208 Score: 180
Period size: 29 Copynumber: 3.1 Consensus size: 29
2109 CTCCAAATTC
2119 AAGATTTCTCCATCAACAAAGCAACAACA
1 AAGATTTCTCCATCAACAAAGCAACAACA
2148 AAGATTTCTCCATCAACAAAGCAACAACA
1 AAGATTTCTCCATCAACAAAGCAACAACA
2177 AAGATTTCTCCATCAACAAAGCAACAACA
1 AAGATTTCTCCATCAACAAAGCAACAACA
2206 AAG
1 AAG
2209 CAAAGTTCTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 61 1.00
ACGTcount: A:0.49, C:0.27, G:0.08, T:0.17
Consensus pattern (29 bp):
AAGATTTCTCCATCAACAAAGCAACAACA
Found at i:2235 original size:46 final size:46
Alignment explanation
Indices: 2182--2270 Score: 169
Period size: 46 Copynumber: 1.9 Consensus size: 46
2172 CAACAAAGAT
2182 TTCTCCATCAACAAAGCAACAACAAAGCAAAGTTCTTCTCCATTTC
1 TTCTCCATCAACAAAGCAACAACAAAGCAAAGTTCTTCTCCATTTC
*
2228 TTCTCCATCAACAAAGCAACAACAAAGCAAAGTTGTTCTCCAT
1 TTCTCCATCAACAAAGCAACAACAAAGCAAAGTTCTTCTCCAT
2271 CAACAAAGCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.38, C:0.29, G:0.08, T:0.25
Consensus pattern (46 bp):
TTCTCCATCAACAAAGCAACAACAAAGCAAAGTTCTTCTCCATTTC
Found at i:2286 original size:46 final size:45
Alignment explanation
Indices: 2190--2290 Score: 114
Period size: 46 Copynumber: 2.2 Consensus size: 45
2180 ATTTCTCCAT
** * *
2190 CAACAAAGCAACAACAAAGCAAAGTTCTTCTCCATTTCTTCTCCAT
1 CAACAAAGCAACAACAAAGCAAAGTTCTTCTCCA-TTCAACACCAA
* *
2236 CAACAAAGCAACAACAAAGCAAAGTTGTTCTCCA-TCAACAAAGCAA
1 CAACAAAGCAACAACAAAGCAAAGTTCTTCTCCATTCAAC--ACCAA
2282 CAACAAAGC
1 CAACAAAGC
2291 GCCTACGAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 3 0.06
46 44 0.94
ACGTcount: A:0.45, C:0.29, G:0.09, T:0.18
Consensus pattern (45 bp):
CAACAAAGCAACAACAAAGCAAAGTTCTTCTCCATTCAACACCAA
Found at i:2499 original size:42 final size:42
Alignment explanation
Indices: 2436--2528 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
2426 TCAAATCTAA
* *
2436 CAAATCCGACAACGAGGAATAACAAGCCTTCAGCCATTTCTCT
1 CAAATCC-ACAACGAGAAATAACAAGCCTTCAGCCATTCCTCT
**
2479 CAAATCCACAACGAGAAATAACAAGCCTTTGGCCATTCCTCT
1 CAAATCCACAACGAGAAATAACAAGCCTTCAGCCATTCCTCT
*
2521 CATATCCA
1 CAAATCCA
2529 TTTCATCGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 38 0.84
43 7 0.16
ACGTcount: A:0.35, C:0.31, G:0.12, T:0.22
Consensus pattern (42 bp):
CAAATCCACAACGAGAAATAACAAGCCTTCAGCCATTCCTCT
Found at i:14309 original size:11 final size:11
Alignment explanation
Indices: 14293--14327 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
14283 TTTCTCAAAC
14293 ATATATACTAA
1 ATATATACTAA
14304 ATATATACT-A
1 ATATATACTAA
14314 A-ATATACTAA
1 ATATATACTAA
14324 ATAT
1 ATAT
14328 TATTTGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 7 0.32
10 4 0.18
11 11 0.50
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATATACTAA
Found at i:15882 original size:32 final size:32
Alignment explanation
Indices: 15841--15926 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 32
15831 CTAGACGCGA
* *
15841 AGCCGTCCTGA-GGGGACGGCACCACCATGGCG
1 AGCCGTCCTGACAGGG-CAGCACCACCATGGCG
*
15873 AGCCGTCCTGACAGGGCAGCACCACCATGGTG
1 AGCCGTCCTGACAGGGCAGCACCACCATGGCG
* * *
15905 TGCCGTCCTCACAGGGCGGCAC
1 AGCCGTCCTGACAGGGCAGCAC
15927 GGTCATCAGC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 44 0.94
33 3 0.06
ACGTcount: A:0.19, C:0.36, G:0.34, T:0.12
Consensus pattern (32 bp):
AGCCGTCCTGACAGGGCAGCACCACCATGGCG
Found at i:18705 original size:26 final size:26
Alignment explanation
Indices: 18676--18730 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
18666 GTCCCATTGC
18676 CCCAGACTCGGTTGTCCACGTGTAGA
1 CCCAGACTCGGTTGTCCACGTGTAGA
18702 CCCAGACTCGGTTGTCCACGTGTAGA
1 CCCAGACTCGGTTGTCCACGTGTAGA
18728 CCC
1 CCC
18731 GATGTGTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.18, C:0.35, G:0.25, T:0.22
Consensus pattern (26 bp):
CCCAGACTCGGTTGTCCACGTGTAGA
Found at i:20060 original size:21 final size:21
Alignment explanation
Indices: 20036--20104 Score: 65
Period size: 22 Copynumber: 3.4 Consensus size: 21
20026 ACTATATATA
* *
20036 TAATAACTGAAATACTTACAT
1 TAATAAATGTAATACTTACAT
20057 TAATTAAATGTAATAC-T--A-
1 TAA-TAAATGTAATACTTACAT
*
20075 TAATAATTGTAATACTTACAT
1 TAATAAATGTAATACTTACAT
20096 TAATTAAAT
1 TAA-TAAAT
20105 TCTTAGATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
17 11 0.29
18 4 0.11
19 1 0.03
20 1 0.03
21 7 0.18
22 14 0.37
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (21 bp):
TAATAAATGTAATACTTACAT
Found at i:20122 original size:24 final size:25
Alignment explanation
Indices: 20095--20141 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
20085 AATACTTACA
20095 TTAATT-AAATTCTTAGATATTTTT
1 TTAATTCAAATTCTTAGATATTTTT
*
20119 TTAATTCAAATTCTTAGGTATTT
1 TTAATTCAAATTCTTAGATATTT
20142 GTGCAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (25 bp):
TTAATTCAAATTCTTAGATATTTTT
Found at i:22596 original size:58 final size:56
Alignment explanation
Indices: 22506--22613 Score: 162
Period size: 58 Copynumber: 1.9 Consensus size: 56
22496 ATCATGCTTC
*
22506 GGTCCTAAAACGTCTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGCCTT
1 GGTCCGAAAACGTCTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGCCTT
* * *
22562 GGTCCGAAAACGTCTTTTTTTATGCATCTAATAAAGAACATGTCACTTGATA
1 GGTCCGAAAACGTC--TTTTTAGGCATCTAATAAAAAACATGTCACTCGATA
22614 TTTGATTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
56 13 0.28
58 33 0.72
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (56 bp):
GGTCCGAAAACGTCTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGCCTT
Found at i:23800 original size:14 final size:14
Alignment explanation
Indices: 23771--23799 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
23761 GATAATCTTA
23771 TTCTTATTCTTTTT
1 TTCTTATTCTTTTT
23785 TTCTT-TTCTTTTT
1 TTCTTATTCTTTTT
23798 TT
1 TT
23800 TGCATCAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTTATTCTTTTT
Found at i:25244 original size:41 final size:41
Alignment explanation
Indices: 25197--25361 Score: 287
Period size: 41 Copynumber: 4.0 Consensus size: 41
25187 TTGATTCAAT
25197 CTTGTGAGTACATGGACTAAATTGACCAACTCCTGTGAATA
1 CTTGTGAGTACATGGACTAAATTGACCAACTCCTGTGAATA
*
25238 CTTGTGAGTACATGGACTAAATTGACCAACTCCTGTAAATA
1 CTTGTGAGTACATGGACTAAATTGACCAACTCCTGTGAATA
*
25279 CTTGTGAGTACATGGACTAAATTGACCCACTCCTGTGAATA
1 CTTGTGAGTACATGGACTAAATTGACCAACTCCTGTGAATA
*
25320 CTTGTGAATACATGGACTAAATTGATCC-ACTCCTGTGAATA
1 CTTGTGAGTACATGGACTAAATTGA-CCAACTCCTGTGAATA
25361 C
1 C
25362 AGGAACTAAA
Statistics
Matches: 119, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
41 117 0.98
42 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (41 bp):
CTTGTGAGTACATGGACTAAATTGACCAACTCCTGTGAATA
Found at i:31230 original size:14 final size:14
Alignment explanation
Indices: 31211--31239 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
31201 CTTTCTTTAG
31211 AAAGCATTAAAGTT
1 AAAGCATTAAAGTT
31225 AAAGCATTAAAGTT
1 AAAGCATTAAAGTT
31239 A
1 A
31240 TATCAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (14 bp):
AAAGCATTAAAGTT
Found at i:32031 original size:14 final size:14
Alignment explanation
Indices: 32012--32039 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
32002 TAGCGCATGA
32012 TTTGGCACACATTG
1 TTTGGCACACATTG
32026 TTTGGCACACATTG
1 TTTGGCACACATTG
32040 ATTGCTCTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (14 bp):
TTTGGCACACATTG
Found at i:36936 original size:30 final size:30
Alignment explanation
Indices: 36902--36963 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
36892 ATTTTTATCT
*
36902 TGACTTTCCTCTTATATCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
*
36932 TGACTTTTCTCTTATACCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
36962 TG
1 TG
36964 GCTTATTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.23, G:0.05, T:0.47
Consensus pattern (30 bp):
TGACTTTCCTCTTATACCCTCAAATTTTAA
Found at i:45768 original size:29 final size:30
Alignment explanation
Indices: 45736--45796 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
45726 ATAATATAAT
* *
45736 ATAATATAATTAAATAA-TTATATTTATAC
1 ATAATAAAATTAAATAATTTATATGTATAC
*
45765 ATAATAAAATTGAATAATTTATATGTATAC
1 ATAATAAAATTAAATAATTTATATGTATAC
45795 AT
1 AT
45797 TAATTAGAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (30 bp):
ATAATAAAATTAAATAATTTATATGTATAC
Found at i:45946 original size:25 final size:26
Alignment explanation
Indices: 45897--45946 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
45887 TGTTTAAATT
*
45897 TTATTTTTTATTAAAAAATTTAATAA
1 TTATTTTTTATTAAAAAATTAAATAA
45923 TTATTTTATT-TTAAAAAA-TAAATA
1 TTATTTT-TTATTAAAAAATTAAATA
45947 TGAGCGGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 15 0.68
27 2 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTATTTTTTATTAAAAAATTAAATAA
Found at i:49224 original size:42 final size:42
Alignment explanation
Indices: 49173--49262 Score: 128
Period size: 45 Copynumber: 2.1 Consensus size: 42
49163 AATGCATTAC
* *
49173 CTAAATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAAATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
49214 CTAAGATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
1 CTAA-ATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
49259 CTAA
1 CTAA
49263 TATTAATTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.14
45 33 0.77
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (42 bp):
CTAAATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:57736 original size:116 final size:111
Alignment explanation
Indices: 57607--57834 Score: 296
Period size: 116 Copynumber: 2.0 Consensus size: 111
57597 TAATAAGTTG
* * * * *
57607 ATCGGCTCACGCTGGTGCATTGAGCATTCTTGATTTGTGGCTAGCAAATTAGTTTAGTTTTAGAG
1 ATCGGCTCACGCTGGCGCATCGAGCATTCTTGATGTGTGGCTAGCAAATCAGTTTAGTTATA-A-
**
57672 TTTTTTTTTTTTTTTCT-TCTCGGTTCTTATCATATATGTGAGGAGGTGGTT
64 ----ACTTTTTTTTTCTATCTCGGTTCTTATCATATATGTGAGGAGGTGGTT
* * *
57723 ATCGGCTCACGCTGGCGCGTCGAGCATTCTTGATGTGTGGTTAGCAAATCATTTTAGTTATAAAC
1 ATCGGCTCACGCTGGCGCATCGAGCATTCTTGATGTGTGGCTAGCAAATCAGTTTAGTTATAAAC
*
57788 TTTTTTTTTCTATCTCGGTTCTTATCATATATGTGAGTAGGTGGTT
66 TTTTTTTTTCTATCTCGGTTCTTATCATATATGTGAGGAGGTGGTT
57834 A
1 A
57835 GCAAATTTGA
Statistics
Matches: 100, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
110 11 0.11
111 34 0.34
115 1 0.01
116 54 0.54
ACGTcount: A:0.19, C:0.14, G:0.23, T:0.44
Consensus pattern (111 bp):
ATCGGCTCACGCTGGCGCATCGAGCATTCTTGATGTGTGGCTAGCAAATCAGTTTAGTTATAAAC
TTTTTTTTTCTATCTCGGTTCTTATCATATATGTGAGGAGGTGGTT
Done.