Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011261.1 Corchorus olitorius cultivar O-4 contig11294, 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: 76484
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:1508 original size:29 final size:30
Alignment explanation
Indices: 1458--1517 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
1448 CTAATTAACG
*
1458 TATAAATATAAATTATTCAATTTTATTATA
1 TATAAATATAAATTATTCAATTATATTATA
*
1488 TATAAATAT-AATTATTTAATTATATTATA
1 TATAAATATAAATTATTCAATTATATTATA
1517 T
1 T
1518 TATTTATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
TATAAATATAAATTATTCAATTATATTATA
Found at i:1529 original size:18 final size:19
Alignment explanation
Indices: 1483--1532 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
1473 TTCAATTTTA
1483 TTATATATAAATATAATTAT
1 TTATATAT-AATATAATTAT
*
1503 TTA-ATTATATTAT-ATTAT
1 TTATA-TATAATATAATTAT
1521 TTATATATAATA
1 TTATATATAATA
1533 CAGGCTGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 14 0.54
19 6 0.23
20 6 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTATATATAATATAATTAT
Found at i:3089 original size:29 final size:29
Alignment explanation
Indices: 3047--3102 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
3037 TACAAGTTTA
*
3047 CAACACCACAATTACAAGTTTTCAACAGT
1 CAACACCACAATTACAAGCTTTCAACAGT
3076 CAACACCACAATTACAAGCTTTCAACA
1 CAACACCACAATTACAAGCTTTCAACA
3103 CCGTACAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.43, C:0.30, G:0.05, T:0.21
Consensus pattern (29 bp):
CAACACCACAATTACAAGCTTTCAACAGT
Found at i:3257 original size:2 final size:2
Alignment explanation
Indices: 3252--3298 Score: 64
Period size: 2 Copynumber: 24.5 Consensus size: 2
3242 AAAATGTGTG
3252 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TGA -A TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
3292 TA TA TA T
1 TA TA TA T
3299 TTCGGGGACG
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.07
2 37 0.90
3 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19965 original size:21 final size:23
Alignment explanation
Indices: 19941--19996 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 23
19931 GAATGTGATA
19941 TTTCAAAATTAAT-AAAA-AGGT
1 TTTCAAAATTAATAAAAACAGGT
19962 TTTCAAAATTAATCAAAAATCAGGT
1 TTTCAAAATTAAT-AAAAA-CAGGT
19987 TTTCAAAATT
1 TTTCAAAATT
19997 TCCAATTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 13 0.42
23 4 0.13
25 14 0.45
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (23 bp):
TTTCAAAATTAATAAAAACAGGT
Found at i:23403 original size:435 final size:432
Alignment explanation
Indices: 22864--23749 Score: 1149
Period size: 435 Copynumber: 2.0 Consensus size: 432
22854 ATAATTACCA
* * *
22864 ATCCTCATGTCCGATTAAAGTTATTCAAGTGTCCGTTAAAATGTTATTGCATGACCTACGACTTT
1 ATCCACATGTCCGATTAAAGTTATTCAAGTGTCCGTTAAAAGGTTATTGCATCACCTACGACTTT
* * * *
22929 TATGAAGTATCCGAAAGCTAAATTTGATCAACGAGTTTCATGAAAGGTTCAAAAGAGAATTTATA
66 CATGAAGGACCCGAAAGCTAAATTTGATCAACAAGTTTCATGAAAGGTTC-AAAGAGAATTTATA
* *
22994 TGTTTCAAGATCTCCAT-AAAAAACATTTTCTTATTTAGATTATTTATCAAATGACCCTCATATT
130 TATTTCAAGATCTACATCAAAAAACATTTTCTTATTTAGATTATTTATCAAATGACCCTCATATT
* **
23058 TTTCTACTTTATACTATTTAGTCCTTTAC-TAATTCTATCTTAATCGATTTAACGC-TCAAGC-T
195 TTTCTACTTTATAC----TA--CCTTTACAAAATTCTATCTTAATCGATAAAACGCTTC-AGCTT
* * **
23120 TTATTTTTT-TTTGTTATATTTGTCCGATTAAGGTGGTTCA-AATGTCTATTAAAAGGTAATTTC
253 TTATTTTTTCTTTGTTATATTTGTCCAATTAAGCTCATTCAGAA--TCTATTAAAAGGTAATTTC
* *
23183 ATTATCTACAACTTT-ATGAAGGACTCAAAAGCCAATTTTTAAGTTTCAATTC-AAACAAATGCT
316 ATGATCTACAACTTTCATGAAGGACTCAAAAGCCAATTTTTAAGTTTCAATTCTAAA-AAAGGCT
*
23246 ACCCAAATTGGATAGTTTCGATTGTCGGTCTATATAATACCATATAATTTTGG
380 ACCCAAATTGGATAGTTTCGATTGACGGTCTATATAATACCATATAATTTTGG
*
23299 ATCCACATGTCCGATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTATTGCATCACCTACGACTTT
1 ATCCACATGTCCGATTAAAGTTATTCAAGTGTCCGTTAAAAGGTTATTGCATCACCTACGACTTT
* ** * * *
23364 CATGAAGGACCCGAAAGTTAAATTTGATCTGCAAGTTTCATGAAGGGTTCAAAGGGAATTTTTAT
66 CATGAAGGACCCGAAAGCTAAATTTGATCAACAAGTTTCATGAAAGGTTCAAAGAGAATTTATAT
* * *
23429 ATTTCAAGATCTACATCAACAAATATTTTCTTATTTGGATTATTTATCAAATGACCCTCATATTT
131 ATTTCAAGATCTACATCAAAAAACATTTTCTTATTTAGATTATTTATCAAATGACCCTCATATTT
* * *
23494 TTCTACTTTATACTACTTTTACAAAATTCTATCTTACTCGATAAAACGCTTCAGCTTTTTTTTTT
196 TTCTACTTTATACTACCTTTACAAAATTCTATCTTAATCGATAAAACGCTTCAGCTTTTATTTTT
* *
23559 TCTTTGTTCTATTTGTCCAATTAAGCTCATTCAGGAATCTATTATAAGGTAATTTCATGATCTAC
261 TCTTTGTTATATTTGTCCAATTAAGCTCATTCA-GAATCTATTAAAAGGTAATTTCATGATCTAC
* ** * * * ** *
23624 CACTTTCATTTAGGACTCAAAAGCTAATTTTTATGTTTCAATTCTAAAAAAGGCTTCCGGAATTT
325 AACTTTCATGAAGGACTCAAAAGCCAATTTTTAAGTTTCAATTCTAAAAAAGGCTACCCAAATTG
* * * * * *
23689 TATGGTTTCGATTGACGGTCTATTTAATATCATATCATTTTTG
390 GATAGTTTCGATTGACGGTCTATATAATACCATATAATTTTGG
* *
23732 ATCCAGATGTCCAATTAA
1 ATCCACATGTCCGATTAA
23750 CAAAGATCCC
Statistics
Matches: 391, Mismatches: 51, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
429 6 0.02
430 25 0.06
431 13 0.03
432 57 0.15
433 97 0.25
434 32 0.08
435 161 0.41
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (432 bp):
ATCCACATGTCCGATTAAAGTTATTCAAGTGTCCGTTAAAAGGTTATTGCATCACCTACGACTTT
CATGAAGGACCCGAAAGCTAAATTTGATCAACAAGTTTCATGAAAGGTTCAAAGAGAATTTATAT
ATTTCAAGATCTACATCAAAAAACATTTTCTTATTTAGATTATTTATCAAATGACCCTCATATTT
TTCTACTTTATACTACCTTTACAAAATTCTATCTTAATCGATAAAACGCTTCAGCTTTTATTTTT
TCTTTGTTATATTTGTCCAATTAAGCTCATTCAGAATCTATTAAAAGGTAATTTCATGATCTACA
ACTTTCATGAAGGACTCAAAAGCCAATTTTTAAGTTTCAATTCTAAAAAAGGCTACCCAAATTGG
ATAGTTTCGATTGACGGTCTATATAATACCATATAATTTTGG
Found at i:27058 original size:21 final size:21
Alignment explanation
Indices: 27015--27059 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
27005 GCTGCTCTAA
* *
27015 TAATCTCATCTATACAGTACC
1 TAATCTAATCTATACAATACC
* *
27036 TAATCTAATCTGTACAATTCC
1 TAATCTAATCTATACAATACC
27057 TAA
1 TAA
27060 ATAGTGTCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (21 bp):
TAATCTAATCTATACAATACC
Found at i:28224 original size:30 final size:30
Alignment explanation
Indices: 28184--28281 Score: 124
Period size: 30 Copynumber: 3.3 Consensus size: 30
28174 TTCTGAAGAT
28184 GATTTTGACCCGTATGAGGATCCCGAGGAG
1 GATTTTGACCCGTATGAGGATCCCGAGGAG
* * * * *
28214 GATTTCGACCCGGACGAGGATACCGAAGAG
1 GATTTTGACCCGTATGAGGATCCCGAGGAG
* * *
28244 GATTTTGACCCATATGAGGATCCTGAGGAA
1 GATTTTGACCCGTATGAGGATCCCGAGGAG
28274 GATTTTGA
1 GATTTTGA
28282 GATGTCAGCC
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (30 bp):
GATTTTGACCCGTATGAGGATCCCGAGGAG
Found at i:29876 original size:11 final size:12
Alignment explanation
Indices: 29860--29890 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
29850 GAAGTTCGTG
29860 TTTGAAGAC-CA
1 TTTGAAGACTCA
29871 TTTGAAGACTCA
1 TTTGAAGACTCA
29883 TTTGAAGA
1 TTTGAAGA
29891 TTTGAAGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (12 bp):
TTTGAAGACTCA
Found at i:29914 original size:29 final size:31
Alignment explanation
Indices: 29860--29919 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
29850 GAAGTTCGTG
*
29860 TTTGAAGACCATTTGAAGACTCATTTGAAGA
1 TTTGAAGACCATTTGAAGACTCATTTCAAGA
* *
29891 TTTGAAGA-C-TTTGAAGATTTATTTCAAGA
1 TTTGAAGACCATTTGAAGACTCATTTCAAGA
29920 GGAAGGATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 17 0.65
30 1 0.04
31 8 0.31
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (31 bp):
TTTGAAGACCATTTGAAGACTCATTTCAAGA
Found at i:29968 original size:11 final size:11
Alignment explanation
Indices: 29952--29980 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
29942 TTAATTGAAG
29952 ACAAGCCATGA
1 ACAAGCCATGA
29963 ACAAGCCATGA
1 ACAAGCCATGA
29974 ACAAGCC
1 ACAAGCC
29981 CTTAAGCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.31, G:0.17, T:0.07
Consensus pattern (11 bp):
ACAAGCCATGA
Found at i:31324 original size:15 final size:15
Alignment explanation
Indices: 31291--31332 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
31281 TTACTTTGCT
31291 TTGTTTTCTAGTATAA
1 TTGTTTTCT-GTATAA
*
31307 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTATAA
31322 TTGTTTTCTGT
1 TTGTTTTCTGT
31333 CAACCTCTGT
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:0.14, C:0.07, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTATAA
Found at i:44021 original size:71 final size:70
Alignment explanation
Indices: 43878--44023 Score: 165
Period size: 71 Copynumber: 2.1 Consensus size: 70
43868 TTGTAAGCCC
* * * *
43878 TCAAACATTTCTATTTTATGTGATTTGTCCTTCATCTTTATTTCTTTTATTTTTATAATATTTTC
1 TCAAACATTTATATTTTATGTGATTTATCATTCATCTTTATTTCTTTTATTTTTAT-ATAATTTC
43943 AATTTT
65 AATTTT
*
43949 TCAAACATTTATCTTTTATGTGATTTAATCATTCAAT-TTTATTTCTTTAATATTTTT-T-TAAT
1 TCAAACATTTATATTTTATGTGATTT-ATCATTC-ATCTTTATTTCTTT--TATTTTTATATAAT
44011 TT-AATATTT
62 TTCAAT-TTT
44020 TCAA
1 TCAA
44024 TTTCTTTTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
70 3 0.05
71 36 0.55
72 16 0.25
73 3 0.05
74 7 0.11
ACGTcount: A:0.27, C:0.11, G:0.03, T:0.59
Consensus pattern (70 bp):
TCAAACATTTATATTTTATGTGATTTATCATTCATCTTTATTTCTTTTATTTTTATATAATTTCA
ATTTT
Found at i:48840 original size:23 final size:23
Alignment explanation
Indices: 48814--48881 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 23
48804 ATCATGAAGG
*
48814 AAAAGAAGAAAAAGAAAGGAAAA
1 AAAAGAAGAAAAAGAAAAGAAAA
* * * ** *
48837 AAAATAGGAAAAGGAAAATCAGA
1 AAAAGAAGAAAAAGAAAAGAAAA
48860 AAAAG-AGAAAAAGAAAATGAAA
1 AAAAGAAGAAAAAGAAAA-GAAA
48882 GGAAAAAATT
Statistics
Matches: 31, Mismatches: 13, Indels: 2
0.67 0.28 0.04
Matches are distributed among these distances:
22 10 0.32
23 21 0.68
ACGTcount: A:0.74, C:0.01, G:0.21, T:0.04
Consensus pattern (23 bp):
AAAAGAAGAAAAAGAAAAGAAAA
Found at i:70898 original size:6 final size:6
Alignment explanation
Indices: 70887--70927 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
70877 GTAGAGTAGA
**
70887 CCTTCT CCTTCT CCTTCT CCTTCT TTTTCT CCTTCT CCTTC
1 CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT CCTTC
70928 AATTGAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (6 bp):
CCTTCT
Found at i:74755 original size:15 final size:15
Alignment explanation
Indices: 74735--74766 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
74725 AATCCACTAA
74735 ATCTAAGTGCACGAT
1 ATCTAAGTGCACGAT
74750 ATCTAAGTGCACGAT
1 ATCTAAGTGCACGAT
74765 AT
1 AT
74767 GAGTCAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (15 bp):
ATCTAAGTGCACGAT
Found at i:75864 original size:31 final size:31
Alignment explanation
Indices: 75826--75887 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
75816 GAGTTTTGTA
*
75826 AAACTTTTGAATCGCCTATTATATCCTTATT
1 AAACTTTTGAATCGCCTATTATACCCTTATT
75857 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATCGCCTATTATACCCTTATT
75888 TTTGGAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATTATACCCTTATT
Found at i:75978 original size:14 final size:14
Alignment explanation
Indices: 75959--75997 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
75949 TATCCTTATA
*
75959 ACTATTTTATTTTT
1 ACTATTTTACTTTT
75973 ACTATTTTACTTTT
1 ACTATTTTACTTTT
75987 A-TAGTTTTACT
1 ACTA-TTTTACT
75998 CAACTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 2 0.09
14 21 0.91
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.64
Consensus pattern (14 bp):
ACTATTTTACTTTT
Found at i:76001 original size:85 final size:83
Alignment explanation
Indices: 75902--76066 Score: 267
Period size: 85 Copynumber: 2.0 Consensus size: 83
75892 GAATATATTC
*
75902 ATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTATTTT
1 ATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACT-TTTT
* *
75967 ATTTTTACTATTTTACTTTT
65 -TTTTTACGATATTACTTTT
* *
75987 ATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTTTTTT
1 ATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTTTTTT
76052 TTTTACGATATTACT
66 TTTTACGATATTACT
76067 AATTTAATTA
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
83 14 0.19
84 4 0.05
85 57 0.76
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.52
Consensus pattern (83 bp):
ATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTTTTTT
TTTTACGATATTACTTTT
Done.