Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020628.1 Corchorus olitorius cultivar O-4 contig20661, 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: 69642
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--48 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43 TA TA TA
1 TA TA TA
49 CATAACAAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4521 original size:2 final size:2
Alignment explanation
Indices: 4514--4561 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
4504 TAATGCAATC
4514 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4555 TA TA TA T
1 TA TA TA T
4562 CATTATTCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7545 original size:40 final size:40
Alignment explanation
Indices: 7490--7571 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
7480 TCACACCCTA
*
7490 GAAAAAAGATTAGTGACGACTCCTCTTTTCCAGTCGTTTC
1 GAAAAAAGATTAGTGACGACTCCTCTTTTCCAATCGTTTC
7530 GAAAAAAGATTAGTGACGACTCCTCTTTTCCAATCGTTTC
1 GAAAAAAGATTAGTGACGACTCCTCTTTTCCAATCGTTTC
7570 GA
1 GA
7572 TAGGGTTCCC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (40 bp):
GAAAAAAGATTAGTGACGACTCCTCTTTTCCAATCGTTTC
Found at i:10974 original size:2 final size:2
Alignment explanation
Indices: 10967--10994 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10957 GTAACCAACT
10967 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10995 CCAAATTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14207 original size:30 final size:30
Alignment explanation
Indices: 14171--14275 Score: 201
Period size: 30 Copynumber: 3.5 Consensus size: 30
14161 AGTAAATGCC
*
14171 AGGAAAGGATGGGAAAGGAATGACCCTTGA
1 AGGAAAGGATGGGAAAGGAAGGACCCTTGA
14201 AGGAAAGGATGGGAAAGGAAGGACCCTTGA
1 AGGAAAGGATGGGAAAGGAAGGACCCTTGA
14231 AGGAAAGGATGGGAAAGGAAGGACCCTTGA
1 AGGAAAGGATGGGAAAGGAAGGACCCTTGA
14261 AGGAAAGGATGGGAA
1 AGGAAAGGATGGGAA
14276 TGACCAATTC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 74 1.00
ACGTcount: A:0.41, C:0.09, G:0.40, T:0.10
Consensus pattern (30 bp):
AGGAAAGGATGGGAAAGGAAGGACCCTTGA
Found at i:34466 original size:30 final size:30
Alignment explanation
Indices: 34430--34497 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
34420 GAAACTCGGT
34430 TCGAGCTCGACGGGCTTCCATTTTTCAAAC
1 TCGAGCTCGACGGGCTTCCATTTTTCAAAC
34460 TCGAGCTCGACGGGCTTCCATTTTTCAAAC
1 TCGAGCTCGACGGGCTTCCATTTTTCAAAC
34490 TCGAGCTC
1 TCGAGCTC
34498 TGGTTGCCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.19, C:0.31, G:0.21, T:0.29
Consensus pattern (30 bp):
TCGAGCTCGACGGGCTTCCATTTTTCAAAC
Found at i:39773 original size:19 final size:20
Alignment explanation
Indices: 39743--39806 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
39733 TTAACACTGT
*
39743 TTAGCAACTGTACAGATGAGA
1 TTAGC-ACTGTACAAATGAGA
* *
39764 TTA-CACTGTACATATTAGA
1 TTAGCACTGTACAAATGAGA
*
39783 TTAGGTACTGTACAAATGAGA
1 TTA-GCACTGTACAAATGAGA
39804 TTA
1 TTA
39807 TTAGAGCAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 16 0.44
20 1 0.03
21 19 0.53
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (20 bp):
TTAGCACTGTACAAATGAGA
Found at i:55840 original size:19 final size:19
Alignment explanation
Indices: 55816--55855 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
55806 TTAGGGATCC
55816 AGTAGATAATTATTTGAAT
1 AGTAGATAATTATTTGAAT
55835 AGTAGATAATTATTTGAAT
1 AGTAGATAATTATTTGAAT
55854 AG
1 AG
55856 ACATTAGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.40
Consensus pattern (19 bp):
AGTAGATAATTATTTGAAT
Found at i:57497 original size:22 final size:22
Alignment explanation
Indices: 57313--57881 Score: 181
Period size: 22 Copynumber: 25.4 Consensus size: 22
57303 CTTCAACGTA
* * **
57313 GAAATATTGACAACCACACTGC
1 GAAATTTTGATAACCACACTAT
* * * *
57335 GAAAATTTGATAACCTCATTGT
1 GAAATTTTGATAACCACACTAT
* * * *
57357 GAAGTTTCGATAACCTCCCTAT
1 GAAATTTTGATAACCACACTAT
* * *
57379 GAAAATTTGATAACCACAATGT
1 GAAATTTTGATAACCACACTAT
*
57401 GAAATTTTGATAACCACACTGT
1 GAAATTTTGATAACCACACTAT
* *
57423 GAAATTCTGATAACCACACAAT
1 GAAATTTTGATAACCACACTAT
* *
57445 GAAGTTTTGATAACCTCATTGTCTAT
1 GAAATTTTGATAACCACA----CTAT
*
57471 GAAATTTTGATAATCACACTAT
1 GAAATTTTGATAACCACACTAT
* * * *
57493 -AAA-ATTGGTAATCGCACTAT
1 GAAATTTTGATAACCACACTAT
* *
57513 GAAAATTTTGGTAACCACACCAT
1 G-AAATTTTGATAACCACACTAT
* * *
57536 GAAATTTCGACAACTTCCCTA-TAAGAAT
1 GAAATTTTGATAAC--CAC-ACT----AT
* ** *
57564 GAAATTGTGATATTCTCTA-TAT
1 GAAATTTTGATAACCAC-ACTAT
* * * *
57586 GTAATTTTGATAACCTCTCCAT
1 GAAATTTTGATAACCACACTAT
* * * *
57608 -AATATTTTCATAAGCTCCCTAT
1 GAA-ATTTTGATAACCACACTAT
* *
57630 GAAATTTTGTTAACCATC-CTAG
1 GAAATTTTGATAACCA-CACTAT
***
57652 GAAATTTTGATAA-CGTTCTAAT
1 GAAATTTTGATAACCACACT-AT
* *
57674 -TAATTTTGATAATCACACTAT
1 GAAATTTTGATAACCACACTAT
* ** * * *
57695 AAAATTTCAAAAACCTTC-GTAT
1 GAAATTTTGATAACC-ACACTAT
*
57717 GAAATTTTGATAATCTC-CA-TAA
1 GAAATTTTGATAA-C-CACACTAT
* ****
57739 GAGATTTTGATAACCTTTTTTTAT
1 GAAATTTTGATAACC--ACACTAT
* * **
57763 GAAATTTTGGTAACCTCTGTAT
1 GAAATTTTGATAACCACACTAT
** *
57785 GAAATTTTGATAATTACACTAC
1 GAAATTTTGATAACCACACTAT
* *
57807 GAAGTTTTGATAACCTC-CATAT
1 GAAATTTTGATAACCACAC-TAT
*
57829 GAAATTTTGGTAACCACACTAT
1 GAAATTTTGATAACCACACTAT
* **
57851 GAAATTTTAATAACCTTACTAT
1 GAAATTTTGATAACCACACTAT
*
57873 GTAATTTTG
1 GAAATTTTG
57882 GTTTGATTGT
Statistics
Matches: 401, Mismatches: 114, Indels: 64
0.69 0.20 0.11
Matches are distributed among these distances:
20 15 0.04
21 22 0.05
22 291 0.73
23 20 0.05
24 18 0.04
25 1 0.00
26 23 0.06
28 11 0.03
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (22 bp):
GAAATTTTGATAACCACACTAT
Found at i:57537 original size:23 final size:23
Alignment explanation
Indices: 57467--57539 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
57457 ACCTCATTGT
*
57467 CTATG-AAATTTTGATAATCACA
1 CTATGAAAATTTTGGTAATCACA
*
57489 CTAT-AAAA--TTGGTAATCGCA
1 CTATGAAAATTTTGGTAATCACA
*
57509 CTATGAAAATTTTGGTAACCACA
1 CTATGAAAATTTTGGTAATCACA
*
57532 CCATGAAA
1 CTATGAAA
57540 TTTCGACAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
20 14 0.33
21 4 0.10
22 7 0.17
23 17 0.40
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.30
Consensus pattern (23 bp):
CTATGAAAATTTTGGTAATCACA
Found at i:59686 original size:22 final size:22
Alignment explanation
Indices: 59618--60114 Score: 185
Period size: 22 Copynumber: 22.4 Consensus size: 22
59608 CTCCAATATA
* * * *
59618 GAAATATTGATAACCACATTTT
1 GAAATTTTGATAACCTCACTAT
*
59640 GCAAA-TTTGATAACCT-AATAT
1 G-AAATTTTGATAACCTCACTAT
* *
59661 GAAATTTCGATAACCTCCCTAT
1 GAAATTTTGATAACCTCACTAT
* * **
59683 GAAAATTCGATAACCAGACTAT
1 GAAATTTTGATAACCTCACTAT
* * * *
59705 GATATTTGGGTAACCACACTAT
1 GAAATTTTGATAACCTCACTAT
* * *
59727 GAAATTTTGATAATCTCAGTGT
1 GAAATTTTGATAACCTCACTAT
*
59749 GAAATTTTGATAATCTGC-CTAT
1 GAAATTTTGATAACCT-CACTAT
* * * *
59771 AAAATTTTAATAATCACACTAAAT
1 GAAATTTTGATAACCTCACT--AT
* * * *
59795 -AAAATTAG-TAACCGCAATAT
1 GAAATTTTGATAACCTCACTAT
* *
59815 GAAAATTTTGATAACCACACCAT
1 G-AAATTTTGATAACCTCACTAT
* *
59838 GAAATTTCGATAACCTCCCTAT
1 GAAATTTTGATAACCTCACTAT
* * *
59860 GAGAATGAAACTGTGATATCCTCTCTAT
1 GA-AAT-----TTTGATAACCTCACTAT
* * * *
59888 G-TATTTTCAATAACCTCTCCAT
1 GAAATTTT-GATAACCTCACTAT
* * *
59910 AAAATTTTCATAACCTCCCTAT
1 GAAATTTTGATAACCTCACTAT
* * * * *
59932 AAAATTCTGTTAACCTCTCTAG
1 GAAATTTTGATAACCTCACTAT
*
59954 GAAATTTTGATAA--GCAC---
1 GAAATTTTGATAACCTCACTAT
* *
59971 -AAATTTTGGTAACCTCCCTCCCTAT
1 GAAATTTTGATAA----CCTCACTAT
* **
59996 GAAATTTTGGTAACCTCTGTAT
1 GAAATTTTGATAACCTCACTAT
60018 GAAATTTTGATAA-CTACACTAT
1 GAAATTTTGATAACCT-CACTAT
* *
60040 GAAGTTTTGATAATCTCTA-TAT
1 GAAATTTTGATAACCTC-ACTAT
* * *
60062 GAAATTTTGGTAACCACACTAC
1 GAAATTTTGATAACCTCACTAT
* **
60084 GAAATTTTGATAATCTTTCTAT
1 GAAATTTTGATAACCTCACTAT
*
60106 GTAATTTTG
1 GAAATTTTG
60115 GTTTGATTGT
Statistics
Matches: 355, Mismatches: 88, Indels: 64
0.70 0.17 0.13
Matches are distributed among these distances:
16 11 0.03
20 7 0.02
21 20 0.06
22 257 0.72
23 30 0.08
24 2 0.01
26 14 0.04
28 14 0.04
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (22 bp):
GAAATTTTGATAACCTCACTAT
Found at i:64552 original size:2 final size:2
Alignment explanation
Indices: 64545--64603 Score: 52
Period size: 2 Copynumber: 30.0 Consensus size: 2
64535 TATTTATCAA
* * *
64545 AT AT AT AT AT AT AT AT AT TT AT CA- AT -T AT -T AT AT TT AT CAA
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT -AT
64586 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
64604 GATCAACAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
1 3 0.07
2 41 0.89
3 2 0.04
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:64576 original size:41 final size:41
Alignment explanation
Indices: 64526--64603 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
64516 TATGCATATA
64526 CAATCATTATATTTATCAAATATATATATATATATATTTAT
1 CAATCATTATATTTATCAAATATATATATATATATATTTAT
*
64567 CAATTATTATATTTATCAAATATATATATATATATAT
1 CAATCATTATATTTATCAAATATATATATATATATAT
64604 GATCAACAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (41 bp):
CAATCATTATATTTATCAAATATATATATATATATATTTAT
Found at i:64579 original size:16 final size:17
Alignment explanation
Indices: 64553--64595 Score: 70
Period size: 16 Copynumber: 2.6 Consensus size: 17
64543 AAATATATAT
64553 ATATATATATTTATCAA
1 ATATATATATTTATCAA
*
64570 TTAT-TATATTTATCAA
1 ATATATATATTTATCAA
64586 ATATATATAT
1 ATATATATAT
64596 ATATATATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATATATATTTATCAA
Found at i:65829 original size:21 final size:21
Alignment explanation
Indices: 65766--65829 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
65756 TTAGCTTCGT
65766 TTAGGTACTGTACAGATGAGA
1 TTAGGTACTGTACAGATGAGA
* * * *
65787 TTA--CACTATACAGATCAAA
1 TTAGGTACTGTACAGATGAGA
*
65806 TTAGGTACTGTACAAATGAGA
1 TTAGGTACTGTACAGATGAGA
65827 TTA
1 TTA
65830 TTAAAGCAGC
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
19 15 0.47
21 17 0.53
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (21 bp):
TTAGGTACTGTACAGATGAGA
Found at i:67578 original size:22 final size:22
Alignment explanation
Indices: 67550--67617 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
67540 GTCCGCCTCG
67550 TTATCTCAACTAAGCTCCGTGC
1 TTATCTCAACTAAGCTCCGTGC
*
67572 TTATCTCAAACT-TGCTCCGTGC
1 TTATCTC-AACTAAGCTCCGTGC
*
67594 --A--ACAACTAAGCTCCGTGC
1 TTATCTCAACTAAGCTCCGTGC
67612 TTATCT
1 TTATCT
67618 TATCTCAGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
17 4 0.11
18 10 0.28
20 2 0.06
22 16 0.44
23 4 0.11
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.32
Consensus pattern (22 bp):
TTATCTCAACTAAGCTCCGTGC
Done.