Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023491.1 Corchorus olitorius cultivar O-4 contig23524, 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: 13623
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:545 original size:22 final size:22
Alignment explanation
Indices: 520--562 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
510 TTTTTGATGA
* *
520 CCTTCTTATAAAATTTTAATAG
1 CCTTCCTATAAAACTTTAATAG
*
542 CCTTCCTATGAAACTTTAATA
1 CCTTCCTATAAAACTTTAATA
563 ATGATACTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.42
Consensus pattern (22 bp):
CCTTCCTATAAAACTTTAATAG
Found at i:1083 original size:20 final size:22
Alignment explanation
Indices: 608--1089 Score: 153
Period size: 22 Copynumber: 22.0 Consensus size: 22
598 TTTTCTTTTA
* *
608 AACCTTCTTATGAAATTTTGTT
1 AACCTTCATATGAAATTTTGAT
* * *
630 AACC-TCGCTAAGGAATTTTGA-
1 AACCTTC-ATATGAAATTTTGAT
*
651 AGACC-TCACTATAAAATTTTGAT
1 A-ACCTTCA-TATGAAATTTTGAT
674 AA-CTTCCGA-ATGAAATTTTGAT
1 AACCTT-C-ATATGAAATTTTGAT
** * *
696 AACCAACACTATATGAGATGTTGAT
1 AACC--TTC-ATATGAAATTTTGAT
* * *
721 AACCTCCATATGATATATTGAT
1 AACCTTCATATGAAATTTTGAT
* * * * *
743 AACC-ACGTTATGAAAATTTAAA
1 AACCTTC-ATATGAAATTTTGAT
*
765 AACCTCCATATG-AATTGTT-AGT
1 AACCTTCATATGAAATT-TTGA-T
* * *
787 AATC-ACACTCTGAAATTTTGAT
1 AACCTTCA-TATGAAATTTTGAT
* * * *
809 AATC-ACACTATGAAATTGTGCT
1 AACCTTCA-TATGAAATTTTGAT
* *
831 AACC-TCGCTATAAAATTTTGAT
1 AACCTTC-ATATGAAATTTTGAT
* * *
853 AAACCTCCTTATAAAATTTTGAT
1 -AACCTTCATATGAAATTTTGAT
* * *
876 AACCTCCTTATGAAATCTTGAT
1 AACCTTCATATGAAATTTTGAT
*
898 AA----C-TA-CAAATTTTGAT
1 AACCTTCATATGAAATTTTGAT
* * **
914 AACCTTCCTTTGATTTTTTGAT
1 AACCTTCATATGAAATTTTGAT
* *
936 GACC-TCATTATGAAATTTTGTT
1 AACCTTCA-TATGAAATTTTGAT
* * *
958 AATCTCCCTATGAAATTTTGAT
1 AACCTTCATATGAAATTTTGAT
* *
980 CTACATAT-ACTATGAAATTTTGAT
1 -AACCT-TCA-TATGAAATTTTGAT
* * *
1004 AACCCTCTTATGAAACTTTGA-
1 AACCTTCATATGAAATTTTGAT
* **
1025 AAACTAAACTATGAAATTTTGAT
1 AACCTTCA-TATGAAATTTTGAT
1048 AACCTTCATATGAAATTTTGAT
1 AACCTTCATATGAAATTTTGAT
*
1070 ATCC-TCAT-TGAAATTTTGAT
1 AACCTTCATATGAAATTTTGAT
1090 TACTCCATAG
Statistics
Matches: 343, Mismatches: 82, Indels: 72
0.69 0.16 0.14
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 13 0.04
21 21 0.06
22 224 0.65
23 38 0.11
24 18 0.05
25 15 0.04
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
AACCTTCATATGAAATTTTGAT
Found at i:1311 original size:22 final size:22
Alignment explanation
Indices: 1193--1319 Score: 91
Period size: 22 Copynumber: 5.8 Consensus size: 22
1183 GTAATCACAT
* *
1193 TTTGAAAATTTGATAACCT-TT
1 TTTGAAATTTTGATAACCTCTC
1214 TTATGAAATTTTGATAACCTCTC
1 TT-TGAAATTTTGATAACCTCTC
* * *
1237 TATAAAATTTTGTTGAACC-CTC
1 TTTGAAATTTTGAT-AACCTCTC
* ** *
1259 TATGAAATTTTGAT--GTTTTC
1 TTTGAAATTTTGATAACCTCTC
* *
1279 ATTATGTAATTTTGATAACCTCGC
1 -TT-TGAAATTTTGATAACCTCTC
1303 TTTGAAATTTTGATAAC
1 TTTGAAATTTTGATAAC
1320 AACACTATGA
Statistics
Matches: 81, Mismatches: 17, Indels: 15
0.72 0.15 0.13
Matches are distributed among these distances:
20 2 0.02
21 3 0.04
22 66 0.81
23 8 0.10
24 2 0.02
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.46
Consensus pattern (22 bp):
TTTGAAATTTTGATAACCTCTC
Found at i:1330 original size:22 final size:21
Alignment explanation
Indices: 1215--1424 Score: 102
Period size: 22 Copynumber: 9.6 Consensus size: 21
1205 ATAACCTTTT
*
1215 TATGAAATTTTGATAACCTCTC
1 TATGAAATTTTGATAACATC-C
* * *
1237 TATAAAATTTTGTTGAAC-CCTC
1 TATGAAATTTTGAT-AACATC-C
**** *
1259 TATGAAATTTTGATGTTTTCAT
1 TATGAAATTTTGATAACATC-C
* *
1281 TATGTAATTTTGATAACCTCGC
1 TATGAAATTTTGATAACATC-C
* *
1303 TTTGAAATTTTGATAACAACAC
1 TATGAAATTTTGATAACATC-C
*
1325 TATGAAATTTTGTTAATCATCC
1 TATGAAATTTTGATAA-CATCC
1347 TAT-AAATTTTGATAATCTGATCTC
1 TATGAAATTTTGATAA-C--ATC-C
** *
1371 TATGAAATTCCGATAATCATTC
1 TATGAAATTTTGATAA-CATCC
* * *
1393 TATGAGA-TTTGATAACTTTC
1 TATGAAATTTTGATAACATCC
*
1413 TATCAAATTTTG
1 TATGAAATTTTG
1425 CTATCCCTTA
Statistics
Matches: 144, Mismatches: 36, Indels: 17
0.73 0.18 0.09
Matches are distributed among these distances:
20 9 0.06
21 23 0.16
22 85 0.59
23 11 0.08
24 4 0.03
25 12 0.08
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.43
Consensus pattern (21 bp):
TATGAAATTTTGATAACATCC
Found at i:1531 original size:22 final size:22
Alignment explanation
Indices: 1461--1608 Score: 108
Period size: 22 Copynumber: 6.7 Consensus size: 22
1451 ATAACCTTTA
* *
1461 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCTCCC
** *
1483 TAAAAAATTTT-AGTAACCACACC
1 TATGAAATTTTGA-TAACCTC-CC
1506 -ATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCC
* *
1527 TATGAAATATT-AGTAACCTCCT
1 TATGAAATTTTGA-TAACCTCCC
* *
1549 TATGAAATTTTGTTAACCAT-AC
1 TATGAAATTTTGATAACC-TCCC
**
1571 TATGAAATTCTT-ATAACCTGGC
1 TATGAAATT-TTGATAACCTCCC
*
1593 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
1609 TCTCTTTGAT
Statistics
Matches: 101, Mismatches: 15, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
21 7 0.07
22 89 0.88
23 5 0.05
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:1531 original size:66 final size:66
Alignment explanation
Indices: 1461--1608 Score: 151
Period size: 66 Copynumber: 2.2 Consensus size: 66
1451 ATAACCTTTA
1461 TATGAAATTTTGATAACCACAC-TAAAAAATTTTAG-TAACCACACCATGAAATT-TTGATAACC
1 TATGAAATTTTGATAACCAC-CTTAAAAAATTTT-GTTAACCACACCATGAAATTCTT-ATAACC
1523 TCCC
63 TCCC
* * ** * * *
1527 TATGAAATATT-AGTAACCTCCTTATGAAATTTTGTTAACCATACTATGAAATTCTTATAACCTG
1 TATGAAATTTTGA-TAACCACCTTAAAAAATTTTGTTAACCACACCATGAAATTCTTATAACCTC
*
1591 GC
65 CC
*
1593 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
1609 TCTCTTTGAT
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
65 3 0.04
66 61 0.91
67 3 0.04
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (66 bp):
TATGAAATTTTGATAACCACCTTAAAAAATTTTGTTAACCACACCATGAAATTCTTATAACCTCC
C
Found at i:1588 original size:44 final size:44
Alignment explanation
Indices: 1461--1837 Score: 187
Period size: 44 Copynumber: 8.8 Consensus size: 44
1451 ATAACCTTTA
* ** *
1461 TATGAAATTTTGATAACCACACTAAAAAATTTTAGTAACCACAC
1 TATGAAATTTTGATAACCATACTATGAAATTTTAGTAACCTCAC
* * *
1505 CATGAAATTTTGATAACC-TCCCTATGAAATATTAGTAACCTC-C
1 TATGAAATTTTGATAACCAT-ACTATGAAATTTTAGTAACCTCAC
* **
1548 TTATGAAATTTTGTTAACCATACTATGAAATTCTTA-TAACCTGGC
1 -TATGAAATTTTGATAACCATACTATGAAATT-TTAGTAACCTCAC
* * * **
1593 TATGACATTTTGAT-A--AT-C--T---CTTTGA-TAACCTTTC
1 TATGAAATTTTGATAACCATACTATGAAATTTTAGTAACCTCAC
* * * * * * *
1627 TATAAAATTGTGATAACCAGAATATAAAATTTCAATAACCTTC-C
1 TATGAAATTTTGATAACCATACTATGAAATTTTAGTAACC-TCAC
** * * * *
1671 TAAAAAATTTTAATAACCTGATCCTATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGATAACC--ATACTATGAAATTTTAGTAACCTCAC
* * * *
1717 TATGAAATTTTGATAACCTTCCCATGAAATTTT-GATAACTTTCA-
1 TATGAAATTTTGATAACCATACTATGAAATTTTAG-TAAC-CTCAC
* * *
1761 TATGAAATTTTGGTAACCACACTATGGAATTTT-GATAACCTC-C
1 TATGAAATTTTGATAACCATACTATGAAATTTTAG-TAACCTCAC
* * **
1804 TCATGAAATTATAATAACCATGTTATGAAATTTT
1 T-ATGAAATTTTGATAACCATACTATGAAATTTT
1838 GATAACCACA
Statistics
Matches: 252, Mismatches: 58, Indels: 46
0.71 0.16 0.13
Matches are distributed among these distances:
34 20 0.08
35 3 0.01
37 1 0.00
38 1 0.00
40 2 0.01
41 2 0.01
43 10 0.04
44 173 0.69
45 9 0.04
46 31 0.12
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.36
Consensus pattern (44 bp):
TATGAAATTTTGATAACCATACTATGAAATTTTAGTAACCTCAC
Found at i:1713 original size:68 final size:66
Alignment explanation
Indices: 1626--1847 Score: 176
Period size: 66 Copynumber: 3.3 Consensus size: 66
1616 GATAACCTTT
* * * * *
1626 CTATAAAATTGTGATAACCAGAATATAAAATTTCAATAACCTTCCTAAAAAATTTTAATAACCTG
1 CTATGAAATTTTGGTAACCACAATATAAAATTTCAATAACCTTCCCAAAAAATTTTAATAA-CT-
1691 ATC
64 ATC
* * ** ** * *
1694 CTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTTGATAACTTT
1 CTATGAAATTTTGGTAACCACAATATAAAATTTCAATAACCTTCCCAAAAAATTTTAATAACTAT
1759 C
66 C
* * ** ** ** * *
1760 ATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC-TCCTCATGAAATTATAATAACCA
1 CTATGAAATTTTGGTAACCACAATATAAAATTTCAATAACCTTCC-CAAAAAATTTTAATAACTA
*
1824 TG
65 TC
* *
1826 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGGTAACCACA
1848 CAGAGACAAG
Statistics
Matches: 131, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
65 3 0.02
66 77 0.59
67 2 0.02
68 49 0.37
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (66 bp):
CTATGAAATTTTGGTAACCACAATATAAAATTTCAATAACCTTCCCAAAAAATTTTAATAACTAT
C
Found at i:1722 original size:22 final size:22
Alignment explanation
Indices: 1694--1848 Score: 145
Period size: 22 Copynumber: 7.0 Consensus size: 22
1684 TAACCTGATC
*
1694 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
*
1716 CTATGAAATTTTGATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
* **
1738 CCATGAAATTTTGATAACTTTCA
1 CTATGAAATTTTGATAAC-CACA
*
1761 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* *
1782 CTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* * **
1803 CTCATGAAATTATAATAACCATG
1 CT-ATGAAATTTTGATAACCACA
*
1826 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
1848 C
1 C
1849 AGAGACAAGA
Statistics
Matches: 105, Mismatches: 22, Indels: 12
0.76 0.16 0.09
Matches are distributed among these distances:
21 4 0.04
22 99 0.94
23 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:1792 original size:66 final size:66
Alignment explanation
Indices: 1675--1848 Score: 224
Period size: 66 Copynumber: 2.6 Consensus size: 66
1665 CCTTCCTAAA
* *
1675 AAATTTTAATAACCTGATCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCC-
1 AAATTATAATAACC--ATCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACC-TCCT
1739 CATG
63 CATG
* * ** *
1743 AAATTTTGATAACTTTCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACCTCCTCAT
1 AAATTATAATAACCATCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCTCAT
1808 G
66 G
** *
1809 AAATTATAATAACCATGTTATGAAATTTTGATAACCACAC
1 AAATTATAATAACCATCATATGAAATTTTGGTAACCACAC
1849 AGAGACAAGA
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 3 0.03
66 78 0.84
68 12 0.13
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (66 bp):
AAATTATAATAACCATCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCTCAT
G
Found at i:2139 original size:11 final size:11
Alignment explanation
Indices: 2125--2149 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2115 TCTAAATTGA
2125 AATTTTTAAAT
1 AATTTTTAAAT
2136 AATTTTTAAAT
1 AATTTTTAAAT
2147 AAT
1 AAT
2150 AAAATTATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTTTTAAAT
Found at i:4094 original size:17 final size:17
Alignment explanation
Indices: 4056--4093 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
4046 TTTTCTTTCT
*
4056 TTTTATGTTTTTAATGG
1 TTTTATGTTTTTAACGG
4073 TTTTATGTTTTTAACGTG
1 TTTTATGTTTTTAACG-G
4091 TTT
1 TTT
4094 AAAAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.16, C:0.03, G:0.16, T:0.66
Consensus pattern (17 bp):
TTTTATGTTTTTAACGG
Done.