Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018083.1 Corchorus olitorius cultivar O-4 contig18116, 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: 10652
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:105 original size:25 final size:24
Alignment explanation
Indices: 54--110 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
44 GTCAGTCTTG
*
54 AATTT-TTTAATGTTTAATTCTTA
1 AATTTATTTAATGTTTAATTATTA
*
77 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATGT-TTAATTATTA
102 AATTTATTT
1 AATTTATTT
111 TACAATCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (24 bp):
AATTTATTTAATGTTTAATTATTA
Found at i:7264 original size:22 final size:22
Alignment explanation
Indices: 7239--7291 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
7229 ATTACACTAT
*
7239 TTTTAATGA-CCTCCTTATGAAA
1 TTTTAATAATCCTCC-TATGAAA
* *
7261 TTTTGATAATCTTCCTATGAAA
1 TTTTAATAATCCTCCTATGAAA
7283 TTTTAATAA
1 TTTTAATAA
7292 CGATATTATG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (22 bp):
TTTTAATAATCCTCCTATGAAA
Found at i:7595 original size:22 final size:21
Alignment explanation
Indices: 7520--7769 Score: 152
Period size: 22 Copynumber: 11.7 Consensus size: 21
7510 GAAAATCACA
* *
7520 CTATGAAATTGTGATAACCTC
1 CTATGAAATTTTGATAACTTC
7541 GCTATGAAATTTTGATAAAGCTTC
1 -CTATGAAATTTTGAT-AA-CTTC
* *
7565 TTATAAAATTTTGATAACTTC
1 CTATGAAATTTTGATAACTTC
*
7586 CTTATGAAATCTTGATAA----
1 C-TATGAAATTTTGATAACTTC
* *
7604 CTA-CAAATTTTGATAATCTCC
1 CTATGAAATTTTGATAA-CTTC
** **
7625 CTATGATTTTTTGATAACCAC
1 CTATGAAATTTTGATAACTTC
* * *
7646 ATTATGAAATTTTGTTAATCTCC
1 -CTATGAAATTTTGATAA-CTTC
* * *
7669 CTATGAAATTTTGATCTACATA
1 CTATGAAATTTTGAT-AACTTC
* **
7691 CTATGAAATTTTGAAAACTAAA
1 CTATGAAATTTTGATAACT-TC
*
7713 CTATGAAATTTTGATAGCCTTC
1 CTATGAAATTTTGATA-ACTTC
* * *
7735 ATATGAAATTTTGATATCCTC
1 CTATGAAATTTTGATAACTTC
7756 CT-TGAAATTTTGAT
1 CTATGAAATTTTGAT
7770 TACTCCATAA
Statistics
Matches: 176, Mismatches: 38, Indels: 30
0.72 0.16 0.12
Matches are distributed among these distances:
16 11 0.06
17 2 0.01
18 1 0.01
20 12 0.07
21 15 0.09
22 112 0.64
23 20 0.11
24 3 0.02
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (21 bp):
CTATGAAATTTTGATAACTTC
Found at i:7897 original size:22 final size:21
Alignment explanation
Indices: 7869--7918 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
7859 TCACATTTTA
*
7869 AAAATTTAATAAACTCTTTAT
1 AAAATTTAATAAACTCTCTAT
* *
7890 GAAAATTTGATAACCTCTCTAT
1 -AAAATTTAATAAACTCTCTAT
7912 AAAATTT
1 AAAATTT
7919 TGTTGACCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (21 bp):
AAAATTTAATAAACTCTCTAT
Found at i:7920 original size:22 final size:22
Alignment explanation
Indices: 7877--8285 Score: 169
Period size: 22 Copynumber: 18.4 Consensus size: 22
7867 TAAAAATTTA
* * *
7877 ATAAACTCTTTATGAAAATTTG
1 ATAACCTCTCTATGAAATTTTG
*
7899 ATAACCTCTCTATAAAATTTTG
1 ATAACCTCTCTATGAAATTTTG
* * *
7921 TTGACCCCTCTATGAAATTTTG
1 ATAACCTCTCTATGAAATTTTG
* * *
7943 ATAATCACAT-TATGTAATTTTG
1 ATAACCTC-TCTATGAAATTTTG
* *
7965 ATAACCTCACTTTGAAATTTTG
1 ATAACCTCTCTATGAAATTTTG
** *
7987 ATAACAACACTATGAAATTTTG
1 ATAACCTCTCTATGAAATTTTG
*
8009 ATAATCT-TCCTAT-AAATTTTG
1 ATAACCTCT-CTATGAAATTTTG
* * ***
8030 ATATTTCGATCTCTAT-ATAATAACG
1 ATA--AC-CTCTCTATGA-AATTTTG
* * *
8055 ATAATCACTCTATGAGA-TTTG
1 ATAACCTCTCTATGAAATTTTG
* *
8076 ATAATCT-TCTATCAAATTTTG
1 ATAACCTCTCTATGAAATTTTG
* * ** *
8097 GTACTCCTCATGAAATGGAGACTTTT-
1 ATA-ACCTC-T-CTAT-GA-AATTTTG
8123 ATAACCT-TCATATGAAATTTTG
1 ATAACCTCTC-TATGAAATTTTG
* * ** *
8145 ATAACCACACTAAAAAATTTCG
1 ATAACCTCTCTATGAAATTTTG
* *
8167 ATAACCACACTATGAAATTTTG
1 ATAACCTCTCTATGAAATTTTG
* *
8189 ATAACCT-TCCCATGAAATATT-
1 ATAACCTCT-CTATGAAATTTTG
8210 AGTAACCTC-CTTATGAAATTTTG
1 A-TAACCTCTC-TATGAAATTTTG
* *
8233 TTAACCACAT-TATGAAATTCTT-
1 ATAACCTC-TCTATGAAATT-TTG
* *
8255 ATAACCTCGCTATGACATTTTG
1 ATAACCTCTCTATGAAATTTTG
*
8277 ATAATCTCT
1 ATAACCTCT
8286 TTGATAACCT
Statistics
Matches: 282, Mismatches: 76, Indels: 58
0.68 0.18 0.14
Matches are distributed among these distances:
20 7 0.02
21 33 0.12
22 206 0.73
23 8 0.03
24 7 0.02
25 13 0.05
26 3 0.01
27 5 0.02
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (22 bp):
ATAACCTCTCTATGAAATTTTG
Done.