Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012962.1 Corchorus olitorius cultivar O-4 contig12995, 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: 16551
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:76 original size:21 final size:21
Alignment explanation
Indices: 36--89 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
26 ATAACGATAC
* *
36 TATAAAATTTCGAGAACCTTTT
1 TATAAAATTT-TAGAACCTTCT
*
58 TATAAAATTTTATAACCTTCT
1 TATAAAATTTTAGAACCTTCT
*
79 TATGAAATTTT
1 TATAAAATTTT
90 GTTAACCTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (21 bp):
TATAAAATTTTAGAACCTTCT
Found at i:354 original size:46 final size:44
Alignment explanation
Indices: 258--361 Score: 138
Period size: 46 Copynumber: 2.3 Consensus size: 44
248 AATCACACTC
* *
258 TAAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCTA
1 TAAAATTTTGATAAACACACTATAAAATTGTGATAACCTCGCTA
* *
302 TGAAATTTTGATAAACATTC-CTATAAAATTTTGATAAACCTCGCTA
1 TAAAATTTTGATAAACA--CACTATAAAATTGTGAT-AACCTCGCTA
348 TAAAATTTTGATAA
1 TAAAATTTTGATAA
362 CCTCCTTATG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 15 0.29
45 13 0.25
46 24 0.46
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (44 bp):
TAAAATTTTGATAAACACACTATAAAATTGTGATAACCTCGCTA
Found at i:364 original size:68 final size:67
Alignment explanation
Indices: 258--383 Score: 173
Period size: 68 Copynumber: 1.9 Consensus size: 67
248 AATCACACTC
* * *
258 TAAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGC-TATGAAATTTTGATAAACATTC
1 TAAAATTTTGATAACCACACTATAAAATTGTGATAACCTC-CTTATGAAATCTTGATAAACATTC
322 CTA
65 CTA
* * *
325 TAAAATTTTGATAAACCTCGCTATAAAATTTTGATAACCTCCTTATGAAATCTTGATAA
1 TAAAATTTTGAT-AACCACACTATAAAATTGTGATAACCTCCTTATGAAATCTTGATAA
384 CTACAAATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
67 13 0.25
68 38 0.75
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.37
Consensus pattern (67 bp):
TAAAATTTTGATAACCACACTATAAAATTGTGATAACCTCCTTATGAAATCTTGATAAACATTCC
TA
Found at i:375 original size:22 final size:21
Alignment explanation
Indices: 62--552 Score: 228
Period size: 22 Copynumber: 22.5 Consensus size: 21
52 CCTTTTTATA
*
62 AAATTTT-ATAACCTTCTTATG
1 AAATTTTGATAACC-TCCTATG
* *
83 AAATTTTGTTAACCTCCGTAAG
1 AAATTTTGATAACCTCC-TATG
*
105 AAATTTTGAAGAACCTCACTATG
1 AAATTTTG-ATAACCTC-CTATG
* *
128 AAAATTTTGATAACTTCCCAATG
1 -AAATTTTGATAACCT-CCTATG
* **
151 AAATTTTGATAGCCAAC-ACTG
1 AAATTTTGATAACCTCCTA-TG
* ** *
172 AGACGTTGATAACTTCCATATG
1 AAATTTTGATAACCTCC-TATG
* * * *
194 ATATATTGATAACCACGTTATG
1 AAATTTTGATAACCTC-CTATG
* * * * *
216 AAAATTTAAAAACATTCATATG
1 AAATTTTGATAAC-CTCCTATG
* * * *
238 -AATTATT-AGTAATCACACTCTA
1 AAATT-TTGA-TAACCTC-CTATG
* *
260 AAATTTTGATAATCACACTATG
1 AAATTTTGATAACCTC-CTATG
*
282 AAATTGTGATAACCTCGCTATG
1 AAATTTTGATAACCTC-CTATG
* *
304 AAATTTTGATAAACATTCCTATA
1 AAATTTTGAT-AAC-CTCCTATG
*
327 AAATTTTGATAAACCTCGCTATA
1 AAATTTTGAT-AACCTC-CTATG
350 AAATTTTGATAACCTCCTTATG
1 AAATTTTGATAACCTCC-TATG
* *
372 AAATCTTGATAA----CTA-C
1 AAATTTTGATAACCTCCTATG
388 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCT-CCTATG
** * *
410 ATTTTTTGATAATCTCATTATG
1 AAATTTTGATAACCTC-CTATG
** *
432 AAATTTTTTTAATCTCCCTATG
1 AAATTTTGATAACCT-CCTATG
* * *
454 AAATTTTGATCTACATACTATG
1 AAATTTTGAT-AACCTCCTATG
*
476 AAATTTTGATAATCCTCTTATG
1 AAATTTTGATAA-CCTCCTATG
* *
498 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCT--CCTATG
*
520 AAATTTTGATAACCTTCATATG
1 AAATTTTGATAACC-TCCTATG
542 AAATTTTGATA
1 AAATTTTGATA
553 TCATGCCTGA
Statistics
Matches: 354, Mismatches: 82, Indels: 67
0.70 0.16 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 3 0.01
21 35 0.10
22 222 0.63
23 67 0.19
24 13 0.04
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (21 bp):
AAATTTTGATAACCTCCTATG
Found at i:700 original size:22 final size:22
Alignment explanation
Indices: 664--998 Score: 232
Period size: 22 Copynumber: 15.2 Consensus size: 22
654 ATGAAATTTT
*
664 ACCTCTTTATGAAATTTTGATA
1 ACCTCTCTATGAAATTTTGATA
* * *
686 ACCTCTCTATAAAATTTTGTTG
1 ACCTCTCTATGAAATTTTGATA
* *
708 ACCCCTCTATAAAATTTTGATA
1 ACCTCTCTATGAAATTTTGATA
* * *
730 ATCACAT-TATGTAATTTTGATA
1 ACCTC-TCTATGAAATTTTGATA
* * *
752 ACCTCGCTTTGAAATTTTGGTA
1 ACCTCTCTATGAAATTTTGATA
* * * *
774 ATCACAT-TTTGAAAATTTGATA
1 ACCTC-TCTATGAAATTTTGATA
*
796 ACCTCTTTATGAAATTTTGATA
1 ACCTCTCTATGAAATTTTGATA
* * *
818 ACCTCTCTATAAAATTTTGTTG
1 ACCTCTCTATGAAATTTTGATA
* *
840 ACCCCTCTATAAAATTTTGATA
1 ACCTCTCTATGAAATTTTGATA
* * *
862 ATCACAT-TATGTAATTTTGATA
1 ACCTC-TCTATGAAATTTTGATA
* *
884 ACCTCGCTTTGAAATTTTGATA
1 ACCTCTCTATGAAATTTTGATA
*** * *
906 ATAACACTATAAAATTTTGATA
1 ACCTCTCTATGAAATTTTGATA
*
928 ATCT-TCTTAT-AAATTTTGATA
1 ACCTCTC-TATGAAATTTTGATA
* *
949 ATCTGATCTCTATGAAATTTCGATA
1 A-C--CTCTCTATGAAATTTTGATA
* *
974 ACCACTCTATGAGA-TTTGATA
1 ACCTCTCTATGAAATTTTGATA
995 ACCT
1 ACCT
999 TCTCAAATCT
Statistics
Matches: 242, Mismatches: 59, Indels: 25
0.74 0.18 0.08
Matches are distributed among these distances:
21 23 0.10
22 199 0.82
23 2 0.01
24 5 0.02
25 13 0.05
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (22 bp):
ACCTCTCTATGAAATTTTGATA
Found at i:805 original size:132 final size:132
Alignment explanation
Indices: 664--949 Score: 488
Period size: 132 Copynumber: 2.2 Consensus size: 132
654 ATGAAATTTT
664 ACCTCTTTATGAAATTTTGATAACCTCTCTATAAAATTTTGTTGACCCCTCTATAAAATTTTGAT
1 ACCTCTTTATGAAATTTTGATAACCTCTCTATAAAATTTTGTTGACCCCTCTATAAAATTTTGAT
* * * *
729 AATCACATTATGTAATTTTGATAACCTCGCTTTGAAATTTTGGTAATCACATTTTGAAAA-TTTG
66 AATCACATTATGTAATTTTGATAACCTCGCTTTGAAATTTTGATAATAACACTAT-AAAATTTTG
793 ATA
130 ATA
796 ACCTCTTTATGAAATTTTGATAACCTCTCTATAAAATTTTGTTGACCCCTCTATAAAATTTTGAT
1 ACCTCTTTATGAAATTTTGATAACCTCTCTATAAAATTTTGTTGACCCCTCTATAAAATTTTGAT
861 AATCACATTATGTAATTTTGATAACCTCGCTTTGAAATTTTGATAATAACACTATAAAATTTTGA
66 AATCACATTATGTAATTTTGATAACCTCGCTTTGAAATTTTGATAATAACACTATAAAATTTTGA
926 TA
131 TA
*
928 ATCT-TCTTAT-AAATTTTGATAA
1 ACCTCT-TTATGAAATTTTGATAA
950 TCTGATCTCT
Statistics
Matches: 147, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
131 17 0.12
132 130 0.88
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (132 bp):
ACCTCTTTATGAAATTTTGATAACCTCTCTATAAAATTTTGTTGACCCCTCTATAAAATTTTGAT
AATCACATTATGTAATTTTGATAACCTCGCTTTGAAATTTTGATAATAACACTATAAAATTTTGA
TA
Found at i:1941 original size:2 final size:2
Alignment explanation
Indices: 1934--1981 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
1924 TTCGTACTTT
* *
1934 TA TA TA TA CTA TA GA TA TA GA 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
1977 TA TA T
1 TA TA T
1982 TGTGGAAATG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:12665 original size:2 final size:2
Alignment explanation
Indices: 12658--12689 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12648 TTAATATTGT
12658 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
12690 AATTGTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13026 original size:25 final size:25
Alignment explanation
Indices: 12992--13041 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
12982 TGTTAGTTTG
12992 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
13017 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
13042 ATTGTTTGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.20, G:0.32, T:0.12
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:13697 original size:19 final size:19
Alignment explanation
Indices: 13673--13709 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13663 TGTATTCGTA
13673 ACCGTTTCACCACCGTTTG
1 ACCGTTTCACCACCGTTTG
*
13692 ACCGTTTCATCACCGTTT
1 ACCGTTTCACCACCGTTT
13710 TGGGGCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.35, G:0.14, T:0.35
Consensus pattern (19 bp):
ACCGTTTCACCACCGTTTG
Found at i:13785 original size:21 final size:19
Alignment explanation
Indices: 13760--13817 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
13750 ACTGCTCTAA
13760 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
13781 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
13800 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
13818 TGCTAAACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Done.