Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020291.1 Corchorus olitorius cultivar O-4 contig20324, 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: 4751
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:1392 original size:21 final size:21
Alignment explanation
Indices: 1368--1431 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
1358 CCTTAGGCAA
1368 CTCCAATGAGCTTGAAACCTT
1 CTCCAATGAGCTTGAAACCTT
*
1389 CTCCAATGAGCTTGAAACTTT
1 CTCCAATGAGCTTGAAACCTT
1410 CTCCAATGAGCTTGAAA-CTT
1 CTCCAATGAGCTTGAAACCTT
1430 CT
1 CT
1432 TTGTGAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 4 0.10
21 37 0.90
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (21 bp):
CTCCAATGAGCTTGAAACCTT
Found at i:1622 original size:22 final size:22
Alignment explanation
Indices: 1594--2177 Score: 133
Period size: 22 Copynumber: 26.9 Consensus size: 22
1584 TCAGGGAAGA
1594 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
1616 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
1638 TTTCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
1659 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
* *
1682 TAACAAAATTTCATAATG-ACGT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
1704 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
* *
1726 AATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * * *
1742 TATCAAGATTTCAGAAGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * * *
1764 TATCAAAATTTTAGAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
1787 TTTCAAAATTTTATAGGAAGGTT
1 TATCAAAATTTCATATGAAGG-T
*
1810 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * * * *
1832 TATTACAATTTCAAAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
1854 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * * *
1876 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* *
1898 TATCAATATATCATAT-AGAGGT
1 TATCAAAATTTCATATGA-AGGT
* * **
1920 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
1943 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
1965 TATCAAAATTTCATAGTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
1987 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* *
2009 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** ** *
2031 TAAAAAAAATTT-ATAAAAAGAT
1 T-ATCAAAATTTCATATGAAGGT
* ** * **
2053 TCTTGAAATTCCATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* * * *
2075 TATTAAAAATTCATAGGAATGT
1 TATCAAAATTTCATATGAAGGT
* *
2097 TATCAAAATTTCATAAGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
2119 CATCAAAA----ATAGTGTAA--T
1 TATCAAAATTTCATA-TG-AAGGT
* * *
2137 TATCATAATTTAATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
*
2159 TATCATAATTTCATATGAA
1 TATCAAAATTTCATATGAA
2178 TATTTCATTT
Statistics
Matches: 411, Mismatches: 105, Indels: 92
0.68 0.17 0.15
Matches are distributed among these distances:
16 8 0.02
17 2 0.00
18 12 0.03
19 1 0.00
20 6 0.01
21 20 0.05
22 284 0.69
23 76 0.18
24 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:1709 original size:44 final size:43
Alignment explanation
Indices: 1575--1736 Score: 125
Period size: 44 Copynumber: 3.7 Consensus size: 43
1565 TTGTGGAGTA
* * *
1575 ATCAAAATTTC--AGGGAAGATATCAAAATTTCAT-ATGAAGGTT
1 ATCAAAATTTCATAGGG-AGTTAACAAAATTTCATAATG-ACGTT
** ** * * *
1617 ATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATAGT-ATGTAG
1 ATCAAAATTTCATAG-GGAGTTAACAAAATTTCATAATGACGT-T
1661 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGACGTT
1 ATCAAAATTTCATAGGGAG-TTAACAAAATTTCATAATGACGTT
** *
1705 ATCAAAAAATCATAGGGAGGTAATCAAAATTT
1 ATCAAAATTTCATAGGGAGTTAA-CAAAATTT
1737 GTAGTTATCA
Statistics
Matches: 95, Mismatches: 17, Indels: 14
0.75 0.13 0.11
Matches are distributed among these distances:
42 11 0.12
43 8 0.08
44 72 0.76
45 4 0.04
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (43 bp):
ATCAAAATTTCATAGGGAGTTAACAAAATTTCATAATGACGTT
Found at i:1718 original size:66 final size:66
Alignment explanation
Indices: 1595--1736 Score: 153
Period size: 66 Copynumber: 2.2 Consensus size: 66
1585 CAGGGAAGAT
* * * * * * ** * *
1595 ATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATA-GTATGT
1 ATCAAAATTTCATAGGAAGATTAACAAAATTTCATAGATGAGTTATCAAAAAATCATAGGGAGGT
1659 A
66 A
*
1660 GATCAAAATTTCATAGGGAGATTAACAAAATTTCATA-ATGACGTTATCAAAAAATCATAGGGAG
1 -ATCAAAATTTCATAGGAAGATTAACAAAATTTCATAGATGA-GTTATCAAAAAATCATAGGGAG
1724 GTA
64 GTA
1727 ATCAAAATTT
1 ATCAAAATTT
1737 GTAGTTATCA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
65 2 0.03
66 56 0.89
67 5 0.08
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (66 bp):
ATCAAAATTTCATAGGAAGATTAACAAAATTTCATAGATGAGTTATCAAAAAATCATAGGGAGGT
A
Found at i:1796 original size:23 final size:23
Alignment explanation
Indices: 1741--1820 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
1731 AAATTTGTAG
* * *
1741 TTATCAAGATTTCAGAAGGAGG-
1 TTATCAAAATTTTAGAGGGAGGT
1763 TTATCAAAATTTTAGAGGGAGGT
1 TTATCAAAATTTTAGAGGGAGGT
* * *
1786 TTTTCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTAGAGGGAGGT
1809 TTATCAAAATTT
1 TTATCAAAATTT
1821 CATAGCGAGG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 19 0.38
23 31 0.62
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTTAGAGGGAGGT
Found at i:1825 original size:23 final size:22
Alignment explanation
Indices: 1594--2023 Score: 134
Period size: 22 Copynumber: 19.7 Consensus size: 22
1584 TCAGGGAAGA
*
1594 TATCAAAATTTCATATGAAGG-T
1 TATCAAAATTTCATA-GGAGGTT
*
1616 TATCAAAATTTCATAGTTTA-GTT
1 TATCAAAATTTCATAG--GAGGTT
* * *
1639 T-TCAAAATTTCATAGTATGTA
1 TATCAAAATTTCATAGGAGGTT
* *
1660 GATCAAAATTTCATAGG-GAGAT
1 TATCAAAATTTCATAGGAG-GTT
* * *
1682 TAACAAAATTTCATAATGACG-T
1 TATCAAAATTTCAT-AGGAGGTT
**
1704 TATCAAAAAATCATAGGGAGG-T
1 TATCAAAATTTCATA-GGAGGTT
* *
1726 AATCAAAA-TT--T-GTA-G-T
1 TATCAAAATTTCATAGGAGGTT
* *
1742 TATCAAGATTTCAGAAGGAGG-T
1 TATCAAAATTTCA-TAGGAGGTT
* *
1764 TATCAAAATTTTAGAGGGAGGTT
1 TATCAAAATTTCATA-GGAGGTT
* *
1787 TTTCAAAATTTTATAGGAAGGTT
1 TATCAAAATTTCATAGG-AGGTT
1810 TATCAAAATTTCATAGCGAGG-T
1 TATCAAAATTTCATAG-GAGGTT
* * * * *
1832 TATTACAATTTCAAAGTG-TGAT
1 TATCAAAATTTCATAG-GAGGTT
1854 TA-CTAACAA-TTCATATGGAGGTT
1 TATC-AA-AATTTCATA-GGAGGTT
* * * *
1877 T-TTAAATTTTCATAACGTGG-T
1 TATCAAAATTTCAT-AGGAGGTT
* * *
1898 TATCAATATATCATATAGAGG-T
1 TATCAAAATTTCATA-GGAGGTT
* * *
1920 TATCAACATCTCATAGTGTTGG-T
1 TATCAAAATTTCATAG-G-AGGTT
* *
1943 TATCAAAATTTCATTGGGAAG-T
1 TATCAAAATTTCA-TAGGAGGTT
*
1965 TATCAAAATTTCATAGTGAGGTC
1 TATCAAAATTTCATAG-GAGGTT
* *
1988 T-TCAAAATTCCTTAGGGAGG-T
1 TATCAAAATTTCATA-GGAGGTT
*
2009 TAACAAAATTTCATA
1 TATCAAAATTTCATA
2024 AGAAGGTTAA
Statistics
Matches: 304, Mismatches: 68, Indels: 72
0.68 0.15 0.16
Matches are distributed among these distances:
16 8 0.03
17 4 0.01
19 1 0.00
20 2 0.01
21 16 0.05
22 204 0.67
23 66 0.22
24 3 0.01
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAGGAGGTT
Done.