Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009853.1 Corchorus olitorius cultivar O-4 contig09885, 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: 3979
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:204 original size:8 final size:8
Alignment explanation
Indices: 191--224 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
181 AATAATGTTA
191 TATTATAT
1 TATTATAT
199 TATTATAT
1 TATTATAT
207 TATTATAT
1 TATTATAT
*
215 CA-TATAT
1 TATTATAT
222 TAT
1 TAT
225 CAATAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTATAT
Found at i:393 original size:23 final size:23
Alignment explanation
Indices: 361--408 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
351 CTCGAGCCCA
*
361 AACCCGACCCGAGCCCGAACCCG
1 AACCCGACCCGAGACCGAACCCG
*
384 AACCCTACCCGAGACCGAACCCG
1 AACCCGACCCGAGACCGAACCCG
407 AA
1 AA
409 AATACCCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.48, G:0.19, T:0.02
Consensus pattern (23 bp):
AACCCGACCCGAGACCGAACCCG
Found at i:419 original size:16 final size:16
Alignment explanation
Indices: 398--517 Score: 181
Period size: 16 Copynumber: 7.6 Consensus size: 16
388 CTACCCGAGA
398 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
414 CCGAACCCG-ACATAAC
1 CCGAACCCGAAAAT-AC
430 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
446 CCAAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
462 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
478 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
494 CCGAACCCG-AAGTAC
1 CCGAACCCGAAAATAC
509 CCGAACCCG
1 CCGAACCCG
518 CCCGAGCCCG
Statistics
Matches: 95, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
15 17 0.18
16 75 0.79
17 3 0.03
ACGTcount: A:0.40, C:0.40, G:0.14, T:0.06
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:1480 original size:26 final size:25
Alignment explanation
Indices: 1425--1484 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
1415 ATATATCTCT
*
1425 AAATTTTCATTATTAAAATTTAGTA
1 AAATTTTCATTATTAAAATTAAGTA
* *
1450 TAATTTT-ATTATTTAAAAATTAATTA
1 AAATTTTCATTA-TT-AAAATTAAGTA
1476 AAATTTTCA
1 AAATTTTCA
1485 ATTTAGACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 4 0.14
25 8 0.29
26 15 0.54
27 1 0.04
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (25 bp):
AAATTTTCATTATTAAAATTAAGTA
Found at i:1593 original size:20 final size:20
Alignment explanation
Indices: 1556--1594 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1546 TACTATTATT
1556 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
1576 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
1595 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:1788 original size:22 final size:22
Alignment explanation
Indices: 1760--1908 Score: 103
Period size: 22 Copynumber: 6.9 Consensus size: 22
1750 TGTCTCTGTG
1760 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
*** *
1782 TGGTTATTGTAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
1805 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
1826 TGGTTACCAAAATTTCATAAGGA
1 TGGTTATCAAAATTTCATAA-GA
* **
1849 -AGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* *
1870 AGGTTATCAAAATCTCAGT--G-
1 TGGTTATCAAAATTTCA-TAAGA
*
1890 TGGTTACCAAAATTTCATA
1 TGGTTATCAAAATTTCATA
1909 GGATCATGTT
Statistics
Matches: 97, Mismatches: 22, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
19 1 0.01
20 15 0.15
21 3 0.03
22 72 0.74
23 5 0.05
24 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:1830 original size:44 final size:44
Alignment explanation
Indices: 1761--1861 Score: 114
Period size: 44 Copynumber: 2.3 Consensus size: 44
1751 GTCTCTGTGT
* **** *
1761 GGTTATCAAAATTTCATAAGATGGTTATTGTAATTTCATGAGGA
1 GGTTATCAAAATTCCATAAGATGGTTACCAAAATTTCATAAGGA
*
1805 GGTTATCAAAATTCCAT-AGTGTGGTTACCAAAATTTCATAAGGA
1 GGTTATCAAAATTCCATAAG-ATGGTTACCAAAATTTCATAAGGA
*
1849 AGTTATCAAAATT
1 GGTTATCAAAATT
1862 TCATGGGAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 2 0.04
44 46 0.96
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.36
Consensus pattern (44 bp):
GGTTATCAAAATTCCATAAGATGGTTACCAAAATTTCATAAGGA
Found at i:1863 original size:66 final size:66
Alignment explanation
Indices: 1752--1942 Score: 225
Period size: 66 Copynumber: 2.9 Consensus size: 66
1742 GATTTTCTTG
* * * **
1752 TCTCTGTGTGGTTATCAAAATTTCATAA-GATGGTTATTGTAATTTCATGAGG-AGGTTATCAAA
1 TCTCAGTGTGGTTACCAAAATTTCATAAGGATAGTTATTAAAATTTCATGAGGAAGGTTATCAAA
1815 A
66 A
*
1816 T-TCCATAGTGTGGTTACCAAAATTTCATAAGGA-AGTTATCAAAATTTCATG-GGAAGGTTATC
1 TCT-C--AGTGTGGTTACCAAAATTTCATAAGGATAGTTATTAAAATTTCATGAGGAAGGTTATC
1878 AAAA
63 AAAA
*
1882 TCTCAGTGTGGTTACCAAAATTTCAT-AGGATCATGTTATTAAAATTTC-TTAGGAAGGTTAT
1 TCTCAGTGTGGTTACCAAAATTTCATAAGGAT-A-GTTATTAAAATTTCATGAGGAAGGTTAT
1943 TGAAATTTTA
Statistics
Matches: 109, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
63 5 0.05
64 24 0.22
65 4 0.04
66 73 0.67
67 3 0.03
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.37
Consensus pattern (66 bp):
TCTCAGTGTGGTTACCAAAATTTCATAAGGATAGTTATTAAAATTTCATGAGGAAGGTTATCAAA
A
Found at i:2050 original size:22 final size:23
Alignment explanation
Indices: 2025--2074 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
2015 GGTTACTAAT
*
2025 ATTTTATGGGGAGGTTATC-AAA
1 ATTTTATGGGGAGATTATCAAAA
* * *
2047 ATTTCATGGTGTGATTATCAAAA
1 ATTTTATGGGGAGATTATCAAAA
2070 ATTTT
1 ATTTT
2075 TAGTGTAGTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.32, C:0.06, G:0.20, T:0.42
Consensus pattern (23 bp):
ATTTTATGGGGAGATTATCAAAA
Found at i:2233 original size:22 final size:23
Alignment explanation
Indices: 2194--2252 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 23
2184 ATAGATATCG
2194 GATTATCAAAA-TTTATAG-GAA
1 GATTATCAAAATTTTATAGTGAA
**
2215 GATTATCAAAATTTTATAGTGTT
1 GATTATCAAAATTTTATAGTGAA
2238 G-TTATCAAAATTTTA
1 GATTATCAAAATTTTA
2253 AAAAGAGGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 11 0.32
22 21 0.62
23 2 0.06
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.42
Consensus pattern (23 bp):
GATTATCAAAATTTTATAGTGAA
Found at i:2263 original size:22 final size:22
Alignment explanation
Indices: 2238--2384 Score: 64
Period size: 22 Copynumber: 6.7 Consensus size: 22
2228 TTATAGTGTT
2238 GTTATCAAAATTTTAAAAAGAG
1 GTTATCAAAATTTTAAAAAGAG
** ** * * *
2260 GTTATCAGTATTACATAATGTG
1 GTTATCAAAATTTTAAAAAGAG
* * * * *
2282 ATTATCAAAATTTCATAGAGGG
1 GTTATCAAAATTTTAAAAAGAG
* * *
2304 GTCAACAAAATTTTATAGAA-AG
1 GTTATCAAAATTTTA-AAAAGAG
* * *
2326 GTTATCGAAATTTCATAAAGAG
1 GTTATCAAAATTTTAAAAAGAG
* *
2348 TTTATC-AAATTTTCAAAAAGTG
1 GTTATCAAAATTTT-AAAAAGAG
* *
2370 ATTACCAAAATTTTA
1 GTTATCAAAATTTTA
2385 TAGTGGTATT
Statistics
Matches: 87, Mismatches: 34, Indels: 8
0.67 0.26 0.06
Matches are distributed among these distances:
21 8 0.09
22 71 0.82
23 8 0.09
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.35
Consensus pattern (22 bp):
GTTATCAAAATTTTAAAAAGAG
Found at i:2343 original size:66 final size:66
Alignment explanation
Indices: 2214--2362 Score: 149
Period size: 66 Copynumber: 2.3 Consensus size: 66
2204 ATTTATAGGA
* * ** * * * *
2214 AGATTATCAAAATTTTATAGTGTTGTTATCAAAATTTTAAAAAGAGGTTATCAGTATTACATAAT
1 AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTAAAAAGAGGTTATCAGAATTACATAAA
2279 G
66 G
* * *
2280 TGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAGAA-AGGTTATC-GAAATTTCATA
1 AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTA-AAAAGAGGTTATCAG-AATTACATA
2343 AAG
64 AAG
* *
2346 AGTTTATCAAATTTTCA
1 AGATTATCAAAATTTCA
2363 AAAAGTGATT
Statistics
Matches: 67, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
65 1 0.01
66 63 0.94
67 3 0.04
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (66 bp):
AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTAAAAAGAGGTTATCAGAATTACATAAA
G
Found at i:2714 original size:23 final size:23
Alignment explanation
Indices: 2685--2767 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
2675 AAGGAGATAA
2685 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTTATAGGGAGGTTT
*
2708 ATTAAAATTTTATA-GGATGGTTT
1 ATCAAAATTTTATAGGGA-GGTTT
* *
2731 ATCAAAATTTCATAGCGAGG-TT
1 ATCAAAATTTTATAGGGAGGTTT
* *
2753 ATCACAATTTCATAG
1 ATCAAAATTTTATAG
2768 TGTGATTATG
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.36
23 32 0.60
24 2 0.04
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (23 bp):
ATCAAAATTTTATAGGGAGGTTT
Found at i:2761 original size:22 final size:22
Alignment explanation
Indices: 2533--2767 Score: 125
Period size: 22 Copynumber: 10.9 Consensus size: 22
2523 TTATGGTTTA
*
2533 GTTT-TCAAAATTTCATAAGAG
1 GTTTATCAAAATTTCATAGGAG
* * *
2554 GGTTATCAAAATTTCATAGTAT
1 GTTTATCAAAATTTCATAGGAG
** *
2576 GTAGATCAAAATTTCATTGG-G
1 GTTTATCAAAATTTCATAGGAG
* * *
2597 AGATTAACAAAATTTCATAATGAG
1 -GTTTATCAAAATTTCAT-AGGAG
**
2621 G-TTAT-AAAGAAATCATAGGGAG
1 GTTTATCAAA-ATTTCATA-GGAG
*
2643 G-TTATCAAAA-TT--T-GTA-
1 GTTTATCAAAATTTCATAGGAG
*
2659 G-TTATCAAGATTTCATAAGGAG
1 GTTTATCAAAATTTCAT-AGGAG
* ** *
2681 ATAAATCAAAATTTTATAGGGAG
1 GTTTATCAAAATTTCATA-GGAG
* *
2704 GTTTATTAAAATTTTATAGGATG
1 GTTTATCAAAATTTCATAGGA-G
2727 GTTTATCAAAATTTCATAGCGAG
1 GTTTATCAAAATTTCATAG-GAG
*
2750 G-TTATCACAATTTCATAG
1 GTTTATCAAAATTTCATAG
2768 TGTGATTATG
Statistics
Matches: 161, Mismatches: 36, Indels: 33
0.70 0.16 0.14
Matches are distributed among these distances:
16 9 0.06
17 4 0.02
19 2 0.01
21 10 0.06
22 79 0.49
23 54 0.34
24 3 0.02
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.35
Consensus pattern (22 bp):
GTTTATCAAAATTTCATAGGAG
Found at i:2776 original size:22 final size:22
Alignment explanation
Indices: 2729--2797 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
2719 ATAGGATGGT
* * *
2729 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTCATAGTGTGA
*
2751 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
* **
2773 TTATGAAAATTTCAGGGTGTGA
1 TTATCAAAATTTCATAGTGTGA
2795 TTA
1 TTA
2798 CTAACAATTC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGA
Done.