Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014706.1 Corchorus olitorius cultivar O-4 contig14739, 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: 5929
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Found at i:1254 original size:35 final size:36
Alignment explanation
Indices: 1208--1699 Score: 596
Period size: 35 Copynumber: 13.8 Consensus size: 36
1198 ATCAATGTGA
* *
1208 AGATCAACTCTGATCAT-TAAGAACTTCTTGAAACG
1 AGATCAACTCTGATCATAAAAAAACTTCTTGAAACG
** *
1243 AGATCAACTCTGATCAT-CGAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCATAAAAAAACTTCTTGAAACG
* *
1278 AGATCAACTCTGATCATAAAAAAACTTCTTGGAATG
1 AGATCAACTCTGATCATAAAAAAACTTCTTGAAACG
* *
1314 AGATCAACTCTGATCATGAAAAAAAAAAAGAACATCTTGAAATG
1 AGATCAACTCTGATCAT-------AAAAA-AACTTCTTGAAACG
** * *
1358 AGATCAACTCTGATCA-ACGAAATCTTCTTGAAAGG
1 AGATCAACTCTGATCATAAAAAAACTTCTTGAAACG
1393 AGATCAACTCTGATCAT-AAAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATAAAAAAACTTCTTGAAACG
1428 AGATCAACTCTG---ATAAAAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATAAAAAAACTTCTTGAAACG
1461 AGATCAACTCTGATCATAAAAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATAAAAAAACTTCTTGAAACG
** * *
1497 AGATCAACTCTGATCAT-CGAAAAGTTCTTGAAAGG
1 AGATCAACTCTGATCATAAAAAAACTTCTTGAAACG
*
1532 AGATCAACTCTGATCAT-CAAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATAAAAAAACTTCTTGAAACG
** *
1567 AGATCAACTCTGATCAT-CGAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCATAAAAAAACTTCTTGAAACG
1602 AGATCAACTCTGATCAT-AAAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATAAAAAAACTTCTTGAAACG
* ** *
1637 AGACCAACTCTGATCAT-CGAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCATAAAAAAACTTCTTGAAACG
1672 AGATCAACTCTGATCAT-AAAAAACTTCT
1 AGATCAACTCTGATCATAAAAAAACTTCT
1700 CTGATCATAA
Statistics
Matches: 405, Mismatches: 38, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
32 2 0.00
33 30 0.07
35 268 0.66
36 72 0.18
43 5 0.01
44 28 0.07
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.25
Consensus pattern (36 bp):
AGATCAACTCTGATCATAAAAAAACTTCTTGAAACG
Found at i:1287 original size:70 final size:70
Alignment explanation
Indices: 1208--2736 Score: 1058
Period size: 70 Copynumber: 21.4 Consensus size: 70
1198 ATCAATGTGA
* * **
1208 AGATCAACTCTGATCAT-TAAGAACTTCTTGAAACGAGATCAACTCTGATCATCGAAAACTTCTT
1 AGATCAACTCTGATCATCGAA-AACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTT
*
1272 GAAAGG
65 GAAACG
** * *
1278 AGATCAACTCTGATCATAAAAAAACTTCTTGGAATGAGATCAACTCTGATCATGAAAAAAAAAAA
1 AGATCAACTCTGATCAT-CGAAAACTTCTTGAAAGGAGATCAACTCTGATCAT--------AAAA
* *
1343 GAACATCTTGAAATG
57 -AACTTCTTGAAACG
* *
1358 AGATCAACTCTGATCAACGAAATCTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTG
1423 AAACG
66 AAACG
** *
1428 AGATCAACTCTGAT-A-AAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAAAAAACTTCTT
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCAT-AAAAAACTTCTT
1491 GAAACG
65 GAAACG
* *
1497 AGATCAACTCTGATCATCGAAAAGTTCTTGAAAGGAGATCAACTCTGATCATCAAAAACTTCTTG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTG
1562 AAACG
66 AAACG
1567 AGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTG
1632 AAACG
66 AAACG
*
1637 AGACCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTCT
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCT-T
* **
1702 GATCATA
65 GA-AACG
* ** * * ** * * * *
1709 AAAAAAACTTCTTGA-AAT-GAGATCAAC-TC-TGATACAACGA-AAACTTCTTGA-AAGGAGAT
1 AGATCAAC-TC-TGATCATCGA-A--AACTTCTTGAAAGGA-GATCAAC-TC-TGATCA-TA-AA
* * *
1768 CAAC-TC-TG-ATCAT
56 AAACTTCTTGAAAC-G
* ** * ** * ** * ** *
1781 AAAAAAACTTACTTGGAATGAGATC-AACTCTGATCATGAAAAAAAAAAAGAACATCTTGA-AAT
1 AGATCAAC-T-C-T-G-AT--CATCGAAAACT--TCTTG--AAAGGAGATCAAC-TC-TGATCAT
**
1844 GAGATCAAC-TC-TGATCAACG
53 -A-AAAAACTTCTTGA--AACG
* ** ** * ** * * **
1864 AAATCTTCT-TGA--AAGGAGATCAAC-TC-TGATCATAAGA--AACTTCTTGAAACGA-GATCA
1 AGATCAACTCTGATCATCGA-A--AACTTCTTGA-AAGGAGATCAAC-TC-TG-ATC-ATAAAAA
1921 AC-T-TTGATCAACG
58 ACTTCTTGA--AACG
* * * ** * *
1934 A-A--AACTTCTTGA--AACGAGATCAAC-T-TTGATCA-TA-AAAAAGCTTCTTGA-AAGGAGA
1 AGATCAAC-TC-TGATCATCGA-A--AACTTCTTGA-AAGGAGATCAA-C-TC-TGATCA-TA-A
** *
1989 TCAAC-TC-TGATCATA-A
55 AAAACTTCTTGA--A-ACG
* * ** ** *
2005 AAAACTTCTCTGATCATAAAAAAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAAACTTCT
1 AGATCAACTCTGATCAT--CGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCT
*
2070 TGAAAGG
64 TGAAACG
* **
2077 AGATCAACTCTGATCATCGAAAACTTCTTAAAATTAGATCAACTCTGATCATAAAAAAAACTTCT
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCAT--AAAAAACTTCT
*
2142 TGAAATG
64 TGAAACG
* * *
2149 AGATCAACTCTGATCAACGAAAACTTCTTGAAATGAGATCAACTTTGATCATAAAAAACTTCTTG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTG
2214 AAACG
66 AAACG
*
2219 AGATCAACTCTGATCATCGAAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAAACTTCTTG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTG
2284 AAACG
66 AAACG
* * * *
2289 AGATCAACTCTGATCATCGAAAACTTCTTTAAATGAGATCAACTCTAATCATCAAAAACTTCTTG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTG
*
2354 AAACA
66 AAACG
2359 AGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTG
2424 AAACG
66 AAACG
* ** * * *
2429 AGATCAACTCTGATAATAAAAAAAAACTTCTTGAAATGAGATCAACTTTGATCA-ACGAAAACTT
1 AGATCAACTCTGATCAT---CGAAAACTTCTTGAAAGGAGATCAACTCTGATCATA-AAAAACTT
*
2493 ACTTGAAAGG
62 -CTTGAAACG
* * *
2503 AGATCAACTCTGATCAT-AAAAACTTCTTGAAATGAGATCAACTCTGATCA-ACGAAAACTTCTT
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATA-AAAAACTTCTT
*
2566 GAAAGG
65 GAAACG
*
2572 AGATCAACTCTGATCAACGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTG
2637 AAACG
66 AAACG
* * *
2642 AGATCAACTCTGATCAT-AAAAACTTCTTGAAACGAGATCAACTCTGATCATCAAAAACTTCTTG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTG
* *
2706 GAATG
66 AAACG
2711 AGATCAACT-TCGATCATCGAAAACTT
1 AGATCAACTCT-GATCATCGAAAACTT
2737 ATTGGAACGA
Statistics
Matches: 1229, Mismatches: 138, Indels: 184
0.79 0.09 0.12
Matches are distributed among these distances:
67 1 0.00
68 35 0.03
69 122 0.10
70 614 0.50
71 92 0.07
72 113 0.09
73 70 0.06
74 48 0.04
75 19 0.02
76 8 0.01
77 3 0.00
78 6 0.00
79 35 0.03
80 29 0.02
81 27 0.02
82 1 0.00
83 4 0.00
84 2 0.00
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (70 bp):
AGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTG
AAACG
Found at i:1447 original size:105 final size:105
Alignment explanation
Indices: 1348--2746 Score: 1670
Period size: 105 Copynumber: 13.4 Consensus size: 105
1338 AAAAAGAACA
* * * *
1348 TCTTGAAATGAGATCAACTCTGATCA-ACGAAATCTTCTTGAAAGGAGATCAACTCTGATCATAA
1 TCTTGAAAGGAGATCAACTCTGATCATA-AAAAACTTCTTGAAACGAGATCAACTCTGATCATAA
*
1412 AAAACTTCTTGAAACGAGATCAACTCTGAT-AA-AAAAACT
65 AAAACTTCTTGAAATGAGATCAACTCTGATCAACAAAAACT
* **
1451 TCTTGAAACGAGATCAACTCTGATCATAAAAAAACTTCTTGAAACGAGATCAACTCTGATCATCG
1 TCTTGAAAGGAGATCAACTCTGATCAT-AAAAAACTTCTTGAAACGAGATCAACTCTGATCATAA
* * *
1516 AAAAGTTCTTGAAAGGAGATCAACTCTGATCATCAAAAACT
65 AAAACTTCTTGAAATGAGATCAACTCTGATCAACAAAAACT
* ** *
1557 TCTTGAAACGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAA
1 TCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAA
* * * *
1622 AAACTTCTTGAAACGAGACCAACTCTGATCATCGAAAACT
66 AAACTTCTTGAAATGAGATCAACTCTGATCAACAAAAACT
*
1662 TCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTC-T----C-TGATC-A---T-A--A-AAA
1 TCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAA
*
1713 AAACTTCTTGAAATGAGATCAACTCTGATACAACGAAAACT
66 AAACTTCTTGAAATGAGATCAACTCTGAT-CAACAAAAACT
* *
1754 TCTTGAAAGGAGATCAACTCTGATCATAAAAAAACTTACTTGGAATGAGATCAACTCTGATCATG
1 TCTTGAAAGGAGATCAACTCTGATCAT-AAAAAACTT-CTTGAAACGAGATCAACTCTGATCAT-
* * *
1819 AAAAAAAAAAAGAACATCTTGAAATGAGATCAACTCTGATCAACGAAATCT
63 -------AAAA-AACTTCTTGAAATGAGATCAACTCTGATCAACAAAAACT
* * *
1870 TCTTGAAAGGAGATCAACTCTGATCATAAGAAACTTCTTGAAACGAGATCAACTTTGATCA-ACG
1 TCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCATA-A
* *
1934 AAAACTTCTTGAAACGAGATCAACTTTGATCATA-AAAAAGCT
65 AAAACTTCTTGAAATGAGATCAACTCTGATCA-ACAAAAA-CT
*
1976 TCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTC-T----C-TGATC-A---T-A--A-AAA
1 TCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAA
2027 AAACTTCTTGAAATGAGATCAACTCTGATCATA-AAAAACT
66 AAACTTCTTGAAATGAGATCAACTCTGATCA-ACAAAAACT
** * **
2067 TCTTGAAAGGAGATCAACTCTGATCATCGAAAACTTCTTAAAATTAGATCAACTCTGATCATAAA
1 TCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCAT--A
*
2132 AAAAACTTCTTGAAATGAGATCAACTCTGATCAACGAAAACT
64 AAAAACTTCTTGAAATGAGATCAACTCTGATCAACAAAAACT
* * **
2174 TCTTGAAATGAGATCAACTTTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCATCGA
1 TCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAA
2239 AAACTTCTTGAAATGAGATCAACTCTGATCATA-AAAAACT
66 AAACTTCTTGAAATGAGATCAACTCTGATCA-ACAAAAACT
* ** * * * *
2279 TCTTGAAACGAGATCAACTCTGATCATCGAAAACTTCTTTAAATGAGATCAACTCTAATCATCAA
1 TCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAA
** * *
2344 AAACTTCTTGAAACAAGATCAACTCTGATCATCGAAAACT
66 AAACTTCTTGAAATGAGATCAACTCTGATCAACAAAAACT
*
2384 TCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATAATAAA
1 TCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCAT---
* *
2449 AAAAAACTTCTTGAAATGAGATCAACTTTGATCAACGAAAACT
63 AAAAAACTTCTTGAAATGAGATCAACTCTGATCAACAAAAACT
*
2492 TACTTGAAAGGAGATCAACTCTGATCAT-AAAAACTTCTTGAAATGAGATCAACTCTGATCA-AC
1 T-CTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCATA-
* * *
2555 GAAAACTTCTTGAAAGGAGATCAACTCTGATCAACGAAAACT
64 AAAAACTTCTTGAAATGAGATCAACTCTGATCAACAAAAACT
2597 TCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCAT-AA
1 TCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAA
* *
2661 AAACTTCTTGAAACGAGATCAACTCTGATCATCAAAAACT
66 AAACTTCTTGAAATGAGATCAACTCTGATCAACAAAAACT
* * ** * *
2701 TCTTGGAATGAGATCAACT-TCGATCATCGAAAACTTATTGGAACGA
1 TCTTGAAAGGAGATCAACTCT-GATCATAAAAAACTTCTTGAAACGA
2747 CCGCACTGGA
Statistics
Matches: 1136, Mismatches: 100, Indels: 119
0.84 0.07 0.09
Matches are distributed among these distances:
91 67 0.06
92 76 0.07
93 11 0.01
94 2 0.00
95 3 0.00
96 1 0.00
97 4 0.00
98 2 0.00
99 5 0.00
100 8 0.01
101 3 0.00
102 1 0.00
103 26 0.02
104 165 0.15
105 395 0.35
106 77 0.07
107 96 0.08
108 70 0.06
109 26 0.02
114 22 0.02
115 8 0.01
116 41 0.04
117 27 0.02
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (105 bp):
TCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAA
AAACTTCTTGAAATGAGATCAACTCTGATCAACAAAAACT
Found at i:1754 original size:36 final size:35
Alignment explanation
Indices: 1698--2013 Score: 305
Period size: 35 Copynumber: 8.6 Consensus size: 35
1688 TAAAAAACTT
* *
1698 CTCTGATCATAAAAAAAACTTCTTGAAATGAGATCAA
1 CTCTGATC--AAAGAAAACTTCTTGAAAGGAGATCAA
*
1735 CTCTGATACAACGAAAACTTCTTGAAAGGAGATCAA
1 CTCTGAT-CAAAGAAAACTTCTTGAAAGGAGATCAA
* * *
1771 CTCTGATCATAAAAAAACTTACTTGGAATGAGATCAA
1 CTCTGATCA-AAGAAAACTT-CTTGAAAGGAGATCAA
* * *
1808 CTCTGATCATGAAAAAAAAAAAGAACATCTTGAAATGAGATCAA
1 CTCTGATC--------AAAGAA-AACTTCTTGAAAGGAGATCAA
* *
1852 CTCTGATCAACGAAATCTTCTTGAAAGGAGATCAA
1 CTCTGATCAAAGAAAACTTCTTGAAAGGAGATCAA
*
1887 CTCTGATCATAAG-AAACTTCTTGAAACGAGATCAA
1 CTCTGATCA-AAGAAAACTTCTTGAAAGGAGATCAA
* * *
1922 CTTTGATCAACGAAAACTTCTTGAAACGAGATCAA
1 CTCTGATCAAAGAAAACTTCTTGAAAGGAGATCAA
*
1957 CTTTGATCATAA-AAAAGCTTCTTGAAAGGAGATCAA
1 CTCTGATCA-AAGAAAA-CTTCTTGAAAGGAGATCAA
1993 CTCTGATCATAA-AAAACTTCT
1 CTCTGATCA-AAGAAAACTTCT
2014 CTGATCATAA
Statistics
Matches: 241, Mismatches: 22, Indels: 34
0.81 0.07 0.11
Matches are distributed among these distances:
34 2 0.01
35 97 0.40
36 79 0.33
37 29 0.12
38 1 0.00
44 28 0.12
45 5 0.02
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.26
Consensus pattern (35 bp):
CTCTGATCAAAGAAAACTTCTTGAAAGGAGATCAA
Found at i:1766 original size:92 final size:89
Alignment explanation
Indices: 1609--1786 Score: 302
Period size: 92 Copynumber: 2.0 Consensus size: 89
1599 AGGAGATCAA
*
1609 CTCTGATCATAAAAAACTTCTTGAAACGAGACCAACTCTGATCATCGAAAACTTCTTGAAAGGAG
1 CTCTGATCATAAAAAACTTCTTGAAACGAGACCAACTCTGATCAACGAAAACTTCTTGAAAGGAG
1674 ATCAACTCTGATCATAAAAAACTT
66 ATCAACTCTGATCATAAAAAACTT
* *
1698 CTCTGATCATAAAAAAAACTTCTTGAAATGAGATCAACTCTGATACAACGAAAACTTCTTGAAAG
1 CTCTGATCAT--AAAAAACTTCTTGAAACGAGACCAACTCTGAT-CAACGAAAACTTCTTGAAAG
1763 GAGATCAACTCTGATCATAAAAAA
63 GAGATCAACTCTGATCATAAAAAA
1787 ACTTACTTGG
Statistics
Matches: 83, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
89 10 0.12
91 30 0.36
92 43 0.52
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (89 bp):
CTCTGATCATAAAAAACTTCTTGAAACGAGACCAACTCTGATCAACGAAAACTTCTTGAAAGGAG
ATCAACTCTGATCATAAAAAACTT
Found at i:1933 original size:19 final size:19
Alignment explanation
Indices: 1911--1965 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
1901 AACTTCTTGA
1911 AACGAGATCAACTTTGATC
1 AACGAGATCAACTTTGATC
1930 AACGA-A--AACTTCTTGA--
1 AACGAGATCAAC-T-TTGATC
1946 AACGAGATCAACTTTGATC
1 AACGAGATCAACTTTGATC
1965 A
1 A
1966 TAAAAAAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 14
0.67 0.00 0.33
Matches are distributed among these distances:
16 8 0.28
17 6 0.21
18 6 0.21
19 9 0.31
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (19 bp):
AACGAGATCAACTTTGATC
Found at i:2036 original size:56 final size:55
Alignment explanation
Indices: 1960--2069 Score: 193
Period size: 56 Copynumber: 2.0 Consensus size: 55
1950 AGATCAACTT
*
1960 TGATCATAAAAAAGCTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTC
1 TGATCATAAAAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTC
*
2015 TGATCATAAAAAAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAAACTTCT
1 TGATCAT-AAAAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCT
2070 TGAAAGGAGA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
55 7 0.13
56 45 0.87
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (55 bp):
TGATCATAAAAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCTC
Found at i:2100 original size:91 final size:92
Alignment explanation
Indices: 1934--2104 Score: 299
Period size: 91 Copynumber: 1.9 Consensus size: 92
1924 TTGATCAACG
*
1934 AAAACTTCTTGAAACGAGATCAACTTTGATCATAAAAAAGCTTCTTGAAAGGAGATCAACTCTGA
1 AAAACTTCTTGAAACGAGATCAACTCTGATCATAAAAAAGCTTCTTGAAAGGAGATCAACTCTGA
1999 TCATAAAAAACTTCTCTGATCATAAAA
66 TCATAAAAAACTTCTCTGATCATAAAA
*
2026 AAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAAA-CTTCTTGAAAGGAGATCAACTCTGA
1 AAAACTTCTTGAAACGAGATCAACTCTGATCATAAAAAAGCTTCTTGAAAGGAGATCAACTCTGA
**
2090 TCATCGAAAACTTCT
66 TCATAAAAAACTTCT
2105 TAAAATTAGA
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
91 38 0.51
92 37 0.49
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.27
Consensus pattern (92 bp):
AAAACTTCTTGAAACGAGATCAACTCTGATCATAAAAAAGCTTCTTGAAAGGAGATCAACTCTGA
TCATAAAAAACTTCTCTGATCATAAAA
Found at i:2743 original size:35 final size:35
Alignment explanation
Indices: 2025--2736 Score: 980
Period size: 35 Copynumber: 20.2 Consensus size: 35
2015 TGATCATAAA
*
2025 AAAAACTTCTTGAAATGAGATCAACTCTGATCATA
1 AAAAACTTCTTGAAATGAGATCAACTCTGATCATC
*
2060 AAAAACTTCTTGAAAGGAGATCAACTCTGATCATC
1 AAAAACTTCTTGAAATGAGATCAACTCTGATCATC
* * * *
2095 GAAAACTTCTTAAAATTAGATCAACTCTGATCATAAA
1 AAAAACTTCTTGAAATGAGATCAACTCTGATCAT--C
*
2132 AAAAACTTCTTGAAATGAGATCAACTCTGATCAAC
1 AAAAACTTCTTGAAATGAGATCAACTCTGATCATC
* * *
2167 GAAAACTTCTTGAAATGAGATCAACTTTGATCATA
1 AAAAACTTCTTGAAATGAGATCAACTCTGATCATC
*
2202 AAAAACTTCTTGAAACGAGATCAACTCTGATCATC
1 AAAAACTTCTTGAAATGAGATCAACTCTGATCATC
* *
2237 GAAAACTTCTTGAAATGAGATCAACTCTGATCATA
1 AAAAACTTCTTGAAATGAGATCAACTCTGATCATC
*
2272 AAAAACTTCTTGAAACGAGATCAACTCTGATCATC
1 AAAAACTTCTTGAAATGAGATCAACTCTGATCATC
* * *
2307 GAAAACTTCTTTAAATGAGATCAACTCTAATCATC
1 AAAAACTTCTTGAAATGAGATCAACTCTGATCATC
**
2342 AAAAACTTCTTGAAACAAGATCAACTCTGATCATC
1 AAAAACTTCTTGAAATGAGATCAACTCTGATCATC
* * *
2377 GAAAACTTCTTGAAAGGAGATCAACTCTGATCATA
1 AAAAACTTCTTGAAATGAGATCAACTCTGATCATC
* * *
2412 AAAAACTTCTTGAAACGAGATCAACTCTGATAATAAAA
1 AAAAACTTCTTGAAATGAGATCAACTCTGATCAT---C
* *
2450 AAAAACTTCTTGAAATGAGATCAACTTTGATCAAC
1 AAAAACTTCTTGAAATGAGATCAACTCTGATCATC
* *
2485 GAAAACTTACTTGAAAGGAGATCAACTCTGATCAT-
1 AAAAACTT-CTTGAAATGAGATCAACTCTGATCATC
*
2520 AAAAACTTCTTGAAATGAGATCAACTCTGATCAAC
1 AAAAACTTCTTGAAATGAGATCAACTCTGATCATC
* * *
2555 GAAAACTTCTTGAAAGGAGATCAACTCTGATCAAC
1 AAAAACTTCTTGAAATGAGATCAACTCTGATCATC
* * *
2590 GAAAACTTCTTGAAAGGAGATCAACTCTGATCATA
1 AAAAACTTCTTGAAATGAGATCAACTCTGATCATC
*
2625 AAAAACTTCTTGAAACGAGATCAACTCTGATCAT-
1 AAAAACTTCTTGAAATGAGATCAACTCTGATCATC
*
2659 AAAAACTTCTTGAAACGAGATCAACTCTGATCATC
1 AAAAACTTCTTGAAATGAGATCAACTCTGATCATC
*
2694 AAAAACTTCTTGGAATGAGATCAACT-TCGATCATC
1 AAAAACTTCTTGAAATGAGATCAACTCT-GATCATC
*
2729 GAAAACTT
1 AAAAACTT
2737 ATTGGAACGA
Statistics
Matches: 605, Mismatches: 63, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
34 59 0.10
35 462 0.76
36 23 0.04
37 30 0.05
38 31 0.05
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.27
Consensus pattern (35 bp):
AAAAACTTCTTGAAATGAGATCAACTCTGATCATC
Found at i:2770 original size:54 final size:54
Alignment explanation
Indices: 2712--2843 Score: 155
Period size: 54 Copynumber: 2.5 Consensus size: 54
2702 CTTGGAATGA
* * *
2712 GATCAACTTC-GATCATCGAAAACTTATTGGAACGACCGCACTGGATCATTTGGG
1 GATCAACTTCTGATCATCAAAAACTTATTGGAACGACCGCACTGGACCATCT-GG
* * *
2766 GATCAAC-TCTGATCTTTAAAAACTTCTTGGAACGACCGCACTGGACCATCTGG
1 GATCAACTTCTGATCATCAAAAACTTATTGGAACGACCGCACTGGACCATCTGG
*
2819 GATCAAC-TATGATC-TCTAAAAACTT
1 GATCAACTTCTGATCATC-AAAAACTT
2844 CTTTAAAAGA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
52 1 0.01
53 25 0.37
54 42 0.62
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.27
Consensus pattern (54 bp):
GATCAACTTCTGATCATCAAAAACTTATTGGAACGACCGCACTGGACCATCTGG
Found at i:2844 original size:53 final size:54
Alignment explanation
Indices: 2730--2846 Score: 182
Period size: 54 Copynumber: 2.2 Consensus size: 54
2720 TCGATCATCG
* * * * *
2730 AAAACTTATTGGAACGACCGCACTGGATCATTTGGGGATCAACTCTGATCTTTA
1 AAAACTTCTTGGAACGACCGCACTGGACCATCTGGGGATCAACTATGATCTCTA
2784 AAAACTTCTTGGAACGACCGCACTGGACCATCT-GGGATCAACTATGATCTCTA
1 AAAACTTCTTGGAACGACCGCACTGGACCATCTGGGGATCAACTATGATCTCTA
2837 AAAACTTCTT
1 AAAACTTCTT
2847 TAAAAGACCA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
53 28 0.48
54 30 0.52
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (54 bp):
AAAACTTCTTGGAACGACCGCACTGGACCATCTGGGGATCAACTATGATCTCTA
Found at i:2886 original size:54 final size:54
Alignment explanation
Indices: 2766--2981 Score: 177
Period size: 54 Copynumber: 4.0 Consensus size: 54
2756 ATCATTTGGG
* * * * * ** **
2766 GATCAACTCTGATCTTTAAAAACTTCTTGGAACGACCGCACTGGACCATC-TGG
1 GATCAACTCTGATCTCTAAAAACTTCTTTGAAAGACCACACAGGGTCATCTTAA
* * * *
2819 GATCAACTATGATCTCTAAAAACTTCTTTAAAAGACCACACGGGGTCAACTTAA
1 GATCAACTCTGATCTCTAAAAACTTCTTTGAAAGACCACACAGGGTCATCTTAA
* ** * * *
2873 GATCAACTCTGATCAT-TGAAAACTTCTTATGAAAGACTGCATAGGGTTATCTGAA
1 GATCAACTCTGATC-TCTAAAAACTTCTT-TGAAAGACCACACAGGGTCATCTTAA
* * * *
2928 GATCAACT-TAGATTTCTAAAAACTTCTATGAAAGACCACACTGGCTCATCTTAA
1 GATCAACTCT-GATCTCTAAAAACTTCTTTGAAAGACCACACAGGGTCATCTTAA
2982 ACACCTGTAC
Statistics
Matches: 126, Mismatches: 32, Indels: 9
0.75 0.19 0.05
Matches are distributed among these distances:
53 40 0.32
54 46 0.37
55 40 0.32
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (54 bp):
GATCAACTCTGATCTCTAAAAACTTCTTTGAAAGACCACACAGGGTCATCTTAA
Found at i:4376 original size:26 final size:26
Alignment explanation
Indices: 4321--4376 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
4311 CACCATTTTT
* *
4321 TCTTTTTCAGATTCTTTGTTTCCTTT
1 TCTTTTTCAGATTCTTTCTTTCCTTC
*
4347 TCTTTTTCA-ATTCTTTTCTTTTCTTC
1 TCTTTTTCAGATTC-TTTCTTTCCTTC
4373 TCTT
1 TCTT
4377 CTCATTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.07, C:0.21, G:0.04, T:0.68
Consensus pattern (26 bp):
TCTTTTTCAGATTCTTTCTTTCCTTC
Done.