Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012728.1 Corchorus capsularis cultivar CVL-1 contig12749, 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: 39247
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:163 original size:14 final size:13
Alignment explanation
Indices: 144--185 Score: 59
Period size: 12 Copynumber: 3.2 Consensus size: 13
134 TTCCAAGTGC
144 AATGAAAAATTGAA
1 AATGAAAAA-TGAA
158 AATGAAAAAATGAA
1 AATG-AAAAATGAA
172 AAT-AAAAATGAA
1 AATGAAAAATGAA
184 AA
1 AA
186 AATGAATGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 11 0.41
14 11 0.41
15 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (13 bp):
AATGAAAAATGAA
Found at i:188 original size:14 final size:14
Alignment explanation
Indices: 144--185 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
134 TTCCAAGTGC
*
144 AATGAAAAATTGAA
1 AATGAAAAAATGAA
158 AATGAAAAAATGAA
1 AATGAAAAAATGAA
172 AAT--AAAAATGAA
1 AATGAAAAAATGAA
184 AA
1 AA
186 AATGAATGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 11 0.41
14 16 0.59
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (14 bp):
AATGAAAAAATGAA
Found at i:1247 original size:24 final size:24
Alignment explanation
Indices: 1220--1266 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1210 ATAATCTCTT
1220 TCTTCAACTATTCAATGCTTCAAA
1 TCTTCAACTATTCAATGCTTCAAA
* * *
1244 TCTTCCATTATTCAATTCTTCAA
1 TCTTCAACTATTCAATGCTTCAA
1267 TTCACTTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.02, T:0.43
Consensus pattern (24 bp):
TCTTCAACTATTCAATGCTTCAAA
Found at i:1313 original size:58 final size:58
Alignment explanation
Indices: 1244--1385 Score: 180
Period size: 58 Copynumber: 2.4 Consensus size: 58
1234 ATGCTTCAAA
* * *
1244 TCTTCCATTATTCAATTCTTCAATTCACTTCAATGACCCAGGGTGGTCTTTCTT-CGTT
1 TCTTCAATTATTCAATGCTTCAATTCACTTCAATGACACAGGGTGGTCTTTCTTCCG-T
** * *
1302 TCTTCAATTATTCAATGCTTCAATTTGCTTCAATGATACATGGTGGTCTTTCTTCCGT
1 TCTTCAATTATTCAATGCTTCAATTCACTTCAATGACACAGGGTGGTCTTTCTTCCGT
*
1360 TCCTCAATTATTCAATGCCTT-AATTC
1 TCTTCAATTATTCAATG-CTTCAATTC
1386 CAAATCTTCA
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
58 68 0.93
59 5 0.07
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44
Consensus pattern (58 bp):
TCTTCAATTATTCAATGCTTCAATTCACTTCAATGACACAGGGTGGTCTTTCTTCCGT
Found at i:1395 original size:22 final size:22
Alignment explanation
Indices: 1370--1637 Score: 101
Period size: 22 Copynumber: 12.2 Consensus size: 22
1360 TCCTCAATTA
1370 TTCAATGCCTT-AATTCCAAATC
1 TTCAATG-CTTCAATTCCAAATC
* *
1392 TTCAATGCTTCAATTTCAATTC
1 TTCAATGCTTCAATTCCAAATC
* * * *
1414 TTCAATGTTTC--TTTCAATTA
1 TTCAATGCTTCAATTCCAAATC
* * *
1434 TTTAATGCTTCAGTTTCAATAT-
1 TTCAATGCTTCAATTCCAA-ATC
* *
1456 TTCAATGCTTCAATTTCAGTAT-
1 TTCAATGCTTCAATTCCA-AATC
* * * * *
1478 TTCAATGTTTCGATTTCAATTT
1 TTCAATGCTTCAATTCCAAATC
* *
1500 TTCAATGTTTCAATGCTCC-GAT-
1 TTCAATGCTTCAAT--TCCAAATC
*
1522 TTCAATTCTTCAAATT-C-AATCC
1 TTCAATGCTTC-AATTCCAAAT-C
* * * *
1544 TTCGATG-TTCCAATTTCAATTA
1 TTCAATGCTT-CAATTCCAAATC
*
1566 TTCAAATGCTTCAATTTCAATAT-
1 TTC-AATGCTTCAATTCCAA-ATC
* *
1589 TTCAACGCTTCAAGTT-CAATTC
1 TTCAATGCTTCAA-TTCCAAATC
* *
1611 TTCAATGCTTCAATTTCAATTC
1 TTCAATGCTTCAATTCCAAATC
1633 TTCAA
1 TTCAA
1638 ATTCAATTCT
Statistics
Matches: 196, Mismatches: 30, Indels: 40
0.74 0.11 0.15
Matches are distributed among these distances:
20 20 0.10
21 14 0.07
22 133 0.68
23 24 0.12
24 5 0.03
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.45
Consensus pattern (22 bp):
TTCAATGCTTCAATTCCAAATC
Found at i:1503 original size:30 final size:30
Alignment explanation
Indices: 1469--1593 Score: 89
Period size: 30 Copynumber: 4.2 Consensus size: 30
1459 AATGCTTCAA
* * *
1469 TTTCAGTATTTCAATGTTTCGATTTCAATT
1 TTTCAATATTTCAATGCTCCGATTTCAATT
*
1499 TTTCAATGTTTCAATGCTCCGATTTCAATT
1 TTTCAATATTTCAATGCTCCGATTTCAATT
* * *
1529 CTTCAA-A-TTCAATCCTTCGATGTTCCAA--
1 TTTCAATATTTCAATGCTCCGAT-TT-CAATT
* * *
1557 TTTCAAT-TATTCAAATGCTTCAATTTCAATA
1 TTTCAATAT-TTC-AATGCTCCGATTTCAATT
1588 TTTCAA
1 TTTCAA
1594 CGCTTCAAGT
Statistics
Matches: 76, Mismatches: 11, Indels: 15
0.75 0.11 0.15
Matches are distributed among these distances:
28 17 0.22
29 5 0.07
30 39 0.51
31 15 0.20
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.46
Consensus pattern (30 bp):
TTTCAATATTTCAATGCTCCGATTTCAATT
Found at i:1514 original size:8 final size:8
Alignment explanation
Indices: 1446--1514 Score: 56
Period size: 8 Copynumber: 9.1 Consensus size: 8
1436 TAATGCTTCA
1446 GTTTCAAT
1 GTTTCAAT
*
1454 ATTTCAAT
1 GTTTCAAT
*
1462 GCTTCAA-
1 GTTTCAAT
*
1469 -TTTCAGT
1 GTTTCAAT
*
1476 ATTTCAAT
1 GTTTCAAT
*
1484 GTTTCGA-
1 GTTTCAAT
1491 -TTTCAAT
1 GTTTCAAT
*
1498 TTTTCAAT
1 GTTTCAAT
1506 GTTTCAAT
1 GTTTCAAT
1514 G
1 G
1515 CTCCGATTTC
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
6 9 0.19
8 38 0.81
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.49
Consensus pattern (8 bp):
GTTTCAAT
Found at i:1540 original size:36 final size:35
Alignment explanation
Indices: 1500--1666 Score: 128
Period size: 36 Copynumber: 4.8 Consensus size: 35
1490 ATTTCAATTT
*
1500 TTCAATGTTTCAATGCTCCGATTTCAATTCTTCAAA
1 TTCAAT-TTTCAATGCTCCAATTTCAATTCTTCAAA
* * * *
1536 TTCAATCCTTCGATGTTCCAATTTCAATTATTCAAA
1 TTCAAT-TTTCAATGCTCCAATTTCAATTCTTCAAA
* * * ** *
1572 TGC----TTCAAT-TTCAATATTTCAACGCTTCAAG
1 TTCAATTTTCAATGCTCCA-ATTTCAATTCTTCAAA
*
1603 TTCAATTCTTCAATGCTTCAATTTCAATTCTTCAAA
1 TTCAATT-TTCAATGCTCCAATTTCAATTCTTCAAA
* *
1639 TTCAATTCTTCAATGTTTCAATTTCAAT
1 TTCAATT-TTCAATGCTCCAATTTCAAT
1667 AGTTCAATGC
Statistics
Matches: 103, Mismatches: 21, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
30 4 0.04
31 19 0.18
36 78 0.76
37 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.06, T:0.43
Consensus pattern (35 bp):
TTCAATTTTCAATGCTCCAATTTCAATTCTTCAAA
Found at i:1600 original size:8 final size:8
Alignment explanation
Indices: 1570--1937 Score: 92
Period size: 8 Copynumber: 50.2 Consensus size: 8
1560 CAATTATTCA
1570 AATGCTTC
1 AATGCTTC
1578 AAT--TTC
1 AATGCTTC
**
1584 AATATTTC
1 AATGCTTC
*
1592 AACGCTTC
1 AATGCTTC
1600 AA-G-TTC
1 AATGCTTC
*
1606 AATTCTTC
1 AATGCTTC
1614 AATGCTTC
1 AATGCTTC
1622 AAT--TTC
1 AATGCTTC
*
1628 AATTCTTC
1 AATGCTTC
*
1636 AA--ATTC
1 AATGCTTC
*
1642 AATTCTTC
1 AATGCTTC
*
1650 AATGTTTC
1 AATGCTTC
1658 AAT--TTC
1 AATGCTTC
1664 AATAG-TTC
1 AAT-GCTTC
1672 AATGCTTC
1 AATGCTTC
1680 AAT--TTC
1 AATGCTTC
*
1686 AATTCTTC
1 AATGCTTC
*
1694 AA--ATTC
1 AATGCTTC
* **
1700 AATTCAAC
1 AATGCTTC
1708 AATGCTTC
1 AATGCTTC
1716 AAT--TTC
1 AATGCTTC
*
1722 AATTCTTC
1 AATGCTTC
*
1730 AA--ATTC
1 AATGCTTC
* **
1736 AATTCAAC
1 AATGCTTC
1744 AATGCTTC
1 AATGCTTC
1752 AAT--TTC
1 AATGCTTC
* *
1758 AGTCCTTC
1 AATGCTTC
*
1766 AATGTTTC
1 AATGCTTC
*
1774 AAT--TTT
1 AATGCTTC
***
1780 AATTAGTC
1 AATGCTTC
1788 AATGCTTC
1 AATGCTTC
1796 AAT--TTC
1 AATGCTTC
*
1802 AATCCTTC
1 AATGCTTC
*
1810 AA--ATTC
1 AATGCTTC
*
1816 AATCCTTC
1 AATGCTTC
1824 AATGCTTC
1 AATGCTTC
1832 AAAT-C--C
1 -AATGCTTC
*
1838 AATTCTTC
1 AATGCTTC
*
1846 AACGCTTC
1 AATGCTTC
1854 AAT--TTC
1 AATGCTTC
*
1860 AATTCTTC
1 AATGCTTC
*
1868 AAAT--TCC
1 -AATGCTTC
1875 AAATG--TC
1 -AATGCTTC
1882 AATGCTTC
1 AATGCTTC
1890 AAT--TTC
1 AATGCTTC
* *
1896 GATTCTTC
1 AATGCTTC
*
1904 AATACTTC
1 AATGCTTC
**
1912 AATTTTTC
1 AATGCTTC
*
1920 AATGTTTC
1 AATGCTTC
1928 AATGCTTC
1 AATGCTTC
1936 AA
1 AA
1938 ATCCAATTCT
Statistics
Matches: 273, Mismatches: 48, Indels: 78
0.68 0.12 0.20
Matches are distributed among these distances:
5 3 0.01
6 88 0.32
7 9 0.03
8 167 0.61
9 6 0.02
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.41
Consensus pattern (8 bp):
AATGCTTC
Found at i:1650 original size:22 final size:22
Alignment explanation
Indices: 1603--1937 Score: 116
Period size: 22 Copynumber: 15.2 Consensus size: 22
1593 ACGCTTCAAG
1603 TTCAATTCTTCAATGCTTCAA-T-
1 TTCAATTCTTCAAT--TTCAATTC
*
1625 TTCAATTCTTCAAATTCAATTC
1 TTCAATTCTTCAATTTCAATTC
**
1647 TTCAATGT-TTCAATTTCAATAG
1 TTCAAT-TCTTCAATTTCAATTC
*
1669 TTCAATGCTTCAATTTCAATTC
1 TTCAATTCTTCAATTTCAATTC
*
1691 TTCAAATTCAATTCAA---CAATGC
1 TTC-AATTC--TTCAATTTCAATTC
*
1713 TTCAA-T-TTCAATTCTTCAA--A
1 TTCAATTCTTCAA-T-TTCAATTC
**
1733 TTCAATTCAACAATGCTTCAA-T-
1 TTCAATTCTTCAAT--TTCAATTC
* *
1755 TTCAGTCCTTCAATGTTTCAATT-
1 TTCAATTCTTCAA--TTTCAATTC
**
1778 TT-AATTAGTCAATGCTTCAA-T-
1 TTCAATTCTTCAAT--TTCAATTC
* * *
1799 TTCAATCCTTCAAATTCAATCC
1 TTCAATTCTTCAATTTCAATTC
* * *
1821 TTCAATGCTTCAAATCCAATTC
1 TTCAATTCTTCAATTTCAATTC
**
1843 TTCAACGCTTCAATTTCAATTC
1 TTCAATTCTTCAATTTCAATTC
* *
1865 TTCAAATTC--CAAATGTCAATGC
1 TTC-AATTCTTC-AATTTCAATTC
* *
1887 TTCAA-T-TTCGATTCTTCAATAC
1 TTCAATTCTTC-AAT-TTCAATTC
* *
1909 TTCAATTTTTCAATGTTTCAATGC
1 TTCAATTCTTCAA--TTTCAATTC
1933 TTCAA
1 TTCAA
1938 ATCCAATTCT
Statistics
Matches: 239, Mismatches: 41, Indels: 64
0.69 0.12 0.19
Matches are distributed among these distances:
17 5 0.02
20 18 0.08
21 14 0.06
22 167 0.70
23 13 0.05
24 16 0.07
25 6 0.03
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.42
Consensus pattern (22 bp):
TTCAATTCTTCAATTTCAATTC
Found at i:1651 original size:58 final size:58
Alignment explanation
Indices: 1574--1916 Score: 379
Period size: 58 Copynumber: 5.9 Consensus size: 58
1564 TATTCAAATG
* * *
1574 CTTCAATTTCAATAT-TTCAACGCTTCAAGTTCAATTCTTCAATGCTTCAATTTCAATT
1 CTTCAAATTCAAT-TCTTCAATGCTTCAATTTCAATTCTTCAATGCTTCAATTTCAATT
* **
1632 CTTCAAATTCAATTCTTCAATGTTTCAATTTCAATAGTTCAATGCTTCAATTTCAATT
1 CTTCAAATTCAATTCTTCAATGCTTCAATTTCAATTCTTCAATGCTTCAATTTCAATT
** * * *
1690 CTTCAAATTCAATTCAACAATGCTTCAATTTCAATTCTTCAA--ATTCAATTCAACAATG
1 CTTCAAATTCAATTCTTCAATGCTTCAATTTCAATTCTTCAATGCTTCAATT--TCAATT
* * * * * ** *
1748 CTTCAATTTCAGTCCTTCAATGTTTCAATTTTAATTAGTCAATGCTTCAATTTCAATC
1 CTTCAAATTCAATTCTTCAATGCTTCAATTTCAATTCTTCAATGCTTCAATTTCAATT
* * * *
1806 CTTCAAATTCAATCCTTCAATGCTTCAAATCCAATTCTTCAACGCTTCAATTTCAATT
1 CTTCAAATTCAATTCTTCAATGCTTCAATTTCAATTCTTCAATGCTTCAATTTCAATT
* * * *
1864 CTTCAAATTCCAAAT-GTCAATGCTTCAATTTCGATTCTTCAATACTTCAATTT
1 CTTCAAATT-CAATTCTTCAATGCTTCAATTTCAATTCTTCAATGCTTCAATTT
1917 TTCAATGTTT
Statistics
Matches: 235, Mismatches: 44, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
56 7 0.03
57 1 0.00
58 217 0.92
59 3 0.01
60 7 0.03
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.41
Consensus pattern (58 bp):
CTTCAAATTCAATTCTTCAATGCTTCAATTTCAATTCTTCAATGCTTCAATTTCAATT
Found at i:1862 original size:36 final size:36
Alignment explanation
Indices: 1611--1847 Score: 181
Period size: 36 Copynumber: 6.4 Consensus size: 36
1601 AGTTCAATTC
* *
1611 TTCAATGCTTCAATTTCAATTCTTCAA--ATTCAATT
1 TTCAATGCTTCAAATTCAATTCTTCAATGCTTCAA-T
* * **
1646 CTTCAATGTTTCAATTTCAATAGTTCAATGCTTCAAT
1 -TTCAATGCTTCAAATTCAATTCTTCAATGCTTCAAT
* **
1683 TTCAATTCTTCAAATTCAATTCAACAATGCTTCAAT
1 TTCAATGCTTCAAATTCAATTCTTCAATGCTTCAAT
* **
1719 TTCAATTCTTCAAATTCAATTCAACAATGCTTCAAT
1 TTCAATGCTTCAAATTCAATTCTTCAATGCTTCAAT
* * * *
1755 TTCAGTCCTTCAATGTTTCAATTTTAATTAGTCAATGCTTCAAT
1 TTCAATGCTTCAA--ATTCAA--TT--CT--TCAATGCTTCAAT
* * *
1799 TTCAATCCTTCAAATTCAATCCTTCAATGCTTCAAA
1 TTCAATGCTTCAAATTCAATTCTTCAATGCTTCAAT
* *
1835 TCCAATTCTTCAA
1 TTCAATGCTTCAA
1848 CGCTTCAATT
Statistics
Matches: 167, Mismatches: 24, Indels: 20
0.79 0.11 0.09
Matches are distributed among these distances:
36 123 0.74
37 1 0.01
38 11 0.07
40 3 0.02
42 5 0.03
44 24 0.14
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (36 bp):
TTCAATGCTTCAAATTCAATTCTTCAATGCTTCAAT
Found at i:1868 original size:36 final size:36
Alignment explanation
Indices: 1821--1915 Score: 75
Period size: 36 Copynumber: 2.6 Consensus size: 36
1811 AATTCAATCC
* * ** *
1821 TTCAATGCTTCAAATCCAATTCTTCAACGCTTCAAT
1 TTCAATTCTTCAAATTCAATTCAACAATGCTTCAAT
* **
1857 TTCAATTCTTCAAATTCCAAAT-GTCAATGCTTCAAT
1 TTCAATTCTTCAAATT-CAATTCAACAATGCTTCAAT
*
1893 TTCGATTCTTCAATACTTCAATT
1 TTCAATTCTTCAA-A-TTCAATT
1916 TTTCAATGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
36 38 0.78
37 9 0.18
38 2 0.04
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.40
Consensus pattern (36 bp):
TTCAATTCTTCAAATTCAATTCAACAATGCTTCAAT
Found at i:1966 original size:104 final size:103
Alignment explanation
Indices: 1821--2020 Score: 273
Period size: 104 Copynumber: 1.9 Consensus size: 103
1811 AATTCAATCC
* * *
1821 TTCAATGCTTCAAATCCAATTCTTCAACGCTTCAATTTCAAT-TCTTCAAATTCCAA-ATGTCAA
1 TTCAATGCTTCAAATCCAATTCTCCAAC-ATTCAATGTCAATGT-TTC-AATTCCAATATGTCAA
1884 TGCTTCAATTTCGATTCTT-CAATACTTCAATTTTTCAATGT
63 TGCTTCAATTTCGATTCTTCCAA-ACTTCAATTTTTCAATGT
*
1925 TTCAATGCTTCAAATCCAATTCTCCAA-ATTCCAAATGTCAATGTTTCAATTTCAATATGTCAAT
1 TTCAATGCTTCAAATCCAATTCTCCAACATT-C-AATGTCAATGTTTCAATTCCAATATGTCAAT
*
1989 GCTTCAATTTCGATTCTTCCAAGCTTCAATTT
64 GCTTCAATTTCGATTCTTCCAAACTTCAATTT
2021 CAGTTCTTCG
Statistics
Matches: 86, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
102 2 0.02
103 8 0.09
104 72 0.84
105 4 0.05
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.41
Consensus pattern (103 bp):
TTCAATGCTTCAAATCCAATTCTCCAACATTCAATGTCAATGTTTCAATTCCAATATGTCAATGC
TTCAATTTCGATTCTTCCAAACTTCAATTTTTCAATGT
Found at i:1984 original size:22 final size:21
Alignment explanation
Indices: 1951--1999 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
1941 CAATTCTCCA
* *
1951 AATTCCAAATGTCAATGTTTC
1 AATTTCAAATGTCAATGCTTC
1972 AATTTCAATATGTCAATGCTTC
1 AATTTCAA-ATGTCAATGCTTC
1994 AATTTC
1 AATTTC
2000 GATTCTTCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (21 bp):
AATTTCAAATGTCAATGCTTC
Found at i:1988 original size:82 final size:82
Alignment explanation
Indices: 1843--1998 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 82
1833 AATCCAATTC
* * * * *
1843 TTCAACGCTTCAATTTCAATTCTTCAAATTCCAAATGTCAATGCTTCAATTTCGATTCTTCAATA
1 TTCAACGCTTCAAATCCAATTCTCCAAATTCCAAATGTCAATGCTTCAATTTCAATTCGTCAATA
1908 CTTCAATTTTTCAATGT
66 CTTCAATTTTTCAATGT
* *
1925 TTCAATGCTTCAAATCCAATTCTCCAAATTCCAAATGTCAATGTTTCAATTTCAATAT-GTCAAT
1 TTCAACGCTTCAAATCCAATTCTCCAAATTCCAAATGTCAATGCTTCAATTTCAAT-TCGTCAAT
*
1989 GCTTCAATTT
65 ACTTCAATTT
1999 CGATTCTTCC
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
82 64 0.98
83 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (82 bp):
TTCAACGCTTCAAATCCAATTCTCCAAATTCCAAATGTCAATGCTTCAATTTCAATTCGTCAATA
CTTCAATTTTTCAATGT
Found at i:2014 original size:22 final size:22
Alignment explanation
Indices: 1989--2042 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1979 ATATGTCAAT
1989 GCTTCAATTTC-GATTCTTCCAA
1 GCTTCAATTTCAG-TTCTTCCAA
*
2011 GCTTCAATTTCAGTTCTTCGAA
1 GCTTCAATTTCAGTTCTTCCAA
2033 --TTCAATTTCA
1 GCTTCAATTTCA
2043 ATGTTTCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 10 0.33
22 19 0.63
23 1 0.03
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.43
Consensus pattern (22 bp):
GCTTCAATTTCAGTTCTTCCAA
Found at i:2050 original size:14 final size:14
Alignment explanation
Indices: 2033--2065 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2023 GTTCTTCGAA
2033 TTCAATTTCAATGT
1 TTCAATTTCAATGT
*
2047 TTCAATTTCAATTT
1 TTCAATTTCAATGT
2061 TTCAA
1 TTCAA
2066 AGCCTCCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.52
Consensus pattern (14 bp):
TTCAATTTCAATGT
Found at i:15914 original size:11 final size:11
Alignment explanation
Indices: 15898--15929 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
15888 GAAGTTCGTG
15898 TTTGAAGATTA
1 TTTGAAGATTA
*
15909 TTTGAAGATAA
1 TTTGAAGATTA
15920 TTTGAAGATT
1 TTTGAAGATT
15930 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:15926 original size:22 final size:22
Alignment explanation
Indices: 15898--15957 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
15888 GAAGTTCGTG
*
15898 TTTGAAGATTATTTGAAGATAA
1 TTTGAAGATTATTTGAAGACAA
15920 TTTGAAG---ATTTGAAGACAA
1 TTTGAAGATTATTTGAAGACAA
*
15939 -TTGAAGAATTATTTCAAGA
1 TTTGAAG-ATTATTTGAAGA
15958 AGCAAGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
22 15 0.47
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (22 bp):
TTTGAAGATTATTTGAAGACAA
Found at i:15932 original size:19 final size:18
Alignment explanation
Indices: 15908--15945 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
15898 TTTGAAGATT
*
15908 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
15927 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
15945 A
1 A
15946 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:17302 original size:6 final size:6
Alignment explanation
Indices: 17291--17321 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
17281 ATAATTGCTA
17291 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TA
17322 CTTTGCTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (6 bp):
TAGATT
Found at i:17359 original size:15 final size:15
Alignment explanation
Indices: 17339--17368 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17329 TAGTATTTAG
*
17339 TTTAATTGTTTTCTT
1 TTTAATTGCTTTCTT
17354 TTTAATTGCTTTCTT
1 TTTAATTGCTTTCTT
17369 AAAATCCCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (15 bp):
TTTAATTGCTTTCTT
Found at i:18662 original size:13 final size:13
Alignment explanation
Indices: 18644--18674 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
18634 CGCCACATAA
18644 GAAGACATGCAGT
1 GAAGACATGCAGT
18657 GAAGACATGCAGT
1 GAAGACATGCAGT
18670 GAAGA
1 GAAGA
18675 GATTTGTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.13, G:0.32, T:0.13
Consensus pattern (13 bp):
GAAGACATGCAGT
Found at i:19011 original size:6 final size:6
Alignment explanation
Indices: 19000--19030 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
18990 ATAATTGCTA
19000 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TA
19031 CTTTGCTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (6 bp):
TAGATT
Found at i:23837 original size:69 final size:71
Alignment explanation
Indices: 23726--23866 Score: 232
Period size: 69 Copynumber: 2.0 Consensus size: 71
23716 TAACAATCTC
*
23726 ATGGCGAAATGGGGTCATATATCTAATATAATATTC-AAA-ACTACTTTTTATCTCACACTCACA
1 ATGGCGAAATGCGGTCATATATCTAATATAATATTCAAAACACTACTTTTTATCTCACACTCACA
23789 GCTGTT
66 GCTGTT
* *
23795 ATGGCGAAGTGCGGTCATATATCTAATATAATATTCACAACTACTACTTTTTATCTCACACTCAC
1 ATGGCGAAATGCGGTCATATATCTAATATAATATTCAAAAC-ACTACTTTTTATCTCACACTCAC
23860 AGCTGTT
65 AGCTGTT
23867 TTTCATCATA
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
69 34 0.52
70 2 0.03
72 30 0.45
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.35
Consensus pattern (71 bp):
ATGGCGAAATGCGGTCATATATCTAATATAATATTCAAAACACTACTTTTTATCTCACACTCACA
GCTGTT
Found at i:24044 original size:32 final size:32
Alignment explanation
Indices: 23957--24044 Score: 140
Period size: 32 Copynumber: 2.8 Consensus size: 32
23947 CGGGTTTAAG
* *
23957 TCGGGTTCGGGTTGAATTTGGGTCAGGTCAAT
1 TCGGGTTCGGGTTGAATTTGGGTTAGCTCAAT
*
23989 TCGGGTTCAGGTTGAATTTGGGTTAGCTCAAT
1 TCGGGTTCGGGTTGAATTTGGGTTAGCTCAAT
*
24021 TCGGGTTTGGGTTGAATTTGGGTT
1 TCGGGTTCGGGTTGAATTTGGGTT
24045 TTAGCCAGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.15, C:0.10, G:0.36, T:0.39
Consensus pattern (32 bp):
TCGGGTTCGGGTTGAATTTGGGTTAGCTCAAT
Found at i:24045 original size:17 final size:17
Alignment explanation
Indices: 23939--24044 Score: 76
Period size: 17 Copynumber: 6.5 Consensus size: 17
23929 CGGGCGGGTT
*
23939 TTTGGGTTCGGGTTTAA
1 TTTGGGTTCGGGTTGAA
* *
23956 GTCGGGTTCGGGTTGAA
1 TTTGGGTTCGGGTTGAA
* *
23973 TTTGGG-TCAGG-TCAA
1 TTTGGGTTCGGGTTGAA
* *
23988 TTCGGGTTCAGGTTGAA
1 TTTGGGTTCGGGTTGAA
* * *
24005 TTTGGGTT--AGCTCAA
1 TTTGGGTTCGGGTTGAA
* *
24020 TTCGGGTTTGGGTTGAA
1 TTTGGGTTCGGGTTGAA
24037 TTTGGGTT
1 TTTGGGTT
24045 TTAGCCAGAT
Statistics
Matches: 67, Mismatches: 18, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
15 19 0.28
16 9 0.13
17 39 0.58
ACGTcount: A:0.14, C:0.09, G:0.37, T:0.40
Consensus pattern (17 bp):
TTTGGGTTCGGGTTGAA
Found at i:24235 original size:16 final size:16
Alignment explanation
Indices: 24188--24249 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
24178 AACTTTTGGA
*
24188 TTCGAGTTCTGATTTT
1 TTCGAGTTCGGATTTT
* **
24204 TTCGGGTT-TAAGTTTT
1 TTCGAGTTCGGA-TTTT
*
24220 TTCGGGTTCGGATTTT
1 TTCGAGTTCGGATTTT
24236 TTCGAGTTCGGATT
1 TTCGAGTTCGGATT
24250 CAAACGGATT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
15 2 0.05
16 36 0.92
17 1 0.03
ACGTcount: A:0.11, C:0.11, G:0.26, T:0.52
Consensus pattern (16 bp):
TTCGAGTTCGGATTTT
Found at i:29957 original size:12 final size:12
Alignment explanation
Indices: 29940--29964 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29930 GTAAGAGGAA
29940 TAATAATAATTT
1 TAATAATAATTT
29952 TAATAATAATTT
1 TAATAATAATTT
29964 T
1 T
29965 TTAATTTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATAATAATTT
Found at i:30796 original size:16 final size:16
Alignment explanation
Indices: 30775--30806 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
30765 AAAGTATATA
30775 AATTTTTGAAATTTGG
1 AATTTTTGAAATTTGG
30791 AATTTTTGAAATTTGG
1 AATTTTTGAAATTTGG
30807 CTATAAGGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (16 bp):
AATTTTTGAAATTTGG
Found at i:38787 original size:32 final size:31
Alignment explanation
Indices: 38741--38807 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 31
38731 AACTTTATGT
*
38741 TTTCCGATTATACCCTTATT-TTTAAAACATTA
1 TTTCCAATTATACCCTT-TTCTTTAAAACA-TA
*
38773 TTTCCAATTGTACCCTTTTCTTTAAAACATA
1 TTTCCAATTATACCCTTTTCTTTAAAACATA
38804 TTTC
1 TTTC
38808 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 8 0.25
32 24 0.75
ACGTcount: A:0.28, C:0.21, G:0.03, T:0.48
Consensus pattern (31 bp):
TTTCCAATTATACCCTTTTCTTTAAAACATA
Found at i:38814 original size:32 final size:32
Alignment explanation
Indices: 38751--38814 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
38741 TTTCCGATTA
*
38751 TACCCTTATTTTTAAAACATTATTTCCAATTG
1 TACCCTTATTTTTAAAACATTATTTCAAATTG
38783 TACCCTT-TTCTTTAAAACA-TATTTCTAAATTG
1 TACCCTTATT-TTTAAAACATTATTTC-AAATTG
38815 CCATTACTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 8 0.28
32 21 0.72
ACGTcount: A:0.31, C:0.19, G:0.03, T:0.47
Consensus pattern (32 bp):
TACCCTTATTTTTAAAACATTATTTCAAATTG
Found at i:38976 original size:37 final size:36
Alignment explanation
Indices: 38907--38983 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 36
38897 AATTTGAATT
*
38907 TTTGTTTCCAACGTCCTATTTAATTTTGTCTTTTGTC
1 TTTGTTTCCAACGTCATATTTAATTTTGTC-TTTGTC
*
38944 TTTGTTTCCAATCGTTATATTTAATTTT-TCTTTGTC
1 TTTGTTTCCAA-CGTCATATTTAATTTTGTCTTTGTC
38980 TTTG
1 TTTG
38984 GTCTTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 10 0.27
37 13 0.35
38 14 0.38
ACGTcount: A:0.14, C:0.16, G:0.10, T:0.60
Consensus pattern (36 bp):
TTTGTTTCCAACGTCATATTTAATTTTGTCTTTGTC
Found at i:39147 original size:19 final size:20
Alignment explanation
Indices: 39120--39157 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
39110 TACTATTATT
39120 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
39140 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
39158 AATCTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Done.