Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167903.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_169, 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: 59706
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:1239 original size:87 final size:88
Alignment explanation
Indices: 1092--1300 Score: 294
Period size: 88 Copynumber: 2.4 Consensus size: 88
1082 TATAATAATA
* * * *
1092 AATCGATCGAGATAACACACGCGAATTGAAATTATGCCTGGAGGTCTTACAGAATAGACTGGGAT
1 AATCGATCGGGATAACAC-CGCGAATCGAAATTATGCCTGAAGGTCTTACAAAATAGACTGGGAT
* *
1157 AACATCGC-AGTTAAAAGATAAAG
65 AACACCGCAAGTCAAAAGATAAAG
* *
1180 AATCGATCGGGATAACACCGCGAATCGAAATTATGTCTGAAGGTCTTACAAAATCGACTGGGATA
1 AATCGATCGGGATAACACCGCGAATCGAAATTATGCCTGAAGGTCTTACAAAATAGACTGGGATA
*
1245 ACACCGCAAGTCAAAAGATAAGG
66 ACACCGCAAGTCAAAAGATAAAG
* * *
1268 AATCAATCGGGATAACTCCGTGAATCGAAATTA
1 AATCGATCGGGATAACACCGCGAATCGAAATTA
1301 CATTCGAAGG
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
87 48 0.44
88 60 0.56
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.21
Consensus pattern (88 bp):
AATCGATCGGGATAACACCGCGAATCGAAATTATGCCTGAAGGTCTTACAAAATAGACTGGGATA
ACACCGCAAGTCAAAAGATAAAG
Found at i:1336 original size:22 final size:23
Alignment explanation
Indices: 1308--1368 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
1298 TTACATTCGA
**
1308 AGGTCTTA-AGAATCATGCCTGG
1 AGGTCTTACAGAATCATGCCCAG
*
1330 AGGTCTTATAGAATCATGCCCAG
1 AGGTCTTACAGAATCATGCCCAG
1353 AGGTCTTACAGAATCA
1 AGGTCTTACAGAATCA
1369 ACTGGAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 8 0.23
23 27 0.77
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (23 bp):
AGGTCTTACAGAATCATGCCCAG
Found at i:1458 original size:22 final size:22
Alignment explanation
Indices: 1427--1470 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1417 ACCGCGAATT
*
1427 GAAATTATGCCCGGAGGTCTTA
1 GAAATCATGCCCGGAGGTCTTA
**
1449 GAAATCATGCTTGGAGGTCTTA
1 GAAATCATGCCCGGAGGTCTTA
1471 CAGGATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (22 bp):
GAAATCATGCCCGGAGGTCTTA
Found at i:1458 original size:133 final size:133
Alignment explanation
Indices: 1220--1470 Score: 324
Period size: 133 Copynumber: 1.9 Consensus size: 133
1210 TTATGTCTGA
* * * * *
1220 AGGTCTTACAAAATCGACTGGGATAACACCGCAAGTCAAAAGATAAGGAATCAATCGGGATAACT
1 AGGTCTTACAAAATCAACTGGAATAACACCGCAAGTCAAAAGATAAGAAATCAACCGGGATAACA
* **
1285 CCGTGAATCGAAATTACATTCGAAGGTCTTAAGAATCATGCCTGGAGGTCTTATAGAATCATGCC
66 CCGCGAATCGAAATTACACCCGAAGGTCTTAAGAATCATGCCTGGAGGTCTTATAGAATCATGCC
1350 CAG
131 CAG
* * * * *
1353 AGGTCTTACAGAATCAACTGGAATAACATCGTAAGTCGAAAGATAAGAAATCGACCGGGATAACA
1 AGGTCTTACAAAATCAACTGGAATAACACCGCAAGTCAAAAGATAAGAAATCAACCGGGATAACA
* ** * *
1418 CCGCGAATTGAAATTATGCCCGGAGGTCTT-AGAAATCATGCTTGGAGGTCTTA
66 CCGCGAATCGAAATTACACCCGAAGGTCTTAAG-AATCATGCCTGGAGGTCTTA
1471 CAGGATAAAT
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
132 2 0.02
133 97 0.98
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (133 bp):
AGGTCTTACAAAATCAACTGGAATAACACCGCAAGTCAAAAGATAAGAAATCAACCGGGATAACA
CCGCGAATCGAAATTACACCCGAAGGTCTTAAGAATCATGCCTGGAGGTCTTATAGAATCATGCC
CAG
Found at i:1525 original size:109 final size:110
Alignment explanation
Indices: 1322--1585 Score: 350
Period size: 109 Copynumber: 2.4 Consensus size: 110
1312 CTTAAGAATC
* * * *
1322 ATGCCTGGAGGTCTTATAGAATCATGCCCAGAGGTCTTACAGAATCAACTGGAATAACATCGTAA
1 ATGCCCGGAGGTCTTAGA-AATCATGCCCGGAGGTCTTACAGAATAAACTGGAATAACATCGTAA
* *
1387 GTCGAAAGATAAGAAATCGACCGGGATAACACCGCGAATTGAAATT
65 GTCAAAAGATAAGAAATCGACCGGGATAACACCGCGAATCGAAATT
** * * * *
1433 ATGCCCGGAGGTCTTAGAAATCATGCTTGGAGGTCTTACAGGATAAATTGGGATAACATCG-CAG
1 ATGCCCGGAGGTCTTAGAAATCATGCCCGGAGGTCTTACAGAATAAACTGGAATAACATCGTAAG
* * * *
1497 TCAAAAGATAAGGAATCGATCGGGATAACATCGTGAATCGAAATT
66 TCAAAAGATAAGAAATCGACCGGGATAACACCGCGAATCGAAATT
**
1542 ATGCCCAAAGGTCTTAGAAATCATGCCCGGAGGTCTTACAGAAT
1 ATGCCCGGAGGTCTTAGAAATCATGCCCGGAGGTCTTACAGAAT
1586 CATGTTCGGA
Statistics
Matches: 132, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
109 80 0.61
110 36 0.27
111 16 0.12
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (110 bp):
ATGCCCGGAGGTCTTAGAAATCATGCCCGGAGGTCTTACAGAATAAACTGGAATAACATCGTAAG
TCAAAAGATAAGAAATCGACCGGGATAACACCGCGAATCGAAATT
Found at i:1567 original size:22 final size:22
Alignment explanation
Indices: 1536--1589 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1526 ATCGTGAATC
*
1536 GAAATTATGCCCAAAGGTCTTA
1 GAAATCATGCCCAAAGGTCTTA
**
1558 GAAATCATGCCCGGAGGTCTTA
1 GAAATCATGCCCAAAGGTCTTA
*
1580 CAGAATCATG
1 GA-AATCATG
1590 TTCGGAGGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 20 0.74
23 7 0.26
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (22 bp):
GAAATCATGCCCAAAGGTCTTA
Found at i:1595 original size:23 final size:22
Alignment explanation
Indices: 1550--1606 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 22
1540 TTATGCCCAA
*
1550 AGGTCTTAGAAATCATGCCCGG
1 AGGTCTTACAAATCATGCCCGG
**
1572 AGGTCTTACAGAATCATGTTCGG
1 AGGTCTTACA-AATCATGCCCGG
1595 AGGTCTTACAAA
1 AGGTCTTACAAA
1607 ATTGACTGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 11 0.35
23 20 0.65
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (22 bp):
AGGTCTTACAAATCATGCCCGG
Found at i:1645 original size:132 final size:132
Alignment explanation
Indices: 1427--1717 Score: 381
Period size: 132 Copynumber: 2.2 Consensus size: 132
1417 ACCGCGAATT
* * ** *
1427 GAAATTATGCCCGGAGGTCTTAGA-AATCATGCTTGGAGGTCTTACAGGATAAATTGGGATAACA
1 GAAATCATGCCCGGAGGTCTTACAGAATCATGCTTGGAGGTCTTACAAAATAAACTGGGATAACA
* ** * * *
1491 TCGCAGTCAAAAGATAAGGAATCGATCGGGATAACATCGTGAATCGAAATTATGCCCAAAGGTCT
66 TCGCAGTCAAAAGATAAAGAATCGATCAAGACAACATCGCGAATCGAAATTATGCCCAAAGGCCT
1556 TA
131 TA
**
1558 GAAATCATGCCCGGAGGTCTTACAGAATCATG-TTCGGAGGTCTTACAAAATTGACTGGGATAAC
1 GAAATCATGCCCGGAGGTCTTACAGAATCATGCTT-GGAGGTCTTACAAAATAAACTGGGATAAC
* ** *
1622 ATCGCAAGTCAGAA-ATAAAGAATCGATCAAGACAACATCGCGAATCGAAATTATGCCCGGATGC
65 ATCGC-AGTCAAAAGATAAAGAATCGATCAAGACAACATCGCGAATCGAAATTATGCCCAAAGGC
1686 CTTA
129 CTTA
*
1690 GAAATCATGCCCGGAGGTCTTATAGAAT
1 GAAATCATGCCCGGAGGTCTTACAGAAT
1718 TGCCCGAAGG
Statistics
Matches: 139, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
131 24 0.17
132 108 0.78
133 7 0.05
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (132 bp):
GAAATCATGCCCGGAGGTCTTACAGAATCATGCTTGGAGGTCTTACAAAATAAACTGGGATAACA
TCGCAGTCAAAAGATAAAGAATCGATCAAGACAACATCGCGAATCGAAATTATGCCCAAAGGCCT
TA
Found at i:1711 original size:22 final size:22
Alignment explanation
Indices: 1668--1754 Score: 88
Period size: 22 Copynumber: 4.0 Consensus size: 22
1658 ATCGCGAATC
* * *
1668 GAAATTATGCCCGGATGCCTTA
1 GAAATCATGCCCGGAGGTCTTA
1690 GAAATCATGCCCGGAGGTCTTA
1 GAAATCATGCCCGGAGGTCTTA
* *
1712 TAGAAT--TGCCCGAAGGTCTTA
1 GA-AATCATGCCCGGAGGTCTTA
* *
1733 AAAATCATGTCCGGAGGTCTTA
1 GAAATCATGCCCGGAGGTCTTA
1755 CAGAATTGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.06
21 15 0.28
22 33 0.61
23 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (22 bp):
GAAATCATGCCCGGAGGTCTTA
Found at i:1723 original size:21 final size:20
Alignment explanation
Indices: 1697--1762 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
1687 TTAGAAATCA
1697 TGCCCGGAGGTCTTATAGAAT
1 TGCCCGGAGGTCTTA-AGAAT
* *
1718 TGCCCGAAGGTCTTAAAAAT
1 TGCCCGGAGGTCTTAAGAAT
*
1738 CATGTCCGGAGGTCTTACAGAAT
1 --TGCCCGGAGGTCTTA-AGAAT
1761 TG
1 TG
1763 AATGGGATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
20 4 0.11
21 16 0.43
22 13 0.35
23 4 0.11
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (20 bp):
TGCCCGGAGGTCTTAAGAAT
Found at i:1788 original size:152 final size:153
Alignment explanation
Indices: 1565--1886 Score: 441
Period size: 152 Copynumber: 2.1 Consensus size: 153
1555 TTAGAAATCA
* * * * * *
1565 TGCCCGGAGGTCTTACAGAATCATGTTCGGAGGTCTTACAAAATTGACTGGGATAACATCGCAAG
1 TGCCCGAAGGTCTTACAAAATCATGTCCGGAGGTCTTACAAAATTGAATGGGATAACACCACAAG
* * * *
1630 TCAGAAATAAAGAATCGATCAAGACAACA-TCGCGAATCGAAATTATGCCCGGATGCCTTAGAAA
66 TCAGAAACAAAGAATCGATCAAGACAACACT-GCGAATCAAAATTATACCCGGAGGCCTTAGAAA
*
1694 TCATGCCCGGAGGTCTTATAGAAT
130 TCATGCCCGGAGGTCTTACAGAAT
* *
1718 TGCCCGAAGGTCTTA-AAAATCATGTCCGGAGGTCTTACAGAATTGAATGGGATAACACCATAAG
1 TGCCCGAAGGTCTTACAAAATCATGTCCGGAGGTCTTACAAAATTGAATGGGATAACACCACAAG
* ** * *
1782 TTAGAAACAAAGAATCGATCGGGATAACACTGCGAATCAAAATTATACCCGGAGGTCTTAGAAAT
66 TCAGAAACAAAGAATCGATCAAGACAACACTGCGAATCAAAATTATACCCGGAGGCCTTAGAAAT
**
1847 CATGTTCGGAGGTCTTACAGAAT
131 CATGCCCGGAGGTCTTACAGAAT
1870 TGCCCGAAGGTCTTACA
1 TGCCCGAAGGTCTTACA
1887 GAATTGAATG
Statistics
Matches: 147, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
152 131 0.89
153 16 0.11
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (153 bp):
TGCCCGAAGGTCTTACAAAATCATGTCCGGAGGTCTTACAAAATTGAATGGGATAACACCACAAG
TCAGAAACAAAGAATCGATCAAGACAACACTGCGAATCAAAATTATACCCGGAGGCCTTAGAAAT
CATGCCCGGAGGTCTTACAGAAT
Found at i:1896 original size:130 final size:130
Alignment explanation
Indices: 1747--2014 Score: 446
Period size: 130 Copynumber: 2.1 Consensus size: 130
1737 TCATGTCCGG
* *
1747 AGGTCTTACAGAATTGAATGGGATAACACCATAAGTTAGAAACAAAGAATCGATCGGGATAACAC
1 AGGTCTTACAGAATTGAATGGGATAACACCACAAGTTAGAAACAAAGAATCGATCGAGATAACAC
** * * *
1812 TGCGAATCAAAATTATACCCGGAGGTCTTAGAAATCATGTTCGGAGGTCTTACAGAATTGCCCGA
66 CACGAATCAAAATTATACCCGGAGGTCTTAGAAATCATGTCCGGAGGTCTTACAAAATTACCCGA
*
1877 AGGTCTTACAGAATTGAATGGGATAACACCACAAGTTAGAAACAAAGAATCGATCGAGATAATAC
1 AGGTCTTACAGAATTGAATGGGATAACACCACAAGTTAGAAACAAAGAATCGATCGAGATAACAC
* *
1942 CACGAATCAAAATTATGCCCGGAGGTCTTAGAAATCATGTCCGGAGGTCTTACAAAATTACCCGG
66 CACGAATCAAAATTATACCCGGAGGTCTTAGAAATCATGTCCGGAGGTCTTACAAAATTACCCGA
2007 AGGTCTTA
1 AGGTCTTA
2015 AAAATCATGC
Statistics
Matches: 128, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 128 1.00
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (130 bp):
AGGTCTTACAGAATTGAATGGGATAACACCACAAGTTAGAAACAAAGAATCGATCGAGATAACAC
CACGAATCAAAATTATACCCGGAGGTCTTAGAAATCATGTCCGGAGGTCTTACAAAATTACCCGA
Found at i:2012 original size:43 final size:44
Alignment explanation
Indices: 1949--2043 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 44
1939 TACCACGAAT
* * * *
1949 CAAAATTATGCCCGGAGGTCTTAGAAATCATGTCCGGAGGTCTTA
1 CAAAATTA-GCCCGGAGGTCTTAAAAATCATGCCCGAAAGTCTTA
1994 CAAAATTA-CCCGGAGGTCTTAAAAATCATGCCCGAAAGTCTTA
1 CAAAATTAGCCCGGAGGTCTTAAAAATCATGCCCGAAAGTCTTA
*
2037 CAGAATT
1 CAAAATT
2044 GATGGGATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
43 37 0.82
45 8 0.18
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (44 bp):
CAAAATTAGCCCGGAGGTCTTAAAAATCATGCCCGAAAGTCTTA
Found at i:2034 original size:22 final size:22
Alignment explanation
Indices: 1950--2036 Score: 97
Period size: 22 Copynumber: 4.0 Consensus size: 22
1940 ACCACGAATC
*
1950 AAAATTATGCCCGGAGGTCTTA
1 AAAATCATGCCCGGAGGTCTTA
* *
1972 GAAATCATGTCCGGAGGTCTTA
1 AAAATCATGCCCGGAGGTCTTA
*
1994 CAAAAT--TACCCGGAGGTCTTA
1 -AAAATCATGCCCGGAGGTCTTA
* *
2015 AAAATCATGCCCGAAAGTCTTA
1 AAAATCATGCCCGGAGGTCTTA
2037 CAGAATTGAT
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
20 5 0.09
21 13 0.25
22 31 0.58
23 4 0.08
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (22 bp):
AAAATCATGCCCGGAGGTCTTA
Found at i:2037 original size:282 final size:282
Alignment explanation
Indices: 1509--2128 Score: 893
Period size: 282 Copynumber: 2.2 Consensus size: 282
1499 AAAAGATAAG
* * *
1509 GAATCGATCGGGATAACA-TCGTGAATCGAAATTATGCCCAAAGGTCTTAGAAATCATGCCCGGA
1 GAATCGATCGGGATAACACT-GCGAATCAAAATTATGCCCAGAGGTCTTAGAAATCATGCCCGGA
** * * * * *
1573 GGTCTTACAGAATCATGTTCGGAGGTCTTACAAAATTGACTGGGATAACATCGCAAGTCAGAAAT
65 GGTCTTACAGAAT-ATGCCCGAAGGTCTTACAAAATTGAATGGGATAACACCACAAGTCAGAAAC
* * * *
1638 AAAGAATCGATCAAGACAACATCGCGAATCGAAATTATGCCCGGATGCCTTAGAAATCATGCCCG
129 AAAGAATCGATCAAGACAACACCACGAATCAAAATTATGCCCGGAGGCCTTAGAAATCATGCCCG
* * * * * *
1703 GAGGTCTTATAGAATTGCCCGAAGGTCTTAAAAATCATGTCCGGAGGTCTTACAGAATTGAATGG
194 GAGGTCTTACAAAATTACCCGAAGGTCTTAAAAATCATGCCCGAAAGTCTTACAGAATTG-ATGG
*
1768 GATAACACCATAAGTTAGAAACAAA
258 GATAACACCACAAGTTAGAAACAAA
* * **
1793 GAATCGATCGGGATAACACTGCGAATCAAAATTATACCCGGAGGTCTTAGAAATCATGTTCGGAG
1 GAATCGATCGGGATAACACTGCGAATCAAAATTATGCCCAGAGGTCTTAGAAATCATGCCCGGAG
* *
1858 GTCTTACAGAAT-TGCCCGAAGGTCTTACAGAATTGAATGGGATAACACCACAAGTTAGAAACAA
66 GTCTTACAGAATATGCCCGAAGGTCTTACAAAATTGAATGGGATAACACCACAAGTCAGAAACAA
* * * * *
1922 AGAATCGATCGAGATAATACCACGAATCAAAATTATGCCCGGAGGTCTTAGAAATCATGTCCGGA
131 AGAATCGATCAAGACAACACCACGAATCAAAATTATGCCCGGAGGCCTTAGAAATCATGCCCGGA
*
1987 GGTCTTACAAAATTACCCGGAGGTCTTAAAAATCATGCCCGAAAGTCTTACAGAATTGATGGGAT
196 GGTCTTACAAAATTACCCGAAGGTCTTAAAAATCATGCCCGAAAGTCTTACAGAATTGATGGGAT
2052 AACACCACAAGTTAGAAACAAA
261 AACACCACAAGTTAGAAACAAA
*
2074 GAATCGATCGGGATAACACCGCGAATCAAAATTATGCCCAGAGGTCTTAGAAATC
1 GAATCGATCGGGATAACACTGCGAATCAAAATTATGCCCAGAGGTCTTAGAAATC
2129 TCAAAATCTT
Statistics
Matches: 299, Mismatches: 36, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
281 80 0.27
282 150 0.50
284 68 0.23
285 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (282 bp):
GAATCGATCGGGATAACACTGCGAATCAAAATTATGCCCAGAGGTCTTAGAAATCATGCCCGGAG
GTCTTACAGAATATGCCCGAAGGTCTTACAAAATTGAATGGGATAACACCACAAGTCAGAAACAA
AGAATCGATCAAGACAACACCACGAATCAAAATTATGCCCGGAGGCCTTAGAAATCATGCCCGGA
GGTCTTACAAAATTACCCGAAGGTCTTAAAAATCATGCCCGAAAGTCTTACAGAATTGATGGGAT
AACACCACAAGTTAGAAACAAA
Found at i:2073 original size:151 final size:151
Alignment explanation
Indices: 1853--2128 Score: 466
Period size: 151 Copynumber: 1.8 Consensus size: 151
1843 AAATCATGTT
* *
1853 CGGAGGTCTTACAGAATTGCCCGAAGGTCTTACAGAATTGAATGGGATAACACCACAAGTTAGAA
1 CGGAGGTCTTACAAAATTGCCCGAAAGTCTTACAGAATTGAATGGGATAACACCACAAGTTAGAA
* *
1918 ACAAAGAATCGATCGAGATAATACCACGAATCAAAATTATGCCCGGAGGTCTTAGAAATCATGTC
66 ACAAAGAATCGATCGAGATAACACCACGAATCAAAATTATGCCCAGAGGTCTTAGAAATCATGTC
1983 CGGAGGTCTTACAAAATTACC
131 CGGAGGTCTTACAAAATTACC
2004 CGGAGGTCTTA-AAAATCATGCCCGAAAGTCTTACAGAATTG-ATGGGATAACACCACAAGTTAG
1 CGGAGGTCTTACAAAAT--TGCCCGAAAGTCTTACAGAATTGAATGGGATAACACCACAAGTTAG
* *
2067 AAACAAAGAATCGATCGGGATAACACCGCGAATCAAAATTATGCCCAGAGGTCTTAGAAATC
64 AAACAAAGAATCGATCGAGATAACACCACGAATCAAAATTATGCCCAGAGGTCTTAGAAATC
2129 TCAAAATCTT
Statistics
Matches: 117, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
150 4 0.03
151 91 0.78
152 22 0.19
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (151 bp):
CGGAGGTCTTACAAAATTGCCCGAAAGTCTTACAGAATTGAATGGGATAACACCACAAGTTAGAA
ACAAAGAATCGATCGAGATAACACCACGAATCAAAATTATGCCCAGAGGTCTTAGAAATCATGTC
CGGAGGTCTTACAAAATTACC
Found at i:2282 original size:21 final size:21
Alignment explanation
Indices: 2229--2289 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
2219 AATCAAATTT
* *
2229 ATGCTCGGAGGTCTTAGAAATT
1 ATGCTCGGAGGTCTTA-CAATC
*
2251 ATGTTCGGAGGTCTTACAATC
1 ATGCTCGGAGGTCTTACAATC
*
2272 ATGCCCGGAGGTCTTACA
1 ATGCTCGGAGGTCTTACA
2290 GAATTGAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 19 0.56
22 15 0.44
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.30
Consensus pattern (21 bp):
ATGCTCGGAGGTCTTACAATC
Found at i:2286 original size:403 final size:404
Alignment explanation
Indices: 1790--2532 Score: 1285
Period size: 403 Copynumber: 1.8 Consensus size: 404
1780 AGTTAGAAAC
*
1790 AAAGAATCGATCGGGATAACACTGCGAATCAAAATTATACCCGGAGGTCTTAGAAATCATGTTCG
1 AAAGAATCGATCGGGATAACACCGCGAATCAAAATTATACCCGGAGGTCTTAGAAATCATGTTCG
1855 GAGGTCTTACAGAATTGCCCGAAGGTCTTACAGAATTGAATGGGATAACACCACAAGTTAGAAAC
66 GAGGTCTTACAGAATTGCCCGAAGGTCTTACAGAATTGAATGGGATAACACCACAAGTTAGAAAC
* * *
1920 AAAGAATCGATCGAGATAATACCACGAATCAAAATTATGCCCGGAGGTCTTAGAAATCATGTCCG
131 AAAAAATCGATCGAGATAACACCACGAATCAAAATTATGCCCGGAGGTCTTAGAAATCATGCCCG
1985 GAGGTCTTACAAAATTACCCGGAGGTCTTAAAAATCATGCCCGAAAGTCTTACAGAATTG-ATGG
196 GAGGTCTTACAAAATTACCCGGAGGTCTTAAAAATCATGCCCGAAAGTCTTACAGAATTGAATGG
* *
2049 GATAACACCACAAGTTAGAAACAAAGAATCGATCGGGATAACACCGCGAATCAAAATTATGCCCA
261 GATAACACCACAAGTTAGAAACAAAGAATCAATCGGGATAACACCGCGAATCAAAATTATACCCA
2114 GAGGTCTTAGAAATCTCAAAATCTTTGAATGCTAATCATAATCAGAGGCAATAAAACTTTAAAAT
326 GAGGTCTTAGAAATCTCAAAATCTTTGAATGCTAATCATAATCAGAGGCAATAAAACTTTAAAAT
2179 TCAAGTTAAAAGAT
391 TCAAGTTAAAAGAT
* * * *
2193 AAAGAATCGATCGGGATAACACCGCGAATCAAATTTATGCTCGGAGGTCTTAGAAATTATGTTCG
1 AAAGAATCGATCGGGATAACACCGCGAATCAAAATTATACCCGGAGGTCTTAGAAATCATGTTCG
*
2258 GAGGTCTTAC--AATCATGCCCGGAGGTCTTACAGAATTGAATGGGATAACACCACAAGTTAGAA
66 GAGGTCTTACAGAAT--TGCCCGAAGGTCTTACAGAATTGAATGGGATAACACCACAAGTTAGAA
* * *
2321 ACAAAAAATCGATCTAGATAACACCGCGAATCGAAATTATGCCCGGAGGTCTTAGAAATCATGCC
129 ACAAAAAATCGATCGAGATAACACCACGAATCAAAATTATGCCCGGAGGTCTTAGAAATCATGCC
* * * *
2386 CGGAGGTCTTACAGAATTACCTGGAGGTCTTAAAAATCATGTCCGAAGGTCTTACAGAATTGAAT
194 CGGAGGTCTTACAAAATTACCCGGAGGTCTTAAAAATCATGCCCGAAAGTCTTACAGAATTGAAT
2451 GGGATAACACCACAAGTTAGAAACAAAGAATCAATCGGGATAACACCGCGAATCAAAATTATACC
259 GGGATAACACCACAAGTTAGAAACAAAGAATCAATCGGGATAACACCGCGAATCAAAATTATACC
2516 CAGAGGTCTTAGAAATC
324 CAGAGGTCTTAGAAATC
2533 ATGCCCGAAG
Statistics
Matches: 319, Mismatches: 18, Indels: 5
0.93 0.05 0.01
Matches are distributed among these distances:
401 3 0.01
403 234 0.73
404 82 0.26
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (404 bp):
AAAGAATCGATCGGGATAACACCGCGAATCAAAATTATACCCGGAGGTCTTAGAAATCATGTTCG
GAGGTCTTACAGAATTGCCCGAAGGTCTTACAGAATTGAATGGGATAACACCACAAGTTAGAAAC
AAAAAATCGATCGAGATAACACCACGAATCAAAATTATGCCCGGAGGTCTTAGAAATCATGCCCG
GAGGTCTTACAAAATTACCCGGAGGTCTTAAAAATCATGCCCGAAAGTCTTACAGAATTGAATGG
GATAACACCACAAGTTAGAAACAAAGAATCAATCGGGATAACACCGCGAATCAAAATTATACCCA
GAGGTCTTAGAAATCTCAAAATCTTTGAATGCTAATCATAATCAGAGGCAATAAAACTTTAAAAT
TCAAGTTAAAAGAT
Found at i:2384 original size:22 final size:22
Alignment explanation
Indices: 2353--2439 Score: 88
Period size: 22 Copynumber: 4.0 Consensus size: 22
2343 ACCGCGAATC
*
2353 GAAATTATGCCCGGAGGTCTTA
1 GAAATCATGCCCGGAGGTCTTA
2375 GAAATCATGCCCGGAGGTCTTA
1 GAAATCATGCCCGGAGGTCTTA
* * *
2397 CAGAAT--TACCTGGAGGTCTTA
1 GA-AATCATGCCCGGAGGTCTTA
* * *
2418 AAAATCATGTCCGAAGGTCTTA
1 GAAATCATGCCCGGAGGTCTTA
2440 CAGAATTGAA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
20 3 0.06
21 14 0.26
22 33 0.62
23 3 0.06
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (22 bp):
GAAATCATGCCCGGAGGTCTTA
Found at i:2423 original size:43 final size:43
Alignment explanation
Indices: 2365--2446 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
2355 AATTATGCCC
* *
2365 GGAGGTCTTAGAAATCATGCCCGGAGGTCTTACAGAATTACCT
1 GGAGGTCTTAAAAATCATGCCCGAAGGTCTTACAGAATTACCT
*
2408 GGAGGTCTTAAAAATCATGTCCGAAGGTCTTACAGAATT
1 GGAGGTCTTAAAAATCATGCCCGAAGGTCTTACAGAATT
2447 GAATGGGATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (43 bp):
GGAGGTCTTAAAAATCATGCCCGAAGGTCTTACAGAATTACCT
Found at i:2449 original size:152 final size:151
Alignment explanation
Indices: 2257--2555 Score: 490
Period size: 152 Copynumber: 2.0 Consensus size: 151
2247 AATTATGTTC
* *
2257 GGAGGTCTTACAATCATGCCCGGAGGTCTTACAGAATTGAATGGGATAACACCACAAGTTAGAAA
1 GGAGGTCTTAAAATCATGCCCGAAGGTCTTACAGAATTGAATGGGATAACACCACAAGTTAGAAA
* * * * *
2322 CAAAAAATCGATCTAGATAACACCGCGAATCGAAATTATGCCCGGAGGTCTTAGAAATCATGCCC
66 CAAAAAATCAATCGAGATAACACCGCGAATCAAAATTATACCCAGAGGTCTTAGAAATCATGCCC
*
2387 GGAGGTCTTACAGAATTACCT
131 GAAGGTCTTACAGAATTACCT
*
2408 GGAGGTCTTAAAAATCATGTCCGAAGGTCTTACAGAATTGAATGGGATAACACCACAAGTTAGAA
1 GGAGGTCTT-AAAATCATGCCCGAAGGTCTTACAGAATTGAATGGGATAACACCACAAGTTAGAA
* *
2473 ACAAAGAATCAATCGGGATAACACCGCGAATCAAAATTATACCCAGAGGTCTTAGAAATCATGCC
65 ACAAAAAATCAATCGAGATAACACCGCGAATCAAAATTATACCCAGAGGTCTTAGAAATCATGCC
2538 CGAAGGTCTTACAGAATT
130 CGAAGGTCTTACAGAATT
2556 GAATGAGATA
Statistics
Matches: 136, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
151 9 0.07
152 127 0.93
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (151 bp):
GGAGGTCTTAAAATCATGCCCGAAGGTCTTACAGAATTGAATGGGATAACACCACAAGTTAGAAA
CAAAAAATCAATCGAGATAACACCGCGAATCAAAATTATACCCAGAGGTCTTAGAAATCATGCCC
GAAGGTCTTACAGAATTACCT
Found at i:2600 original size:109 final size:108
Alignment explanation
Indices: 2409--2641 Score: 376
Period size: 109 Copynumber: 2.1 Consensus size: 108
2399 GAATTACCTG
* * *
2409 GAGGTCTTAAAAATCATGTCCGAAGGTCTTACAGAATTGAATGGGATAACACCACAAGTTAGAAA
1 GAGGTCTTAGAAATCATGCCCGAAGGTCTTACAGAATTGAATGAGATAACACCACAAGTTAGAAA
*
2474 CAAAGAATCAATCGGGATAACACCGCGAATCAAAATTATACCC
66 CAAAAAATCAATCGGGATAACACCGCGAATCAAAATTATACCC
2517 AGAGGTCTTAGAAATCATGCCCGAAGGTCTTACAGAATTGAATGAGATAACACCACAAGTTAGAA
1 -GAGGTCTTAGAAATCATGCCCGAAGGTCTTACAGAATTGAATGAGATAACACCACAAGTTAGAA
* * * *
2582 ACAAAAAATCTATCGGGATAACATCGCGAATCGAAATTATGCCC
65 ACAAAAAATCAATCGGGATAACACCGCGAATCAAAATTATACCC
2626 GAAGGTCTTAGAAATC
1 G-AGGTCTTAGAAATC
2642 TCAAAATCTT
Statistics
Matches: 115, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
108 1 0.01
109 114 0.99
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (108 bp):
GAGGTCTTAGAAATCATGCCCGAAGGTCTTACAGAATTGAATGAGATAACACCACAAGTTAGAAA
CAAAAAATCAATCGGGATAACACCGCGAATCAAAATTATACCC
Found at i:2950 original size:41 final size:41
Alignment explanation
Indices: 2889--3001 Score: 142
Period size: 41 Copynumber: 2.8 Consensus size: 41
2879 TTTTTTTTTA
2889 AGAA-GGTT-CTCTCTAAACAGAGGCTTTAAAATCTTGATTG
1 AGAATGGTTCCTCT-TAAACAGAGGCTTTAAAATCTTGATTG
*
2929 A-AATTGGTTCCTCTTAAACAGAGGCTTTGAAATCTTGATTG
1 AGAA-TGGTTCCTCTTAAACAGAGGCTTTAAAATCTTGATTG
** * *
2970 AGAATAATTCTTCTTAAACAGAGACTTTAAAA
1 AGAATGGTTCCTCTTAAACAGAGGCTTTAAAA
3002 CTTTAAAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
39 2 0.03
40 1 0.02
41 54 0.86
42 6 0.10
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (41 bp):
AGAATGGTTCCTCTTAAACAGAGGCTTTAAAATCTTGATTG
Found at i:4726 original size:17 final size:15
Alignment explanation
Indices: 4682--4732 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
4672 AATATGTCCC
* *
4682 TTTTTTT-TTTCTTC
1 TTTTTTTGTTTTTTT
4696 TTTTTTTGTTTTTTGT
1 TTTTTTTGTTTTTT-T
4712 TTTTTTTGTCTTTTTT
1 TTTTTTTGT-TTTTTT
4728 TTTTT
1 TTTTT
4733 GCCTCATCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 7 0.22
15 5 0.16
16 15 0.47
17 5 0.16
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (15 bp):
TTTTTTTGTTTTTTT
Found at i:11291 original size:16 final size:15
Alignment explanation
Indices: 11270--11305 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
11260 TTAGGGTTTT
11270 GATTTTAGAGTTTGG
1 GATTTTAGAGTTTGG
*
11285 AGATTTTAGGGTTTGG
1 -GATTTTAGAGTTTGG
11301 GATTT
1 GATTT
11306 GTGGTTTGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.47
Consensus pattern (15 bp):
GATTTTAGAGTTTGG
Found at i:11425 original size:32 final size:33
Alignment explanation
Indices: 11317--11459 Score: 153
Period size: 31 Copynumber: 4.6 Consensus size: 33
11307 TGGTTTGGGG
11317 TTTTG-ATTTTA-GGGTTTGGATTTTAA-A-GA
1 TTTTGAATTTTAGGGGTTTGGATTTTAAGAGGA
*
11346 TTTTGAATTTT-GAGGGTTTGGATTTT--GTGGA
1 TTTTGAATTTTAG-GGGTTTGGATTTTAAGAGGA
*
11377 TTTCGAATTTTAGGGGTTTGGA-TTTAAG-GGA
1 TTTTGAATTTTAGGGGTTTGGATTTTAAGAGGA
* *
11408 TTTTAGATTTTTAGGGGTTTGGATTTTATGAGG-
1 TTTT-GAATTTTAGGGGTTTGGATTTTAAGAGGA
*
11441 TTTTGGATTTTAGGGGTTT
1 TTTTGAATTTTAGGGGTTT
11460 TAGAAACCTA
Statistics
Matches: 96, Mismatches: 7, Indels: 19
0.79 0.06 0.16
Matches are distributed among these distances:
29 5 0.05
30 8 0.08
31 40 0.42
32 32 0.33
33 9 0.09
34 2 0.02
ACGTcount: A:0.19, C:0.01, G:0.30, T:0.50
Consensus pattern (33 bp):
TTTTGAATTTTAGGGGTTTGGATTTTAAGAGGA
Found at i:11432 original size:16 final size:15
Alignment explanation
Indices: 11313--11459 Score: 102
Period size: 15 Copynumber: 9.5 Consensus size: 15
11303 TTTGTGGTTT
*
11313 GGGGTTTTGATTTTA
1 GGGGTTTGGATTTTA
11328 -GGGTTTGGATTTTAA
1 GGGGTTTGGATTTT-A
* ** *
11343 AGATTTTGAATTTT-
1 GGGGTTTGGATTTTA
11357 GAGGGTTTGGATTTT-
1 G-GGGTTTGGATTTTA
* *
11372 GTGGATTTCGAATTTTA
1 G-GGGTTT-GGATTTTA
*
11389 GGGGTTTGGATTTAA
1 GGGGTTTGGATTTTA
* *
11404 GGGATTTTAGATTTTTA
1 GGG-GTTTGGA-TTTTA
11421 GGGGTTTGGATTTTA
1 GGGGTTTGGATTTTA
*
11436 TGAGGTTTTGGATTTTA
1 -G-GGGTTTGGATTTTA
11453 GGGGTTT
1 GGGGTTT
11460 TAGAAACCTA
Statistics
Matches: 102, Mismatches: 21, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
14 12 0.12
15 36 0.35
16 33 0.32
17 21 0.21
ACGTcount: A:0.18, C:0.01, G:0.32, T:0.49
Consensus pattern (15 bp):
GGGGTTTGGATTTTA
Found at i:11460 original size:16 final size:16
Alignment explanation
Indices: 11313--11460 Score: 105
Period size: 16 Copynumber: 9.5 Consensus size: 16
11303 TTTGTGGTTT
11313 GGGGTTTT-GATTTTA
1 GGGGTTTTGGATTTTA
11328 -GGG-TTTGGATTTTA
1 GGGGTTTTGGATTTTA
** * *
11342 AAGATTTTGAATTTT-
1 GGGGTTTTGGATTTTA
11357 GAGGG-TTTGGATTTT-
1 G-GGGTTTTGGATTTTA
* * *
11372 GTGGATTTCGAATTTTA
1 G-GGGTTTTGGATTTTA
*
11389 GGGG-TTTGGATTTAA
1 GGGGTTTTGGATTTTA
* *
11404 GGGATTTTAGATTTTTA
1 GGGGTTTTGGA-TTTTA
11421 GGGG-TTTGGATTTTA
1 GGGGTTTTGGATTTTA
*
11436 TGAGGTTTTGGATTTTA
1 -GGGGTTTTGGATTTTA
11453 GGGGTTTT
1 GGGGTTTT
11461 AGAAACCTAG
Statistics
Matches: 101, Mismatches: 22, Indels: 19
0.71 0.15 0.13
Matches are distributed among these distances:
13 3 0.03
14 10 0.10
15 29 0.29
16 40 0.40
17 19 0.19
ACGTcount: A:0.18, C:0.01, G:0.32, T:0.49
Consensus pattern (16 bp):
GGGGTTTTGGATTTTA
Found at i:12833 original size:14 final size:14
Alignment explanation
Indices: 12814--12854 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
12804 GCTGTTCTTC
12814 TTTTTTTGTA-TTA
1 TTTTTTTGTATTTA
12827 TTTTTTTTGTATTTA
1 -TTTTTTTGTATTTA
12842 TTTTTTTGTATTT
1 TTTTTTTGTATTT
12855 CGTATAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 23 0.88
15 3 0.12
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.80
Consensus pattern (14 bp):
TTTTTTTGTATTTA
Found at i:18589 original size:9 final size:9
Alignment explanation
Indices: 18575--18603 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
18565 ATAATTATTT
18575 AATTTTAAA
1 AATTTTAAA
18584 AATTTT-AA
1 AATTTTAAA
18592 AATTTTAAA
1 AATTTTAAA
18601 AAT
1 AAT
18604 GTAGTTTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
AATTTTAAA
Found at i:20865 original size:9 final size:9
Alignment explanation
Indices: 20847--20881 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
20837 TTTTTTTCCG
20847 TTTG-TTTT
1 TTTGTTTTT
20855 TTTGTTTTT
1 TTTGTTTTT
20864 TTTGTTTTT
1 TTTGTTTTT
20873 TTTGTTTTT
1 TTTGTTTTT
20882 GTTCTTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.15
9 22 0.85
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (9 bp):
TTTGTTTTT
Found at i:22637 original size:19 final size:20
Alignment explanation
Indices: 22601--22639 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
22591 GATAAAGTGC
*
22601 TAATATAATTAATTATTTAT
1 TAATATAATTAATAATTTAT
*
22621 TAATA-AATTTATAATTTAT
1 TAATATAATTAATAATTTAT
22640 ATATCACATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAATATAATTAATAATTTAT
Found at i:22659 original size:28 final size:29
Alignment explanation
Indices: 22628--22686 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
22618 TATTAATAAA
* * *
22628 TTTATAATTTATATATCACATTAAA-ATT
1 TTTAAAATTTAAATATCAAATTAAATATT
22656 TTTAAAATTTAAATATCAAATTAAATATT
1 TTTAAAATTTAAATATCAAATTAAATATT
22685 TT
1 TT
22687 ATTTTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (29 bp):
TTTAAAATTTAAATATCAAATTAAATATT
Found at i:26824 original size:526 final size:526
Alignment explanation
Indices: 25829--27214 Score: 1753
Period size: 530 Copynumber: 2.6 Consensus size: 526
25819 TTTTTTTTTG
25829 CACATGGATTGCTTAACTTGATGTCACGTGAC-ATTAATTAATGCAAATTAATTATTAATTTTAA
1 CACATGGATTGCTTAACTTGATGTCACGTG-CTATTAATTAATGCAAATTAATTATTAATTTTAA
* * * *
25893 AATACTTAATAAGTAAC-AAATTAATTAAGTTAATTTATAAAATTAGCTAGCAAAATTTTTTGAA
65 AATACTTAATAAATAACAAAATAAATTAAATTAATTTATAAAATTGGCTAGCAAAA-TTTTTGAA
* * *
25957 TCATACTATTATTATTTCAATAAGAATGAGATTTTATTTAAATTTGTATTATTTTCATGATCTAA
129 TCATATTATTACTATTTCAATAAGAATGAGATTTTATTTAAATTTGTATTATTTTTATGATCTAA
* * * * * *
26022 TTTCAAGTTTGAATATCCTTTATTTTTTGCAATATTACTAAAAAAT-TATGATAATTTAATTACA
194 TTCCAAGTTTGAATATCCTTTA-TTTTGGCAAAATTAATGAAAAATATATAATAATTTAATTACA
* *
26086 AATTTCAAATTTCAAAACCTAAATGAGTAAAT-A-ATATCTATTACCGCTCAAAAATTAATGCAA
258 AATTTCAAA-TTCAAAACCTAAA-GAGTAAATAATATATATATTATCGCTCAAAAATTAATGCAA
*** * * ** *
26149 ATTAGAGGTGTTCATGGGTCAGACTGGGTCAAATTTGAACTAAGCTCATGATTGGTATTAATCAT
321 ATTAGAGGTGTTCATGGGTCAGACCAAGCCAAATTAGAACTAAGCTCATGATTAATATTAATCAC
* *
26214 TTATATGCTTATCTAAACCTGACTCAGTCCAAAATTTTAAGTCTAAAAATTTTTTTAAGTCCAAT
386 TTATATACTTATCTAAACCTGACTCAGTCCAAAATTTTAAGTCTAAAAATTTTTCTAAGTCCAAT
* * *
26279 CCAAATCTTATATAAATATAT-AAAATTAAAACCTTACGT-AAAA-AAAAAAT-AATGTGGATGG
451 CCAAATCTTATATAAATATATAAAAATCAAAACCTTACATAAAAAGAAAAAATCAATATGGATGG
26340 TTAATTT-TTTAA
516 TT--TTTCTTTAA
* * *
26352 CACATGGATTGCTTAACTTGATGTCACGTGTCTATTAATTAATGCGAGTTAATTATTAGTTTTAA
1 CACATGGATTGCTTAACTTGATGTCACGTG-CTATTAATTAATGCAAATTAATTATTAATTTTAA
*
26417 AATACTTAATAAATAACAAAATCAATTAAATTAATTTATAAAATTGGCTAGCAAAATTTTTGAAA
65 AATACTTAATAAATAACAAAATAAATTAAATTAATTTATAAAATTGGCTAGCAAAATTTTTG-AA
* * *
26482 TCATATTATTACTATTTCACTAAGAATGAGATTTTATTTAACTTTGTATTATTTTTATGATATAA
129 TCATATTATTACTATTTCAATAAGAATGAGATTTTATTTAAATTTGTATTATTTTTATGATCTAA
* * *
26547 TTCCAAGCTTGAATATCTTTTATATTTGGCAAAATTAATGAAAAATATATAATAATTTAGTTACA
194 TTCCAAGTTTGAATATCCTTTAT-TTTGGCAAAATTAATGAAAAATATATAATAATTTAATTACA
* *
26612 AATTTCAAATTCAAAACCTTAAAGAGTAAATAATATATATATTATTG-TCCAAAATTAATGCAAA
258 AATTTCAAATTCAAAACC-TAAAGAGTAAATAATATATATATTATCGCTCAAAAATTAATGCAAA
* *** * *
26676 TTAGAGGTGTTTATGGGTCA-AGCCAAGCCGCGTTCAGATC-AAGTTCAT-ATTTAATATTAAT-
322 TTAGAGGTGTTCATGGGTCAGA-CCAAGCCAAATT-AGAACTAAGCTCATGA-TTAATATTAATC
* * ** * * * * *
26737 AGCTTATATACTTGTTTAAACCTGGTTTAGTCTAAAATTTTGAGTTTCAAAATTTTTCTAAG-CT
384 A-CTTATATACTTATCTAAACCTGACTCAGTCCAAAATTTTAAGTCTAAAAATTTTTCTAAGTC-
*** *
26801 TGGTCCAAATCTTATATAAATATATAAAAATCAAAACCTTACATAAAAAAGGGAAAAAATCACTA
447 CAATCCAAATCTTATATAAATATATAAAAATCAAAACCTTACAT-AAAAA--GAAAAAATCAATA
**
26866 TGGATGGTTTTTCTTTTT
509 TGGATGGTTTTTCTTTAA
* * ** *
26884 TACATGAATTGCTTAACTTGATGTTGCATG-TATTAATTAATGCAAATTAATTATTAATTTTAAA
1 CACATGGATTGCTTAACTTGATGTCACGTGCTATTAATTAATGCAAATTAATTATTAATTTTAAA
* *
26948 TTACTTAATAAATAATAAAATAAATTAAATTAATTTATAAAATTGGCTAGCAAAATTTTTGGAAT
66 ATACTTAATAAATAACAAAATAAATTAAATTAATTTATAAAATTGGCTAGCAAAATTTTT-GAAT
*
27013 CATATTATTACTATTTCATTAAGAATGAGATTTTATTTAAATTTGTATTATTTTTATGATCTAAT
130 CATATTATTACTATTTCAATAAGAATGAGATTTTATTTAAATTTGTATTATTTTTATGATCTAAT
** *
27078 TCCAAGTTTGAATATCCTTTATTTTGGCAACTTTAATGAAAAATATACAATAATTTAATTACAAA
195 TCCAAGTTTGAATATCCTTTATTTTGGCAAAATTAATGAAAAATATATAATAATTTAATTACAAA
** * * *
27143 TTTCAAAATTTGAAACCTAAAGAAGTAAATATTATATATATTATCGCTTAAAAATTAATACAAAT
260 TTTC-AAATTCAAAACCTAAAG-AGTAAATAATATATATATTATCGCTCAAAAATTAATGCAAAT
*
27208 TAAAGGT
323 TAGAGGT
27215 ATCCATGGAT
Statistics
Matches: 749, Mismatches: 89, Indels: 42
0.85 0.10 0.05
Matches are distributed among these distances:
523 31 0.04
524 52 0.07
525 154 0.21
526 156 0.21
527 29 0.04
529 52 0.07
530 204 0.27
531 25 0.03
532 35 0.05
533 11 0.01
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.39
Consensus pattern (526 bp):
CACATGGATTGCTTAACTTGATGTCACGTGCTATTAATTAATGCAAATTAATTATTAATTTTAAA
ATACTTAATAAATAACAAAATAAATTAAATTAATTTATAAAATTGGCTAGCAAAATTTTTGAATC
ATATTATTACTATTTCAATAAGAATGAGATTTTATTTAAATTTGTATTATTTTTATGATCTAATT
CCAAGTTTGAATATCCTTTATTTTGGCAAAATTAATGAAAAATATATAATAATTTAATTACAAAT
TTCAAATTCAAAACCTAAAGAGTAAATAATATATATATTATCGCTCAAAAATTAATGCAAATTAG
AGGTGTTCATGGGTCAGACCAAGCCAAATTAGAACTAAGCTCATGATTAATATTAATCACTTATA
TACTTATCTAAACCTGACTCAGTCCAAAATTTTAAGTCTAAAAATTTTTCTAAGTCCAATCCAAA
TCTTATATAAATATATAAAAATCAAAACCTTACATAAAAAGAAAAAATCAATATGGATGGTTTTT
CTTTAA
Found at i:29017 original size:49 final size:50
Alignment explanation
Indices: 28959--29053 Score: 138
Period size: 49 Copynumber: 1.9 Consensus size: 50
28949 TTCTTTTTGT
*
28959 CATTAATTTGTCACTTATAAATTGA-TTGGTCCAATAATTAAAATTTTAG
1 CATTAATTTGTCACTTATAAATTGATTTAGTCCAATAATTAAAATTTTAG
* * * *
29008 CATTTATTTGTCATTTATAAATTGATTTAGTCTAATAGTTAAAATT
1 CATTAATTTGTCACTTATAAATTGATTTAGTCCAATAATTAAAATT
29054 GTTTGCTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
49 23 0.57
50 17 0.43
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.46
Consensus pattern (50 bp):
CATTAATTTGTCACTTATAAATTGATTTAGTCCAATAATTAAAATTTTAG
Found at i:30258 original size:20 final size:21
Alignment explanation
Indices: 30229--30268 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
30219 TATTTTGGTA
*
30229 TTATTATT-AAGTTTATTTTT
1 TTATTATTAAAGTTCATTTTT
*
30249 TTATTTTTAAAGTTCATTTT
1 TTATTATTAAAGTTCATTTT
30269 AAAAATTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.68
Consensus pattern (21 bp):
TTATTATTAAAGTTCATTTTT
Found at i:30981 original size:20 final size:21
Alignment explanation
Indices: 30943--30992 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
30933 GTAAAACTAT
**
30943 TTTTTTTTTTGTATTCTGAC-
1 TTTTTTTTTTGTAAACTGACA
30963 TCTTTTTTTTT-TAAACTGACA
1 T-TTTTTTTTTGTAAACTGACA
30984 TTTTTTTTT
1 TTTTTTTTT
30993 CTTTGTGCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.14, C:0.10, G:0.06, T:0.70
Consensus pattern (21 bp):
TTTTTTTTTTGTAAACTGACA
Found at i:31304 original size:14 final size:12
Alignment explanation
Indices: 31283--31316 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 12
31273 GAGGACTGTG
31283 TTTTTTTTTTACA
1 TTTTTTTTTT-CA
31296 TTATTTTTTTTCA
1 TT-TTTTTTTTCA
31309 TTTTTTTT
1 TTTTTTTT
31317 GCAACGTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 6 0.30
14 8 0.40
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTTCA
Found at i:31343 original size:237 final size:238
Alignment explanation
Indices: 30898--31375 Score: 721
Period size: 237 Copynumber: 2.0 Consensus size: 238
30888 CACCAAAAAG
* *
30898 GTCCTCATTTCCTTAGATCTACTTTCAAAGTTTCGGTAAAACTATTTTTTTTTTTGTATTCTGAC
1 GTCCTCATTTCCTTAGATCTACTTTCAAAGTTTCAGTAAAACTA--TTTTTTTTTATATTCTGAC
* * * *
30963 TCTTTTTTTTTTAAACTGACATTTTTTTTTCTTTGTGCAGAAAGCCCTCGGTGTTGGGTTCCTCT
64 TCTTTTTTTTTGAAACTGACATTTTTTTTTCTTTATGCAGAAAGCCCTCAGTGTTGGGTTCCTAT
* **
31028 CTACGGGGAAGACTGTGTTTTCTTTTTTATAGTATTTTTTTTCATTTTTTTTGCAGTGTCTCTCC
129 CTACGGGGAAGACTGTGTTTTCTTTTTTACAGTATTTTTTTTCATTTTTTTTGCAACGTCTCTCC
*
31093 TTCCTTCCTTTCTTTTTTGTTGTCCGGCTATGAGCTCTATTTATA
194 TTCCTTCCTTTCTTTTTTGTTGTCCGGCCATGAGCTCTATTTATA
* *
31138 GTCCTCATTT-CTCTAGATCTGCTTTCAAAGTTTCAGTGAAACTA-TTTTTTTTATATT-TGGAC
1 GTCCTCATTTCCT-TAGATCTACTTTCAAAGTTTCAGTAAAACTATTTTTTTTTATATTCT-GAC
* * *
31200 TCTTTTTTTTTGAAACTGACCCTTTTTTTTTCTTTATGCAGAAAGCTCTCAGTGTTGGGTTTCTA
64 TCTTTTTTTTTGAAACTGA-CATTTTTTTTTCTTTATGCAGAAAGCCCTCAGTGTTGGGTTCCTA
* *
31265 TCTACGGGGAGGACTGTGTTTT-TTTTTTACATTATTTTTTTTCATTTTTTTTGCAACGTCTCTC
128 TCTACGGGGAAGACTGTGTTTTCTTTTTTACAGTATTTTTTTTCATTTTTTTTGCAACGTCTCTC
*
31329 CTTCCTTTCTTTCTTTTTTGTTGTCCGGCCATGAGCTCTATTTATA
193 CTTCCTTCCTTTCTTTTTTGTTGTCCGGCCATGAGCTCTATTTATA
31375 G
1 G
31376 AGCTCTGGTA
Statistics
Matches: 217, Mismatches: 18, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
236 1 0.00
237 116 0.53
238 60 0.28
239 2 0.01
240 38 0.18
ACGTcount: A:0.16, C:0.18, G:0.15, T:0.51
Consensus pattern (238 bp):
GTCCTCATTTCCTTAGATCTACTTTCAAAGTTTCAGTAAAACTATTTTTTTTTATATTCTGACTC
TTTTTTTTTGAAACTGACATTTTTTTTTCTTTATGCAGAAAGCCCTCAGTGTTGGGTTCCTATCT
ACGGGGAAGACTGTGTTTTCTTTTTTACAGTATTTTTTTTCATTTTTTTTGCAACGTCTCTCCTT
CCTTCCTTTCTTTTTTGTTGTCCGGCCATGAGCTCTATTTATA
Found at i:32882 original size:19 final size:20
Alignment explanation
Indices: 32846--32884 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
32836 AATAAGGACT
32846 GCTAAAAAAAAAGGAAGGAAG
1 GCTAAAAAAAAA-GAAGGAAG
*
32867 GCTAAAAAAGAA-AAGGAA
1 GCTAAAAAAAAAGAAGGAA
32885 AAAAGAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.64, C:0.05, G:0.26, T:0.05
Consensus pattern (20 bp):
GCTAAAAAAAAAGAAGGAAG
Found at i:32888 original size:13 final size:14
Alignment explanation
Indices: 32870--32902 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
32860 AAGGAAGGCT
*
32870 AAAAAAGAA-AAGG
1 AAAAAAGAAGAAGC
32883 AAAAAAGAAGAAGC
1 AAAAAAGAAGAAGC
32897 AAAAAA
1 AAAAAA
32903 AAATAGAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAGAAGC
Found at i:33032 original size:14 final size:14
Alignment explanation
Indices: 33013--33060 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
33003 GTTTAGCCGT
33013 AGCAAAAAGAGAAA
1 AGCAAAAAGAGAAA
33027 AGCAAAAA-A-AAA
1 AGCAAAAAGAGAAA
**
33039 AAAAAAAAGAGAAGA
1 AGCAAAAAGAGAA-A
33054 AGCAAAA
1 AGCAAAA
33061 CCAGAAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
12 9 0.33
13 2 0.07
14 10 0.37
15 6 0.22
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (14 bp):
AGCAAAAAGAGAAA
Found at i:34268 original size:3 final size:3
Alignment explanation
Indices: 34260--34289 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
34250 TATGTCATAA
34260 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
34290 GATACAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:37026 original size:17 final size:16
Alignment explanation
Indices: 36998--37030 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
36988 AAAGTTATTT
36998 AAATTCAATTTGATTC
1 AAATTCAATTTGATTC
37014 AAATTCGAATTTGATTC
1 AAATTC-AATTTGATTC
37031 GATAATTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (16 bp):
AAATTCAATTTGATTC
Found at i:37171 original size:20 final size:20
Alignment explanation
Indices: 37143--37181 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
37133 AGCTTTTTTA
* *
37143 TTATATATATATTTATTATT
1 TTATATATAAAATTATTATT
*
37163 TTATTTATAAAATTATTAT
1 TTATATATAAAATTATTAT
37182 CTTACCTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATATATAAAATTATTATT
Found at i:38246 original size:62 final size:63
Alignment explanation
Indices: 38137--38269 Score: 180
Period size: 62 Copynumber: 2.1 Consensus size: 63
38127 AAAAAATGCC
* *
38137 TTGAATAATCCCCTTAAAAAAATTTGAAGGGGATTATTTAATACGTTTTTGGCTAA-AAACACT
1 TTGAATAATCCCCTTAAAAAAATTTGAAGGGGATTATTTAAGACGTTTTTGGC-AACAAACACA
* ** * *
38200 TTGAATAATCTCCTTCTAAAAA-TTGAAGGGGATTATTTAAGGCGTTTTTGGCAACAAACGCA
1 TTGAATAATCCCCTTAAAAAAATTTGAAGGGGATTATTTAAGACGTTTTTGGCAACAAACACA
38262 TTGAATAA
1 TTGAATAA
38270 CCCTATTCAA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
61 2 0.03
62 41 0.66
63 19 0.31
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.34
Consensus pattern (63 bp):
TTGAATAATCCCCTTAAAAAAATTTGAAGGGGATTATTTAAGACGTTTTTGGCAACAAACACA
Found at i:39393 original size:15 final size:15
Alignment explanation
Indices: 39373--39432 Score: 65
Period size: 15 Copynumber: 4.3 Consensus size: 15
39363 TAAAAATTAA
* *
39373 ACAAAAATATATAAT
1 ACAAAAATACAAAAT
39388 ACAAAAATACAAAAT
1 ACAAAAATACAAAAT
39403 AC--AAA-A-AAAAT
1 ACAAAAATACAAAAT
*
39414 ATAAAAATACAAAAT
1 ACAAAAATACAAAAT
39429 ACAA
1 ACAA
39433 TAAAAAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 6 0.16
12 1 0.03
13 6 0.16
14 1 0.03
15 23 0.62
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (15 bp):
ACAAAAATACAAAAT
Found at i:39401 original size:7 final size:7
Alignment explanation
Indices: 39385--39461 Score: 58
Period size: 7 Copynumber: 11.6 Consensus size: 7
39375 AAAAATATAT
39385 AATACAAA
1 AATAC-AA
39393 AATACAA
1 AATACAA
39400 AATACAA
1 AATACAA
39407 AA-A-AA
1 AATACAA
39412 ATATA-AA
1 A-ATACAA
39419 AATACAA
1 AATACAA
39426 AATAC--
1 AATACAA
*
39431 AATAAAA
1 AATACAA
39438 AATA-AA
1 AATACAA
* *
39444 AACAAAA
1 AATACAA
*
39451 AAAACAA
1 AATACAA
39458 AATA
1 AATA
39462 ATAAAAAACA
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
5 7 0.12
6 10 0.17
7 36 0.62
8 5 0.09
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.13
Consensus pattern (7 bp):
AATACAA
Found at i:39411 original size:32 final size:31
Alignment explanation
Indices: 39353--39462 Score: 90
Period size: 32 Copynumber: 3.6 Consensus size: 31
39343 AATATTATTA
*
39353 AATACAATAATA-AAAATTAAACAAAAATATAT
1 AATACAAAAATACAAAA-TAAACAAAAA-ATAT
39385 AATACAAAAATACAAAAT--AC-AAAAA-A-
1 AATACAAAAATACAAAATAAACAAAAAATAT
* *
39411 AATATAAAAATACAAAATACAATAAAAAATA-
1 AATACAAAAATACAAAATA-AACAAAAAATAT
* *
39442 AAAACAAAAAAAACAAAATAA
1 AATAC-AAAAATACAAAATAA
39463 TAAAAAACAA
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
26 17 0.26
27 1 0.02
28 1 0.02
29 5 0.08
30 7 0.11
31 5 0.08
32 25 0.38
33 4 0.06
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.16
Consensus pattern (31 bp):
AATACAAAAATACAAAATAAACAAAAAATAT
Found at i:39412 original size:33 final size:34
Alignment explanation
Indices: 39352--39432 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 34
39342 TAATATTATT
* *
39352 AAATACAATAATA-AAAATTAAACAAAAATAT-A
1 AAATACAAAAATACAAAATTAAAAAAAAATATAA
*
39384 TAATACAAAAATACAAAA-TACAAAAAAAATATAA
1 AAATACAAAAATACAAAATTA-AAAAAAAATATAA
39418 AAATAC-AAAATACAA
1 AAATACAAAAATACAA
39433 TAAAAAATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 13 0.31
33 23 0.55
34 6 0.14
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.19
Consensus pattern (34 bp):
AAATACAAAAATACAAAATTAAAAAAAAATATAA
Found at i:39414 original size:26 final size:26
Alignment explanation
Indices: 39385--39445 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 26
39375 AAAAATATAT
39385 AATACAAAAATACAAAATACAA-AAAA
1 AATA-AAAAATACAAAATACAATAAAA
39411 AATATAAAAATACAAAATACAATAAAA
1 AATA-AAAAATACAAAATACAATAAAA
39438 AATAAAAA
1 AATAAAAA
39446 CAAAAAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
26 25 0.76
27 8 0.24
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (26 bp):
AATAAAAAATACAAAATACAATAAAA
Found at i:39420 original size:19 final size:19
Alignment explanation
Indices: 39391--39454 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
39381 ATATAATACA
*
39391 AAAATACAAAATACAAAA-
1 AAAATAAAAAATACAAAAC
*
39409 AAAATATAAAAATACAAAAT
1 AAAATA-AAAAATACAAAAC
*
39429 ACAATAAAAAATA-AAAAC
1 AAAATAAAAAATACAAAAC
39447 AAAA-AAAA
1 AAAATAAAA
39455 CAAAATAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
17 4 0.10
18 13 0.32
19 18 0.45
20 5 0.12
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (19 bp):
AAAATAAAAAATACAAAAC
Found at i:52835 original size:47 final size:48
Alignment explanation
Indices: 52779--53650 Score: 890
Period size: 47 Copynumber: 17.9 Consensus size: 48
52769 AGAACATATG
* * * *
52779 AGATTTTTAAAGTTGTTGAACTTCTACTGAGATGAGCTTTTTCAAGAT
1 AGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAT
* * * *
52827 -TATTTTTAAAGTTGTTGAGCCTATGTTGAGATGAGCTTTTTCAAG-T
1 AGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAT
* * *
52873 -GAAATTTTAAAGTTGTTGAGCCTTTGCTGAAAGGAGCTTTTTCAAGAT
1 AG-ATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAT
* ** * *
52921 -GATTTTTAAAATTGTTGAGCCTCTATTAAGAAGAGCTTTTTCAAG-T
1 AGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAT
* * * * * **
52967 -GAAATTTTAAAATTATTGAGCCTTTGCTGAGAGAAGCCCTTTCAAGAT
1 AG-ATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAT
* * *
53015 GAGATTTTTAAAGTCGTTGAGCCTCTGCTGAGAGGAACTTTTCCAAGAT
1 -AGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAT
* ** **
53064 -GATTTTTAAAGTTGTTGAGCCTTTATTGAGAAAAGCTTTTTCAAG-T
1 AGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAT
* *
53110 GAGA-TTTTAAAGTTGTTGAGCCTCTACTGATAGGAGCTTTTTCAA-AT
1 -AGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAT
* *
53157 GAGA-TTTTAAAGTTGTTGAGCCTTTGCTGAGAGGAGCCTTTTTGAAGAT
1 -AGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCAAGAT
* * * *
53206 AAGAATTTTTAAAGTTATTGAGCCTCTGCTAAGAGGAACCCTTTTCAAGAT
1 -AG-ATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGG-AGCTTTTTCAAGAT
* * *
53257 GAGATTTTTAAAGTCGTTGAGCCTCTGCTGAGAAGTGCCTTTTTCAAGAT
1 -AGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCAAGAT
* * * *
53307 GAAAATTTTTAAAGTTGTTGAGCCTTTGCTGATAAGAGCTTTTTCAA-AT
1 --AGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAT
*
53356 AAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGTCCTTTTCAAGAT
1 -AGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCAAGAT
* * *
53406 GAGATTTTTAAAGTCGTTGAGCCTCTGCTAAGAAGAGCCTTTTTCAAGAT
1 -AGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCAAGAT
*
53456 GAGAATTTTTAAAGTCGTTGAGCCTCTGCTGAGAGGAGCTTTTTC-AGAT
1 -AG-ATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAT
53505 AAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGTCCTTTTT-AAGAT
1 -AGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG--CTTTTTCAAGAT
* *
53555 GAGATTTTTAAAGTTGTTGAGCTTCTGCTGAGATGAGCCTTTTTCAAGAT
1 -AGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCAAGAT
* * * * *
53605 AAAATTTTTAAAGTTATTGAGTCTTTACTGAGAGGAGTCTTTTTCA
1 -AGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCA
53651 GATTTTAAAT
Statistics
Matches: 696, Mismatches: 105, Indels: 44
0.82 0.12 0.05
Matches are distributed among these distances:
46 4 0.01
47 255 0.37
48 79 0.11
49 63 0.09
50 192 0.28
51 102 0.15
52 1 0.00
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (48 bp):
AGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAT
Found at i:53376 original size:149 final size:149
Alignment explanation
Indices: 52779--53650 Score: 1011
Period size: 149 Copynumber: 6.0 Consensus size: 149
52769 AGAACATATG
* * * * *
52779 AGATTTTTAAAGTTGTTGAACTTCTACTGAGATG-AGCTTTTTCAAGAT--TATTTTTAAAGTTG
1 AGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAAGCCTTTTCAAGATGAGATTTTTAAAGTTG
* * *
52841 TTGAGCCTATGTTGAGATGAG-CTTTTTCAAG-TGAAA-TTTTAAAGTTGTTGAGCCTTTGCTGA
66 TTGAGCCTCTGCTGAGAAGAGCCTTTTTCAAGATGAAATTTTTAAAGTTGTTGAGCCTTTGCTGA
*
52903 AAGGAGCTTTTTCAAGAT-
131 GAGGAGCTTTTTCAAGATA
* * * * * * * *
52921 -GATTTTTAAAATTGTTGAGCCTCTATTAAGAAG-AGCTTTTTCAAG-TGA-AATTTTAAAATTA
1 AGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAAGCCTTTTCAAGATGAGATTTTTAAAGTTG
* * * * *
52982 TTGAGCCTTTGCTGAG-AGAAGCC-CTTTCAAGATGAGATTTTTAAAGTCGTTGAGCCTCTGCTG
66 TTGAGCCTCTGCTGAGAAG-AGCCTTTTTCAAGATGAAATTTTTAAAGTTGTTGAGCCTTTGCTG
* *
53045 AGAGGAACTTTTCCAAGAT-
130 AGAGGAGCTTTTTCAAGATA
* * * *
53064 -GATTTTTAAAGTTGTTGAGCCTTTATTGAGA-AAAGCTTTTTCAAG-TGAGA-TTTTAAAGTTG
1 AGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAAGCCTTTTCAAGATGAGATTTTTAAAGTTG
* * * *
53125 TTGAGCCTCTACTGATAGGAG-CTTTTTCAA-ATGAGA-TTTTAAAGTTGTTGAGCCTTTGCTGA
66 TTGAGCCTCTGCTGAGAAGAGCCTTTTTCAAGATGAAATTTTTAAAGTTGTTGAGCCTTTGCTGA
*
53187 GAGGAGCCTTTTTGAAGATA
131 GAGGAG-CTTTTTCAAGATA
* * * * *
53207 AGAATTTTTAAAGTTATTGAGCCTCTGCTAAGAGGAACCCTTTTCAAGATGAGATTTTTAAAGTC
1 AG-ATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAAGCCTTTTCAAGATGAGATTTTTAAAGTT
*
53272 GTTGAGCCTCTGCTGAGAAGTGCCTTTTTCAAGATGAAAATTTTTAAAGTTGTTGAGCCTTTGCT
65 GTTGAGCCTCTGCTGAGAAGAGCCTTTTTCAAGATG-AAATTTTTAAAGTTGTTGAGCCTTTGCT
* *
53337 GATAAGAGCTTTTTCAA-ATA
129 GAGAGGAGCTTTTTCAAGATA
* *
53357 AGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGG-AGTCCTTTTCAAGATGAGATTTTTAAAGTC
1 AGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAAG-CCTTTTCAAGATGAGATTTTTAAAGTT
* * *
53421 GTTGAGCCTCTGCTAAGAAGAGCCTTTTTCAAGATGAGAATTTTTAAAGTCGTTGAGCCTCTGCT
65 GTTGAGCCTCTGCTGAGAAGAGCCTTTTTCAAGATGA-AATTTTTAAAGTTGTTGAGCCTTTGCT
53486 GAGAGGAGCTTTTTC-AGATA
129 GAGAGGAGCTTTTTCAAGATA
* *
53506 AGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGG-AGTCCTTTTTAAGATGAGATTTTTAAAGTT
1 AGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAAG-CCTTTTCAAGATGAGATTTTTAAAGTT
* * * * * *
53570 GTTGAGCTTCTGCTGAGATGAGCCTTTTTCAAGATAAAATTTTTAAAGTTATTGAGTCTTTACTG
65 GTTGAGCCTCTGCTGAGAAGAGCCTTTTTCAAGATGAAATTTTTAAAGTTGTTGAGCCTTTGCTG
53635 AGAGGAGTCTTTTTCA
130 AGAGGAG-CTTTTTCA
53651 GATTTTAAAT
Statistics
Matches: 632, Mismatches: 72, Indels: 44
0.84 0.10 0.06
Matches are distributed among these distances:
140 2 0.00
141 101 0.16
142 22 0.03
143 112 0.18
144 3 0.00
145 25 0.04
146 11 0.02
147 5 0.01
148 60 0.09
149 243 0.38
150 8 0.01
151 10 0.02
152 30 0.05
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (149 bp):
AGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAAGCCTTTTCAAGATGAGATTTTTAAAGTTG
TTGAGCCTCTGCTGAGAAGAGCCTTTTTCAAGATGAAATTTTTAAAGTTGTTGAGCCTTTGCTGA
GAGGAGCTTTTTCAAGATA
Found at i:53959 original size:15 final size:14
Alignment explanation
Indices: 53939--54025 Score: 85
Period size: 15 Copynumber: 6.4 Consensus size: 14
53929 AAAATTAAAT
*
53939 AAAAATACATAATAC
1 AAAAATA-AAAATAC
53954 AAAAATATAAAATAC
1 AAAAATA-AAAATAC
53969 ---AA-AAAAATAC
1 AAAAATAAAAATAC
53979 AAAAATACAAAATAC
1 AAAAATA-AAAATAC
* *
53994 AATAA-AAAAATAA
1 AAAAATAAAAATAC
54007 AAAAATAAAAATAC
1 AAAAATAAAAATAC
54021 AAAAA
1 AAAAA
54026 GGGGCTGGTG
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
10 7 0.12
11 1 0.02
12 2 0.03
13 12 0.20
14 14 0.23
15 24 0.40
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAAATAAAAATAC
Found at i:53965 original size:8 final size:8
Alignment explanation
Indices: 53939--54025 Score: 64
Period size: 7 Copynumber: 11.6 Consensus size: 8
53929 AAAATTAAAT
53939 AAAAATAC
1 AAAAATAC
*
53947 -ATAATAC
1 AAAAATAC
53954 AAAAATA-
1 AAAAATAC
*
53961 TAAAATAC
1 AAAAATAC
53969 AAAAAAATAC
1 --AAAAATAC
53979 AAAAATAC
1 AAAAATAC
53987 -AAAATAC
1 AAAAATAC
*
53994 ---AATAA
1 AAAAATAC
53999 AAAAATA-
1 AAAAATAC
*
54006 AAAAA-AT
1 AAAAATAC
54013 AAAAATAC
1 AAAAATAC
54021 AAAAA
1 AAAAA
54026 GGGGCTGGTG
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
5 4 0.06
6 1 0.02
7 29 0.45
8 23 0.36
10 7 0.11
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (8 bp):
AAAAATAC
Found at i:53977 original size:25 final size:24
Alignment explanation
Indices: 53949--54025 Score: 100
Period size: 25 Copynumber: 3.0 Consensus size: 24
53939 AAAAATACAT
53949 AATACAAAAATATAAAATACAAAAA
1 AATACAAAAATA-AAAATACAAAAA
53974 AATACAAAAATACAAAATACAATAAAAA
1 AATACAAAAATA-AAAATAC---AAAAA
*
54002 AATAAAAAAATAAAAATACAAAAA
1 AATACAAAAATAAAAATACAAAAA
54026 GGGGCTGGTG
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.11
25 19 0.40
27 7 0.15
28 16 0.34
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (24 bp):
AATACAAAAATAAAAATACAAAAA
Found at i:57014 original size:24 final size:21
Alignment explanation
Indices: 56976--57033 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 21
56966 GAATAAATTT
56976 AAAATTAT-TTAATTTGTAATTAAA
1 AAAATTATCTT-ATTT-TAA-T-AA
*
57000 AAAATTATCTTATTTTTATAA
1 AAAATTATCTTATTTTAATAA
57021 AAAATTATCTTAT
1 AAAATTATCTTAT
57034 GTGCCATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 15 0.47
22 1 0.03
23 2 0.06
24 12 0.38
25 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (21 bp):
AAAATTATCTTATTTTAATAA
Found at i:58332 original size:9 final size:9
Alignment explanation
Indices: 58318--58347 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
58308 ATGATTATTT
58318 AATTTTAAA
1 AATTTTAAA
58327 AATTTT-AA
1 AATTTTAAA
58335 AATTTTAAA
1 AATTTTAAA
58344 AATT
1 AATT
58348 AGTTTGTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
AATTTTAAA
Found at i:59587 original size:20 final size:19
Alignment explanation
Indices: 59541--59588 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
59531 AAATGAAATA
*
59541 ATTTTAAATTTTAAATAAT
1 ATTTTAAATTTTAAACAAT
*
59560 AGTATTAAATTTTAAACAACT
1 A-TTTTAAATTTTAAACAA-T
59581 ATTTTAAA
1 ATTTTAAA
59589 AAGTGTTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 21 0.88
21 2 0.08
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (19 bp):
ATTTTAAATTTTAAACAAT
Done.