Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005946.1 Hibiscus syriacus cultivar Beakdansim tig00013960_pilon, 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: 2465359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:1790815 original size:46 final size:45
Alignment explanation
Indices: 1790724--1790849 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 45
1790714 TATTAAAAAT
*
1790724 ATATATTTTATTTTTATCTTAATTTTAAAATATTATAATAATAAA
1 ATATATTTTATTTTTATCTTAATTTTAAAATATTACAATAATAAA
**
1790769 ATATATTTTATTTTTATCTTAAATTTTAAAATAGTT-CAATTTTAAA
1 ATATATTTTATTTTTATCTT-AATTTTAAAATA-TTACAATAATAAA
1790815 ATATATTTTATTTTTATCTTAATTTTAAAATATTA
1 ATATATTTTATTTTTATCTTAATTTTAAAATATTA
1790850 TAAGAACAAA
Statistics
Matches: 75, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
44 2 0.03
45 32 0.43
46 39 0.52
47 2 0.03
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (45 bp):
ATATATTTTATTTTTATCTTAATTTTAAAATATTACAATAATAAA
Found at i:1797232 original size:16 final size:16
Alignment explanation
Indices: 1797213--1797258 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
1797203 TTGGCTAAAA
*
1797213 TTCGGGTTGCTTTCGG
1 TTCGGGTTACTTTCGG
*
1797229 TTCGGGTTACTTTCGT
1 TTCGGGTTACTTTCGG
**
1797245 TTTAGGTTACTTTC
1 TTCGGGTTACTTTC
1797259 TGTTTAACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.07, C:0.17, G:0.26, T:0.50
Consensus pattern (16 bp):
TTCGGGTTACTTTCGG
Found at i:1817488 original size:43 final size:43
Alignment explanation
Indices: 1817435--1817538 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 43
1817425 AATTATGCAT
*
1817435 TAAATAACCTCTGAAAAAGCCAATCATTGCATTATTGCTACAA
1 TAAATAACCTCTGAAAAAGCCAACCATTGCATTATTGCTACAA
* * * *
1817478 TAAATGACCTCTGAAAAAGCCAACCGTTTCATTATTGCTGCAA
1 TAAATAACCTCTGAAAAAGCCAACCATTGCATTATTGCTACAA
* *
1817521 TAAATTACCTCTAAAAAA
1 TAAATAACCTCTGAAAAA
1817539 TAACTAAAAC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (43 bp):
TAAATAACCTCTGAAAAAGCCAACCATTGCATTATTGCTACAA
Found at i:1822483 original size:18 final size:19
Alignment explanation
Indices: 1822462--1822504 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1822452 ATTAGATAAC
* *
1822462 AATAATTAAATTAAAA-AT
1 AATAAATAAATGAAAAGAT
*
1822480 AATAAATACATGAAAAGAT
1 AATAAATAAATGAAAAGAT
1822499 AATAAA
1 AATAAA
1822505 ATACTAGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (19 bp):
AATAAATAAATGAAAAGAT
Found at i:1826472 original size:20 final size:22
Alignment explanation
Indices: 1826449--1826492 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
1826439 TTCATGATAC
*
1826449 AAATGGCATTT-AAA-TCAATT
1 AAATGGAATTTAAAATTCAATT
*
1826469 AAATTGAATTTAAAATTCAATT
1 AAATGGAATTTAAAATTCAATT
1826491 AA
1 AA
1826493 TGAAAAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.45
21 3 0.15
22 8 0.40
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (22 bp):
AAATGGAATTTAAAATTCAATT
Found at i:1827279 original size:30 final size:30
Alignment explanation
Indices: 1827226--1827314 Score: 169
Period size: 30 Copynumber: 2.9 Consensus size: 30
1827216 AATTGTTACG
1827226 TGTATAACTTTTTAATAAAAATATTTTTTCT
1 TGTATAACTTTTTAAT-AAAATATTTTTTCT
1827257 TGTATAACTTTTTAATAAAATATTTTTTCT
1 TGTATAACTTTTTAATAAAATATTTTTTCT
1827287 TGTATAACTTTTTAATAAAATATTTTTT
1 TGTATAACTTTTTAATAAAATATTTTTT
1827315 TCTTTTTAGA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 42 0.72
31 16 0.28
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (30 bp):
TGTATAACTTTTTAATAAAATATTTTTTCT
Found at i:1829250 original size:24 final size:24
Alignment explanation
Indices: 1829218--1829263 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1829208 ATATAACTTA
1829218 TAGCGAATCGGTCATGCTACCGGT
1 TAGCGAATCGGTCATGCTACCGGT
1829242 TAGCGAATCGGTCATGCTACCG
1 TAGCGAATCGGTCATGCTACCG
1829264 ATAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.24
Consensus pattern (24 bp):
TAGCGAATCGGTCATGCTACCGGT
Found at i:1831460 original size:21 final size:21
Alignment explanation
Indices: 1831430--1831472 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1831420 ACTTAATATT
*
1831430 ACAATGTCAAAATTAGGTGCA
1 ACAATATCAAAATTAGGTGCA
1831451 ACAATATCAAAATTAGGTGCA
1 ACAATATCAAAATTAGGTGCA
1831472 A
1 A
1831473 TAATGTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (21 bp):
ACAATATCAAAATTAGGTGCA
Found at i:1836137 original size:23 final size:21
Alignment explanation
Indices: 1836079--1836126 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1836069 CCTAATATTG
*
1836079 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAAGTGCAA
1836100 CAATGTCAAAATTAAGTGCAA
1 CAATGTCAAAATTAAGTGCAA
*
1836121 TAATGT
1 CAATGT
1836127 TTGAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAAGTGCAA
Found at i:1837886 original size:21 final size:21
Alignment explanation
Indices: 1837856--1837899 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1837846 ATGATGATCT
*
1837856 GATTGCAATGCATCTAATAAA
1 GATTGAAATGCATCTAATAAA
*
1837877 GATTGAAATGTATCTAATAAA
1 GATTGAAATGCATCTAATAAA
1837898 GA
1 GA
1837900 AATGAAGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (21 bp):
GATTGAAATGCATCTAATAAA
Found at i:1843409 original size:11 final size:11
Alignment explanation
Indices: 1843393--1843422 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1843383 GTTTTATGAC
1843393 TTGAAATTGAT
1 TTGAAATTGAT
1843404 TTGAAATTGAT
1 TTGAAATTGAT
1843415 TTGAAATT
1 TTGAAATT
1843423 CTTTCAGTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.47
Consensus pattern (11 bp):
TTGAAATTGAT
Found at i:1847491 original size:3 final size:3
Alignment explanation
Indices: 1847483--1847600 Score: 173
Period size: 3 Copynumber: 39.0 Consensus size: 3
1847473 TTATTTATTA
*
1847483 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
1847529 AAT AAT AAT AAT AAT AAT AAT AAT ACT AAT ACT AAT AAT AAT ACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
1847577 AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
1847601 TTTAAATGAA
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
3 99 0.97
4 3 0.03
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1848204 original size:76 final size:76
Alignment explanation
Indices: 1847732--1848675 Score: 1746
Period size: 76 Copynumber: 12.4 Consensus size: 76
1847722 GAAACGTTGA
*
1847732 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1847797 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1847808 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
*
1847872 CGGCTTTTTGG
66 AGGCTTTTTGG
* *
1847883 AAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-ATTTGAAAACATCAAAAAGCTCCCG
1847948 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
1847960 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-ATTTGAAAACATCAAAAAGCTCCCG
1848025 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* *
1848037 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-ATTTGAAAACATCAAAAAGCTCCCG
1848102 AAGGCTTTTTGG
65 AAGGCTTTTTGG
1848114 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1848179 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
1848190 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGACAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1848255 AGGCTTTTTGG
66 AGGCTTTTTGG
1848266 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1848331 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1848342 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1848407 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1848418 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1848483 AGGCTTTTTGG
66 AGGCTTTTTGG
1848494 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1848559 AGGCTTTTTGG
66 AGGCTTTTTGG
1848570 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1848635 AGGCTTTTTGG
66 AGGCTTTTTGG
1848646 AAACATCATGCACTGAAGGACTTACAGATG
1 AAACATCATGCACTGAAGGACTTACAGATG
1848676 TGAGAAATAG
Statistics
Matches: 851, Mismatches: 15, Indels: 4
0.98 0.02 0.00
Matches are distributed among these distances:
75 68 0.08
76 563 0.66
77 220 0.26
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:1849867 original size:54 final size:54
Alignment explanation
Indices: 1849785--1849954 Score: 286
Period size: 54 Copynumber: 3.1 Consensus size: 54
1849775 AGAATAGCAG
* *** * *
1849785 GTTCGTAAAACATTTGATAGTGCATTCATCCTTTCCTGTGGCTTCTGTTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTTAGAT
1849839 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTTAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTTAGAT
1849893 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTTAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTTAGAT
1849947 GTTCGTAA
1 GTTCGTAA
1849955 TTATTGAAGT
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 110 1.00
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTTAGAT
Found at i:1852419 original size:92 final size:92
Alignment explanation
Indices: 1852213--1852549 Score: 577
Period size: 92 Copynumber: 3.7 Consensus size: 92
1852203 TGATTTTAGA
* * * *
1852213 GTTCATACCAAATCATATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT-GT
1 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCT
* *
1852277 CTTCCAAATTCAATGATTGGTTCTGTG
66 CTTCCAAATTCAATAACTGGTTCTGTG
*
1852304 GTTCATACCAAAACAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCT
1 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCT
* *
1852369 CTTCCAAATTCAATAACTAGTTCTATG
66 CTTCCAAATTCAATAACTGGTTCTGTG
1852396 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCT
1 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCT
1852461 CTTCCAAATTCAATAACTGGTTCTGTG
66 CTTCCAAATTCAATAACTGGTTCTGTG
*
1852488 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGGCACATT
1 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
1852550 ATTTCTACTA
Statistics
Matches: 233, Mismatches: 12, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
91 59 0.25
92 174 0.75
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.26
Consensus pattern (92 bp):
GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCT
CTTCCAAATTCAATAACTGGTTCTGTG
Found at i:1854829 original size:17 final size:16
Alignment explanation
Indices: 1854807--1854840 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
1854797 TTCAATTTTC
1854807 TTTTTTCTTCTTCTCTT
1 TTTTTTCTTCTT-TCTT
1854824 TTTTTTCTTCTTTCTT
1 TTTTTTCTTCTTTCTT
1854840 T
1 T
1854841 GTTGGATAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTCTTCTTTCTT
Found at i:1855141 original size:2 final size:2
Alignment explanation
Indices: 1855134--1855218 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
1855124 ACAACAAAGG
1855134 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1855176 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1855218 A
1 A
1855219 AAGGATAAAT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1861907 original size:3 final size:3
Alignment explanation
Indices: 1861899--1862023 Score: 160
Period size: 3 Copynumber: 41.0 Consensus size: 3
1861889 TTATTTATTA
*
1861899 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAT AAAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
* * * *
1861946 AAT AAT AAT AAT AAT TAT TAT AAT AAT AAT ACT AAT ACT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* **
1861994 ACT AAT AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1862024 TTTAAATGAA
Statistics
Matches: 106, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
3 100 0.94
4 6 0.06
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:1866304 original size:2 final size:2
Alignment explanation
Indices: 1866297--1866325 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1866287 ATCTTGTTTC
1866297 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1866326 TGTGATAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1874014 original size:60 final size:60
Alignment explanation
Indices: 1873909--1874027 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 60
1873899 CCCATGACCC
* *
1873909 TAATCAATAATGAGTATTATTTCAATAATAAATAACTTTAAATATCAATTTAATAAAATG
1 TAATCAATAATGAGTAATATTTCAATAATAAATAACTTCAAATATCAATTTAATAAAATG
* * * * * * *
1873969 TAATTAATAATGAGTAATATTTCGATCATTAATGAGTTCAGATATCAATTTAATAAAAT
1 TAATCAATAATGAGTAATATTTCAATAATAAATAACTTCAAATATCAATTTAATAAAAT
1874028 ATCCTTTAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.39
Consensus pattern (60 bp):
TAATCAATAATGAGTAATATTTCAATAATAAATAACTTCAAATATCAATTTAATAAAATG
Found at i:1879413 original size:42 final size:43
Alignment explanation
Indices: 1879333--1879441 Score: 130
Period size: 42 Copynumber: 2.5 Consensus size: 43
1879323 AACAAATACC
* *
1879333 ACAAAAGATCAGGTTCTTTAGCGGCATTGTGCATACAAACG-CG
1 ACAAAAG-TCAAGTTCTTTAGCGGCATTGTGCAAACAAACGTCG
* *
1879376 ACAAAAGTCAAGTTCTTTAGCGTCATTTTGCAAACAAACGTCG
1 ACAAAAGTCAAGTTCTTTAGCGGCATTGTGCAAACAAACGTCG
** * *
1879419 TGAAATGTCATGTTCTTTAGCGG
1 ACAAAAGTCAAGTTCTTTAGCGG
1879442 TGTTTTGTAC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 29 0.52
43 27 0.48
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (43 bp):
ACAAAAGTCAAGTTCTTTAGCGGCATTGTGCAAACAAACGTCG
Found at i:1879448 original size:43 final size:41
Alignment explanation
Indices: 1879345--1879490 Score: 116
Period size: 43 Copynumber: 3.4 Consensus size: 41
1879335 AAAAGATCAG
* * *
1879345 GTTCTTTAGCGGCATTGTGCATACAAACGCGACAAAA-GTCAA
1 GTTCTTTAGCGGTATTTTGCAAACAAACGCGA-AAAATGTC-A
**
1879387 GTTCTTTAGC-GTCATTTTGCAAACAAACGTCGTGAAATGTCA
1 GTTCTTTAGCGGT-ATTTTGCAAACAAACG-CGAAAAATGTCA
* * * * *
1879429 TGTTCTTTAGCGGTGTTTTGTACACAAACGCCGCAAAATGTTA
1 -GTTCTTTAGCGGTATTTTGCAAACAAACG-CGAAAAATGTCA
*
1879472 GTTTCTTTAGCGGTGTTTT
1 G-TTCTTTAGCGGTATTTT
1879491 AGATTCAAAC
Statistics
Matches: 86, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
41 1 0.01
42 29 0.34
43 54 0.63
44 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (41 bp):
GTTCTTTAGCGGTATTTTGCAAACAAACGCGAAAAATGTCA
Found at i:1880190 original size:81 final size:80
Alignment explanation
Indices: 1880031--1880216 Score: 275
Period size: 82 Copynumber: 2.3 Consensus size: 80
1880021 ATTTCTGTAA
* * *
1880031 AAAACGCCACTAAAGTAATAGTCAGTAGAGGCATTTTTTAAAAAATGTCACTATATATAAATCTT
1 AAAACGCCACTAAAGTAATAGTCAATAGAGGCATTTTTTAAAAAACGCCACTATATATAAATCTT
*
1880096 ATTGCGTCGTTTGTGAC
66 ATTGCGGCGTTTGT--C
* *
1880113 AAAACGCCACTAAAGTAGTAGTCAATAGCGGCATTTTTT-AAAAACGCCACTATATATAAATCTT
1 AAAACGCCACTAAAGTAATAGTCAATAGAGGCATTTTTTAAAAAACGCCACTATATATAAATCTT
*
1880177 ATTGTGGCGTTTGTC
66 ATTGCGGCGTTTGTC
1880192 AAACACGCCACTAAAGTAATAGTCA
1 AAA-ACGCCACTAAAGTAATAGTCA
1880217 GTAAAACACC
Statistics
Matches: 95, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
79 4 0.04
80 20 0.21
81 35 0.37
82 36 0.38
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (80 bp):
AAAACGCCACTAAAGTAATAGTCAATAGAGGCATTTTTTAAAAAACGCCACTATATATAAATCTT
ATTGCGGCGTTTGTC
Found at i:1880280 original size:68 final size:66
Alignment explanation
Indices: 1880153--1880282 Score: 188
Period size: 66 Copynumber: 1.9 Consensus size: 66
1880143 GCATTTTTTA
* * * *
1880153 AAAACGCCACTATATATAAATCTTATTGTGGCGTTTGTCAAACACGCCACTAAAGTAATAGTCAG
1 AAAACACCACTATATATAAACCTTATTGTGGCGTTTGTAAAAAACGCCACTAAAGTAATAGTCAG
1880218 T
66 T
* *
1880219 AAAACACCGCTATATATAAACCTTATTGTGGCTTTTCTGTAAAAAACGCCACTAAAGTAATAGT
1 AAAACACCACTATATATAAACCTTATTGTGGC-GTT-TGTAAAAAACGCCACTAAAGTAATAGT
1880283 ATGTAGTGGC
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
66 29 0.52
67 2 0.04
68 25 0.45
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (66 bp):
AAAACACCACTATATATAAACCTTATTGTGGCGTTTGTAAAAAACGCCACTAAAGTAATAGTCAG
T
Found at i:1887529 original size:2 final size:2
Alignment explanation
Indices: 1887422--1887512 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
1887412 GATGTGTAAG
1887422 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1887464 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1887506 AT AT AT A
1 AT AT AT A
1887513 CACGAATGTA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1888503 original size:23 final size:23
Alignment explanation
Indices: 1888473--1888516 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1888463 AGAGAATTGA
1888473 AATAAAGAGTGAAAAGCTCTTGG
1 AATAAAGAGTGAAAAGCTCTTGG
1888496 AATAAAGAGTGAAAAGCTCTT
1 AATAAAGAGTGAAAAGCTCTT
1888517 CTCTTGTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (23 bp):
AATAAAGAGTGAAAAGCTCTTGG
Found at i:1904992 original size:31 final size:30
Alignment explanation
Indices: 1904953--1905041 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 30
1904943 AGCCCCTAAA
*
1904953 AATAAAATATTAATTTGATCCTTAAATTTC
1 AATAAAATATTAATTTGATCTTTAAATTTC
* *
1904983 AGATAAAATATCAATTTGA-CATTTAAATTTTT
1 A-ATAAAATATTAATTTGATC-TTTAAA-TTTC
*
1905015 AATAAAATATTAATTTAATCTTTAAAT
1 AATAAAATATTAATTTGATCTTTAAAT
1905042 CGAATCAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
30 3 0.06
31 42 0.84
32 5 0.10
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (30 bp):
AATAAAATATTAATTTGATCTTTAAATTTC
Found at i:1908572 original size:141 final size:138
Alignment explanation
Indices: 1908405--1908656 Score: 432
Period size: 141 Copynumber: 1.8 Consensus size: 138
1908395 GGTCATCCAT
* *
1908405 GGGCACTCGGTTTTTATTGGGATCTACGGTATTTTTTACATTGTTCATGAAAATCTTCACATTGA
1 GGGCACTCGGTTTTTATTGGGATCTACGGTATTTTTTACATTGTTCATGAAAATCATCACATCGA
1908470 TGTGATGAGTTCTAATAAAAAAATATTTTATTCAAAATCATCACCTCGATAGGTTTTTTTATTTA
66 TGTGATGAGTTCTAATAAAAAAATATTTTATTCAAAATCATCACCTCGATAGGTTTTTTTATTTA
1908535 GTCCAATA
131 GTCCAATA
1908543 GGGCACTCGGATTTTTAATTTGGGATCTACGGTATTTTTTACATTGTTCATGAAAATCATCACAT
1 GGGCACTCGG-TTTTT-A-TTGGGATCTACGGTATTTTTTACATTGTTCATGAAAATCATCACAT
* * *
1908608 CGATGTGATGAGTTCTAATAAAAATATTTTTTATTCAAACTCATCACCT
63 CGATGTGATGAGTTCTAATAAAAAAATATTTTATTCAAAATCATCACCT
1908657 AGATGATGAG
Statistics
Matches: 106, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
138 10 0.09
139 5 0.05
140 1 0.01
141 90 0.85
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (138 bp):
GGGCACTCGGTTTTTATTGGGATCTACGGTATTTTTTACATTGTTCATGAAAATCATCACATCGA
TGTGATGAGTTCTAATAAAAAAATATTTTATTCAAAATCATCACCTCGATAGGTTTTTTTATTTA
GTCCAATA
Found at i:1909150 original size:17 final size:17
Alignment explanation
Indices: 1909128--1909165 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1909118 ATCACAAATG
*
1909128 ATGATT-AGTGATGAACA
1 ATGATTGAGTGA-CAACA
1909145 ATGATTGAGTGACAACA
1 ATGATTGAGTGACAACA
1909162 ATGA
1 ATGA
1909166 CTACAGGAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (17 bp):
ATGATTGAGTGACAACA
Found at i:1910841 original size:40 final size:40
Alignment explanation
Indices: 1910772--1910847 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
1910762 GAGTTTACCG
* *
1910772 CATCAAAAAATTTAGTTTTTACTTCATTTTAGTATCTCGT
1 CATCAAAAAATTCAGTTTTTACTTCATTTTAATATCTCGT
* ** *
1910812 CATCAAAAACTTCAGTTTTTGTTTTATTTTAATATC
1 CATCAAAAAATTCAGTTTTTACTTCATTTTAATATC
1910848 CCAAACAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.49
Consensus pattern (40 bp):
CATCAAAAAATTCAGTTTTTACTTCATTTTAATATCTCGT
Found at i:1911308 original size:18 final size:19
Alignment explanation
Indices: 1911268--1911310 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1911258 CATTATGATT
* *
1911268 TTATTTTATAATTTATTTA
1 TTATTTTATAAATTATTCA
*
1911287 TTATTTTA-AAATTATTCG
1 TTATTTTATAAATTATTCA
1911305 TTATTT
1 TTATTT
1911311 CTAAGTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
TTATTTTATAAATTATTCA
Found at i:1912652 original size:2 final size:2
Alignment explanation
Indices: 1912647--1912696 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
1912637 ATTTTCAATA
1912647 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1912689 AT AT -T AT A
1 AT AT AT AT A
1912697 AATGTTTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1929925 original size:29 final size:30
Alignment explanation
Indices: 1929885--1929947 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
1929875 TAAGCATTAA
1929885 TTTTATGCATTTACATTTCT-TCCCTTTAC
1 TTTTATGCATTTACATTTCTATCCCTTTAC
* * * *
1929914 TTTTATGTATTTATATTTCTATCCTTTTAT
1 TTTTATGCATTTACATTTCTATCCCTTTAC
1929944 TTTT
1 TTTT
1929948 GTTATTCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.17, C:0.16, G:0.03, T:0.63
Consensus pattern (30 bp):
TTTTATGCATTTACATTTCTATCCCTTTAC
Found at i:1931375 original size:31 final size:31
Alignment explanation
Indices: 1931327--1931385 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1931317 TTTAGAACAC
*
1931327 TTTTATTACTATCATTAAACGTTTAAAATAT
1 TTTTATTACTATCATTAAAAGTTTAAAATAT
* *
1931358 TTTTATTA-TAATTATTAAAATTTTAAAA
1 TTTTATTACT-ATCATTAAAAGTTTAAAA
1931386 CTTACATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.04
31 23 0.96
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (31 bp):
TTTTATTACTATCATTAAAAGTTTAAAATAT
Found at i:1931617 original size:21 final size:21
Alignment explanation
Indices: 1931572--1931617 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
1931562 CTACTGAGAG
* *
1931572 TAATATTCATTAAAATTTTTA
1 TAATATTCATTAAAAATGTTA
1931593 -AATATT-ACTTAAAAATGTTA
1 TAATATTCA-TTAAAAATGTTA
1931613 TAATA
1 TAATA
1931618 ATTATAGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
19 1 0.05
20 16 0.76
21 4 0.19
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (21 bp):
TAATATTCATTAAAAATGTTA
Found at i:1933941 original size:2 final size:2
Alignment explanation
Indices: 1933934--1933963 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1933924 GCATGCAAAC
1933934 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1933964 TGTACAGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1944782 original size:23 final size:23
Alignment explanation
Indices: 1944752--1944799 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1944742 ATAGAAGAAG
1944752 AAGAAAAAAACT-GCAATTCGAAA
1 AAGAAAAAAA-TAGCAATTCGAAA
*
1944775 AAGAAAAAAATAGCAGTTCGAAA
1 AAGAAAAAAATAGCAATTCGAAA
1944798 AA
1 AA
1944800 AAGAGTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.62, C:0.10, G:0.15, T:0.12
Consensus pattern (23 bp):
AAGAAAAAAATAGCAATTCGAAA
Found at i:1953515 original size:2 final size:2
Alignment explanation
Indices: 1953510--1953728 Score: 406
Period size: 2 Copynumber: 110.5 Consensus size: 2
1953500 ATATATATAT
1953510 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1953552 AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1953593 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1953635 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* *
1953677 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G GG GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1953718 AG AG AG AG AG A
1 AG AG AG AG AG A
1953729 AAAAAGTAAT
Statistics
Matches: 214, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
1 2 0.01
2 212 0.99
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1957671 original size:50 final size:50
Alignment explanation
Indices: 1957594--1957694 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
1957584 GAACGCCGGC
1957594 AGATTCATACCCTGATTTCAAGCTTCCTTAGAATTCTTAAGTTTTGAAAA
1 AGATTCATACCCTGATTTCAAGCTTCCTTAGAATTCTTAAGTTTTGAAAA
*
1957644 AGATTCATACCCTGATTTCAAGTTTCCTTAGAATTCTTAAGTTTTGAAAA
1 AGATTCATACCCTGATTTCAAGCTTCCTTAGAATTCTTAAGTTTTGAAAA
1957694 A
1 A
1957695 CATGTTGGAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.39
Consensus pattern (50 bp):
AGATTCATACCCTGATTTCAAGCTTCCTTAGAATTCTTAAGTTTTGAAAA
Found at i:1961942 original size:20 final size:23
Alignment explanation
Indices: 1961904--1961945 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 23
1961894 ATCATTAACT
1961904 ATAATATATATATATATATAATA
1 ATAATATATATATATATATAATA
1961927 ATAATA-ATA-ATA-ATATAAT
1 ATAATATATATATATATATAAT
1961946 TGATTCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 3 0.16
22 3 0.16
23 6 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
ATAATATATATATATATATAATA
Found at i:1965213 original size:2 final size:2
Alignment explanation
Indices: 1965208--1965244 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1965198 TGAGTGTGTG
1965208 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1965245 GGAAATAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1965877 original size:29 final size:29
Alignment explanation
Indices: 1965826--1965883 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1965816 GTGTTGGCCG
**
1965826 TAGGTCGCCATGCCTTCTGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
1965855 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
1965884 AAGAGATTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.14, C:0.34, G:0.28, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:1965945 original size:14 final size:14
Alignment explanation
Indices: 1965926--1965992 Score: 62
Period size: 14 Copynumber: 4.4 Consensus size: 14
1965916 CGCTGGGCAT
1965926 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
1965940 CCGAGGTCATCCGAGAGCA
1 CCGAGGCCATCC----G-A
1965959 TCCGAGGCCATCCGA
1 -CCGAGGCCATCCGA
1965974 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
1965988 ACGAG
1 CCGAG
1965993 CTATGCGAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
14 29 0.66
15 1 0.02
16 1 0.02
18 1 0.02
19 1 0.02
20 11 0.25
ACGTcount: A:0.24, C:0.37, G:0.30, T:0.09
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:1965960 original size:34 final size:34
Alignment explanation
Indices: 1965922--1965987 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
1965912 AACACGCTGG
*
1965922 GCATCCGAGGCCATCCGACCGAGGTCATCCGAGA
1 GCATCCGAGGCCATCCGACCGAGGCCATCCGAGA
1965956 GCATCCGAGGCCATCCGACCGAGGCCATCCGA
1 GCATCCGAGGCCATCCGACCGAGGCCATCCGA
1965988 ACGAGCTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.23, C:0.38, G:0.29, T:0.11
Consensus pattern (34 bp):
GCATCCGAGGCCATCCGACCGAGGCCATCCGAGA
Found at i:1966031 original size:33 final size:33
Alignment explanation
Indices: 1965984--1966058 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
1965974 CCGAGGCCAT
* *
1965984 CCGAACGAGCTATGCGAGGGCATCCAAGGGCAA-
1 CCGAGCGAGCTATGCGAGGGAATCCAAGGG-AAG
**
1966017 CCGAGCGAGCTATGCGAGGGAATCTGAGGGAAG
1 CCGAGCGAGCTATGCGAGGGAATCCAAGGGAAG
1966050 CCGAGCGAG
1 CCGAGCGAG
1966059 GGTAGGTCGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
32 2 0.05
33 35 0.95
ACGTcount: A:0.28, C:0.24, G:0.39, T:0.09
Consensus pattern (33 bp):
CCGAGCGAGCTATGCGAGGGAATCCAAGGGAAG
Found at i:1973010 original size:2 final size:2
Alignment explanation
Indices: 1973003--1973034 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1972993 AATTTTGTAA
1973003 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1973035 TATTAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1973293 original size:61 final size:62
Alignment explanation
Indices: 1973193--1973309 Score: 157
Period size: 61 Copynumber: 1.9 Consensus size: 62
1973183 CCAACCAAAC
*
1973193 ACAAAATAAAACATTTCCAGAAATCATATTCCCCGGTAATCTTACATTCATTCTCAAAATACA
1 ACAAAAT-AAACATTTCCAGAAATCATATTCCCCAGTAATCTTACATTCATTCTCAAAATACA
* * * *
1973256 ACAAAAT-AACA-TTCTCAGAAATCATATTCTCTAGTAATCTTACGTTCTTTCTCA
1 ACAAAATAAACATTTC-CAGAAATCATATTCCCCAGTAATCTTACATTCATTCTCA
1973310 TAATCTTACA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 3 0.06
61 38 0.79
63 7 0.15
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.32
Consensus pattern (62 bp):
ACAAAATAAACATTTCCAGAAATCATATTCCCCAGTAATCTTACATTCATTCTCAAAATACA
Found at i:1976470 original size:8 final size:9
Alignment explanation
Indices: 1976422--1976470 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
1976412 ATAATATATA
1976422 TATTTTTGT
1 TATTTTTGT
*
1976431 TATTTTTAT
1 TATTTTTGT
* *
1976440 GA-TTCT-T
1 TATTTTTGT
1976447 TATTTTTGT
1 TATTTTTGT
1976456 TATTTTTGT
1 TATTTTTGT
1976465 TATTTT
1 TATTTT
1976471 CTTTTTCTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
7 2 0.06
8 6 0.18
9 25 0.76
ACGTcount: A:0.14, C:0.02, G:0.08, T:0.76
Consensus pattern (9 bp):
TATTTTTGT
Found at i:1976497 original size:22 final size:22
Alignment explanation
Indices: 1976446--1976502 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
1976436 TTATGATTCT
* **
1976446 TTATTTTTGTTATTTTTGTTATT
1 TTATTTTTCTT-TTTTTGTTACA
*
1976469 TTCTTTTTCTTTTTTTGTTACA
1 TTATTTTTCTTTTTTTGTTACA
1976491 TTA-TTTTCTTTT
1 TTATTTTTCTTTT
1976503 ATTCTATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 9 0.31
22 11 0.38
23 9 0.31
ACGTcount: A:0.11, C:0.07, G:0.05, T:0.77
Consensus pattern (22 bp):
TTATTTTTCTTTTTTTGTTACA
Found at i:1976899 original size:20 final size:20
Alignment explanation
Indices: 1976855--1977102 Score: 236
Period size: 20 Copynumber: 12.2 Consensus size: 20
1976845 AATGACCAAC
*
1976855 AAAATCGCAACGCGA--AATA
1 AAAATCGCAACGCGATTAA-G
*
1976874 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
1976894 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
1976914 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
1976934 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
1976955 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
1976976 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
* *
1976997 AAGAATCGCAATGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
1977018 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
*
1977038 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
1977058 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
*
1977078 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
1977098 AAAAT
1 AAAAT
1977103 GAGTAAATTT
Statistics
Matches: 190, Mismatches: 28, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
18 1 0.01
19 15 0.08
20 133 0.70
21 14 0.07
22 27 0.14
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:1977208 original size:6 final size:6
Alignment explanation
Indices: 1977197--1977260 Score: 128
Period size: 6 Copynumber: 10.7 Consensus size: 6
1977187 AGACACGTAT
1977197 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1977245 GACCAC GACCAC GACC
1 GACCAC GACCAC GACC
1977261 CGAGACGAGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:1977834 original size:20 final size:20
Alignment explanation
Indices: 1977809--1978116 Score: 260
Period size: 20 Copynumber: 15.2 Consensus size: 20
1977799 GAATTTACTC
1977809 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
1977829 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
1977849 A--TTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCG
1977869 A--TTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCG
1977889 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
1977909 A--TTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCG
* *
1977929 ATTTTCTGAATCGCATTGCG
1 ATTTTCTTAATCGCGTTGCG
***
1977949 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
* *
1977971 ATTCTCTTAATCGCATTGCG
1 ATTTTCTTAATCGCGTTGCG
***
1977991 ATTCTTGGAATATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
*
1978013 ATTTTCTT--TTGACCGTTGCG
1 ATTTTCTTAATCG--CGTTGCG
* *
1978033 ATTTTCTT-TTCAACGTTGCG
1 ATTTTCTTAATC-GCGTTGCG
* *
1978053 ATTTTCTAAATCACGTTGCG
1 ATTTTCTTAATCGCGTTGCG
*
1978073 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
*
1978093 A-TTT-TTATTTCGCGTTGCG
1 ATTTTCTTA-ATCGCGTTGCG
1978112 ATTTT
1 ATTTT
1978117 GTTGGTCATT
Statistics
Matches: 242, Mismatches: 27, Indels: 38
0.79 0.09 0.12
Matches are distributed among these distances:
18 14 0.06
19 14 0.06
20 167 0.69
21 12 0.05
22 35 0.14
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
ATTTTCTTAATCGCGTTGCG
Found at i:1978032 original size:42 final size:40
Alignment explanation
Indices: 1977809--1978114 Score: 290
Period size: 40 Copynumber: 7.6 Consensus size: 40
1977799 GAATTTACTC
1977809 ATTTTCTTAATCGCGTTGCGATTTTCTT--AATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGA--TTCTTGGAATCGCGTTGCG
1977849 A--TTCTTGGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1977889 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
* *
1977929 ATTTTCTGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
* *
1977971 ATTCTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
* **** *
1978013 ATTTTCTT--TTGACCGTTGCGATT-TTCTTTTCAACGTTGCG
1 ATTTTCTTAATCG--CGTTGCGATTCTTGGAATC-GCGTTGCG
* * **
1978053 ATTTTCTAAATCACGTTGCGATT-TTCTAAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
*
1978093 A-TTT-TTATTTCGCGTTGCGATT
1 ATTTTCTTA-ATCGCGTTGCGATT
1978115 TTGTTGGTCA
Statistics
Matches: 227, Mismatches: 24, Indels: 31
0.80 0.09 0.11
Matches are distributed among these distances:
38 12 0.05
39 17 0.07
40 121 0.53
41 5 0.02
42 72 0.32
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.42
Consensus pattern (40 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:1981290 original size:21 final size:21
Alignment explanation
Indices: 1981253--1981292 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1981243 TTATGATTTT
*
1981253 TAAAATTAATAAGAAAGTGTA
1 TAAAATTAATAAAAAAGTGTA
1981274 TAAAATTAA-AATAAAAGTG
1 TAAAATTAATAA-AAAAGTG
1981293 ATTGATCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (21 bp):
TAAAATTAATAAAAAAGTGTA
Found at i:1981845 original size:11 final size:11
Alignment explanation
Indices: 1981831--1981875 Score: 65
Period size: 11 Copynumber: 4.0 Consensus size: 11
1981821 TCGTTAAGAA
1981831 CTCGAGTCGAG
1 CTCGAGTCGAG
1981842 CTCGAGCTCGAG
1 CTCGAG-TCGAG
1981854 -TCGAGTCCGAG
1 CTCGAGT-CGAG
1981865 CTCGAGTCGAG
1 CTCGAGTCGAG
1981876 TCCATTCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 1 0.03
11 19 0.61
12 11 0.35
ACGTcount: A:0.18, C:0.29, G:0.36, T:0.18
Consensus pattern (11 bp):
CTCGAGTCGAG
Found at i:1981853 original size:17 final size:17
Alignment explanation
Indices: 1981831--1981878 Score: 80
Period size: 17 Copynumber: 2.8 Consensus size: 17
1981821 TCGTTAAGAA
1981831 CTCGAGTCGAG-CTCGAG
1 CTCGAGTCGAGTC-CGAG
1981848 CTCGAGTCGAGTCCGAG
1 CTCGAGTCGAGTCCGAG
1981865 CTCGAGTCGAGTCC
1 CTCGAGTCGAGTCC
1981879 ATTCAATCCG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 29 0.97
18 1 0.03
ACGTcount: A:0.17, C:0.31, G:0.33, T:0.19
Consensus pattern (17 bp):
CTCGAGTCGAGTCCGAG
Found at i:1981857 original size:5 final size:5
Alignment explanation
Indices: 1981832--1981877 Score: 56
Period size: 6 Copynumber: 8.4 Consensus size: 5
1981822 CGTTAAGAAC
1981832 TCGAG TCGAG CTCGAG CTCGAG TCGAG TCCGAG CTCGAG TCGAG TC
1 TCGAG TCGAG -TCGAG -TCGAG TCGAG T-CGAG -TCGAG TCGAG TC
1981878 CATTCAATCC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 18 0.47
6 19 0.50
7 1 0.03
ACGTcount: A:0.17, C:0.28, G:0.35, T:0.20
Consensus pattern (5 bp):
TCGAG
Found at i:1982339 original size:82 final size:84
Alignment explanation
Indices: 1982253--1982415 Score: 240
Period size: 82 Copynumber: 2.0 Consensus size: 84
1982243 AAATTTTATT
*
1982253 ATGATTATATGTCAATATTATTATTAAATTTTTAATAACAAGATATTAAAATAAAA-TAAAATTA
1 ATGATTATATGTCAATATCATTATTAAATTTTTAATAACAAGATATTAAAATAAAATTAAAATTA
*
1982317 AAATTTTAAAA-ATATTTG
66 AAATTTGAAAACATATTTG
** ** *
1982335 ATGATTATATGTCAATATCATTATTTTATTTTTAATAATGAGATATTAAAATAAAATTTAAATTA
1 ATGATTATATGTCAATATCATTATTAAATTTTTAATAACAAGATATTAAAATAAAATTAAAATTA
*
1982400 AACTTTGAAAACATAT
66 AAATTTGAAAACATAT
1982416 AAACTTTAGG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
82 51 0.72
83 16 0.23
84 4 0.06
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (84 bp):
ATGATTATATGTCAATATCATTATTAAATTTTTAATAACAAGATATTAAAATAAAATTAAAATTA
AAATTTGAAAACATATTTG
Found at i:1986038 original size:16 final size:17
Alignment explanation
Indices: 1985999--1986040 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
1985989 TTCTTATTTT
1985999 AATTAAATATAATTTTAA
1 AATT-AATATAATTTTAA
*
1986017 CA-TAATATAA-TTTAA
1 AATTAATATAATTTTAA
1986032 AATTAATAT
1 AATTAATAT
1986041 TAAAATAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 6 0.29
16 13 0.62
17 1 0.05
18 1 0.05
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTAATATAATTTTAA
Found at i:1987102 original size:32 final size:34
Alignment explanation
Indices: 1987039--1987113 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 34
1987029 TCGGACCGGG
1987039 TATATATA-TTTAAATTAAATATATAAATATT-A
1 TATATATATTTTAAATTAAATATATAAATATTAA
*
1987071 TATATATATTTTAAATTAAAT-TA-AATTTATTAA
1 TATATATATTTTAAATTAAATATATAA-ATATTAA
1987104 TATTATATAT
1 TA-TATATAT
1987114 ATATAATCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
31 2 0.05
32 14 0.37
33 15 0.39
34 7 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
TATATATATTTTAAATTAAATATATAAATATTAA
Found at i:1987111 original size:34 final size:34
Alignment explanation
Indices: 1987039--1987118 Score: 99
Period size: 38 Copynumber: 2.2 Consensus size: 34
1987029 TCGGACCGGG
1987039 TATATATATTTAAATTAAATATATAAATATTATA
1 TATATATATTTAAATTAAATATATAAATATTATA
*
1987073 TATATAT-TTTAAATTAAATTAAATTTATTAATATTATA
1 TATATATATTTAAATTAAA-T--A--TATAAATATTATA
1987111 TATATATA
1 TATATATA
1987119 ATCATTATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
33 11 0.28
34 8 0.21
36 1 0.03
38 19 0.49
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (34 bp):
TATATATATTTAAATTAAATATATAAATATTATA
Found at i:1995872 original size:21 final size:20
Alignment explanation
Indices: 1995846--1995885 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
1995836 TAATTTTAAA
1995846 TAAAGGTTTTGAAACCTCCTT
1 TAAAGGTTTTGAAA-CTCCTT
1995867 TAAAGGTTTTGAAACTCCT
1 TAAAGGTTTTGAAACTCCT
1995886 ACACAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (20 bp):
TAAAGGTTTTGAAACTCCTT
Found at i:1996778 original size:27 final size:27
Alignment explanation
Indices: 1996739--1996793 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 27
1996729 TAATATTATT
1996739 TTTTGTTATAATTATATTATTATACATA
1 TTTTGTTATAATTATATTATTATA-ATA
1996767 TTTT-TTATAATTATATTATTATAATA
1 TTTTGTTATAATTATATTATTATAATA
1996793 T
1 T
1996794 ATAATATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 4 0.15
27 19 0.70
28 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTGTTATAATTATATTATTATAATA
Found at i:1996925 original size:24 final size:24
Alignment explanation
Indices: 1996894--1996940 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1996884 TTCTAATATT
1996894 TTAAAAATAATAATA-TTATTTTG
1 TTAAAAATAATAATATTTATTTTG
*
1996917 TTAATAAATAATATTATTTATTTT
1 TTAA-AAATAATAATATTTATTTT
1996941 ATTTGATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TTAAAAATAATAATATTTATTTTG
Found at i:1998113 original size:21 final size:21
Alignment explanation
Indices: 1998089--1998158 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
1998079 AAATAAATCG
1998089 CAACGCGAACTTTGACTATCA
1 CAACGCGAACTTTGACTATCA
** *
1998110 CAA--CGAA-TTTGGAAAATCG
1 CAACGCGAACTTT-GACTATCA
*
1998129 CAACGCGAACTTCGACTATCA
1 CAACGCGAACTTTGACTATCA
*
1998150 CAATGCGAA
1 CAACGCGAA
1998159 TATGTAAATC
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
18 3 0.08
19 12 0.32
21 20 0.54
22 2 0.05
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (21 bp):
CAACGCGAACTTTGACTATCA
Found at i:1998138 original size:40 final size:42
Alignment explanation
Indices: 1998060--1998152 Score: 145
Period size: 40 Copynumber: 2.3 Consensus size: 42
1998050 TGCGATTTGG
* *
1998060 GACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTT
1 GACTATCACAACGAATTTGAAATAAATCGCAACGCGAACTTC
*
1998102 GACTATCACAACGAATTTG-GA-AAATCGCAACGCGAACTTC
1 GACTATCACAACGAATTTGAAATAAATCGCAACGCGAACTTC
1998142 GACTATCACAA
1 GACTATCACAA
1998153 TGCGAATATG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
40 29 0.60
41 1 0.02
42 18 0.38
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.22
Consensus pattern (42 bp):
GACTATCACAACGAATTTGAAATAAATCGCAACGCGAACTTC
Found at i:1998196 original size:21 final size:21
Alignment explanation
Indices: 1998167--1998219 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1998157 AATATGTAAA
*
1998167 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
*
1998188 TCGCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
1998209 TCGCGTTGCGA
1 TCGCGTTGCGA
1998220 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:2012015 original size:15 final size:15
Alignment explanation
Indices: 2011995--2012076 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
2011985 TTCCAGAAAA
*
2011995 TGAATTATTGGAATT
1 TGAATTACTGGAATT
2012010 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
2012025 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
2012040 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
2012055 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
2012069 TGAATTAC
1 TGAATTAC
2012077 ATTTCTGTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
14 12 0.20
15 47 0.80
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.37
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:2012041 original size:45 final size:44
Alignment explanation
Indices: 2011990--2012076 Score: 138
Period size: 45 Copynumber: 2.0 Consensus size: 44
2011980 TGGTTTTCCA
* **
2011990 GAAAATGAATTATTGGAATTTGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTACTG
2012035 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
2012077 ATTTCTGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 14 0.36
45 25 0.64
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (44 bp):
GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACTG
Found at i:2012074 original size:29 final size:30
Alignment explanation
Indices: 2011995--2012076 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
2011985 TTCCAGAAAA
* **
2011995 TGAATTATTGGAATTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
2012025 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
2012055 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
2012077 ATTTCTGTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.37
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:2012082 original size:20 final size:20
Alignment explanation
Indices: 2012059--2012128 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
2012049 GGAATTTGAA
2012059 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
2012079 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
2012099 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
2012119 TTCTGGAAAA
1 TTCTGGAAAA
2012129 CATCTGGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:2012351 original size:24 final size:28
Alignment explanation
Indices: 2012294--2012357 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 28
2012284 TTTACTAAAA
2012294 TATTATTGAAATATATAAATAAAATTAT
1 TATTATTGAAATATATAAATAAAATTAT
2012322 TCATTATT-AAATATATAAA-AAAATTTAT
1 T-ATTATTGAAATATATAAATAAAA-TTAT
2012350 TATATATT
1 TAT-TATT
2012358 ATTAAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
27 6 0.18
28 21 0.64
29 6 0.18
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (28 bp):
TATTATTGAAATATATAAATAAAATTAT
Found at i:2012399 original size:23 final size:22
Alignment explanation
Indices: 2012369--2012418 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
2012359 TTAAAATAAA
2012369 AATATAATAT-ATTATATTATTAT
1 AATATAAT-TGATTATATTA-TAT
*
2012392 AATATAATTGATTATTTTATAT
1 AATATAATTGATTATATTATAT
2012414 AATAT
1 AATAT
2012419 TAAAAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
AATATAATTGATTATATTATAT
Found at i:2012436 original size:22 final size:23
Alignment explanation
Indices: 2012411--2012454 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
2012401 GATTATTTTA
2012411 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
2012433 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
2012455 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:2012459 original size:22 final size:22
Alignment explanation
Indices: 2012415--2012471 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
2012405 ATTTTATATA
* *
2012415 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
2012436 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
2012458 ATATTTTAAATATT
1 ATATTATAAATATT
2012472 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:2012470 original size:52 final size:52
Alignment explanation
Indices: 2012351--2012471 Score: 135
Period size: 52 Copynumber: 2.3 Consensus size: 52
2012341 AAAATTTATT
**
2012351 ATATATTATTAAA-A-TAAAAATATAATATATTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAAATATAATATATTATATTATTATAATATAATAA
2012402 AT-TATTTTATATAATATTAAAAATAT-A-ATATTATATTATTATAAATATTAATAA
1 ATATA-TTT-TA-AATATTAAAAATATAATATATTATATTATTAT-AATA-TAATAA
2012456 ATATATTTTAAATATT
1 ATATATTTTAAATATT
2012472 TTAATAATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 23 0.38
53 8 0.13
54 18 0.30
55 2 0.03
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (52 bp):
ATATATTTTAAATATTAAAAATATAATATATTATATTATTATAATATAATAA
Found at i:2012712 original size:42 final size:42
Alignment explanation
Indices: 2012660--2012859 Score: 346
Period size: 42 Copynumber: 4.7 Consensus size: 42
2012650 ATGAATTACA
*
2012660 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
*
2012702 TTCCAGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
*
2012744 TTCCGGAAAACGAATTACGTGAAACAAACACAGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
*
2012786 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
*
2012828 TTCCGGGAAAATGAATTACGTGAAACAAACAC
1 TTCC-GGAAAACGAATTACGTGAAACAAACAC
2012860 ATGAATTCGG
Statistics
Matches: 150, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
42 124 0.83
43 26 0.17
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
Found at i:2014762 original size:17 final size:17
Alignment explanation
Indices: 2014740--2014772 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2014730 GGTTAGGGTC
2014740 AGGATTTTGAGATTTTA
1 AGGATTTTGAGATTTTA
2014757 AGGATTTTGAGATTTT
1 AGGATTTTGAGATTTT
2014773 TTTTTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.48
Consensus pattern (17 bp):
AGGATTTTGAGATTTTA
Found at i:2015402 original size:16 final size:16
Alignment explanation
Indices: 2015377--2015415 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
2015367 CATTTAATAA
2015377 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
* *
2015393 ATAAATGAACATGAAC
1 ATAAACGAACACGAAC
2015409 ATAAACG
1 ATAAACG
2015416 TTGGAGACCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.56, C:0.18, G:0.13, T:0.13
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:2016203 original size:24 final size:26
Alignment explanation
Indices: 2016167--2016230 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 26
2016157 GATTGAGTTA
**
2016167 AACATAAATGAATGAACAT-A-AACG
1 AACATAACCGAATGAACATAATAACG
2016191 AACATAACCGAATGAACATAATTGAACG
1 AACATAACCGAATGAACATAA-T-AACG
2016219 AACATAACCGAA
1 AACATAACCGAA
2016231 CGTTCATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 17 0.50
25 1 0.03
28 16 0.47
ACGTcount: A:0.55, C:0.17, G:0.12, T:0.16
Consensus pattern (26 bp):
AACATAACCGAATGAACATAATAACG
Found at i:2016231 original size:14 final size:14
Alignment explanation
Indices: 2016187--2016232 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
2016177 AATGAACATA
2016187 AACGAACATAACCG
1 AACGAACATAACCG
* **
2016201 AATGAACATAATTG
1 AACGAACATAACCG
2016215 AACGAACATAACCG
1 AACGAACATAACCG
2016229 AACG
1 AACG
2016233 TTCATTAACG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.50, C:0.22, G:0.15, T:0.13
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:2017050 original size:11 final size:11
Alignment explanation
Indices: 2017034--2017064 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
2017024 AGCTCGGTTC
2017034 AAAAAAAAAAT
1 AAAAAAAAAAT
2017045 AAAAAAAAAAT
1 AAAAAAAAAAT
2017056 AAAATAAAA
1 AAAA-AAAA
2017065 CCGAATCGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (11 bp):
AAAAAAAAAAT
Found at i:2017059 original size:16 final size:15
Alignment explanation
Indices: 2017034--2017064 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2017024 AGCTCGGTTC
2017034 AAAAAAAAAATAAAA
1 AAAAAAAAAATAAAA
2017049 AAAAAATAAAATAAAA
1 AAAAAA-AAAATAAAA
2017065 CCGAATCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAAAAAATAAAA
Found at i:2017074 original size:5 final size:5
Alignment explanation
Indices: 2017063--2017110 Score: 60
Period size: 5 Copynumber: 9.6 Consensus size: 5
2017053 AATAAAATAA
* * * *
2017063 AACCG AATCG AATCG AATCG AACCG AACCG AATCG AACCG AACCG AAC
1 AACCG AACCG AACCG AACCG AACCG AACCG AACCG AACCG AACCG AAC
2017111 ATACAAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.42, C:0.31, G:0.19, T:0.08
Consensus pattern (5 bp):
AACCG
Found at i:2017089 original size:15 final size:15
Alignment explanation
Indices: 2017066--2017109 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
2017056 AAAATAAAAC
* *
2017066 CGAATCGAATCGAAT
1 CGAACCGAACCGAAT
2017081 CGAACCGAACCGAAT
1 CGAACCGAACCGAAT
2017096 CGAACCGAACCGAA
1 CGAACCGAACCGAA
2017110 CATACAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.41, C:0.30, G:0.20, T:0.09
Consensus pattern (15 bp):
CGAACCGAACCGAAT
Found at i:2018984 original size:36 final size:36
Alignment explanation
Indices: 2018943--2019018 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
2018933 ATTTTCGGGA
2018943 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
2018979 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
2019015 TTTT
1 TTTT
2019019 TTGCTATAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:2019462 original size:15 final size:15
Alignment explanation
Indices: 2019442--2019471 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2019432 TATCACAATC
2019442 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
2019457 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
2019472 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:2022112 original size:36 final size:36
Alignment explanation
Indices: 2022071--2022146 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
2022061 ATTTTCGGGA
2022071 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
2022107 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
2022143 TTTT
1 TTTT
2022147 TTGCTATAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:2025242 original size:36 final size:36
Alignment explanation
Indices: 2025201--2025276 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2025191 ATTTTCGGGA
*
2025201 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTCGGCAAAATTCGAATAAAGACGAT
2025237 TTTTGCTATTTTCGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTCGGCAAAATTCGAATAAAGACGAT
2025273 TTTT
1 TTTT
2025277 TTGCTATAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTTGCTATTTTCGGCAAAATTCGAATAAAGACGAT
Found at i:2025714 original size:15 final size:15
Alignment explanation
Indices: 2025694--2025723 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2025684 TATCACAATC
2025694 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
2025709 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
2025724 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:2028399 original size:35 final size:36
Alignment explanation
Indices: 2028325--2028399 Score: 143
Period size: 35 Copynumber: 2.1 Consensus size: 36
2028315 ATTTTCGGGA
2028325 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
2028361 TTTTGCTA-TTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
2028396 TTTT
1 TTTT
2028400 TTGCTATAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
35 31 0.79
36 8 0.21
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:2028843 original size:15 final size:15
Alignment explanation
Indices: 2028823--2028852 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2028813 TATCACAATC
2028823 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
2028838 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
2028853 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:2031495 original size:36 final size:36
Alignment explanation
Indices: 2031454--2031529 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2031444 ATTTTCGGGA
*
2031454 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGACAAAATTCGAATAAAGACGAT
2031490 TTTTGCTATTTTTGACAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGACAAAATTCGAATAAAGACGAT
2031526 TTTT
1 TTTT
2031530 TTGCTATAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTTGCTATTTTTGACAAAATTCGAATAAAGACGAT
Found at i:2031972 original size:15 final size:15
Alignment explanation
Indices: 2031952--2031981 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2031942 TATCACAATC
2031952 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
2031967 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
2031982 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:2036492 original size:36 final size:36
Alignment explanation
Indices: 2036451--2036526 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
2036441 ATTTTCGGGA
2036451 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
2036487 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
2036523 TTTT
1 TTTT
2036527 TTGCTATAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:2040143 original size:5 final size:5
Alignment explanation
Indices: 2040133--2040157 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2040123 AAAATTTAAA
2040133 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
2040158 TTATCATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:2040664 original size:13 final size:13
Alignment explanation
Indices: 2040642--2040674 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2040632 ATATTTTTTA
2040642 TTATAATCTAATT
1 TTATAATCTAATT
*
2040655 TTATACTCTAATT
1 TTATAATCTAATT
2040668 TTATAAT
1 TTATAAT
2040675 TTCGTACTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (13 bp):
TTATAATCTAATT
Found at i:2042263 original size:23 final size:23
Alignment explanation
Indices: 2042237--2042281 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2042227 TTAAAAGGCA
2042237 GAGAAAAACATGCCATAAAGGTG
1 GAGAAAAACATGCCATAAAGGTG
* * *
2042260 GAGATAAACGTGTCATAAAGGT
1 GAGAAAAACATGCCATAAAGGT
2042282 AGATAACATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.44, C:0.11, G:0.27, T:0.18
Consensus pattern (23 bp):
GAGAAAAACATGCCATAAAGGTG
Found at i:2045750 original size:19 final size:19
Alignment explanation
Indices: 2045726--2045772 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
2045716 CAACCCACAG
*
2045726 TGTTTATACCCCAAAACTT
1 TGTTTACACCCCAAAACTT
2045745 TGTTTACACCCCAAAACTT
1 TGTTTACACCCCAAAACTT
2045764 TGTTTACAC
1 TGTTTACAC
2045773 TCTTTCCACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (19 bp):
TGTTTACACCCCAAAACTT
Found at i:2046463 original size:21 final size:21
Alignment explanation
Indices: 2046437--2046506 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
2046427 TGAGTTTGGG
*
2046437 ATCGATCCCTTTACAAAAAGA
1 ATCGATCCCTTCACAAAAAGA
* *
2046458 ATCGATCCCTTCACCAAAAGG
1 ATCGATCCCTTCACAAAAAGA
* * * **
2046479 ATTGACCCCTTCCCTTAAAGA
1 ATCGATCCCTTCACAAAAAGA
2046500 ATCGATC
1 ATCGATC
2046507 TATTTCTTGC
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.24
Consensus pattern (21 bp):
ATCGATCCCTTCACAAAAAGA
Found at i:2049752 original size:3 final size:3
Alignment explanation
Indices: 2049744--2049777 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
2049734 CCAACATCTA
2049744 TTC TTC TTC TTC TTC TTC TTC TTC TTCC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC
2049778 CTTTGGAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:2051171 original size:21 final size:22
Alignment explanation
Indices: 2051134--2051209 Score: 77
Period size: 21 Copynumber: 3.6 Consensus size: 22
2051124 CGTTGCAAGA
** *
2051134 AAGGGATTTATCCTTTTCA-TC
1 AAGGGATCGATCCTTTTTAGTC
*
2051155 AAGGGATCGA-CCTTTTTAGTG
1 AAGGGATCGATCCTTTTTAGTC
*
2051176 AAGGGATCGATCCTTTTT-GTA
1 AAGGGATCGATCCTTTTTAGTC
*
2051197 AAAGGATCGATCC
1 AAGGGATCGATCC
2051210 CAAACTCATT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 7 0.15
21 33 0.70
22 7 0.15
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (22 bp):
AAGGGATCGATCCTTTTTAGTC
Found at i:2060236 original size:23 final size:23
Alignment explanation
Indices: 2060192--2060277 Score: 61
Period size: 23 Copynumber: 3.6 Consensus size: 23
2060182 ATTTTTTTTG
* *
2060192 AAAAATAAAAGTTATTCTAAATT
1 AAAAATAAAAATTATTCAAAATT
*
2060215 AAAAATATAAAATTATTAAAATATT
1 AAAAATA-AAAATTATTCAAA-ATT
*
2060240 CAAAAA-AATAAA-TA-TAAAAATACT
1 -AAAAATAA-AAATTATTCAAAAT--T
2060264 AAAAATAAAAATTA
1 AAAAATAAAAATTA
2060278 AATTACTAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 15
0.74 0.04 0.21
Matches are distributed among these distances:
22 2 0.04
23 20 0.38
24 18 0.35
25 7 0.13
26 5 0.10
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.29
Consensus pattern (23 bp):
AAAAATAAAAATTATTCAAAATT
Found at i:2060267 original size:21 final size:21
Alignment explanation
Indices: 2060243--2060289 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2060233 AAATATTCAA
*
2060243 AAAAATAAATATAAAAATACT
1 AAAAATAAAAATAAAAATACT
* *
2060264 AAAAATAAAAATTAAATTACT
1 AAAAATAAAAATAAAAATACT
2060285 AAAAA
1 AAAAA
2060290 AATTTGAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAATAAAAATAAAAATACT
Found at i:2062289 original size:16 final size:16
Alignment explanation
Indices: 2062268--2062318 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
2062258 TTACCCGACA
2062268 TGTTTTCAACCTGACC
1 TGTTTTCAACCTGACC
2062284 TGTTTTCAACCTGACC
1 TGTTTTCAACCTGACC
*
2062300 TGTTTTTAACCTGACC
1 TGTTTTCAACCTGACC
2062316 TGT
1 TGT
2062319 AAATGATCCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.18, C:0.27, G:0.14, T:0.41
Consensus pattern (16 bp):
TGTTTTCAACCTGACC
Found at i:2062613 original size:23 final size:24
Alignment explanation
Indices: 2062579--2062624 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
2062569 ATGCAAAGGA
2062579 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
2062603 AAATT-ATATAGTTTAATTTATA
1 AAATTAATATAGTTTAATTTATA
2062625 CAAAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:2062819 original size:14 final size:14
Alignment explanation
Indices: 2062800--2062858 Score: 73
Period size: 14 Copynumber: 4.2 Consensus size: 14
2062790 TATATTATGA
*
2062800 TTTATGATTTAGTG
1 TTTATGATTTAGGG
* **
2062814 TTTATGGTTTAAAG
1 TTTATGATTTAGGG
*
2062828 TTTAGGATTTAGGG
1 TTTATGATTTAGGG
2062842 TTTATGATTTAGGG
1 TTTATGATTTAGGG
2062856 TTT
1 TTT
2062859 CTATAAATTA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (14 bp):
TTTATGATTTAGGG
Found at i:2062819 original size:21 final size:20
Alignment explanation
Indices: 2062794--2062854 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
2062784 TCCATTTATA
*
2062794 TTATGATTTATGATTTAGTGT
1 TTATGGTTTATGATTTAG-GT
*
2062815 TTATGGTTTA-AAGTTTAGGAT
1 TTATGGTTTATGA-TTTAGG-T
*
2062836 TTAGGGTTTATGATTTAGG
1 TTATGGTTTATGATTTAGG
2062855 GTTTCTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 2 0.06
21 30 0.91
22 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (20 bp):
TTATGGTTTATGATTTAGGT
Found at i:2062894 original size:49 final size:49
Alignment explanation
Indices: 2062851--2062944 Score: 136
Period size: 48 Copynumber: 1.9 Consensus size: 49
2062841 GTTTATGATT
* * *
2062851 TAGGGTTTCTATAAATTATATAATTTA-TTACTTTATATAGTTTATGCA
1 TAGGGTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATGCA
* *
2062899 TAGTGTTTCTATAAACTATATAAGTAATTTATTTTATATAGTTTAT
1 TAGGGTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTAT
2062945 ATATATACAT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 23 0.57
49 17 0.43
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (49 bp):
TAGGGTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATGCA
Found at i:2063022 original size:23 final size:25
Alignment explanation
Indices: 2062996--2063053 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 25
2062986 ATACATACAT
2062996 ATTATATAAAATTATTT-AATA-AA
1 ATTATATAAAATTATTTAAATATAA
*
2063019 ATTA-ATAAAATTGTTTAAATATAA
1 ATTATATAAAATTATTTAAATATAA
2063043 ATTATATAAAA
1 ATTATATAAAA
2063054 CATGATTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 11 0.35
23 8 0.26
24 6 0.19
25 6 0.19
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
ATTATATAAAATTATTTAAATATAA
Found at i:2063375 original size:7 final size:7
Alignment explanation
Indices: 2063345--2063402 Score: 53
Period size: 7 Copynumber: 8.3 Consensus size: 7
2063335 TCCATTTATA
2063345 TTAGGGT
1 TTAGGGT
* *
2063352 TTATGAT
1 TTAGGGT
*
2063359 TTAGGAT
1 TTAGGGT
*
2063366 TTAGTGT
1 TTAGGGT
*
2063373 TTATGGT
1 TTAGGGT
**
2063380 TTAAAGT
1 TTAGGGT
2063387 TTAGGGT
1 TTAGGGT
2063394 TTAGGGT
1 TTAGGGT
2063401 TT
1 TT
2063403 TAATAAACTA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (7 bp):
TTAGGGT
Found at i:2063496 original size:15 final size:15
Alignment explanation
Indices: 2063476--2063527 Score: 77
Period size: 15 Copynumber: 3.4 Consensus size: 15
2063466 TAATATACTT
2063476 TATATAGTTTATATA
1 TATATAGTTTATATA
*
2063491 TATATAGGTTATATA
1 TATATAGTTTATATA
*
2063506 TATATAGTCTATATA
1 TATATAGTTTATATA
2063521 TACTATA
1 TA-TATA
2063528 CATGGTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
15 29 0.88
16 4 0.12
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:2063571 original size:550 final size:551
Alignment explanation
Indices: 2062712--2063827 Score: 1806
Period size: 550 Copynumber: 2.0 Consensus size: 551
2062702 ATTTTGGCAA
* *** *
2062712 TACATTAGTTTACATAGGCCCAATATATAAGTTCACTCTTTTATTACAAATATATATATGCATTA
1 TACATTAGTTTACATAGGCCCAATACATAAACCCACTATTTTATTACAAATATATATATGCATTA
* **
2062777 GTGCTAGTCCATTTATATTATGATTTATGATTTAGTGTTTATGGTTTAAAGTTTAGGATTTAGGG
66 GTGCTAGTCCATTTATATTAGGATTTATGATTTAGTGTTTATGGTTT-AA--TTAGGATTTAAAG
* *
2062842 TTTATGATTTAGGGTTTCTATAAATTATATAATTTATTACTTTATATAGTTTATGCATAGTGTTT
128 TTTAGGATTTAGGGTTTCTATAAACTATATAATTTATTACTTTATATAGTTTATGCATAGTGTTT
* * *
2062907 CTATAAACTATATAAGTAATTTATTTTATATAGTTTATATATATACATATATATAGTTTATATAT
193 CTATAAACTATATAAGTAATATACTTTATATAGTTTATATATATACATATATATAGTCTATATAT
*
2062972 ATTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTGTTTAA
258 ACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTGTTTAA
2063037 ATATAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTAT
323 ATATAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTAT
2063102 ATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCAT
388 ATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCAT
2063167 GTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAAC-AA
453 GTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACTAA
* *
2063231 AAAATAAGTCCATTTGAAATAGTGAT-GTTCTATT
518 AAAATAAGTCAATTTGAAATAGTGATAG-TCCATT
*
2063265 TACATTAGTTTACATAGGCCCAATACATAAACCCATTATTTTATTAC-AA-ATATATATGCATTA
1 TACATTAGTTTACATAGGCCCAATACATAAACCCACTATTTTATTACAAATATATATATGCATTA
*
2063328 GTGCTAGTCCATTTATATTAGGGTTTATGATTTAG-GATTTA-GTGTTT-A-T-GG-TTTAAAGT
66 GTGCTAGTCCATTTATATTAGGATTTATGATTTAGTG-TTTATG-GTTTAATTAGGATTTAAAGT
* *
2063387 TTAGGGTTTAGGGTTT-TAATAAACTATATACTTTATTACTTTATATA-TTTATGCATAGTGTTT
129 TTAGGATTTAGGGTTTCT-ATAAACTATATAATTTATTACTTTATATAGTTTATGCATAGTGTTT
*
2063450 CTATAAACTATATAAGTAATATACTTTATATAGTTTATATATATATAGGTTATATATATATAGTC
193 CTATAAACTATATAAGTAATATACTTTATATAG--T-T-TATATATA---TACATATATATAGTC
2063515 TATATATACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAAT
251 TATATATACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAAT
2063580 TGTTTAAATATAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGC
316 TGTTTAAATATAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGC
2063645 ATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTA
381 ATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTA
*
2063710 GTTGCATGTTAGGTTAATTCACATTAATAGCCTATTTATTTTGTTGTTATGAATAAGTAATAATA
446 GTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATA
* *
2063775 AAACTAAAAAATAAGTCAATTTGCAATAGTGCTAGTCCATT
511 AAACTAAAAAATAAGTCAATTTGAAATAGTGATAGTCCATT
2063816 TACATTAGTTTA
1 TACATTAGTTTA
2063828 TCCTAATACA
Statistics
Matches: 527, Mismatches: 24, Indels: 26
0.91 0.04 0.05
Matches are distributed among these distances:
543 48 0.09
544 47 0.09
545 3 0.01
546 2 0.00
547 8 0.02
549 1 0.00
550 277 0.53
551 97 0.18
552 3 0.01
553 41 0.08
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (551 bp):
TACATTAGTTTACATAGGCCCAATACATAAACCCACTATTTTATTACAAATATATATATGCATTA
GTGCTAGTCCATTTATATTAGGATTTATGATTTAGTGTTTATGGTTTAATTAGGATTTAAAGTTT
AGGATTTAGGGTTTCTATAAACTATATAATTTATTACTTTATATAGTTTATGCATAGTGTTTCTA
TAAACTATATAAGTAATATACTTTATATAGTTTATATATATACATATATATAGTCTATATATACT
ATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTGTTTAAATA
TAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATG
GTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTT
AGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACTAAAAA
ATAAGTCAATTTGAAATAGTGATAGTCCATT
Found at i:2063572 original size:23 final size:25
Alignment explanation
Indices: 2063546--2063603 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 25
2063536 ATACATACAT
2063546 ATTATATAAAATTATTT-AATA-AA
1 ATTATATAAAATTATTTAAATATAA
*
2063569 ATTA-ATAAAATTGTTTAAATATAA
1 ATTATATAAAATTATTTAAATATAA
2063593 ATTATATAAAA
1 ATTATATAAAA
2063604 CATGATTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 11 0.35
23 8 0.26
24 6 0.19
25 6 0.19
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
ATTATATAAAATTATTTAAATATAA
Found at i:2064815 original size:2 final size:2
Alignment explanation
Indices: 2064810--2064857 Score: 53
Period size: 2 Copynumber: 23.0 Consensus size: 2
2064800 AAATTTACTT
*
2064810 TA TA TA GTA TA TA TA TA TA T- TA TA TA TA TA TA GTT TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
2064853 CTA TA
1 -TA TA
2064858 CATGATTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 1 0.03
2 34 0.85
3 5 0.12
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2064826 original size:11 final size:10
Alignment explanation
Indices: 2064810--2064857 Score: 53
Period size: 11 Copynumber: 4.6 Consensus size: 10
2064800 AAATTTACTT
2064810 TATATAGTATA
1 TATATA-TATA
2064821 TATATATAT-
1 TATATATATA
2064830 TATATATATA
1 TATATATATA
*
2064840 TAGTTTATATA
1 TA-TATATATA
2064851 TACTATA
1 TA-TATA
2064858 CATGATTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 9 0.28
10 5 0.16
11 18 0.56
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (10 bp):
TATATATATA
Found at i:2064828 original size:13 final size:13
Alignment explanation
Indices: 2064810--2064852 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
2064800 AAATTTACTT
2064810 TATATAGTATATA
1 TATATAGTATATA
*
2064823 TATATATTATATA
1 TATATAGTATATA
*
2064836 TATATAGTTTATA
1 TATATAGTATATA
2064849 TATA
1 TATA
2064853 CTATACATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (13 bp):
TATATAGTATATA
Found at i:2064835 original size:15 final size:15
Alignment explanation
Indices: 2064817--2064857 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
2064807 CTTTATATAG
2064817 TATATATATATA--T
1 TATATATATATAGTT
2064830 TATATATATATAGTT
1 TATATATATATAGTT
2064845 TATATATACTATA
1 TATATATA-TATA
2064858 CATGATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 12 0.48
15 9 0.36
16 4 0.16
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
TATATATATATAGTT
Found at i:2065063 original size:2 final size:2
Alignment explanation
Indices: 2065056--2065094 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2065046 TTATATTAGT
2065056 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
2065095 GATTAAATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2065201 original size:100 final size:100
Alignment explanation
Indices: 2065075--2065275 Score: 402
Period size: 100 Copynumber: 2.0 Consensus size: 100
2065065 ACACACACAC
2065075 ACACACACACACACACACACGATTAAATTGCATCGAATTGAAAATTCAAGAAGATATATACAATT
1 ACACACACACACACACACACGATTAAATTGCATCGAATTGAAAATTCAAGAAGATATATACAATT
2065140 AAACCATAACTAAAATGAAAGAAATCAAAAATAAA
66 AAACCATAACTAAAATGAAAGAAATCAAAAATAAA
2065175 ACACACACACACACACACACGATTAAATTGCATCGAATTGAAAATTCAAGAAGATATATACAATT
1 ACACACACACACACACACACGATTAAATTGCATCGAATTGAAAATTCAAGAAGATATATACAATT
2065240 AAACCATAACTAAAATGAAAGAAATCAAAAATAAA
66 AAACCATAACTAAAATGAAAGAAATCAAAAATAAA
2065275 A
1 A
2065276 AACAAGTGGA
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 101 1.00
ACGTcount: A:0.55, C:0.18, G:0.08, T:0.19
Consensus pattern (100 bp):
ACACACACACACACACACACGATTAAATTGCATCGAATTGAAAATTCAAGAAGATATATACAATT
AAACCATAACTAAAATGAAAGAAATCAAAAATAAA
Done.