Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006564.1 Hibiscus syriacus cultivar Beakdansim tig00016065_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: 1886890
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1769299 original size:37 final size:38
Alignment explanation
Indices: 1769238--1769591 Score: 233
Period size: 39 Copynumber: 9.2 Consensus size: 38
1769228 GAAACGTTTT
* * * *
1769238 CAAAGTTTATGTTTCAAGAGAAACTGTCTTAAGGGAGG
1 CAAAATTTATGTTTCAAGGGAAACTGTCTCAAGGGAGA
*
1769276 CAAAATTT-TCTTTCAAGGGAAACTGTCTCAAGGGAGA
1 CAAAATTTATGTTTCAAGGGAAACTGTCTCAAGGGAGA
* ** * *
1769313 CAAAACTTTCTGTTTTGAGGGAAACTATCTCAAGCGAGA
1 CAAAA-TTTATGTTTCAAGGGAAACTGTCTCAAGGGAGA
* * **
1769352 TAAAATCTTATGTTTCAAGGGAAACTATCTCAAGCAAGA
1 CAAAAT-TTATGTTTCAAGGGAAACTGTCTCAAGGGAGA
* * * * *
1769391 CAAAATCTTCTATTTCGAGGGAAACTATCTCAAGCGAGA
1 CAAAAT-TTATGTTTCAAGGGAAACTGTCTCAAGGGAGA
* * ** * **
1769430 TAAAATCTTCTGTTTTGAGGGAAACTATCTCAAGCAAGA
1 CAAAAT-TTATGTTTCAAGGGAAACTGTCTCAAGGGAGA
* * * * **
1769469 TAAAATCTTCTATTTCAAGGGAAACTATCTCAAGAAAGA
1 CAAAAT-TTATGTTTCAAGGGAAACTGTCTCAAGGGAGA
* * * * *
1769508 TAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGA
1 CAAAAT-TTATGTTTCAAGGGAAACTGTCTCAAGGGAGA
* * * ** * *
1769547 TAAGATCTTCTGTTTTGAGGGAAACTATCTCAAGCGAGA
1 CAAAAT-TTATGTTTCAAGGGAAACTGTCTCAAGGGAGA
*
1769586 TAAAAT
1 CAAAAT
1769592 CGTCTTTAAA
Statistics
Matches: 278, Mismatches: 35, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
37 30 0.11
38 11 0.04
39 237 0.85
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (38 bp):
CAAAATTTATGTTTCAAGGGAAACTGTCTCAAGGGAGA
Found at i:1769345 original size:39 final size:39
Alignment explanation
Indices: 1769286--1769592 Score: 436
Period size: 39 Copynumber: 7.9 Consensus size: 39
1769276 CAAAATTTTC
* * * *
1769286 TTTCAAGGGAAACTGTCTCAAGGGAGACAAAA-CTTTCTG
1 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATC-TTCTG
* *
1769325 TTTTGAGGGAAACTATCTCAAGCGAGATAAAATCTTATG
1 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
* * * *
1769364 TTTCAAGGGAAACTATCTCAAGCAAGACAAAATCTTCTA
1 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
1769403 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
1 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
* * *
1769442 TTTTGAGGGAAACTATCTCAAGCAAGATAAAATCTTCTA
1 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
* **
1769481 TTTCAAGGGAAACTATCTCAAGAAAGATAAAATCTTCTG
1 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
*
1769520 TTTCGAGGGAAACTATCTCAAGCGAGATAAGATCTTCTG
1 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
*
1769559 TTTTGAGGGAAACTATCTCAAGCGAGATAAAATC
1 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATC
1769593 GTCTTTAAAA
Statistics
Matches: 238, Mismatches: 29, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
39 237 1.00
40 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (39 bp):
TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
Found at i:1769448 original size:117 final size:117
Alignment explanation
Indices: 1769244--1769592 Score: 506
Period size: 117 Copynumber: 3.0 Consensus size: 117
1769234 TTTTCAAAGT
* * * ** * * * *
1769244 TTATGTTTCAAGAGAAACTGTCTTAAGGGAGGCAAAAT-TT-TCTTTCAAGGGAAACTGTCTCAA
1 TTATGTTTCAAGGGAAACTATCTCAAGAAAGACAAAATCTTCTATTTCGAGGGAAACTATCTCAA
* *
1769307 GGGAGACAAAA-CTTTCTGTTTTGAGGGAAACTATCTCAAGCGAGATAAAATC
66 GCGAGATAAAATC-TTCTGTTTTGAGGGAAACTATCTCAAGCGAGATAAAATC
*
1769359 TTATGTTTCAAGGGAAACTATCTCAAGCAAGACAAAATCTTCTATTTCGAGGGAAACTATCTCAA
1 TTATGTTTCAAGGGAAACTATCTCAAGAAAGACAAAATCTTCTATTTCGAGGGAAACTATCTCAA
*
1769424 GCGAGATAAAATCTTCTGTTTTGAGGGAAACTATCTCAAGCAAGATAAAATC
66 GCGAGATAAAATCTTCTGTTTTGAGGGAAACTATCTCAAGCGAGATAAAATC
* * * *
1769476 TTCTATTTCAAGGGAAACTATCTCAAGAAAGATAAAATCTTCTGTTTCGAGGGAAACTATCTCAA
1 TTATGTTTCAAGGGAAACTATCTCAAGAAAGACAAAATCTTCTATTTCGAGGGAAACTATCTCAA
*
1769541 GCGAGATAAGATCTTCTGTTTTGAGGGAAACTATCTCAAGCGAGATAAAATC
66 GCGAGATAAAATCTTCTGTTTTGAGGGAAACTATCTCAAGCGAGATAAAATC
1769593 GTCTTTAAAA
Statistics
Matches: 212, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
115 32 0.15
116 2 0.01
117 177 0.83
118 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (117 bp):
TTATGTTTCAAGGGAAACTATCTCAAGAAAGACAAAATCTTCTATTTCGAGGGAAACTATCTCAA
GCGAGATAAAATCTTCTGTTTTGAGGGAAACTATCTCAAGCGAGATAAAATC
Found at i:1769787 original size:75 final size:76
Alignment explanation
Indices: 1769599--1769834 Score: 318
Period size: 75 Copynumber: 3.1 Consensus size: 76
1769589 AATCGTCTTT
* * * *
1769599 AAAAACAATATTGAGTGAAATGAAATGCCTTCTTTCGAGTAAAAAACCGTCTAAAGCGAGACAAA
1 AAAAACAATATTGAGTGAAATGAAATGTCTTCTTTCGAGT-AAAAACAGTCTCAAGTGAGACAAA
*
1769664 TATTGTTTTAAG
65 TCTTGTTTTAAG
* * *
1769676 AAAAACAATATTGAGTGAAAT-AAATCTTCTTGTTTCGAGTAAAAACTGTCTCAAGTGAGACAAA
1 AAAAACAATATTGAGTGAAATGAAAT-GTCTTCTTTCGAGTAAAAACAGTCTCAAGTGAGACAAA
1769740 TCTTG-TTTAAG
65 TCTTGTTTTAAG
* *
1769751 AAAAACAATCTTGAGTCAAATGAAATGTCTTCTTTCGAGT-AAAACAGTCTCAAGTGAGACAAAG
1 AAAAACAATATTGAGTGAAATGAAATGTCTTCTTTCGAGTAAAAACAGTCTCAAGTGAGACAAA-
*
1769815 TC-CGTTTTAAG
65 TCTTGTTTTAAG
1769826 AAAAACAAT
1 AAAAACAAT
1769835 CTATAGTGAG
Statistics
Matches: 142, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
74 23 0.16
75 54 0.38
76 33 0.23
77 32 0.23
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (76 bp):
AAAAACAATATTGAGTGAAATGAAATGTCTTCTTTCGAGTAAAAACAGTCTCAAGTGAGACAAAT
CTTGTTTTAAG
Found at i:1770687 original size:18 final size:16
Alignment explanation
Indices: 1770648--1770691 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
1770638 CAAAGCATTT
*
1770648 TATTTTTGCTACTTTA
1 TATTTTTGCTACTTAA
*
1770664 TTTTTTTAGTCTACTTAA
1 TATTTTT-G-CTACTTAA
1770682 TATTTTTGCT
1 TATTTTTGCT
1770692 TTATTCTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 8 0.35
17 2 0.09
18 13 0.57
ACGTcount: A:0.18, C:0.11, G:0.07, T:0.64
Consensus pattern (16 bp):
TATTTTTGCTACTTAA
Found at i:1772562 original size:59 final size:59
Alignment explanation
Indices: 1772470--1772590 Score: 188
Period size: 59 Copynumber: 2.1 Consensus size: 59
1772460 AAATAGATGA
* * *
1772470 TAAGTGTCCTATCGAACCCTCCTAGTCACAATGAAAAGGCAAACTCGATAATATGGATC
1 TAAGTATCCTATCAAACCCTCCTAGTCACAATGAAAAGACAAACTCGATAATATGGATC
** *
1772529 TAAGTATCCTATCAAACCCTCCTAGTTGCAATGAAAAGACAAACTCGATAATATGGCTC
1 TAAGTATCCTATCAAACCCTCCTAGTCACAATGAAAAGACAAACTCGATAATATGGATC
1772588 TAA
1 TAA
1772591 CCAATCCTCC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (59 bp):
TAAGTATCCTATCAAACCCTCCTAGTCACAATGAAAAGACAAACTCGATAATATGGATC
Found at i:1787175 original size:3 final size:3
Alignment explanation
Indices: 1787163--1787234 Score: 128
Period size: 3 Copynumber: 24.3 Consensus size: 3
1787153 CTTGTAATCT
1787163 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
1787210 ATA ATA ATA ATA ATA ATG ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1787235 ATGTTTTTGA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 64 0.97
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1789680 original size:23 final size:25
Alignment explanation
Indices: 1789647--1789707 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 25
1789637 ATGTCCATCC
*
1789647 ACCTTCCAGAAG-G-TGCTGACTAG
1 ACCTTCTAGAAGCGCTGCTGACTAG
* *
1789670 ATCTTCTAGAAAGCTGCTGCTGACTGG
1 ACCTTCTAG-AAGC-GCTGCTGACTAG
1789697 ACCTTCTAGAA
1 ACCTTCTAGAA
1789708 ACTGCCATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
23 7 0.23
24 3 0.10
26 3 0.10
27 17 0.57
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (25 bp):
ACCTTCTAGAAGCGCTGCTGACTAG
Found at i:1789702 original size:27 final size:26
Alignment explanation
Indices: 1789660--1789712 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
1789650 TTCCAGAAGG
*
1789660 TGCTGACTAGATCTTCTAGAAAGCTGC
1 TGCTGACTAGACCTTCTAGAAA-CTGC
*
1789687 TGCTGACTGGACCTTCTAGAAACTGC
1 TGCTGACTAGACCTTCTAGAAACTGC
1789713 CATGTGAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (26 bp):
TGCTGACTAGACCTTCTAGAAACTGC
Found at i:1795993 original size:54 final size:55
Alignment explanation
Indices: 1795928--1796044 Score: 164
Period size: 54 Copynumber: 2.1 Consensus size: 55
1795918 GTAGTTAAAA
* *
1795928 ATGATTGAGTGCCTCTGTGCTTCAGTCTAGAATCTGACACATCTATGC-TTTGGG
1 ATGATTGAGTGCCTCTGTACTTCAATCTAGAATCTGACACATCTATGCTTTTGGG
* ** * *
1795982 ATGATTGAGTGCCTCTGTACTTCAATCTAGGATCTGGTACCTCTGTGCTTTTGGG
1 ATGATTGAGTGCCTCTGTACTTCAATCTAGAATCTGACACATCTATGCTTTTGGG
1796037 ATGATTGA
1 ATGATTGA
1796045 TCACATCAGT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
54 41 0.75
55 14 0.25
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (55 bp):
ATGATTGAGTGCCTCTGTACTTCAATCTAGAATCTGACACATCTATGCTTTTGGG
Found at i:1796257 original size:57 final size:57
Alignment explanation
Indices: 1796085--1796258 Score: 206
Period size: 57 Copynumber: 3.1 Consensus size: 57
1796075 ATCTTTGTAT
* * *
1796085 ATTAAAGAAACGATTGAGCACCTCTGTGCATCTATCTTTAAACTGACACCTCTGTGT
1 ATTAAAGAAACGATTGAGCACCTCTGTGCATCAATCTTTAAACTGACACCTTTGTGC
* ** * * *
1796142 ATTAAAGAAACGATTGAGAATTTATGTGCATCAATCTTTAAACTGGCA-CTTGTATGC
1 ATTAAAGAAACGATTGAGCACCTCTGTGCATCAATCTTTAAACTGACACCTT-TGTGC
* * * * *
1796199 ATTAAATAAATGATTGAGCACCTCTCTGCATCAATCCTTAAGCTGACACCTTTGTGC
1 ATTAAAGAAACGATTGAGCACCTCTGTGCATCAATCTTTAAACTGACACCTTTGTGC
1796256 ATT
1 ATT
1796259 TACTATACTA
Statistics
Matches: 95, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
56 2 0.02
57 90 0.95
58 3 0.03
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.33
Consensus pattern (57 bp):
ATTAAAGAAACGATTGAGCACCTCTGTGCATCAATCTTTAAACTGACACCTTTGTGC
Found at i:1802789 original size:24 final size:24
Alignment explanation
Indices: 1802757--1802804 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1802747 AAGTCTTCCT
1802757 GATGATGTATAAAACATCTATGTA
1 GATGATGTATAAAACATCTATGTA
1802781 GATGATGTATAAAACATCTATGTA
1 GATGATGTATAAAACATCTATGTA
1802805 CAATGTCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (24 bp):
GATGATGTATAAAACATCTATGTA
Found at i:1817391 original size:29 final size:27
Alignment explanation
Indices: 1817318--1817383 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
1817308 TTGATGCATA
*
1817318 CTTGTTTCTGCATGGGATTATTCCCTT
1 CTTGTTTCTGCATGGGATTATTCCCAT
* *
1817345 CTTGATTCTACATGGGATTAAATTCCCAT
1 CTTGTTTCTGCATGGGATT--ATTCCCAT
1817374 CTTGTTTCTG
1 CTTGTTTCTG
1817384 TTTGGGATCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 17 0.53
29 15 0.47
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (27 bp):
CTTGTTTCTGCATGGGATTATTCCCAT
Found at i:1817498 original size:43 final size:43
Alignment explanation
Indices: 1817430--1817515 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
1817420 GATTTCTAAC
* * *
1817430 TCTGCTTGGGATCCTCTACGAAGGGCAATATCCCCATTCTGAT
1 TCTGATTGGGATCCTCTACGAAGGGCAACATCCCCATCCTGAT
* *
1817473 TCTGATTGGGATCCTCTACGGAGGGCTACATCCCCATCCTGAT
1 TCTGATTGGGATCCTCTACGAAGGGCAACATCCCCATCCTGAT
1817516 ATTCTGTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (43 bp):
TCTGATTGGGATCCTCTACGAAGGGCAACATCCCCATCCTGAT
Found at i:1819645 original size:15 final size:15
Alignment explanation
Indices: 1819622--1819653 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1819612 TGTTGTTGGC
*
1819622 CAACTAATTTTTGCA
1 CAACAAATTTTTGCA
1819637 CAACAAATTTTTGCA
1 CAACAAATTTTTGCA
1819652 CA
1 CA
1819654 TCAGGGGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (15 bp):
CAACAAATTTTTGCA
Found at i:1821721 original size:90 final size:90
Alignment explanation
Indices: 1821568--1821745 Score: 311
Period size: 90 Copynumber: 2.0 Consensus size: 90
1821558 CCTAACACAC
* *
1821568 CCTTTTATAGCCAAGTTACCCTAATCATATTAGTGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGGTTTTATTATTTCAAATTAATTAAATCTAT
* *
1821633 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
*
1821658 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGGTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGGTTTTATTATTTCAAATTAATTAAATCTAT
1821723 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
1821746 TTCAGGATTA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.46
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGGTTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:1822898 original size:27 final size:27
Alignment explanation
Indices: 1822843--1822898 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
1822833 CCGCCATCAC
* *
1822843 CACTTTGAACTTGAAACTCCATAGCAT
1 CACTTTGAACTTGAAACTCCACAACAT
* *
1822870 CACTTTGAACTTGAAAGTCCACAATAT
1 CACTTTGAACTTGAAACTCCACAACAT
1822897 CA
1 CA
1822899 AGATCTTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.29
Consensus pattern (27 bp):
CACTTTGAACTTGAAACTCCACAACAT
Found at i:1824449 original size:23 final size:23
Alignment explanation
Indices: 1824392--1824452 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1824382 CTCGTATAAA
*
1824392 TGCACCGAAGTACCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1824415 TACACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1824438 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
1824453 TATAAGATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.31, C:0.28, G:0.23, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1831373 original size:23 final size:23
Alignment explanation
Indices: 1831347--1831396 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1831337 CACCACAGCT
1831347 CGTACAAATGCACCGAAGTGCCA
1 CGTACAAATGCACCGAAGTGCCA
* * *
1831370 CGTAGAATTGCACCGAAGTGCCG
1 CGTACAAATGCACCGAAGTGCCA
1831393 CGTA
1 CGTA
1831397 GAATTGTACC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (23 bp):
CGTACAAATGCACCGAAGTGCCA
Found at i:1831397 original size:23 final size:23
Alignment explanation
Indices: 1831355--1831407 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
1831345 CTCGTACAAA
1831355 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1831378 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1831401 TGTACCG
1 TGCACCG
1831408 TAGTTCCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1840530 original size:10 final size:11
Alignment explanation
Indices: 1840503--1840595 Score: 61
Period size: 11 Copynumber: 8.6 Consensus size: 11
1840493 GAAAGTACCT
*
1840503 AAATAATAATA
1 AAATAAAAATA
*
1840514 AATTAAAAA-A
1 AAATAAAAATA
*
1840524 GAATAAAAATA
1 AAATAAAAATA
*
1840535 AAATAAAAGTGA
1 AAATAAAAAT-A
1840547 AAA-AAGTAAA-A
1 AAATAA--AAATA
1840558 AAAT-AAAA-A
1 AAATAAAAATA
1840567 AAATAAAAATA
1 AAATAAAAATA
* * *
1840578 ATACAATAATA
1 AAATAAAAATA
1840589 AAATAAA
1 AAATAAA
1840596 TTATATATAT
Statistics
Matches: 62, Mismatches: 13, Indels: 14
0.70 0.15 0.16
Matches are distributed among these distances:
9 8 0.13
10 12 0.19
11 36 0.58
12 4 0.06
13 2 0.03
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:1840539 original size:26 final size:26
Alignment explanation
Indices: 1840503--1840598 Score: 90
Period size: 28 Copynumber: 3.6 Consensus size: 26
1840493 GAAAGTACCT
1840503 AAATAATAATAAATTAAAAAAGAATAA
1 AAATAA-AATAAATTAAAAAAGAATAA
*
1840530 AAATAAAATAAAAGTGAAAAAAGTAA-AA
1 AAATAAAAT-AAA-TTAAAAAAG-AATAA
* *
1840558 AAATAAAA-AAAAT-AAAAATAATACA
1 AAATAAAATAAATTAAAAAAGAATA-A
1840583 ATAATAAAATAAATTA
1 A-AATAAAATAAATTA
1840599 TATATATATA
Statistics
Matches: 56, Mismatches: 5, Indels: 15
0.74 0.07 0.20
Matches are distributed among these distances:
23 2 0.04
24 6 0.11
25 2 0.04
26 13 0.23
27 13 0.23
28 18 0.32
29 2 0.04
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (26 bp):
AAATAAAATAAATTAAAAAAGAATAA
Found at i:1840568 original size:8 final size:8
Alignment explanation
Indices: 1840503--1840595 Score: 53
Period size: 8 Copynumber: 10.9 Consensus size: 8
1840493 GAAAGTACCT
1840503 AAATAATAA
1 AAATAA-AA
*
1840512 TAAATTAAA
1 -AAATAAAA
*
1840521 AAAGAATAA
1 AAATAA-AA
1840530 AAATAAAATA
1 AAAT-AAA-A
1840540 AAAGTGAAAA
1 AAA-T-AAAA
*
1840550 AAGTAAAA
1 AAATAAAA
1840558 AAATAAAA
1 AAATAAAA
*
1840566 AAA-ATAA
1 AAATAAAA
*
1840573 AAATAATA
1 AAATAAAA
* *
1840581 CAATAATA
1 AAATAAAA
1840589 AAATAAA
1 AAATAAA
1840596 TTATATATAT
Statistics
Matches: 65, Mismatches: 13, Indels: 12
0.72 0.14 0.13
Matches are distributed among these distances:
7 6 0.09
8 32 0.49
9 9 0.14
10 14 0.22
11 4 0.06
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (8 bp):
AAATAAAA
Found at i:1840568 original size:9 final size:9
Alignment explanation
Indices: 1840518--1840580 Score: 56
Period size: 9 Copynumber: 6.9 Consensus size: 9
1840508 ATAATAAATT
*
1840518 AAAAAAGAA
1 AAAAAATAA
*
1840527 TAAAAATAA
1 AAAAAATAA
*
1840536 AATAAAAGTGA
1 AA-AAAA-TAA
*
1840547 AAAAAGT-A
1 AAAAAATAA
1840555 AAAAAATAA
1 AAAAAATAA
1840564 AAAAAATAA
1 AAAAAATAA
*
1840573 AAATAATA
1 AAAAAATA
1840581 CAATAATAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
8 7 0.16
9 26 0.59
10 7 0.16
11 4 0.09
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.14
Consensus pattern (9 bp):
AAAAAATAA
Found at i:1840580 original size:18 final size:17
Alignment explanation
Indices: 1840503--1840580 Score: 57
Period size: 17 Copynumber: 4.3 Consensus size: 17
1840493 GAAAGTACCT
* *
1840503 AAATAATAATAAATTAAA
1 AAATAA-AAAAAATAAAA
* *
1840521 AAAGAATAAAAATAAAATA
1 AAATAAAAAAAAT-AAA-A
* *
1840540 AAAGTGAAAAAAGTAAAA
1 AAA-TAAAAAAAATAAAA
1840558 AAATAAAAAAAATAAAA
1 AAATAAAAAAAATAAAA
1840575 ATAATA
1 A-AATA
1840581 CAATAATAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
17 18 0.39
18 15 0.33
19 7 0.15
20 6 0.13
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (17 bp):
AAATAAAAAAAATAAAA
Found at i:1843885 original size:29 final size:29
Alignment explanation
Indices: 1843842--1843943 Score: 89
Period size: 29 Copynumber: 3.5 Consensus size: 29
1843832 GAACATAATG
*
1843842 AATAGTCGAGTGACTATTTTGTAACTTTT
1 AATAGTCGAGAGACTATTTTGTAACTTTT
* **** * **
1843871 AATAGTCGAGGGACTCAACAAAGCAACTCAT
1 AATAGTCGAGAGACT--ATTTTGTAACTTTT
*
1843902 -ATAGTCGAAAGACTATTTTGTAACTTTT
1 AATAGTCGAGAGACTATTTTGTAACTTTT
1843930 AATAGTCGAGAGAC
1 AATAGTCGAGAGAC
1843944 CCAACAAATC
Statistics
Matches: 52, Mismatches: 18, Indels: 6
0.68 0.24 0.08
Matches are distributed among these distances:
28 7 0.13
29 26 0.50
30 12 0.23
31 7 0.13
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (29 bp):
AATAGTCGAGAGACTATTTTGTAACTTTT
Found at i:1843916 original size:59 final size:60
Alignment explanation
Indices: 1843843--1843988 Score: 199
Period size: 59 Copynumber: 2.5 Consensus size: 60
1843833 AACATAATGA
* * * *
1843843 ATAGTCGAGTGACTATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGCAA-CTCAT
1 ATAGTCGAATGACTATTTTGTAACTTTTAATAGTCGAGAGACCCAACAAAGCAATATCAT
* *
1843902 ATAGTCGAAAGACTATTTTGTAACTTTTAATAGTCGAGAGACCCAACAAATCAATATCAT
1 ATAGTCGAATGACTATTTTGTAACTTTTAATAGTCGAGAGACCCAACAAAGCAATATCAT
1843962 ATAGTC-AGATGACTATTTGTGT-ACTTT
1 ATAGTCGA-ATGACTATTT-TGTAACTTT
1843989 ATCCTAAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
59 50 0.65
60 24 0.31
61 3 0.04
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (60 bp):
ATAGTCGAATGACTATTTTGTAACTTTTAATAGTCGAGAGACCCAACAAAGCAATATCAT
Found at i:1845413 original size:73 final size:71
Alignment explanation
Indices: 1845297--1845440 Score: 254
Period size: 73 Copynumber: 2.0 Consensus size: 71
1845287 AACCTATATG
1845297 TTGCTTTTATAGCACTCAATAGTACACAGCTATCCCTAACAGACTTAAAA-CTATATGTTAGGTT
1 TTGCTTTTATAGCACTCAATAGTACACAGCTATCCCTAACAGACTTAAAACCTATATGTTAGGTT
1845361 AACAGC
66 AACAGC
1845367 TTGCTTTTATAGCACTCATATGACGTACACAGCTATCCCTAACAGACTTAAAACCTATATGTTAG
1 TTGCTTTTATAGCACTCA-AT-A-GTACACAGCTATCCCTAACAGACTTAAAACCTATATGTTAG
1845432 GTTAACAGC
63 GTTAACAGC
1845441 CAAGGTCAAA
Statistics
Matches: 70, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
70 18 0.26
71 2 0.03
72 1 0.01
73 29 0.41
74 20 0.29
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.31
Consensus pattern (71 bp):
TTGCTTTTATAGCACTCAATAGTACACAGCTATCCCTAACAGACTTAAAACCTATATGTTAGGTT
AACAGC
Found at i:1846900 original size:12 final size:12
Alignment explanation
Indices: 1846883--1846907 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1846873 ATATTTTTGA
1846883 TAAAATATTATT
1 TAAAATATTATT
1846895 TAAAATATTATT
1 TAAAATATTATT
1846907 T
1 T
1846908 TTTATAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:1851751 original size:52 final size:52
Alignment explanation
Indices: 1851644--1851752 Score: 139
Period size: 52 Copynumber: 2.1 Consensus size: 52
1851634 AGAGACAGAG
* * * * *
1851644 GAAGAAGATGATGAACAATATCAGTTAGGGTTAGAGAAGATGTATAGAAGAA
1 GAAGAAGAAGATGAACAATAACAGTTAGGGTTAGAAAAGATGAACAGAAGAA
* *
1851696 GAAGAAGAAGATGAATAATAAGAGTTAGGGTTAGAAAAGATGAACA-AAGACA
1 GAAGAAGAAGATGAACAATAACAGTTAGGGTTAGAAAAGATGAACAGAAGA-A
1851748 GAAGA
1 GAAGA
1851753 TGAAAATGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
51 4 0.08
52 45 0.92
ACGTcount: A:0.50, C:0.04, G:0.28, T:0.17
Consensus pattern (52 bp):
GAAGAAGAAGATGAACAATAACAGTTAGGGTTAGAAAAGATGAACAGAAGAA
Found at i:1851880 original size:53 final size:53
Alignment explanation
Indices: 1851770--1851880 Score: 136
Period size: 53 Copynumber: 2.1 Consensus size: 53
1851760 GTTTAATTTG
* * * *
1851770 GGTTCAGGGTTAGAGAAGATAACCAGAGATAGAAGATGAAGAGGCTATGTTAG
1 GGTTTAGGATTAGAGAAGATAACCAGAGATAAAAGATGAAGAGGCTATGTTAA
* *
1851823 GGTTTAGGATTAGAGAAGATGAA-TAGAGATAAAA-AGTGAAGAGGCTCTGTTAA
1 GGTTTAGGATTAGAGAAGAT-AACCAGAGATAAAAGA-TGAAGAGGCTATGTTAA
1851876 GGTTT
1 GGTTT
1851881 GAGTCAGAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
52 1 0.02
53 47 0.94
54 2 0.04
ACGTcount: A:0.38, C:0.05, G:0.32, T:0.24
Consensus pattern (53 bp):
GGTTTAGGATTAGAGAAGATAACCAGAGATAAAAGATGAAGAGGCTATGTTAA
Found at i:1851975 original size:65 final size:65
Alignment explanation
Indices: 1851905--1852037 Score: 187
Period size: 65 Copynumber: 2.0 Consensus size: 65
1851895 AAATAGTTGT
* * * *
1851905 GGGTTTGATCTAAAAATAGTTTGGGTTTT-TGTTTTCGGTGTTTGTAAGGATCAAATAAGGGTTT
1 GGGTTTGATCTAAAAATAGGTT-AGTTTTAAGTTTTCGGTGTTTGTAAGGATCAAAGAAGGGTTT
1851969 G
65 G
* * *
1851970 GGGTTTGATTTAAAAATAGGTTAGTTTTAAGTTTTTGGTGTTTGTAAGGATCAAAGAATGGTTTG
1 GGGTTTGATCTAAAAATAGGTTAGTTTTAAGTTTTCGGTGTTTGTAAGGATCAAAGAAGGGTTTG
1852035 GGG
1 GGG
1852038 AAGAATAGGG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
64 5 0.08
65 55 0.92
ACGTcount: A:0.25, C:0.03, G:0.30, T:0.42
Consensus pattern (65 bp):
GGGTTTGATCTAAAAATAGGTTAGTTTTAAGTTTTCGGTGTTTGTAAGGATCAAAGAAGGGTTTG
Found at i:1852180 original size:103 final size:103
Alignment explanation
Indices: 1852002--1852255 Score: 282
Period size: 103 Copynumber: 2.5 Consensus size: 103
1851992 AGTTTTAAGT
* * * * * * * * *
1852002 TTTTGGTGTTTGT-AAGGATCAAA-GAATGGTTTGGGGAAGAATAGGGATGAACAAAGGTTGAAT
1 TTTTGGTGTTTGTGAA-GATCAAATGAGTGTTTTGGGGATGAACACGAATAAACAAAGATTGAAA
* * * *
1852065 TTTTGGGTGTTTGATCG-TAAA-CACGGGAATGAGTTTGGG
65 TTTTAGGCGTTTGATCGAAAAACCA-GGAAATG-GTTTGGG
* *
1852104 TTTTGGTGTTTGTGAAGATCAAATGAGTGTTTTGGGGATGAACACGAATAAACAACGATTTAAAT
1 TTTTGGTGTTTGTGAAGATCAAATGAGTGTTTTGGGGATGAACACGAATAAACAAAGATTGAAAT
1852169 TTTAGGCGTTTGATCGAAAAACCAGGAAATGGTTTGGG
66 TTTAGGCGTTTGATCGAAAAACCAGGAAATGGTTTGGG
* * * *
1852207 TTTTGGTGTTTATGAAGATCAAATAAGGGTTTTTGGGATGAACACGAAT
1 TTTTGGTGTTTGTGAAGATCAAATGAGTGTTTTGGGGATGAACACGAAT
1852256 GGACAAAGGA
Statistics
Matches: 129, Mismatches: 19, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
102 20 0.16
103 98 0.76
104 9 0.07
105 2 0.02
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (103 bp):
TTTTGGTGTTTGTGAAGATCAAATGAGTGTTTTGGGGATGAACACGAATAAACAAAGATTGAAAT
TTTAGGCGTTTGATCGAAAAACCAGGAAATGGTTTGGG
Found at i:1852653 original size:29 final size:29
Alignment explanation
Indices: 1852616--1852719 Score: 100
Period size: 33 Copynumber: 3.3 Consensus size: 29
1852606 AATATATGTT
*
1852616 TATATTAATAAATTAATAAATAATTTATA
1 TATACTAATAAATTAATAAATAATTTATA
1852645 TATACTAATAAATTATATAATATATAGTTTATA
1 TATACTAATAAATTA-ATAA-ATA-A-TTTATA
* * *
1852678 TATACTAATGAACTATATACTATATAGTTTATA
1 TATACTAAT-AA--AT-TAATAAATAATTTATA
1852711 TATACTAAT
1 TATACTAAT
1852720 GAACTATATC
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
29 14 0.22
30 4 0.06
31 3 0.05
32 1 0.02
33 30 0.48
34 2 0.03
35 3 0.05
36 4 0.06
37 2 0.03
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (29 bp):
TATACTAATAAATTAATAAATAATTTATA
Found at i:1852666 original size:33 final size:33
Alignment explanation
Indices: 1852629--1853072 Score: 255
Period size: 33 Copynumber: 13.6 Consensus size: 33
1852619 ATTAATAAAT
* * * *
1852629 TAATAAATAATTTATATATACTAATAAATTATA
1 TAATATATAGTTTATATATACTAATGAACTATA
1852662 TAATATATAGTTTATATATACTAATGAACTATA
1 TAATATATAGTTTATATATACTAATGAACTATA
*
1852695 TACTATATAGTTTATATATACTAATGAACTATA
1 TAATATATAGTTTATATATACTAATGAACTATA
** *
1852728 TCCTATATAGTTTCTATATACTAATGAACTATA
1 TAATATATAGTTTATATATACTAATGAACTATA
** * * *
1852761 TCCTATATAGTTTCTATATACT-AT-ATAGTTTA
1 TAATATATAGTTTATATATACTAATGA-ACTATA
* *
1852793 TAA-ATACTA-ATGA-ACTATA-TAAT--A-TATA
1 TAATATA-TAGTTTATA-TATACTAATGAACTATA
* * * *
1852821 TAGTTTATA--TTA-ATAAACT-AT-ACAATATA
1 TAATATATAGTTTATATATACTAATGA-ACTATA
* * * *
1852850 TAGTTTATA-TTTATATATACCAATGAATTATA
1 TAATATATAGTTTATATATACTAATGAACTATA
* * ** *
1852882 TAGTTTATA-TAAACTA-ATGAACTATATGATCTATA
1 TAATATATAGTTTA-TATAT--ACTA-ATGAACTATA
* * *
1852917 TACTATACATTTTATATATAGTTTAAACTAATGAACTATA
1 TAATATATA-GTT-TATATA---T--ACTAATGAACTATA
* *
1852957 TAATATATAATTTATATGTACTAATGAACTATA
1 TAATATATAGTTTATATATACTAATGAACTATA
*
1852990 TACTATATAGTTTATATATACTAATGAAC--TA
1 TAATATATAGTTTATATATACTAATGAACTATA
* * * *
1853021 TAATATATA-TATATATATATTAATAAAGTATA
1 TAATATATAGTTTATATATACTAATGAACTATA
1853053 -AAGTATATAGTTTATATATA
1 TAA-TATATAGTTTATATATA
1853073 GTATATAAAA
Statistics
Matches: 336, Mismatches: 47, Indels: 56
0.77 0.11 0.13
Matches are distributed among these distances:
26 5 0.01
27 4 0.01
28 8 0.02
29 16 0.05
30 20 0.06
31 28 0.08
32 37 0.11
33 166 0.49
34 3 0.01
35 15 0.04
37 3 0.01
38 7 0.02
39 2 0.01
40 16 0.05
41 6 0.02
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.43
Consensus pattern (33 bp):
TAATATATAGTTTATATATACTAATGAACTATA
Found at i:1852830 original size:51 final size:51
Alignment explanation
Indices: 1852723--1852820 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
1852713 TACTAATGAA
* * * *
1852723 CTATATCCTATATAGTTTCTATATACTAATGAACTATATCCTATATAGTTT
1 CTATATACTATATAGTTTATAAATACTAATGAACTATATCATATATAGTTT
*
1852774 CTATATACTATATAGTTTATAAATACTAATGAACTATATAATATATA
1 CTATATACTATATAGTTTATAAATACTAATGAACTATATCATATATA
1852821 TAGTTTATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (51 bp):
CTATATACTATATAGTTTATAAATACTAATGAACTATATCATATATAGTTT
Found at i:1852840 original size:31 final size:31
Alignment explanation
Indices: 1852782--1852891 Score: 93
Period size: 31 Copynumber: 3.5 Consensus size: 31
1852772 TTCTATATAC
*
1852782 TATATAGTTTATAAATACTAATGAACTATATAATA
1 TATATAGTTTAT--AT--TAATAAACTATATAATA
*
1852817 TATATAGTTTATATTAATAAACTATA-CA-A
1 TATATAGTTTATATTAATAAACTATATAATA
* *
1852846 TATATAGTTTATATTTATATATACCA-ATGAAT-
1 TATATAGTTTATA-TTA-ATAAACTATAT-AATA
1852878 TATATAGTTTATAT
1 TATATAGTTTATAT
1852892 AAACTAATGA
Statistics
Matches: 65, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
29 14 0.22
30 5 0.08
31 18 0.28
32 14 0.22
33 2 0.03
35 12 0.18
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (31 bp):
TATATAGTTTATATTAATAAACTATATAATA
Found at i:1852888 original size:26 final size:25
Alignment explanation
Indices: 1852855--1852918 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
1852845 ATATATAGTT
* *
1852855 TATATTTATATATACCAATGAATTA
1 TATATTTATATAAACCAATGAACTA
*
1852880 TATAGTTTATATAAACTAATGAACTA
1 TATA-TTTATATAAACCAATGAACTA
*
1852906 TATGATCTATATA
1 TAT-ATTTATATA
1852919 CTATACATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 4 0.12
26 28 0.85
27 1 0.03
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (25 bp):
TATATTTATATAAACCAATGAACTA
Found at i:1853095 original size:42 final size:43
Alignment explanation
Indices: 1853023--1853120 Score: 137
Period size: 42 Copynumber: 2.3 Consensus size: 43
1853013 ATGAACTATA
* * *
1853023 ATATATATATATATATATTAATAAAGTATAAAGTATATAGTTT
1 ATATATATATATAAAAATTAATAAAGTATAAACTATATAGTTT
1853066 ATATATAGTATATAAAAATT-ATAAA-TATAAACTATATAGTTT
1 ATATATA-TATATAAAAATTAATAAAGTATAAACTATATAGTTT
1853108 ATATATATTATAT
1 ATATATA-TATAT
1853121 TAATATATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
42 28 0.56
43 12 0.24
44 10 0.20
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.44
Consensus pattern (43 bp):
ATATATATATATAAAAATTAATAAAGTATAAACTATATAGTTT
Found at i:1853145 original size:31 final size:31
Alignment explanation
Indices: 1853065--1853160 Score: 82
Period size: 28 Copynumber: 3.3 Consensus size: 31
1853055 GTATATAGTT
1853065 TATATATAGTATATAAA-A-ATTATA--AATA
1 TATATATA-TATATAAATATATTATATTAATA
* * *
1853093 TAAACTATATAGTTTATATATATTATATTAATA
1 TATA-TATATA-TATAAATATATTATATTAATA
1853126 TATATATATATATAAATATA--A-ATTAATA
1 TATATATATATATAAATATATTATATTAATA
1853154 TAT-TATA
1 TATATATA
1853161 ATTGTTTTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
27 4 0.07
28 15 0.27
29 9 0.16
30 1 0.02
31 14 0.25
32 6 0.11
33 7 0.12
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (31 bp):
TATATATATATATAAATATATTATATTAATA
Found at i:1853145 original size:42 final size:41
Alignment explanation
Indices: 1853023--1853160 Score: 120
Period size: 42 Copynumber: 3.3 Consensus size: 41
1853013 ATGAACTATA
* * *
1853023 ATATATA-TATATATATATTAATAAAGTATAAAGTATATAGTTT
1 ATATATATTATATAAAAATT-ATAAA-TATAAA-CATATAGTTT
*
1853066 ATATATAGTATATAAAAATTATAAATATAAACTATATAGTTT
1 ATATATATTATATAAAAATTATAAATATAAAC-ATATAGTTT
* * * **
1853108 ATATATATTATATTAATATATATATATATATAA-ATATAAATT
1 ATATATATTATATAAAAAT-TATAAATATA-AACATATAGTTT
1853150 A-ATATATTATA
1 ATATATATTATA
1853161 ATTGTTTTAA
Statistics
Matches: 82, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
41 10 0.12
42 39 0.48
43 21 0.26
44 12 0.15
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (41 bp):
ATATATATTATATAAAAATTATAAATATAAACATATAGTTT
Found at i:1853156 original size:2 final size:2
Alignment explanation
Indices: 1853019--1853145 Score: 70
Period size: 2 Copynumber: 64.0 Consensus size: 2
1853009 ACTAATGAAC
* *
1853019 TA TA -A TA TA TA TA TA TA TA TA T- TA -A TA AA GTA TA AA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* * * * *
1853060 TA GTT TA TA TA TA GTA TA TA AA AA T- TA TA AA TA TA AA CTA TA
1 TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* *
1853102 TA GTT TA TA TA TA T- TA TA T- TA -A TA TA TA TA TA TA TA TA AA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1853142 TA TA
1 TA TA
1853146 AATTAATATA
Statistics
Matches: 96, Mismatches: 16, Indels: 26
0.70 0.12 0.19
Matches are distributed among these distances:
1 7 0.07
2 82 0.85
3 7 0.07
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1861424 original size:60 final size:60
Alignment explanation
Indices: 1861360--1861475 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
1861350 TCTCTGACTA
* * * ** *
1861360 TCATTCTAAATTAATCCTCAAACTTTTT-ATTATTTCAATCTCATCCCCAAACTATAACTT
1 TCATTCCAAACTAATCCCCAAACTTTTTGAACATTCCAATCTCAT-CCCAAACTATAACTT
* *
1861420 TCATTCCAAACTATTCCCCAAACTTTTTGAACATTCCAATTTCATCCCAAACTATA
1 TCATTCCAAACTAATCCCCAAACTTTTTGAACATTCCAATCTCATCCCAAACTATA
1861476 CGTATATACT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 35 0.74
61 12 0.26
ACGTcount: A:0.34, C:0.28, G:0.01, T:0.38
Consensus pattern (60 bp):
TCATTCCAAACTAATCCCCAAACTTTTTGAACATTCCAATCTCATCCCAAACTATAACTT
Found at i:1864599 original size:2 final size:2
Alignment explanation
Indices: 1864592--1864657 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
1864582 GTATGGCCAT
1864592 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
1864634 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
1864658 AACACTTTAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1864718 original size:2 final size:2
Alignment explanation
Indices: 1864713--1864738 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1864703 ACACACACAC
1864713 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
1864739 GAGAAATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1865683 original size:13 final size:13
Alignment explanation
Indices: 1865667--1865704 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
1865657 TTTTGTTTCG
1865667 TTTTTTCTTTCTA
1 TTTTTTCTTTCTA
1865680 TTTTTTCTTTCTA
1 TTTTTTCTTTCTA
1865693 TTCTTTATCTTT
1 TT-TTT-TCTTT
1865705 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 15 0.65
14 3 0.13
15 5 0.22
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTCTTTCTA
Found at i:1865959 original size:3 final size:3
Alignment explanation
Indices: 1865945--1866001 Score: 73
Period size: 3 Copynumber: 19.3 Consensus size: 3
1865935 AAGAAATACA
*
1865945 AAT AAC AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AGA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
*
1865989 AAT ATT AAT AAT A
1 AAT AAT AAT AAT A
1866002 TTATTAATGA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 3 0.06
3 43 0.91
4 1 0.02
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1866009 original size:9 final size:9
Alignment explanation
Indices: 1865951--1866009 Score: 66
Period size: 9 Copynumber: 6.7 Consensus size: 9
1865941 TACAAATAAC
*
1865951 AATAATAAT
1 AATAATATT
1865960 AATAATA-T
1 AATAATATT
*
1865968 AATAATAAT
1 AATAATATT
**
1865977 AATAATAGA
1 AATAATATT
1865986 AATAATATT
1 AATAATATT
1865995 AATAATATT
1 AATAATATT
*
1866004 ATTAAT
1 AATAAT
1866010 GATTTCGACC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
8 8 0.18
9 36 0.82
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (9 bp):
AATAATATT
Found at i:1866997 original size:131 final size:131
Alignment explanation
Indices: 1866248--1866970 Score: 727
Period size: 131 Copynumber: 5.6 Consensus size: 131
1866238 ATCAGATCTG
* * * * ** *
1866248 GAAAAAGGGGATCTGCTCCGCTGCTTTTCAAGGTAGATC--ATCTAGAAATTTTGATTCACTTTA
1 GAAAAAGGGGATATGTTCCGCTGCTCTTCAGGGTAGATCAGATCTAGAAACGTTGATTCACTTCA
* * * * * * *
1866311 CTGCTATTCAGGGAAGATTGAATTGAGGTAGATTTGTTCCATTTCTCTTCAGGGAAGATCAAATC
66 CTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCCTCAAGGAAGATCAAATA
1866376 T
131 T
* * * * * * *
1866377 AGAAAAAAAAGGGATTTGTTCCGCTACTATTCTGGTTAGATCAGATCTGGAAACGTTGATTCACT
1 -G--AAAAAGGGGATATGTTCCGCTGCTCTTCAGGGTAGATCAGATCTAGAAACGTTGATTCACT
* * * * * * *
1866442 TTACTACTCTTCAGGGAAGATTAAATCGAGGAAGTTTTGTTCCACTGGTACTCAAGGAAGATCAA
63 TCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCCTCAAGGAAGATCAA
1866507 ATAT
128 ATAT
* * * *
1866511 GGAAAAGGGGATCA-GCTCCACTGCTCTTCAGGGTAGACCAGATCT------G--GATTCACTTC
1 GAAAAAGGGGAT-ATGTTCCGCTGCTCTTCAGGGTAGATCAGATCTAGAAACGTTGATTCACTTC
* * * * ** * *
1866567 ACTGCCCTTCAAGGAAGATTGAATCAAGGAAGATTTGTTCCACAACTCCT-AAGGAAGACCAATT
65 ACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCCTCAAGGAAGATCAAAT
1866631 AT
130 AT
** ** * *
1866633 GAAAAAAAGGATATGTTATGCTGTTCTTCAGGGTAGATCAGATCTAGAAATGTTGATTCACTTCA
1 GAAAAAGGGGATATGTTCCGCTGCTCTTCAGGGTAGATCAGATCTAGAAACGTTGATTCACTTCA
* * * *
1866698 CTACTCTTCAGGGAAGATTGAATCGAGGTAGATTT-TTCCACTGTTCCTTAGGGAAGATCAAATA
66 CTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCCTCAAGGAAGATCAAATA
1866762 T
131 T
* * * * *
1866763 GGAAAAAGGGGATATGTTCCGCTGCTCTTCAGGGTAGATCGGATTTAGAAAAGTTGATTAACTTT
1 -GAAAAAGGGGATATGTTCCGCTGCTCTTCAGGGTAGATCAGATCTAGAAACGTTGATTCACTTC
1866828 ACTGCTCTTCAGGGAAGATTGAATCGAGGCT-GATTTGTTCCACTGCTCCTCAAGGAAGATCAAA
65 ACTGCTCTTCAGGGAAGATTGAATCGAGG-TAGATTTGTTCCACTGCTCCTCAAGGAAGATCAAA
*
1866892 TCT
129 TAT
* ** * * * *
1866895 GAAAAAGGGGATATGCTATGCTACTCTTTAGGGTAGATTAGATCTGGAAACGTTGATTCACTTCA
1 GAAAAAGGGGATATGTTCCGCTGCTCTTCAGGGTAGATCAGATCTAGAAACGTTGATTCACTTCA
1866960 CTGCTCTTCAG
66 CTGCTCTTCAG
1866971 AGAATATTAA
Statistics
Matches: 481, Mismatches: 94, Indels: 35
0.79 0.15 0.06
Matches are distributed among these distances:
121 1 0.00
122 48 0.10
123 49 0.10
125 1 0.00
128 1 0.00
129 10 0.02
130 55 0.11
131 184 0.38
132 57 0.12
133 1 0.00
134 74 0.15
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (131 bp):
GAAAAAGGGGATATGTTCCGCTGCTCTTCAGGGTAGATCAGATCTAGAAACGTTGATTCACTTCA
CTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCCTCAAGGAAGATCAAATA
T
Found at i:1868338 original size:20 final size:20
Alignment explanation
Indices: 1868312--1868359 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
1868302 TTTATTTGTT
*
1868312 TTTTCTTTTTCTTTTCTTT-
1 TTTTCTTTTTCTTTTATTTC
1868331 TATTTCTTTTTCTTTTATTTC
1 T-TTTCTTTTTCTTTTATTTC
1868352 TTTTCTTT
1 TTTTCTTT
1868360 AGGCAAAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 24 0.92
21 1 0.04
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTCTTTTTCTTTTATTTC
Found at i:1868343 original size:15 final size:14
Alignment explanation
Indices: 1868301--1868359 Score: 77
Period size: 14 Copynumber: 4.2 Consensus size: 14
1868291 TTGAACCCCT
*
1868301 TTTTATTTGTTTT-
1 TTTTATTTCTTTTC
1868314 TTCTT-TTTCTTTTC
1 TT-TTATTTCTTTTC
1868328 TTTTATTTCTTTTTC
1 TTTTATTTC-TTTTC
1868343 TTTTATTTCTTTTC
1 TTTTATTTCTTTTC
1868357 TTT
1 TTT
1868360 AGGCAAAGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
13 11 0.27
14 16 0.39
15 14 0.34
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (14 bp):
TTTTATTTCTTTTC
Found at i:1881611 original size:2 final size:2
Alignment explanation
Indices: 1881604--1881630 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1881594 CCATGGCCAT
1881604 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 T
1881631 TAGCAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1882662 original size:25 final size:24
Alignment explanation
Indices: 1882612--1882668 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
1882602 CTTTTCCTCT
1882612 TTTTTGTTTCGTTTCTTTTTCATTC
1 TTTTT-TTTCGTTTCTTTTTCATTC
1882637 TATTTTTTTC-TTTCTTTTCTTC-TTC
1 T-TTTTTTTCGTTTC-TTT-TTCATTC
1882662 TTTTTTT
1 TTTTTTT
1882669 CTCTGAACCG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
24 10 0.34
25 12 0.41
26 7 0.24
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.77
Consensus pattern (24 bp):
TTTTTTTTCGTTTCTTTTTCATTC
Found at i:1883106 original size:16 final size:15
Alignment explanation
Indices: 1883081--1883114 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1883071 AAAATAACAA
*
1883081 TAATAGTAATAATAAT
1 TAATAATAATAAT-AT
1883097 TAATAATAATAATAT
1 TAATAATAATAATAT
1883112 TAA
1 TAA
1883115 CGATTTCGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
TAATAATAATAATAT
Done.