Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001700.1 Hibiscus syriacus cultivar Beakdansim tig00003398_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: 2632955
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:1781518 original size:18 final size:19
Alignment explanation
Indices: 1781474--1781536 Score: 69
Period size: 18 Copynumber: 3.3 Consensus size: 19
1781464 TAATAATGAA
1781474 TAATATT-AT-TTATATATT
1 TAATATTAATATTA-ATATT
1781492 TAATATTAATATTAATA-T
1 TAATATTAATATTAATATT
1781510 TAATATTAATATAATAATATTT
1 TAATATTAATAT--TAATA-TT
1781532 TAATA
1 TAATA
1781537 AAGATATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
18 20 0.51
19 5 0.13
20 8 0.21
22 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATATTAATATTAATATT
Found at i:1781558 original size:23 final size:23
Alignment explanation
Indices: 1781532--1781576 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1781522 AATAATATTT
1781532 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
1781555 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
1781577 ATATAACACT
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:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:1784743 original size:17 final size:17
Alignment explanation
Indices: 1784721--1784756 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1784711 TTGAGTCATT
1784721 CAAACTCAAGTCGAGTC
1 CAAACTCAAGTCGAGTC
*
1784738 CAAACTCGAGTCGAGTC
1 CAAACTCAAGTCGAGTC
1784755 CA
1 CA
1784757 TTTGATTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (17 bp):
CAAACTCAAGTCGAGTC
Found at i:1787497 original size:41 final size:41
Alignment explanation
Indices: 1787446--1787534 Score: 142
Period size: 41 Copynumber: 2.2 Consensus size: 41
1787436 AGTCCATTTT
* * *
1787446 CGGTCTCCTCGCATTTACCGCTATGTGTGGTCATATAATAA
1 CGGTCGCCTCGCATTTACCGCTATGCGCGGTCATATAATAA
*
1787487 TGGTCGCCTCGCATTTACCGCTATGCGCGGTCATATAATAA
1 CGGTCGCCTCGCATTTACCGCTATGCGCGGTCATATAATAA
1787528 CGGTCGC
1 CGGTCGC
1787535 GGAGGACACT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.30
Consensus pattern (41 bp):
CGGTCGCCTCGCATTTACCGCTATGCGCGGTCATATAATAA
Found at i:1794321 original size:59 final size:60
Alignment explanation
Indices: 1794248--1794380 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 60
1794238 GTCGAATGAT
* * * * *
1794248 CATTTTGTATCTTTTAAT-AGCAGGGAGACTCAACAAA-CAACACCATATAGTTGA-AGGAC
1 CATTTTATAACTTTTAATAACCAAGG-GACTCAACAAAGCAACACCATATAATTGAGA-GAC
* *
1794307 CATTTTATAACTTTTAGTAACCAAGGGACTCAACAAAGTAACACCATATAATTGAGAGAC
1 CATTTTATAACTTTTAATAACCAAGGGACTCAACAAAGCAACACCATATAATTGAGAGAC
1794367 CATTTGTAT-ACTTT
1 CATTT-TATAACTTT
1794381 ACCAAAAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
59 26 0.41
60 33 0.52
61 4 0.06
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (60 bp):
CATTTTATAACTTTTAATAACCAAGGGACTCAACAAAGCAACACCATATAATTGAGAGAC
Found at i:1800760 original size:15 final size:15
Alignment explanation
Indices: 1800742--1800779 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1800732 ATTTTTTTAC
1800742 ATTTTTA-CATTTATT
1 ATTTTTATCATTT-TT
*
1800757 ATTTTTATTATTTTT
1 ATTTTTATCATTTTT
1800772 ATTTTTAT
1 ATTTTTAT
1800780 TTTTAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTTTATCATTTTT
Found at i:1801866 original size:13 final size:13
Alignment explanation
Indices: 1801848--1801877 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1801838 AGCCTAAGAG
1801848 ATAAATAAATAAA
1 ATAAATAAATAAA
1801861 ATAAATAAATAAA
1 ATAAATAAATAAA
1801874 ATAA
1 ATAA
1801878 TTCTAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
ATAAATAAATAAA
Found at i:1805227 original size:3 final size:3
Alignment explanation
Indices: 1805219--1805313 Score: 111
Period size: 3 Copynumber: 32.0 Consensus size: 3
1805209 TTAATATATT
* * * *
1805219 TAA TAA TAA AAA AAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
1805267 TAA T-A TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1805314 AATGGATAAA
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
2 2 0.03
3 75 0.97
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1805321 original size:12 final size:11
Alignment explanation
Indices: 1805230--1805327 Score: 58
Period size: 12 Copynumber: 8.5 Consensus size: 11
1805220 AATAATAAAA
*
1805230 AAAATAATAAT
1 AAAATGATAAT
*
1805241 AATAATAATAAT
1 AA-AATGATAAT
*
1805253 AAAAATAATAAT
1 -AAAATGATAAT
* *
1805265 GATAAT-ATATT
1 -AAAATGATAAT
1805276 AATAATGATAAT
1 AA-AATGATAAT
1805288 AATAAT-ATTAAT
1 AA-AATGA-TAAT
1805300 AATAATGATAAT
1 AA-AATGATAAT
1805312 AAAATGGATAA-
1 AAAAT-GATAAT
1805323 AAAAT
1 AAAAT
1805328 AGTATCTTCA
Statistics
Matches: 75, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
10 1 0.01
11 18 0.24
12 53 0.71
13 3 0.04
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (11 bp):
AAAATGATAAT
Found at i:1805804 original size:119 final size:118
Alignment explanation
Indices: 1805561--1806015 Score: 749
Period size: 119 Copynumber: 3.9 Consensus size: 118
1805551 GCTCTTGATG
*
1805561 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-T
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
* * * *
1805622 TAC-CTGGAAATGTTGATCCATCAACTGATGAATTCAAGCAAAAGGTTGAACA
66 TTCTCTGGAAAAGATGATCCATCAATTGATGAATTCAAGCAAAAGGTTGAACA
*
1805674 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
* *
1805739 TCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
66 TTCTCTGGAAAAGATGATCCATCAA-TTGATGAATTCAAGCAAAAGGTTGAACA
1805793 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
*
1805858 TTCTCTGGAAAAGATGATCCATCAATTTGATGAATTCAAGCAAAAGATTGAACA
66 TTCTCTGGAAAAGATGATCCATCAA-TTGATGAATTCAAGCAAAAGGTTGAACA
1805912 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
* *
1805977 TTCTCTGGAAAAGATTGATCCATCAAGTGATGGATTCAA
66 TTCTCTGGAAAAGA-TGATCCATCAATTGATGAATTCAA
1806016 ATCTTTGCTA
Statistics
Matches: 324, Mismatches: 11, Indels: 8
0.94 0.03 0.02
Matches are distributed among these distances:
113 37 0.11
116 21 0.06
117 3 0.01
118 20 0.06
119 232 0.72
120 11 0.03
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (118 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
TTCTCTGGAAAAGATGATCCATCAATTGATGAATTCAAGCAAAAGGTTGAACA
Found at i:1806734 original size:50 final size:50
Alignment explanation
Indices: 1806659--1807249 Score: 1155
Period size: 50 Copynumber: 11.8 Consensus size: 50
1806649 CTTACCAAAA
1806659 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
1806709 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
* *
1806759 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATTCTGTCAAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
1806809 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
1806859 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
1806909 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
1806959 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
1807009 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
1807059 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
*
1807109 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCCGTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
1807159 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
1807209 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1807250 AGTCTCTTTC
Statistics
Matches: 535, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 535 1.00
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.24
Consensus pattern (50 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAC
Found at i:1808400 original size:11 final size:11
Alignment explanation
Indices: 1808384--1808444 Score: 51
Period size: 11 Copynumber: 6.0 Consensus size: 11
1808374 TGACCCCCTT
1808384 TCTTTTTCTTC
1 TCTTTTTCTTC
1808395 TC-TTTT-TTC
1 TCTTTTTCTTC
* *
1808404 T-ATTTTC-TA
1 TCTTTTTCTTC
*
1808413 T-TTTTTCTTT
1 TCTTTTTCTTC
*
1808423 TCTTTTTCTTT
1 TCTTTTTCTTC
1808434 TCTTTTTCTTC
1 TCTTTTTCTTC
1808445 AAGCATAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
9 15 0.36
10 6 0.14
11 21 0.50
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (11 bp):
TCTTTTTCTTC
Found at i:1808411 original size:7 final size:6
Alignment explanation
Indices: 1808382--1808443 Score: 56
Period size: 7 Copynumber: 10.0 Consensus size: 6
1808372 CTTGACCCCC
* *
1808382 TTTCTT TTTC-T TCTCTTT TTTCTAT TTTCTAT TTTTTCT TTTCTT TTTC-T
1 TTTCTT TTTCTT TTTC-TT TTTCT-T TTTCT-T TTTCT-T TTTCTT TTTCTT
1808432 TTTCTT TTTCTT
1 TTTCTT TTTCTT
1808444 CAAGCATAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
5 9 0.19
6 17 0.36
7 21 0.45
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTCTT
Found at i:1808411 original size:25 final size:25
Alignment explanation
Indices: 1808382--1808444 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 25
1808372 CTTGACCCCC
1808382 TTTCTTTTTCTTCTCTTT-TTTCTAT
1 TTTCTTTTTCTTCT-TTTCTTTCTAT
* *
1808407 TTTCTATTTT-TTCTTTTCTTTTTCT
1 TTTCT-TTTTCTTCTTTTCTTTCTAT
1808432 TTTCTTTTTCTTC
1 TTTCTTTTTCTTC
1808445 AAGCATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 7 0.21
25 22 0.67
26 4 0.12
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTCTTTTTCTTCTTTTCTTTCTAT
Found at i:1819096 original size:17 final size:17
Alignment explanation
Indices: 1819054--1819104 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
1819044 AAATACTTGC
1819054 AAATAAAACAT-ATAAAT
1 AAATAAAA-ATAATAAAT
*
1819071 ATTATAAAAATAATAAAT
1 A-AATAAAAATAATAAAT
1819089 AAATAAAAATAA-AAAT
1 AAATAAAAATAATAAAT
1819105 TTTTGAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 4 0.13
17 13 0.43
18 13 0.43
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAAAATAATAAAT
Found at i:1820699 original size:3 final size:3
Alignment explanation
Indices: 1820691--1820786 Score: 120
Period size: 3 Copynumber: 32.0 Consensus size: 3
1820681 TTAATATATT
* * * *
1820691 TAA TAA TAA TAA AAA AAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
1820739 TAA TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1820787 AATGGATAAA
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1820794 original size:12 final size:11
Alignment explanation
Indices: 1820708--1820799 Score: 53
Period size: 12 Copynumber: 7.8 Consensus size: 11
1820698 AATAAAAAAA
*
1820708 ATAATAATAATA
1 ATAATAA-AATG
*
1820720 ATAATAAAAATA
1 ATAAT-AAAATG
* *
1820732 ATAATGATAATA
1 ATAAT-AAAATG
*
1820744 ATATTAATAATG
1 ATAATAA-AATG
1820756 ATAATAATAAT-
1 ATAATAA-AATG
1820767 ATTAATAATAATG
1 A-TAATAA-AATG
1820780 ATAATAAAATGG
1 ATAATAAAAT-G
1820792 ATAA-AAAA
1 ATAATAAAA
1820800 AATAGTATCT
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.13
12 57 0.83
13 3 0.04
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (11 bp):
ATAATAAAATG
Found at i:1825610 original size:25 final size:25
Alignment explanation
Indices: 1825576--1825625 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1825566 AGCATAAAAG
* *
1825576 CAAAGCTTGAAAAATAAAGAAGAAA
1 CAAAACTTGAAAAATAAAAAAGAAA
*
1825601 CAAAACTTGAAAAGTAAAAAAGAAA
1 CAAAACTTGAAAAATAAAAAAGAAA
1825626 AGCTTTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.66, C:0.08, G:0.14, T:0.12
Consensus pattern (25 bp):
CAAAACTTGAAAAATAAAAAAGAAA
Found at i:1831155 original size:18 final size:19
Alignment explanation
Indices: 1831124--1831162 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1831114 GTAGAAAGAT
*
1831124 AATAAAAGCGATTAAA-TA
1 AATAAAAGCAATTAAAGTA
*
1831142 AATAAAAGTAATTAAAGTA
1 AATAAAAGCAATTAAAGTA
1831161 AA
1 AA
1831163 AATAAGAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.64, C:0.03, G:0.10, T:0.23
Consensus pattern (19 bp):
AATAAAAGCAATTAAAGTA
Found at i:1831793 original size:24 final size:25
Alignment explanation
Indices: 1831747--1831795 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1831737 GCATAAAAAG
1831747 CAAAACTTGAAAAATAAAGAAGAAA
1 CAAAACTTGAAAAATAAAGAAGAAA
*
1831772 CAAAACTTGAAAAGTAAA-AAGAAA
1 CAAAACTTGAAAAATAAAGAAGAAA
1831796 AGCTTTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.67, C:0.08, G:0.12, T:0.12
Consensus pattern (25 bp):
CAAAACTTGAAAAATAAAGAAGAAA
Found at i:1833661 original size:37 final size:39
Alignment explanation
Indices: 1833587--1833662 Score: 93
Period size: 37 Copynumber: 2.0 Consensus size: 39
1833577 ATGAATAAGG
* **
1833587 TTTTCTGTTCGTTTAATTAAATAAATGAACATGAACAAAA
1 TTTTCTGCTCGTTTAA-TAAATAAATGAACACAAACAAAA
*
1833627 TTTTCTGCTCGTTT-A-AAATGAATGAACACAAACAAA
1 TTTTCTGCTCGTTTAATAAATAAATGAACACAAACAAA
1833663 TGACTCATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 18 0.56
39 1 0.03
40 13 0.41
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (39 bp):
TTTTCTGCTCGTTTAATAAATAAATGAACACAAACAAAA
Found at i:1833710 original size:32 final size:32
Alignment explanation
Indices: 1833669--1833745 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
1833659 CAAATGACTC
* *
1833669 ATTCATTCATTTATATTCATGAATGTTTGATA
1 ATTCGTTCATTTATATTCATGAATATTTGATA
* ** *
1833701 ATTCGTTCATTTATGTTCATTTATATTTGGTA
1 ATTCGTTCATTTATATTCATGAATATTTGATA
*
1833733 ATTCGTTCGTTTA
1 ATTCGTTCATTTA
1833746 GTTAAATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.25, C:0.10, G:0.12, T:0.53
Consensus pattern (32 bp):
ATTCGTTCATTTATATTCATGAATATTTGATA
Found at i:1833758 original size:32 final size:32
Alignment explanation
Indices: 1833694--1833760 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
1833684 TTCATGAATG
* *
1833694 TTTGATAATTCGTTCATTTATGTTCATTTATA
1 TTTGATAATTCGTTCATTTATGTTAATATATA
* *
1833726 TTTGGTAATTCGTTCGTTTA-GTTAAATATATA
1 TTTGATAATTCGTTCATTTATGTT-AATATATA
1833758 TTT
1 TTT
1833761 ATCTTTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 3 0.10
32 27 0.90
ACGTcount: A:0.25, C:0.07, G:0.12, T:0.55
Consensus pattern (32 bp):
TTTGATAATTCGTTCATTTATGTTAATATATA
Found at i:1835488 original size:20 final size:20
Alignment explanation
Indices: 1835459--1835501 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1835449 ATTCCACCAC
*
1835459 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
1835479 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
1835499 ATG
1 ATG
1835502 GGTTCTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:1840364 original size:27 final size:27
Alignment explanation
Indices: 1840326--1840388 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
1840316 AAACCTTAAT
1840326 TTGATGGGTCTTGATGTGTGGGCCTGG
1 TTGATGGGTCTTGATGTGTGGGCCTGG
1840353 TTGATGGGTCTTGATGTGTGGGCCTGG
1 TTGATGGGTCTTGATGTGTGGGCCTGG
1840380 TTGATGGGT
1 TTGATGGGT
1840389 TTAATATGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.08, C:0.10, G:0.44, T:0.38
Consensus pattern (27 bp):
TTGATGGGTCTTGATGTGTGGGCCTGG
Found at i:1840422 original size:18 final size:19
Alignment explanation
Indices: 1840399--1840437 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1840389 TTAATATGTT
1840399 TGGG-TTTAGATTTGTAAA
1 TGGGTTTTAGATTTGTAAA
*
1840417 TGGGTTTTTAGTTTTGTAAA
1 TGGG-TTTTAGATTTGTAAA
1840437 T
1 T
1840438 TTTGGTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
20 14 0.78
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (19 bp):
TGGGTTTTAGATTTGTAAA
Found at i:1843749 original size:33 final size:33
Alignment explanation
Indices: 1843707--1843773 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
1843697 CTTAGTACAG
*
1843707 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACAACCTTATGTGTCATACGGATT
1843740 ATGGTGGACACAACCTTATGTGTCATACGGATT
1 ATGGTGGACACAACCTTATGTGTCATACGGATT
1843773 A
1 A
1843774 GCACTATGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (33 bp):
ATGGTGGACACAACCTTATGTGTCATACGGATT
Found at i:1851205 original size:9 final size:8
Alignment explanation
Indices: 1851175--1851203 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1851165 ACATAACTGC
1851175 AAAAAAT-
1 AAAAAATA
1851182 AAAAAATA
1 AAAAAATA
1851190 AAAAAATA
1 AAAAAATA
1851198 AAAAAA
1 AAAAAA
1851204 ATGGTCGAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAATA
Found at i:1855180 original size:17 final size:17
Alignment explanation
Indices: 1855158--1855193 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1855148 TGACCGGTTT
1855158 CGACCCGACCCGTTGAC
1 CGACCCGACCCGTTGAC
*
1855175 CGACCCGACCTGTTGAC
1 CGACCCGACCCGTTGAC
1855192 CG
1 CG
1855194 TTGACCGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.44, G:0.25, T:0.14
Consensus pattern (17 bp):
CGACCCGACCCGTTGAC
Found at i:1855294 original size:59 final size:59
Alignment explanation
Indices: 1855207--1855358 Score: 211
Period size: 59 Copynumber: 2.6 Consensus size: 59
1855197 ACCGGGTGAC
** **
1855207 ATTTTGGGGAA-TTAATTCGAAATGGGTGCTATTTTGGGAA-TTAATTCGAAATGGGTGCT
1 ATTTT-GGGAATTTAATTCGAAAAAGGTGCTATTTTGGGAATTTAATTCGAAA-AAGTGCT
*
1855266 ATTTTGGGAATTTAATTCGAAAAAGGTGCTATATTGGGAATTTAATTCGAAAAAGTGCT
1 ATTTTGGGAATTTAATTCGAAAAAGGTGCTATTTTGGGAATTTAATTCGAAAAAGTGCT
*
1855325 ATTTTAGGAATTTAATTCG-AAAAGGTGCTATTTT
1 ATTTTGGGAATTTAATTCGAAAAAGGTGCTATTTT
1855359 AGTAATTATT
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
58 19 0.23
59 54 0.64
60 11 0.13
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.38
Consensus pattern (59 bp):
ATTTTGGGAATTTAATTCGAAAAAGGTGCTATTTTGGGAATTTAATTCGAAAAAGTGCT
Found at i:1855365 original size:29 final size:29
Alignment explanation
Indices: 1855207--1855358 Score: 209
Period size: 29 Copynumber: 5.2 Consensus size: 29
1855197 ACCGGGTGAC
*
1855207 ATTTTGGGGAA-TTAATTCGAAATGGGTGCT
1 ATTTT-GGGAATTTAATTCGAAA-AGGTGCT
*
1855237 ATTTTGGGAA-TTAATTCGAAATGGGTGCT
1 ATTTTGGGAATTTAATTCGAAA-AGGTGCT
1855266 ATTTTGGGAATTTAATTCGAAAAAGGTGCT
1 ATTTTGGGAATTTAATTCG-AAAAGGTGCT
* *
1855296 ATATTGGGAATTTAATTCGAAAAAGTGCT
1 ATTTTGGGAATTTAATTCGAAAAGGTGCT
*
1855325 ATTTTAGGAATTTAATTCGAAAAGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAGGTGCT
1855354 ATTTT
1 ATTTT
1855359 AGTAATTATT
Statistics
Matches: 114, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
29 74 0.65
30 37 0.32
31 3 0.03
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.38
Consensus pattern (29 bp):
ATTTTGGGAATTTAATTCGAAAAGGTGCT
Found at i:1855383 original size:59 final size:58
Alignment explanation
Indices: 1855214--1855387 Score: 183
Period size: 59 Copynumber: 3.0 Consensus size: 58
1855204 GACATTTTGG
* * ** * *
1855214 GGAA-TTAATTCGAAATGGGTGCTATTTTGGGAATTAATTCGAAATGGGTGCTATTTTG
1 GGAATTTAATTCGAAA-AGGTGCTATTTTGGGAATTATTTAAAAAAGGGTGCTATTTTA
* **
1855272 GGAATTTAATTCGAAAAAGGTGCTATATTGGGAATTTAATTCGAAAAA--GTGCTATTTTA
1 GGAATTTAATTCG-AAAAGGTGCTATTTTGGGAA-TT-ATTTAAAAAAGGGTGCTATTTTA
* *
1855331 GGAATTTAATTCGAAAAGGTGCTATTTTAGTAATTATTTTAAAAAAGGGTGCTATTT
1 GGAATTTAATTCGAAAAGGTGCTATTTTGGGAATTA-TTTAAAAAAGGGTGCTATTT
1855388 CTTTAAAATG
Statistics
Matches: 96, Mismatches: 13, Indels: 13
0.79 0.11 0.11
Matches are distributed among these distances:
56 1 0.01
57 9 0.09
58 21 0.22
59 55 0.57
60 5 0.05
61 5 0.05
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.38
Consensus pattern (58 bp):
GGAATTTAATTCGAAAAGGTGCTATTTTGGGAATTATTTAAAAAAGGGTGCTATTTTA
Found at i:1871694 original size:29 final size:30
Alignment explanation
Indices: 1871653--1871803 Score: 184
Period size: 29 Copynumber: 5.2 Consensus size: 30
1871643 AGCGGGTGAC
**
1871653 ATTTTGGGAA-TTAATTCGAAATTGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAAGGTGCT
** **
1871682 ATTTTGGTTA-TTAATTCGAAATGGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAAGGTGCT
* *
1871711 ATTTTGAGAATTTAGTTC-AAAAAGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAAGGTGCT
* *
1871740 ATATTGGGAATTTAATTCAAAAAAGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAAGGTGCT
1871770 ATTTTGGGAATTTAATTCG-AAAAGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAAGGTGCT
1871799 ATTTT
1 ATTTT
1871804 AGTAATTATT
Statistics
Matches: 106, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
29 72 0.68
30 34 0.32
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.40
Consensus pattern (30 bp):
ATTTTGGGAATTTAATTCGAAAAAGGTGCT
Found at i:1871825 original size:29 final size:29
Alignment explanation
Indices: 1871653--1871829 Score: 171
Period size: 29 Copynumber: 6.1 Consensus size: 29
1871643 AGCGGGTGAC
**
1871653 ATTTTGGGAA-TTAATTCGAAATTGGTGCT
1 ATTTTGGGAATTTAATTC-AAAAAGGTGCT
** **
1871682 ATTTTGGTTA-TTAATTCGAAATGGGTGCT
1 ATTTTGGGAATTTAATTC-AAAAAGGTGCT
* *
1871711 ATTTTGAGAATTTAGTTCAAAAAGGTGCT
1 ATTTTGGGAATTTAATTCAAAAAGGTGCT
*
1871740 ATATTGGGAATTTAATTCAAAAAAGGTGCT
1 ATTTTGGGAATTTAATTC-AAAAAGGTGCT
*
1871770 ATTTTGGGAATTTAATTCGAAAAGGTGCT
1 ATTTTGGGAATTTAATTCAAAAAGGTGCT
* * * *
1871799 ATTTTAGTAA-TTATTTTAAAAAGGGTGCT
1 ATTTTGGGAATTTAATTCAAAAA-GGTGCT
1871828 AT
1 AT
1871830 GTCTGTAAAA
Statistics
Matches: 126, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 9 0.07
29 83 0.66
30 34 0.27
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.40
Consensus pattern (29 bp):
ATTTTGGGAATTTAATTCAAAAAGGTGCT
Found at i:1871826 original size:88 final size:87
Alignment explanation
Indices: 1871656--1871829 Score: 219
Period size: 88 Copynumber: 2.0 Consensus size: 87
1871646 GGGTGACATT
* ** ** *
1871656 TTGGGAATTAATTCGAAATTGGTGCTATTTTGGTTATTAATTCGAAATGGGTGCTATTTTGAGAA
1 TTGGGAATTAATTCAAAAAAGGTGCTATTTTGGGAATTAATTCGAAATAGGTGCTATTTTGAGAA
1871721 TTTAGTTCAAAAAGGTGCTATA
66 TTTAGTTCAAAAAGGTGCTATA
1871743 TTGGGAATTTAATTCAAAAAAGGTGCTATTTTGGGAATTTAATTCGAAA-AGGTGCTATTTT-AG
1 TTGGGAA-TTAATTCAAAAAAGGTGCTATTTTGGGAA-TTAATTCGAAATAGGTGCTATTTTGAG
* *
1871806 TAA-TTATTTTAAAAAGGGTGCTAT
64 -AATTTAGTTCAAAAA-GGTGCTAT
1871830 GTCTGTAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
87 19 0.25
88 45 0.60
89 11 0.15
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.40
Consensus pattern (87 bp):
TTGGGAATTAATTCAAAAAAGGTGCTATTTTGGGAATTAATTCGAAATAGGTGCTATTTTGAGAA
TTTAGTTCAAAAAGGTGCTATA
Found at i:1873652 original size:31 final size:31
Alignment explanation
Indices: 1873607--1873685 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
1873597 ATAACGATGG
* *
1873607 AGTGACAATTTTGTTTCAAATTA-ATAATGTT
1 AGTGACAATTTTGTTAC-AAGTAGATAATGTT
* *
1873638 ATTGACTATTTTGTTACAAGTAGATAATGTT
1 AGTGACAATTTTGTTACAAGTAGATAATGTT
1873669 AGTGACCAA-TTTGTTAC
1 AGTGA-CAATTTTGTTAC
1873686 TCTAGAAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 4 0.10
31 34 0.85
32 2 0.05
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (31 bp):
AGTGACAATTTTGTTACAAGTAGATAATGTT
Found at i:1881987 original size:22 final size:22
Alignment explanation
Indices: 1881933--1881988 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
1881923 GGAATCGATA
*
1881933 CCCTCATGAGGGAACTGATTCCC
1 CCCTCAAG-GGGAACTGATTCCC
* *
1881956 CCTTTGAAGGGGAACTGATTCCC
1 CC-CTCAAGGGGAACTGATTCCC
1881979 CCCTCAAGGG
1 CCCTCAAGGG
1881989 AATCGATACC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 6 0.22
23 18 0.67
24 3 0.11
ACGTcount: A:0.21, C:0.32, G:0.25, T:0.21
Consensus pattern (22 bp):
CCCTCAAGGGGAACTGATTCCC
Found at i:1887333 original size:49 final size:49
Alignment explanation
Indices: 1887260--1887393 Score: 173
Period size: 49 Copynumber: 2.7 Consensus size: 49
1887250 AAATAAATTT
* * *
1887260 ACATAAATACTAAAAAAGAGTTTGTTATAACAATAAGCACATGACAAA-A
1 ACATAAAAACAAAAAAAGA-TTTGTTACAACAATAAGCACATGACAAATA
** *
1887309 ACATAAAGGCAAAAAAAGAATTTGTTGCAACAATAAGCACATGACAAATA
1 ACATAAAAACAAAAAAAG-ATTTGTTACAACAATAAGCACATGACAAATA
*
1887359 ACATAAAAACAAAAAAAG-TTAGTTACAACAATAAG
1 ACATAAAAACAAAAAAAGATTTGTTACAACAATAAG
1887394 AAAATGAGGA
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
48 15 0.20
49 41 0.55
50 18 0.24
ACGTcount: A:0.57, C:0.13, G:0.11, T:0.19
Consensus pattern (49 bp):
ACATAAAAACAAAAAAAGATTTGTTACAACAATAAGCACATGACAAATA
Found at i:1893244 original size:23 final size:23
Alignment explanation
Indices: 1893199--1893244 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1893189 CCATTAAATG
* *
1893199 GTATCAATATTACTGTTATAGTA
1 GTATCAATACTACTGTTACAGTA
* *
1893222 GTATCAATACTCCTTTTACAGTA
1 GTATCAATACTACTGTTACAGTA
1893245 TCGATACCGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (23 bp):
GTATCAATACTACTGTTACAGTA
Found at i:1894913 original size:26 final size:26
Alignment explanation
Indices: 1894883--1894935 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
1894873 GGTCTGACGT
* *
1894883 GATAGTTTCTAGAAGGTCTATTCAGC
1 GATAGTTTCTAGAAGATCTAGTCAGC
1894909 GATAGTTTCTAGAAGATCTAGTCAGC
1 GATAGTTTCTAGAAGATCTAGTCAGC
1894935 G
1 G
1894936 CGCCTTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (26 bp):
GATAGTTTCTAGAAGATCTAGTCAGC
Found at i:1896291 original size:19 final size:19
Alignment explanation
Indices: 1896248--1896308 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
1896238 ATAGTTGGTA
1896248 TTCTTTATTTTT-T-ATATT
1 TTCTTTATTTTTCTAATA-T
1896266 GTATCTTTATTTTTCTAATAT
1 -T-TCTTTATTTTTCTAATAT
*
1896287 TTCTTTATTTTTC-AATAA
1 TTCTTTATTTTTCTAATAT
1896305 TTCT
1 TTCT
1896309 GCCTTTACGA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
18 8 0.21
19 13 0.34
20 12 0.32
21 2 0.05
22 3 0.08
ACGTcount: A:0.21, C:0.10, G:0.02, T:0.67
Consensus pattern (19 bp):
TTCTTTATTTTTCTAATAT
Found at i:1896303 original size:18 final size:19
Alignment explanation
Indices: 1896247--1896308 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 19
1896237 GATAGTTGGT
*
1896247 ATTCTTTATTTTT-TATATT
1 ATTCTTTATTTTTCTA-ATA
*
1896266 GTATCTTTATTTTTCTAATA
1 AT-TCTTTATTTTTCTAATA
*
1896286 TTTCTTTATTTTTC-AATA
1 ATTCTTTATTTTTCTAATA
1896304 ATTCT
1 ATTCT
1896309 GCCTTTACGA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 8 0.22
19 13 0.35
20 14 0.38
21 2 0.05
ACGTcount: A:0.23, C:0.10, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTCTTTATTTTTCTAATA
Found at i:1899369 original size:28 final size:28
Alignment explanation
Indices: 1899327--1899455 Score: 213
Period size: 28 Copynumber: 4.6 Consensus size: 28
1899317 GAATTCATTG
* *
1899327 ATGCATTTACCAACTGTTAATGTGTACC
1 ATGCATTTACCAACTATAAATGTGTACC
* * *
1899355 ATGCATTTACTAACTATCAATGTGTATC
1 ATGCATTTACCAACTATAAATGTGTACC
1899383 ATGCATTTACCAACTATAAATGTGTACC
1 ATGCATTTACCAACTATAAATGTGTACC
1899411 ATGCATTTACCAACTATAAATGTGTACC
1 ATGCATTTACCAACTATAAATGTGTACC
1899439 ATGCATTTACCAACTAT
1 ATGCATTTACCAACTAT
1899456 CATAAAGCAT
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 94 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (28 bp):
ATGCATTTACCAACTATAAATGTGTACC
Found at i:1899791 original size:19 final size:19
Alignment explanation
Indices: 1899769--1899827 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
1899759 AAAGTTAACG
1899769 GTCAACAGGTTGGGTCAAA
1 GTCAACAGGTTGGGTCAAA
* *
1899788 GTCATCAGGTTGAGTCAAA
1 GTCAACAGGTTGGGTCAAA
* * **
1899807 ATCAATAGGTCAGGTCAAA
1 GTCAACAGGTTGGGTCAAA
1899826 GT
1 GT
1899828 TGATGGGTTG
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (19 bp):
GTCAACAGGTTGGGTCAAA
Found at i:1901004 original size:30 final size:29
Alignment explanation
Indices: 1900968--1901032 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
1900958 CTATTTGCAT
* **
1900968 AAAAAAATAATTACAATGATAAGCAAATG
1 AAAAAAATAACTACAACAATAAGCAAATG
* *
1900997 ACAAAAAATAGCTACAACAATAAGCCAATG
1 A-AAAAAATAACTACAACAATAAGCAAATG
1901027 AAAAAA
1 AAAAAA
1901033 CCATGTTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.63, C:0.12, G:0.09, T:0.15
Consensus pattern (29 bp):
AAAAAAATAACTACAACAATAAGCAAATG
Found at i:1906225 original size:58 final size:58
Alignment explanation
Indices: 1906163--1906347 Score: 194
Period size: 58 Copynumber: 3.2 Consensus size: 58
1906153 GAGCACTGAG
* *
1906163 TGTGCTAAATGATAAGGAAATCATATTAAAAATATAGATTTCCAGATAGGGCATATTA
1 TGTGCTAAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATATTA
** ** * *** * **
1906221 TGTGCTAAAATGGCAAGGGGGATCATACTGAGTGTATGGGTTTCCAGATAAAGCACTA--A
1 TGTGCT-AAATGATAA-GGAAATCATATTGAAAATATGGATTTCCAGATAGGGCA-TATTA
*
1906280 GGGTGCTAAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATATTA
1 -TGTGCTAAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATATTA
1906339 TGTGCTAAA
1 TGTGCTAAA
1906348 ATGGTAACAA
Statistics
Matches: 95, Mismatches: 26, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
57 2 0.02
58 43 0.45
59 16 0.17
60 32 0.34
61 2 0.02
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (58 bp):
TGTGCTAAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATATTA
Found at i:1906379 original size:59 final size:59
Alignment explanation
Indices: 1906163--1906409 Score: 186
Period size: 59 Copynumber: 4.2 Consensus size: 59
1906153 GAGCACTGAG
* * ** *
1906163 TGTGCT-AAATGATAAGGAAATCATATTAAAAATATAGATTTCCAGATAGGGCA-TATTA
1 TGTGCTAAAATGGTAAGGAAATCATACT-AAGGTATGGATTTCCAGATAGGGCACTATTA
* ** * * **
1906221 TGTGCTAAAATGGCAAGGGGGATCATACTGAGTGTATGGGTTTCCAGATAAAGCACTA--A
1 TGTGCTAAAATGGTAA-GGAAATCATACTAAG-GTATGGATTTCCAGATAGGGCACTATTA
* * * **
1906280 GGGTGCT-AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGCA-TATTA
1 -TGTGCTAAAATGGTAAGGAAATCATACT-AAGGTATGGATTTCCAGATAGGGCACTATTA
** * *
1906339 TGTGCTAAAATGGTAACAAAATCATACTAATGGTATGGATTTTC-GAATAGGGCACT-TTG
1 TGTGCTAAAATGGTAAGGAAATCATACTAA-GGTATGGATTTCCAG-ATAGGGCACTATTA
1906398 TGTGCTAAAATG
1 TGTGCTAAAATG
1906410 AAAGGGGAAG
Statistics
Matches: 144, Mismatches: 33, Indels: 23
0.72 0.17 0.12
Matches are distributed among these distances:
57 2 0.01
58 41 0.28
59 67 0.47
60 32 0.22
61 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.30
Consensus pattern (59 bp):
TGTGCTAAAATGGTAAGGAAATCATACTAAGGTATGGATTTCCAGATAGGGCACTATTA
Found at i:1906410 original size:118 final size:118
Alignment explanation
Indices: 1906154--1906376 Score: 333
Period size: 118 Copynumber: 1.9 Consensus size: 118
1906144 TTCTATATGG
*
1906154 AGCACTGAGTGTGCTAAATGATAAGGAAATCATATTAAAAATATAGATTTCCAGATAGGGCATAT
1 AGCACTAAGTGTGCTAAATGATAAGGAAATCATATTAAAAATATAGATTTCCAGATAGGGCATAT
**** *
1906219 TATGTGCTAAAATGGCAAGGGGGATCATACTGAGTGTATGGGTTTCCAGATAA
66 TATGTGCTAAAATGGCAAGCAAAATCATACTAAGTGTATGGGTTTCCAGATAA
* * *
1906272 AGCACTAAGGGTGCTAAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATAT
1 AGCACTAAGTGTGCTAAATGATAAGGAAATCATATTAAAAATATAGATTTCCAGATAGGGCATAT
*
1906337 TATGTGCTAAAATGGTAA-CAAAATCATACTAA-TGGTATGG
66 TATGTGCTAAAATGGCAAGCAAAATCATACTAAGT-GTATGG
1906377 ATTTTCGAAT
Statistics
Matches: 94, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
116 1 0.01
117 15 0.16
118 78 0.83
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (118 bp):
AGCACTAAGTGTGCTAAATGATAAGGAAATCATATTAAAAATATAGATTTCCAGATAGGGCATAT
TATGTGCTAAAATGGCAAGCAAAATCATACTAAGTGTATGGGTTTCCAGATAA
Found at i:1906567 original size:17 final size:18
Alignment explanation
Indices: 1906542--1906575 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1906532 ATTGTAGTAT
1906542 ATTCATTGGA-ATTAAAG
1 ATTCATTGGAGATTAAAG
*
1906559 ATTCCTTGGAGATTAAA
1 ATTCATTGGAGATTAAA
1906576 TATCAGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (18 bp):
ATTCATTGGAGATTAAAG
Found at i:1906910 original size:21 final size:21
Alignment explanation
Indices: 1906884--1906924 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1906874 TTGGCGAAGT
*
1906884 TACTGTAGCAGTGCATCGATG
1 TACTGTAGAAGTGCATCGATG
1906905 TACTGTAGAAGTGCATCGAT
1 TACTGTAGAAGTGCATCGAT
1906925 ACACATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (21 bp):
TACTGTAGAAGTGCATCGATG
Found at i:1907038 original size:22 final size:23
Alignment explanation
Indices: 1906997--1907042 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
1906987 GGTACAATGT
1906997 TCACTGTTCACGAGTATTGTTCA
1 TCACTGTTCACGAGTATTGTTCA
*
1907020 TCACTGTTCATG-GTATTGTTCA
1 TCACTGTTCACGAGTATTGTTCA
1907042 T
1 T
1907043 ACGTATAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (23 bp):
TCACTGTTCACGAGTATTGTTCA
Found at i:1908037 original size:2 final size:2
Alignment explanation
Indices: 1908030--1908088 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1908020 AGATCTTTTA
1908030 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
1908072 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1908089 CCCCCATCAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1917869 original size:24 final size:24
Alignment explanation
Indices: 1917818--1917871 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1917808 CAAAATCCAG
* *
1917818 ATCAGAACAAAATTCATGTTATGT
1 ATCAGAACAAAATTCAAGTTATGA
*
1917842 ATCAGAACAGAATTCAAGTTA-GAA
1 ATCAGAACAAAATTCAAGTTATG-A
1917866 ATCAGA
1 ATCAGA
1917872 TAAAATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAGAACAAAATTCAAGTTATGA
Found at i:1920553 original size:24 final size:24
Alignment explanation
Indices: 1920507--1920572 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
1920497 ATGGAGACAT
* * *
1920507 CAGAAATTAAAACAGATTTCAGAA
1 CAGAAATCAAAACAGAATCCAGAA
* *
1920531 CA-AATATCTAAACAGAATCCAGAT
1 CAGAA-ATCAAAACAGAATCCAGAA
1920555 CAGAAATCAAAACAGAAT
1 CAGAAATCAAAACAGAAT
1920573 TCAGGTTATG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
23 2 0.06
24 30 0.88
25 2 0.06
ACGTcount: A:0.55, C:0.17, G:0.11, T:0.18
Consensus pattern (24 bp):
CAGAAATCAAAACAGAATCCAGAA
Found at i:1929594 original size:58 final size:59
Alignment explanation
Indices: 1929494--1929755 Score: 205
Period size: 58 Copynumber: 4.5 Consensus size: 59
1929484 TGACACTTTT
*** ** * * *
1929494 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATATATTTCTATATAGAACACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAAAATATGGATTTCCAGATAGAACACTAAG
* **
1929553 TGTGCT-AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGCA-TATTA-
1 TGTGCTAAAATGATAAGGAAATCATACTGAAAATATGGATTTCCAGATAGAACACTA--AG
* * *** *
1929611 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGGTTTCCAGATA-AAGCACTAAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAAAATATGGATTTCCAGATAGAA-CACTAAG
* * * * *
1929670 GGTACT-AAATGATAAGGAAACCATATTGAAAATATGGATTTCCAGATAGAGCA-TATTA-
1 TGTGCTAAAATGATAAGGAAATCATACTGAAAATATGGATTTCCAGATAGAACACTA--AG
* **
1929728 TGTGCTAAAATGGTAACAAAATCATACT
1 TGTGCTAAAATGATAAGGAAATCATACT
1929756 AATGGTATGA
Statistics
Matches: 155, Mismatches: 38, Indels: 20
0.73 0.18 0.09
Matches are distributed among these distances:
57 3 0.02
58 84 0.54
59 66 0.43
60 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (59 bp):
TGTGCTAAAATGATAAGGAAATCATACTGAAAATATGGATTTCCAGATAGAACACTAAG
Found at i:1929700 original size:117 final size:117
Alignment explanation
Indices: 1929494--1929755 Score: 382
Period size: 117 Copynumber: 2.2 Consensus size: 117
1929484 TGACACTTTT
* * * * * * *
1929494 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATATATTTCTATATAGAACACTGAGTGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCAGATAGAACACTAAGGGTACT
* *
1929559 AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATATTA
66 AAATGATAAGGAAACCATATTGAAAATATGGATTTCCAGATAGAGCATATTA
* * *
1929611 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGGTTTCCAGATA-AAGCACTAAGGGTAC
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCAGATAGAA-CACTAAGGGTAC
1929675 TAAATGATAAGGAAACCATATTGAAAATATGGATTTCCAGATAGAGCATATTA
65 TAAATGATAAGGAAACCATATTGAAAATATGGATTTCCAGATAGAGCATATTA
**
1929728 TGTGCTAAAATGGTAACAAAATCATACT
1 TGTGCTAAAATGGTAAGGAAATCATACT
1929756 AATGGTATGA
Statistics
Matches: 129, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
116 2 0.02
117 127 0.98
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (117 bp):
TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCAGATAGAACACTAAGGGTACT
AAATGATAAGGAAACCATATTGAAAATATGGATTTCCAGATAGAGCATATTA
Found at i:1929985 original size:17 final size:18
Alignment explanation
Indices: 1929960--1929993 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1929950 ATTGTAGTAT
1929960 ATTCATTGGA-ATTAAAG
1 ATTCATTGGAGATTAAAG
*
1929977 ATTCCTTGGAGATTAAA
1 ATTCATTGGAGATTAAA
1929994 TATCATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (18 bp):
ATTCATTGGAGATTAAAG
Found at i:1936595 original size:3 final size:3
Alignment explanation
Indices: 1936587--1936659 Score: 110
Period size: 3 Copynumber: 24.0 Consensus size: 3
1936577 TAGTTTGCTT
1936587 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1936635 TTA ATA TACA TTA TTA TTG TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA
1936660 AATAAAAATA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
3 61 0.97
4 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1938851 original size:82 final size:82
Alignment explanation
Indices: 1938714--1938875 Score: 270
Period size: 82 Copynumber: 2.0 Consensus size: 82
1938704 AAGAGAATGA
*
1938714 ATTTTGGGTGATAAACGCATACTGATTTATCTTTTAACTGATGTTTTCTTAAAAACTCTTTTAAA
1 ATTTTGGGTGATAAACGCATACTGATTTATCTTTTAACTGATATTTTCTTAAAAACTCTTTTAAA
*
1938779 AGATGAATTTTAGGTGC
66 AGAAGAATTTTAGGTGC
* * *
1938796 ATTTTTGGTGATAAACGCATACTGGTTTATCTTTTAACTGATATTTTCTTTAAAACTCTTTTAAA
1 ATTTTGGGTGATAAACGCATACTGATTTATCTTTTAACTGATATTTTCTTAAAAACTCTTTTAAA
*
1938861 AGAAGATTTTTAGGT
66 AGAAGAATTTTAGGT
1938876 ATTCGACCTA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
82 74 1.00
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.44
Consensus pattern (82 bp):
ATTTTGGGTGATAAACGCATACTGATTTATCTTTTAACTGATATTTTCTTAAAAACTCTTTTAAA
AGAAGAATTTTAGGTGC
Found at i:1948312 original size:22 final size:22
Alignment explanation
Indices: 1948282--1948345 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
1948272 TATCTACATC
* *
1948282 TACATTCTTCAAAGATGATTGA
1 TACACTCTTCAAAGATGATAGA
1948304 TACACTCTTCAAAGATGATAGA
1 TACACTCTTCAAAGATGATAGA
* * *
1948326 TTCTCTTTTCAAAGATGATA
1 TACACTCTTCAAAGATGATA
1948346 TATTCTCTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (22 bp):
TACACTCTTCAAAGATGATAGA
Found at i:1948350 original size:22 final size:22
Alignment explanation
Indices: 1948289--1948365 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
1948279 ATCTACATTC
* * *
1948289 TTCAAAGATGAT-TGATACACTC
1 TTCAAAGATGATAT-ATTCTCTT
*
1948311 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATATATTCTCTT
1948333 TTCAAAGATGATATATTCTCTT
1 TTCAAAGATGATATATTCTCTT
*
1948355 TTTAAAGATGA
1 TTCAAAGATGA
1948366 AAGCCTTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (22 bp):
TTCAAAGATGATATATTCTCTT
Found at i:1949085 original size:45 final size:45
Alignment explanation
Indices: 1949022--1949588 Score: 918
Period size: 45 Copynumber: 12.6 Consensus size: 45
1949012 CTATTTCCCA
* *
1949022 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1949067 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1949112 CATCTGTAAGCCCTTCAATGCATGATGTTTTCAAAACCTTCGGGA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1949157 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1949202 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGTT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
1949247 CCTATATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1949292 CATTTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGC
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1949337 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1949382 CATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1949427 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
1949472 CATTTGTAAGCCCTTCAGTGCATTATGTTCTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * *
1949517 CATGTGTAAGCCCTTCAGTGCATGATATTTTCAAATCCTCCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * *
1949562 CATCTATAAGACCTACAGTGCAAGATG
1 CATCTGTAAGCCCTTCAGTGCATGATG
1949589 ATAAGACCTC
Statistics
Matches: 484, Mismatches: 38, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 484 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:1949770 original size:3 final size:3
Alignment explanation
Indices: 1949762--1949810 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
1949752 CAGTTTGCTT
* *
1949762 TTA TTA TTA TTA TTA TTA TTA ATA TACA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
1949808 TTA
1 TTA
1949811 AATAAAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 39 0.95
4 2 0.05
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1949895 original size:11 final size:11
Alignment explanation
Indices: 1949879--1949906 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1949869 AAGAAGAGGG
1949879 CCAACAATGGC
1 CCAACAATGGC
1949890 CCAACAATGGC
1 CCAACAATGGC
1949901 CCAACA
1 CCAACA
1949907 GTGACCAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.39, G:0.14, T:0.07
Consensus pattern (11 bp):
CCAACAATGGC
Found at i:1957372 original size:9 final size:9
Alignment explanation
Indices: 1957360--1957423 Score: 50
Period size: 9 Copynumber: 7.7 Consensus size: 9
1957350 ATATGTTAAG
1957360 TATATATAT
1 TATATATAT
1957369 TATATATA-
1 TATATATAT
*
1957377 TAAACTATA-
1 TATA-TATAT
*
1957386 TATATAAAT
1 TATATATAT
*
1957395 TATATA-GT
1 TATATATAT
1957403 T-TATAT-T
1 TATATATAT
1957410 TATAT-TAT
1 TATATATAT
1957418 TATATA
1 TATATA
1957424 CCATTTATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
7 7 0.16
8 17 0.38
9 21 0.47
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (9 bp):
TATATATAT
Found at i:1957376 original size:13 final size:13
Alignment explanation
Indices: 1957360--1957400 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
1957350 ATATGTTAAG
*
1957360 TATATATATTATA
1 TATATAAATTATA
*
1957373 TATATAAACTATA
1 TATATAAATTATA
1957386 TATATAAATTATA
1 TATATAAATTATA
1957399 TA
1 TA
1957401 GTTTATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (13 bp):
TATATAAATTATA
Found at i:1957478 original size:2 final size:2
Alignment explanation
Indices: 1957473--1957632 Score: 62
Period size: 2 Copynumber: 79.0 Consensus size: 2
1957463 CTATATAGTT
* *
1957473 TA TA TA TA AA T- TA TA TA TA TA TA TA TA TA TA AA GTA TA -A T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * * *
1957513 TA TA AA GA T- TA AA GTA TA TA -A TA TA AA GTA TA TA TG 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
* * * * *
1957555 AA GTA TA TA TA CA TA TA AA GTA TA -A GTA TG TA TA TA TA TA TG
1 TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
* * * *
1957597 TA TA TA AA CTA TA AA GTG TG 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
1957633 CACACACACA
Statistics
Matches: 115, Mismatches: 29, Indels: 28
0.67 0.17 0.16
Matches are distributed among these distances:
1 6 0.05
2 102 0.89
3 7 0.06
ACGTcount: A:0.50, C:0.01, G:0.08, T:0.41
Consensus pattern (2 bp):
TA
Found at i:1957527 original size:20 final size:21
Alignment explanation
Indices: 1957479--1957540 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
1957469 AGTTTATATA
* * *
1957479 TAAATTATATATATATATATAT
1 TAAAGTATATA-ATATAAAGAT
*
1957501 ATAAAGTATA-ATTATAAAGAT
1 -TAAAGTATATAATATAAAGAT
1957522 TAAAGTATATAATATAAAG
1 TAAAGTATATAATATAAAG
1957541 TATATATGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 9 0.27
21 15 0.45
22 1 0.03
23 8 0.24
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (21 bp):
TAAAGTATATAATATAAAGAT
Found at i:1957557 original size:31 final size:33
Alignment explanation
Indices: 1957484--1957630 Score: 108
Period size: 34 Copynumber: 4.5 Consensus size: 33
1957474 ATATATAAAT
* * *
1957484 TATATATA-TATATATATATAAAGTATAATTATA
1 TATATAAAGTATATA-ATATAAAGTATAAGTATG
* *
1957517 AAGATTAAAGTATATAATATAAAGTAT-A-TATG
1 TATA-TAAAGTATATAATATAAAGTATAAGTATG
1957549 TATATAAAGTATATATACATATAAAGTATAAGTATG
1 TATATAAAG--TATATA-ATATAAAGTATAAGTATG
* * * *
1957585 TATATATA-TATGT-ATATAAACTATAAAGTGTG
1 TATATAAAGTATATAATATAAAGTAT-AAGTATG
*
1957617 TATATATA-TATATA
1 TATATAAAGTATATA
1957631 TACACACACA
Statistics
Matches: 94, Mismatches: 11, Indels: 18
0.76 0.09 0.15
Matches are distributed among these distances:
31 15 0.16
32 23 0.24
33 13 0.14
34 25 0.27
35 7 0.07
36 11 0.12
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.40
Consensus pattern (33 bp):
TATATAAAGTATATAATATAAAGTATAAGTATG
Found at i:1958543 original size:14 final size:14
Alignment explanation
Indices: 1958489--1958562 Score: 71
Period size: 14 Copynumber: 5.2 Consensus size: 14
1958479 GGGTCTTATT
*
1958489 AACTCGACTGAGTC
1 AACTCGATTGAGTC
*
1958503 AACCCGGATTGAGTC
1 AACTC-GATTGAGTC
**
1958518 AACT-TTTCTGAGTC
1 AACTCGAT-TGAGTC
1958532 AACTCGATTGAGTC
1 AACTCGATTGAGTC
1958546 AACTC-ATTTGAGTC
1 AACTCGA-TTGAGTC
1958560 AAC
1 AAC
1958563 CCATTGACTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
13 2 0.04
14 35 0.71
15 12 0.24
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (14 bp):
AACTCGATTGAGTC
Found at i:1958549 original size:28 final size:30
Alignment explanation
Indices: 1958496--1958564 Score: 99
Period size: 28 Copynumber: 2.4 Consensus size: 30
1958486 ATTAACTCGA
*
1958496 CTGAGTCAACCCGGATTGAGTCAACT-TTT
1 CTGAGTCAACCCGGATTGAGTCAACTCATT
*
1958525 CTGAGTCAACTC-GATTGAGTCAACTCATT
1 CTGAGTCAACCCGGATTGAGTCAACTCATT
1958554 -TGAGTCAACCC
1 CTGAGTCAACCC
1958565 ATTGACTTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.64
29 13 0.36
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (30 bp):
CTGAGTCAACCCGGATTGAGTCAACTCATT
Found at i:1958567 original size:14 final size:14
Alignment explanation
Indices: 1958526--1958567 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1958516 TCAACTTTTC
*
1958526 TGAGTCAACTCGA-T
1 TGAGTCAAC-CCATT
*
1958540 TGAGTCAACTCATT
1 TGAGTCAACCCATT
1958554 TGAGTCAACCCATT
1 TGAGTCAACCCATT
1958568 GACTTTGACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 1 0.04
14 23 0.96
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (14 bp):
TGAGTCAACCCATT
Found at i:1959620 original size:18 final size:17
Alignment explanation
Indices: 1959597--1959631 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1959587 TAAAATAACC
1959597 AAAATGCAACTAAAGTGT
1 AAAATG-AACTAAAGTGT
*
1959615 AAAATGACCTAAAGTGT
1 AAAATGAACTAAAGTGT
1959632 CTCCAAGCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.23
Consensus pattern (17 bp):
AAAATGAACTAAAGTGT
Found at i:1964759 original size:12 final size:12
Alignment explanation
Indices: 1964742--1964766 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1964732 GAAAGTGACC
1964742 CTTCATCTTCTT
1 CTTCATCTTCTT
1964754 CTTCATCTTCTT
1 CTTCATCTTCTT
1964766 C
1 C
1964767 CAATCAGTGA
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:0.08, C:0.36, G:0.00, T:0.56
Consensus pattern (12 bp):
CTTCATCTTCTT
Found at i:1971967 original size:29 final size:30
Alignment explanation
Indices: 1971925--1971988 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
1971915 ACAAGCCTCA
* * *
1971925 GAAAAATTGGGGATCATTTCGTAAGTTTT-
1 GAAAAATTGGGGATAAATTCGTAAATTTTG
*
1971954 GAAAAGTTGGGGATAAATTCGTAAATTTTG
1 GAAAAATTGGGGATAAATTCGTAAATTTTG
1971984 GAAAA
1 GAAAA
1971989 TTGATGAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.33
Consensus pattern (30 bp):
GAAAAATTGGGGATAAATTCGTAAATTTTG
Found at i:1972994 original size:33 final size:33
Alignment explanation
Indices: 1972948--1973048 Score: 193
Period size: 33 Copynumber: 3.1 Consensus size: 33
1972938 ACCTAGTGTA
*
1972948 TATGGTGGCCACGACCTTATGTGTCATACGGAT
1 TATGGTGGACACGACCTTATGTGTCATACGGAT
1972981 TATGGTGGACACGACCTTATGTGTCATACGGAT
1 TATGGTGGACACGACCTTATGTGTCATACGGAT
1973014 TATGGTGGACACGACCTTATGTGTCATACGGAT
1 TATGGTGGACACGACCTTATGTGTCATACGGAT
1973047 TA
1 TA
1973049 GCACTACGGT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 67 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.31
Consensus pattern (33 bp):
TATGGTGGACACGACCTTATGTGTCATACGGAT
Found at i:1980460 original size:89 final size:89
Alignment explanation
Indices: 1980339--1980524 Score: 250
Period size: 89 Copynumber: 2.1 Consensus size: 89
1980329 AAAGTTGAGA
* * *
1980339 AGCCTGCAGAAAGTGGTAAGGTCTTACCCTTGCACATAGCAGAG-GAGTCTTTAGAAATAGTAAG
1 AGCCTTCAGAAAGTGGTAAGGTCTTACCCTTGCACATAGCA-AGTGAGCCTTTAGAAACAGTAAG
* * *
1980403 GCCTTACCGTTGCACTTAGCAAAGG
65 GCCTTACCCTTCCACATAGCAAAGG
* *
1980428 AGCCTTCAGAAA-TGGTAAGGTCTTTACTCTTGCACATAGCAAGTGAGCCTTTAGAAACGGTAAG
1 AGCCTTCAGAAAGTGGTAAGGTC-TTACCCTTGCACATAGCAAGTGAGCCTTTAGAAACAGTAAG
* *
1980492 GTCTTACCCTTCCACATAGCAAATG
65 GCCTTACCCTTCCACATAGCAAAGG
1980517 AGCCTTCA
1 AGCCTTCA
1980525 AAAACTTCCT
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
88 12 0.14
89 73 0.86
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (89 bp):
AGCCTTCAGAAAGTGGTAAGGTCTTACCCTTGCACATAGCAAGTGAGCCTTTAGAAACAGTAAGG
CCTTACCCTTCCACATAGCAAAGG
Found at i:1980476 original size:45 final size:43
Alignment explanation
Indices: 1980339--1980524 Score: 210
Period size: 44 Copynumber: 4.2 Consensus size: 43
1980329 AAAGTTGAGA
*
1980339 AGCCTGCAGAAAGTGGTAAGGTCTTACCCTTGCACATAGCAGAGG
1 AGCCTTCAGAAA-TGGTAAGGTCTTACCCTTGCACATAGCA-AGG
* * * * * *
1980384 AGTCTTTAGAAATAGTAAGGCCTTACCGTTGCACTTAGCAAAGG
1 AGCCTTCAGAAATGGTAAGGTCTTACCCTTGCACATAGC-AAGG
*
1980428 AGCCTTCAGAAATGGTAAGGTCTTTACTCTTGCACATAGCAAGTG
1 AGCCTTCAGAAATGGTAAGGTC-TTACCCTTGCACATAGCAAG-G
* * * *
1980473 AGCCTTTAGAAACGGTAAGGTCTTACCCTTCCACATAGCAAATG
1 AGCCTTCAGAAATGGTAAGGTCTTACCCTTGCACATAGC-AAGG
1980517 AGCCTTCA
1 AGCCTTCA
1980525 AAAACTTCCT
Statistics
Matches: 117, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
44 70 0.60
45 47 0.40
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (43 bp):
AGCCTTCAGAAATGGTAAGGTCTTACCCTTGCACATAGCAAGG
Found at i:1988087 original size:516 final size:518
Alignment explanation
Indices: 1987109--1988142 Score: 1876
Period size: 516 Copynumber: 2.0 Consensus size: 518
1987099 CCACAGGCAT
1987109 GGCACTCATAGTGTATCTCTGAAAAGACTCACATCTGCCTTTCTTACTGTTGTGTGCAGAAGAAT
1 GGCACTCATAGTGTATCTCTGAAAAGACTCACATCTGCCTTTCTTACTGTTGTGTGCAGAAGAAT
*
1987174 CAATAGAACCAAAAGGCCTTCTGAATCAATCTCGATCTCGATCTCGATCTCTCTTGCGCTCCATA
66 CAACAGAACCAAAAGGCCTTCTGAATCAATCTCG----CGATCTCGATCTCTCTTGCGCTCCATA
1987239 TCCACTCACTTAATCTCCTTGGTGGTCTTGGATCTCTCAACCAAGGCATCAAAGTTCCTTTCCTG
127 TCCACTCACTTAATCTCCTTGGTGGTCTTGGATCTCTCAACCAAGGCATCAAAGTTCCTTTCCTG
1987304 GAGGGTAGAAACTAGACTCCTTATCTCTTACATGAGTCCATTCTCGAACCTCAAGCACCGATCCG
192 GAGGGTAGAAACTAGACTCCTTATCTCTTACATGAGTCCATTCTCGAACCTCAAGCACCGATCCG
* *
1987369 ATTCAATTTCAATAAGTCTAGTAGTATAACGACTTAGTCTAATGAACTCAACCTCATAGTCCATA
257 ATTCAATGTCAACAAGTCTAGTAGTATAACGACTTAGTCTAATGAACTCAACCTCATAGTCCATA
*
1987434 ACAGACATATCACACTGCTCCAAATTCTAAAACTCCTAACATCGCTCTTGTAGATATCTCTCTCC
322 ACAGACATATCACACTGCTCCAAATTCTAAAACTCCTAACATCGCTCCTGTAGATATCTCTCTCC
1987499 AATGTAGTGACTCCGAAAATGTTCCCAAAAAACGACCAGATATTGATTGCCACTGCATAAAACTC
387 AATGTAGTGACTCCGAAAATGTTCCCAAAAAACGACCAGATATTGATTGCCACTGCATAAAACTC
1987564 TCATTCTTCAGCATAGCTAGGGCCCCTTTAACTGTTGCTCAGGCCTCAAATCATACTAGTGCAGC
452 TCATTCTTCAGCATAGCTAGGGCCCCTTTAACTGTTGCTCAGGCCTCAAATCATACTAGTGCAGC
1987629 AA
517 AA
* * *
1987631 GGCACTCATAGTGTCTCTCTGAAAAGACTTAGC-TCTGCCTTTCTTACTGTTGTTTGCAGAAGAA
1 GGCACTCATAGTGTATCTCTGAAAAGACTCA-CATCTGCCTTTCTTACTGTTGTGTGCAGAAGAA
*
1987695 TCAACAGAACCATAAGGCCTTCTGAATCAATCT-G-GATCTCGATCTCTCTTGCGCTCCATATCC
65 TCAACAGAACCAAAAGGCCTTCTGAATCAATCTCGCGATCTCGATCTCTCTTGCGCTCCATATCC
* *
1987758 ACTTATTTAATCTCCTTGGTGGTCTTGGATCTCTCAACCAAGGCATCAAAGTTCCTTTCCTGGAG
130 ACTCACTTAATCTCCTTGGTGGTCTTGGATCTCTCAACCAAGGCATCAAAGTTCCTTTCCTGGAG
*
1987823 GGTAGAAACTAGACTCCTTATCTCTTACATGAGTCCATTCTCGAACCTCAAGTACCGATCCGATT
195 GGTAGAAACTAGACTCCTTATCTCTTACATGAGTCCATTCTCGAACCTCAAGCACCGATCCGATT
1987888 CAATGTCAACAAGTCTAGTAGTATAACGACTTAGTCTAATGAACTCAACCTCATAGTCCATAACA
260 CAATGTCAACAAGTCTAGTAGTATAACGACTTAGTCTAATGAACTCAACCTCATAGTCCATAACA
*
1987953 GACATATCACACTGCTCCAAATTCTAAAACTCCTGACATCGCTCCTGTAGATATCTCTCTCCAAT
325 GACATATCACACTGCTCCAAATTCTAAAACTCCTAACATCGCTCCTGTAGATATCTCTCTCCAAT
*
1988018 GTTGTGACTCCGAAAATGTTCCCAAAAAACGACCAGATATTGATTGCCACTGCATAAAACTCTCA
390 GTAGTGACTCCGAAAATGTTCCCAAAAAACGACCAGATATTGATTGCCACTGCATAAAACTCTCA
*
1988083 TTCTTCAGCATAGCTAGTGCCCCTTTAACTGTTGCTCAGGCCTCAAATCATACTAGTGCA
455 TTCTTCAGCATAGCTAGGGCCCCTTTAACTGTTGCTCAGGCCTCAAATCATACTAGTGCA
1988143 TCTATTGACA
Statistics
Matches: 497, Mismatches: 14, Indels: 8
0.96 0.03 0.02
Matches are distributed among these distances:
516 405 0.81
521 1 0.00
522 90 0.18
523 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (518 bp):
GGCACTCATAGTGTATCTCTGAAAAGACTCACATCTGCCTTTCTTACTGTTGTGTGCAGAAGAAT
CAACAGAACCAAAAGGCCTTCTGAATCAATCTCGCGATCTCGATCTCTCTTGCGCTCCATATCCA
CTCACTTAATCTCCTTGGTGGTCTTGGATCTCTCAACCAAGGCATCAAAGTTCCTTTCCTGGAGG
GTAGAAACTAGACTCCTTATCTCTTACATGAGTCCATTCTCGAACCTCAAGCACCGATCCGATTC
AATGTCAACAAGTCTAGTAGTATAACGACTTAGTCTAATGAACTCAACCTCATAGTCCATAACAG
ACATATCACACTGCTCCAAATTCTAAAACTCCTAACATCGCTCCTGTAGATATCTCTCTCCAATG
TAGTGACTCCGAAAATGTTCCCAAAAAACGACCAGATATTGATTGCCACTGCATAAAACTCTCAT
TCTTCAGCATAGCTAGGGCCCCTTTAACTGTTGCTCAGGCCTCAAATCATACTAGTGCAGCAA
Found at i:1989574 original size:21 final size:21
Alignment explanation
Indices: 1989552--1989623 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
1989542 GACTCGCACT
* * *
1989552 GACCATTGTCTGCCGTTGACT
1 GACCATTGACTGTCGTTGACC
1989573 GACCATTGACTGTCGTTGACC
1 GACCATTGACTGTCGTTGACC
1989594 GACCATTGACTGTCGTTGACC
1 GACCATTGACTGTCGTTGACC
1989615 GACCATTGA
1 GACCATTGA
1989624 TTTTTTCCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.19, C:0.28, G:0.24, T:0.29
Consensus pattern (21 bp):
GACCATTGACTGTCGTTGACC
Found at i:1989583 original size:11 final size:11
Alignment explanation
Indices: 1989549--1989623 Score: 57
Period size: 11 Copynumber: 7.1 Consensus size: 11
1989539 ATTGACTCGC
1989549 ACTGACCATTG
1 ACTGACCATTG
* *
1989560 TCTG-CCGTTG
1 ACTGACCATTG
1989570 ACTGACCATTG
1 ACTGACCATTG
* *
1989581 ACTG-TCGTTG
1 ACTGACCATTG
*
1989591 ACCGACCATTG
1 ACTGACCATTG
* *
1989602 ACTG-TCGTTG
1 ACTGACCATTG
*
1989612 ACCGACCATTG
1 ACTGACCATTG
1989623 A
1 A
1989624 TTTTTTCCAA
Statistics
Matches: 46, Mismatches: 15, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
10 22 0.48
11 24 0.52
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.29
Consensus pattern (11 bp):
ACTGACCATTG
Found at i:1999605 original size:18 final size:18
Alignment explanation
Indices: 1999560--1999606 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
1999550 CCAGCCGACC
* *
1999560 CGACCCAACCTGACTGCT
1 CGACCCAACTTAACTGCT
*
1999578 CAACCCCAACTTAACTGCT
1 CGA-CCCAACTTAACTGCT
1999597 CGACCCAACT
1 CGACCCAACT
1999607 CGTTGACCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.28, C:0.45, G:0.11, T:0.17
Consensus pattern (18 bp):
CGACCCAACTTAACTGCT
Found at i:2002172 original size:18 final size:18
Alignment explanation
Indices: 2002146--2002184 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
2002136 TCAAAAAGAC
2002146 TGAAGTAAATGATAAGTT
1 TGAAGTAAATGATAAGTT
*
2002164 TGAATTAAATGATAAGTT
1 TGAAGTAAATGATAAGTT
2002182 TGA
1 TGA
2002185 CGGAAGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.36
Consensus pattern (18 bp):
TGAAGTAAATGATAAGTT
Found at i:2004675 original size:39 final size:41
Alignment explanation
Indices: 2004632--2004722 Score: 114
Period size: 44 Copynumber: 2.2 Consensus size: 41
2004622 ATAGTAGAGA
* * *
2004632 AGCCTTTAGAAA-T-GGTCTTACCCTTGCACATAGCAAAGG
1 AGCCTTCAGAAAGTAGGTCTTACACTTACACATAGCAAAGG
2004671 AGCCTTCAGAAATGGTAAGGTCTTACACTTACACATAGCAAAGG
1 AGCCTTCAGAAA--GT-AGGTCTTACACTTACACATAGCAAAGG
2004715 AGCCTTCA
1 AGCCTTCA
2004723 AAAACTCCCT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
39 11 0.25
42 1 0.02
44 32 0.73
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (41 bp):
AGCCTTCAGAAAGTAGGTCTTACACTTACACATAGCAAAGG
Found at i:2007079 original size:76 final size:75
Alignment explanation
Indices: 2006972--2007187 Score: 292
Period size: 76 Copynumber: 2.9 Consensus size: 75
2006962 ATTTTAAACA
*
2006972 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
*
2007037 TG-ATATTATTT
66 -GAATATTA-TC
* * *
2007048 TTATATTTTATCTATGTTTTAGGTATTTTAGTTTAAATAGGTTTAAGTATTTTAATTAGGATTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
2007113 GAATATTATC
66 GAATATTATC
* ** * * *
2007123 TTAAATAGTATTTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTT
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAAGATTT
2007187 A
65 A
2007188 AGATGTTTTA
Statistics
Matches: 126, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
74 4 0.03
75 55 0.44
76 67 0.53
ACGTcount: A:0.29, C:0.01, G:0.13, T:0.56
Consensus pattern (75 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
GAATATTATC
Found at i:2007168 original size:75 final size:76
Alignment explanation
Indices: 2006980--2007187 Score: 287
Period size: 75 Copynumber: 2.8 Consensus size: 76
2006970 CATTATATTT
* *
2006980 TATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAAGTTTTATGATATT
1 TATCTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTATTTTAATTAGGATTTATGATATT
* * **
2007044 ATTTTTATATTT
65 ATTCTTAAATAG
* *
2007056 TATCTATGTTTTAGGTATTTTAGTTTAAATAGGTTTAAGTATTTTAATTAGGATTTA-GAATATT
1 TATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTATG-ATATT
2007120 A-TCTTAAATAG
65 ATTCTTAAATAG
* *
2007131 TATTTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 TATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTA
2007188 AGATGTTTTA
Statistics
Matches: 118, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
75 64 0.54
76 54 0.46
ACGTcount: A:0.29, C:0.01, G:0.14, T:0.56
Consensus pattern (76 bp):
TATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTATGATATTA
TTCTTAAATAG
Found at i:2007862 original size:19 final size:19
Alignment explanation
Indices: 2007840--2007907 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
2007830 TTTTCCCTTT
*
2007840 TTATTTATTATTATTTATA
1 TTATTTATTATTTTTTATA
*
2007859 TTA-TTATTATTTTTTCTA
1 TTATTTATTATTTTTTATA
** * *
2007877 AAAATTATTATTTTTTATT
1 TTATTTATTATTTTTTATA
2007896 TTATTTTATTAT
1 TTA-TTTATTAT
2007908 ATCTTTTTAA
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
18 14 0.37
19 17 0.45
20 7 0.18
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATTTATTATTTTTTATA
Found at i:2007864 original size:15 final size:14
Alignment explanation
Indices: 2007839--2007870 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
2007829 ATTTTCCCTT
2007839 TTTATTTATTATTA
1 TTTATTTATTATTA
2007853 TTTATATTATTATTA
1 TTTAT-TTATTATTA
2007868 TTT
1 TTT
2007871 TTTCTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTATTTATTATTA
Found at i:2009851 original size:21 final size:20
Alignment explanation
Indices: 2009796--2009851 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
2009786 CCATTAATAT
* *
2009796 TTTTATTTTCCTTTTTTCAA
1 TTTTATTTTTCTATTTTCAA
2009816 TTTT-TATTTT-TATTTTCAA
1 TTTTAT-TTTTCTATTTTCAA
2009835 TTTTATTTTTCTGATTT
1 TTTTATTTTTCT-ATTT
2009852 ATTTGTGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 17 0.57
20 9 0.30
21 4 0.13
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTATTTTTCTATTTTCAA
Found at i:2012651 original size:18 final size:19
Alignment explanation
Indices: 2012622--2012658 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2012612 TTATTTCCCT
2012622 TTTTATTTATTATTATTTA
1 TTTTATTTATTATTATTTA
*
2012641 TTTTA-TTATTATTTTTTA
1 TTTTATTTATTATTATTTA
2012659 AATTATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTATTTATTATTATTTA
Found at i:2012664 original size:18 final size:18
Alignment explanation
Indices: 2012628--2012675 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
2012618 CCCTTTTTAT
**
2012628 TTATTATTATTTATTTTA
1 TTATTATTATTTAAATTA
*
2012646 TTATTATTTTTTAAATTA
1 TTATTATTATTTAAATTA
* *
2012664 TAATTTTTATTT
1 TTATTATTATTT
2012676 TATTATATCT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTATTATTTAAATTA
Found at i:2015925 original size:18 final size:18
Alignment explanation
Indices: 2015913--2015954 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
2015903 GCCCTCGTCC
2015913 ACGACCACGCCCTGGCCT
1 ACGACCACGCCCTGGCCT
2015931 ACGACCACGCCCTGGCCT
1 ACGACCACGCCCTGGCCT
2015949 ACGACC
1 ACGACC
2015955 TCTAGTAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.19, C:0.50, G:0.21, T:0.10
Consensus pattern (18 bp):
ACGACCACGCCCTGGCCT
Found at i:2016579 original size:44 final size:44
Alignment explanation
Indices: 2016523--2016697 Score: 269
Period size: 44 Copynumber: 4.0 Consensus size: 44
2016513 TATAGAAAGC
** * *
2016523 GGTAAGGTCTTACCCTTGCACATAATAGAGGAGCCTTTAGAAAT
1 GGTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTTCAGAAAT
* *
2016567 GGTAAGGTCTTACCCTTGAACATAGCAAATGAGCCTTCAGAAAT
1 GGTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTTCAGAAAT
*
2016611 GGTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTTCATAAAT
1 GGTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTTCAGAAAT
* *
2016655 GGAAAGGTCTTACCCTTGCACATAGTAAAGGAGCCTTCAGAAA
1 GGTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTTCAGAAA
2016698 CTTCCTCCAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 119 1.00
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (44 bp):
GGTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTTCAGAAAT
Found at i:2027513 original size:139 final size:138
Alignment explanation
Indices: 2027221--2027483 Score: 402
Period size: 139 Copynumber: 1.9 Consensus size: 138
2027211 GTTACAAAAC
* * *
2027221 TTGTCACTATATAACATTTTTGCACTAAAAAATAGGGAGAAATATTTCTAATAGTATAAGTTTTC
1 TTGTGACTATATAACATTTTTACACTAAAAAATAGGGAGAAATAGTTCTAATAGTATAAGTTTTC
*
2027286 ATAATGATTAAAATATACAACTACAAAAATAATTAATTAAAAAAAACTTAAATTATATTAATTAC
66 ACAATGATTAAAATATACAACTACAAAAATAATTAATTAAAAAAAACTTAAATTATATTAATTAC
2027351 AATATATT
131 AATATATT
* *
2027359 TTGTGACTATATAACATTTTTCACACTAAAAAATAGGGAGAAATAGTTCTGATAGTATAATTTTT
1 TTGTGACTATATAACATTTTT-ACACTAAAAAATAGGGAGAAATAGTTCTAATAGTATAAGTTTT
* * * * * *
2027424 CACAATGATTAAAATATATAAGTAC-AAAATAATTTATTACAAAAAACTTGAATTTTATTA
65 CACAATGATTAAAATATACAACTACAAAAATAATTAATTAAAAAAAACTTAAATTATATTA
2027484 TTTGATGTGA
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
138 51 0.46
139 61 0.54
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.37
Consensus pattern (138 bp):
TTGTGACTATATAACATTTTTACACTAAAAAATAGGGAGAAATAGTTCTAATAGTATAAGTTTTC
ACAATGATTAAAATATACAACTACAAAAATAATTAATTAAAAAAAACTTAAATTATATTAATTAC
AATATATT
Found at i:2028270 original size:15 final size:15
Alignment explanation
Indices: 2028246--2028283 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2028236 AAAAAACTAC
*
2028246 TAATTGTGACAAAAT
1 TAATTTTGACAAAAT
2028261 TAATTTTGACAAAAT
1 TAATTTTGACAAAAT
*
2028276 TAAATTTG
1 TAATTTTG
2028284 TCATAGTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (15 bp):
TAATTTTGACAAAAT
Found at i:2033666 original size:21 final size:21
Alignment explanation
Indices: 2033640--2033679 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2033630 GAGGGAAGAT
2033640 AAGAGAAAAGAAAACAACTAG
1 AAGAGAAAAGAAAACAACTAG
*
2033661 AAGAGAAATGAAAACAACT
1 AAGAGAAAAGAAAACAACT
2033680 GGAAAATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.65, C:0.10, G:0.17, T:0.07
Consensus pattern (21 bp):
AAGAGAAAAGAAAACAACTAG
Found at i:2037780 original size:14 final size:13
Alignment explanation
Indices: 2037761--2037807 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
2037751 GCAAGCACTC
2037761 AAAAGAAGAAAATA
1 AAAAGAAGAAAA-A
2037775 AAAAGAAGAAAAA
1 AAAAGAAGAAAAA
*
2037788 AAGAA-AAGAAAAG
1 AA-AAGAAGAAAAA
2037801 AAAAGAA
1 AAAAGAA
2037808 AAGTTGATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 2 0.07
13 14 0.47
14 14 0.47
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (13 bp):
AAAAGAAGAAAAA
Found at i:2037789 original size:17 final size:18
Alignment explanation
Indices: 2037761--2037804 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
2037751 GCAAGCACTC
* *
2037761 AAAAGAAGAAAATAAAA-
1 AAAAGAAAAAAAGAAAAG
*
2037778 AGAAGAAAAAAAGAAAAG
1 AAAAGAAAAAAAGAAAAG
2037796 AAAAGAAAA
1 AAAAGAAAA
2037805 GAAAAGTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAAAAGAAAAG
Found at i:2037791 original size:22 final size:23
Alignment explanation
Indices: 2037761--2037809 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
2037751 GCAAGCACTC
* * *
2037761 AAAAGAAGAAAATAAAA-AGAAG
1 AAAAAAAGAAAAGAAAAGAAAAG
2037783 AAAAAAAGAAAAGAAAAGAAAAG
1 AAAAAAAGAAAAGAAAAGAAAAG
2037806 AAAA
1 AAAA
2037810 GTTGATAGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (23 bp):
AAAAAAAGAAAAGAAAAGAAAAG
Found at i:2037794 original size:5 final size:5
Alignment explanation
Indices: 2037775--2037810 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
2037765 GAAGAAAATA
*
2037775 AAAAG AAGAAA AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG AAAAG
2037811 TTGATAGCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:2037804 original size:15 final size:16
Alignment explanation
Indices: 2037761--2037810 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
2037751 GCAAGCACTC
*
2037761 AAAAGAAG-AAAATA-
1 AAAAGAAGAAAAAAAG
2037775 AAAAGAAGAAAAAAAG
1 AAAAGAAGAAAAAAAG
*
2037791 AAAAGAA-AAGAAAAG
1 AAAAGAAGAAAAAAAG
2037806 AAAAG
1 AAAAG
2037811 TTGATAGCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
14 8 0.25
15 17 0.53
16 7 0.22
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (16 bp):
AAAAGAAGAAAAAAAG
Found at i:2042070 original size:14 final size:14
Alignment explanation
Indices: 2042051--2042089 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
2042041 GCAAGCACTC
2042051 AAAAGAAGAAAACA
1 AAAAGAAGAAAACA
2042065 AAAAGAAGAAAACA
1 AAAAGAAGAAAACA
*
2042079 AGAA-AAGAAAA
1 AAAAGAAGAAAA
2042090 GAAAGAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAAACA
Found at i:2042081 original size:22 final size:22
Alignment explanation
Indices: 2042051--2042098 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2042041 GCAAGCACTC
*
2042051 AAAAGAAGAAAACAAAAAG-AAG
1 AAAACAAGAAAA-AAAAAGAAAG
*
2042073 AAAACAAGAAAAGAAAAGAAAG
1 AAAACAAGAAAAAAAAAGAAAG
2042095 AAAA
1 AAAA
2042099 GTTGATTGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAACAAGAAAAAAAAAGAAAG
Found at i:2052059 original size:133 final size:132
Alignment explanation
Indices: 2051893--2052230 Score: 410
Period size: 132 Copynumber: 2.6 Consensus size: 132
2051883 ATTTTTCTTA
* * * * * * **
2051893 GATCTGCCTGAATAGTAGGGAAGCAAATCAAGTTCAATTCAATCATCCCTAAAGATCAATGAAGT
1 GATCTTCCTGAATAGCAGTGAAGCAAATCAAGTTCGATTCAATCTTCCCTAAAGAGCAACAAAGT
* *
2051958 TGATCAAAGTTTTTCAAGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATCAT-TCTTCTTTTAG
66 GGATCAAAGTTTTTCAAGTCTGATCT-CCCTAAAGAGTAGTGGAGCAGATCATCT-TTCTTTCAG
*
2052022 ATTTT
129 A-ATT
* * ** *
2052027 G-TCTTCCTGAATAGCAGTGAAGTAAATCAAGTTTGATTTGATCTTCCCTAAAGAGCAGCAAAGT
1 GATCTTCCTGAATAGCAGTGAAGCAAATCAAGTTCGATTCAATCTTCCCTAAAGAGCAACAAAGT
* * *
2052091 GGATCAAAGTTTTTCGAGTCTGATCTCCCTAAAGAGTAGTGGAGCAGGTCATCTTTCTTTCATAA
66 GGATCAAAGTTTTTCAAGTCTGATCTCCCTAAAGAGTAGTGGAGCAGATCATCTTTCTTTCAGAA
2052156 TT
131 TT
* * * * *
2052158 GATCTTCCTGAAGAGCAATGAAGCAAATCAATTTCGATTCAATCTTCCCTGAAGAGCAGCAAAGT
1 GATCTTCCTGAATAGCAGTGAAGCAAATCAAGTTCGATTCAATCTTCCCTAAAGAGCAACAAAGT
*
2052223 GAATCAAA
66 GGATCAAA
2052231 TTCTTTTTCG
Statistics
Matches: 174, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
131 3 0.02
132 95 0.55
133 75 0.43
134 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (132 bp):
GATCTTCCTGAATAGCAGTGAAGCAAATCAAGTTCGATTCAATCTTCCCTAAAGAGCAACAAAGT
GGATCAAAGTTTTTCAAGTCTGATCTCCCTAAAGAGTAGTGGAGCAGATCATCTTTCTTTCAGAA
TT
Found at i:2052264 original size:132 final size:132
Alignment explanation
Indices: 2051912--2052269 Score: 345
Period size: 132 Copynumber: 2.7 Consensus size: 132
2051902 GAATAGTAGG
** * * *** * *
2051912 GAAGCAAATCAAGTTCAATTCAATCATCCCTAAAGATCAATGAAGTTG-ATCAAAGTTTTTCAAG
1 GAAGCAAATCAAGTTTGATTCAATCTTCCCTAAAGAGCAGCAAAG-TGAATCAAACTTTTTCGAG
* * * * * * *
2051976 TCTGATCTCCCCTAAAGAGTAGTGGAGCAGATCAT-TCTTCTTTTAGATTTTG-TCTTCCTGAAT
65 TCCGATCT-CCCTAAAGAGAAGTGGAGCAGGTCATCT-TTCTTTCATA-ATTGATCTTCCTGAAG
*
2052039 AGCAGT
127 AGCAAT
* ** * *
2052045 GAAGTAAATCAAGTTTGATTTGATCTTCCCTAAAGAGCAGCAAAGTGGATCAAAGTTTTTCGAGT
1 GAAGCAAATCAAGTTTGATTCAATCTTCCCTAAAGAGCAGCAAAGTGAATCAAACTTTTTCGAGT
* *
2052110 CTGATCTCCCTAAAGAGTAGTGGAGCAGGTCATCTTTCTTTCATAATTGATCTTCCTGAAGAGCA
66 CCGATCTCCCTAAAGAGAAGTGGAGCAGGTCATCTTTCTTTCATAATTGATCTTCCTGAAGAGCA
2052175 AT
131 AT
*
2052177 GAAGCAAATCAA-TTTCGATTCAATCTTCCCTGAAGAGCAGCAAAGTGAATCAAATTCTTTTTCG
1 GAAGCAAATCAAGTTT-GATTCAATCTTCCCTAAAGAGCAGCAAAGTGAATCAAA--CTTTTTCG
*
2052241 TGATCCGAT-TACCC-AAA-A-AAGTGGAGCAG
63 AG-TCCGATCT-CCCTAAAGAGAAGTGGAGCAG
2052270 ATCAAGTCCG
Statistics
Matches: 191, Mismatches: 26, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
131 6 0.03
132 105 0.55
133 60 0.31
134 12 0.06
135 8 0.04
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (132 bp):
GAAGCAAATCAAGTTTGATTCAATCTTCCCTAAAGAGCAGCAAAGTGAATCAAACTTTTTCGAGT
CCGATCTCCCTAAAGAGAAGTGGAGCAGGTCATCTTTCTTTCATAATTGATCTTCCTGAAGAGCA
AT
Found at i:2054931 original size:14 final size:14
Alignment explanation
Indices: 2054899--2054931 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2054889 ATCATTTTTT
2054899 GTTTTTTAAAATTA
1 GTTTTTTAAAATTA
2054913 GTTTTCTTAAAATTA
1 GTTTT-TTAAAATTA
2054928 -TTTT
1 GTTTT
2054932 AAAGGATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (14 bp):
GTTTTTTAAAATTA
Found at i:2061609 original size:4 final size:4
Alignment explanation
Indices: 2061600--2061635 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
2061590 CGCTAACTTT
*
2061600 TTTA TTTA TTTA TTTA TTTA TTTA TGTA TTTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTT
2061636 TATGTTCGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 26 0.90
5 3 0.10
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:2063946 original size:20 final size:20
Alignment explanation
Indices: 2063917--2063955 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2063907 TTCCTATTTT
*
2063917 TGCATATTTGCATTTACATG
1 TGCATATTTGCATTAACATG
*
2063937 TGCATCTTTGCATTAACAT
1 TGCATATTTGCATTAACAT
2063956 CTATACATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.44
Consensus pattern (20 bp):
TGCATATTTGCATTAACATG
Found at i:2075495 original size:17 final size:19
Alignment explanation
Indices: 2075445--2075499 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 19
2075435 GAGATAGTTA
2075445 ATAATGAGAAGAACTCATCTG
1 ATAATGAGAAGAACT--TCTG
*
2075466 ATGATGAAGAAGAACTT-T-
1 ATAATG-AGAAGAACTTCTG
2075484 ATAATGAGAAGAACTT
1 ATAATGAGAAGAACTT
2075500 GATCAACCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 10 0.32
18 5 0.16
19 1 0.03
20 1 0.03
21 5 0.16
22 9 0.29
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.25
Consensus pattern (19 bp):
ATAATGAGAAGAACTTCTG
Found at i:2075638 original size:118 final size:118
Alignment explanation
Indices: 2075423--2075644 Score: 268
Period size: 118 Copynumber: 1.9 Consensus size: 118
2075413 TAAATTAGTT
* * * *
2075423 AACATTTCCAATGAGATAGTTAATAATGAGAAGAACTCATCTGATGATGAAGAAGAACTTTATAA
1 AACATTTCCAATGAGAGAGTTAATAATGAAAAGAACTCATCCGATGAGGAAGAAGAACTTTATAA
* *
2075488 TGAGAAGAACTTGATCAACCTTGGTTCAATTCCATCACAGAATTAGGTGAATC
66 TGAGAAGAACTTCATCAACCTTGCTTCAATTCCATCACAGAATTAGGTGAATC
* * * * *
2075541 AACATTTCCAATG-GAAGAGTTCATAATGAAAAGAATTCATCCGATGAGGGAGACGAATTTTATA
1 AACATTTCCAATGAG-AGAGTTAATAATGAAAAGAACTCATCCGATGAGGAAGAAGAACTTTATA
** * * *
2075605 ATGAGACTAACTTCTTTAACCTTAGCTT-GATTCCATCACA
65 ATGAGAAGAACTTCATCAACCTT-GCTTCAATTCCATCACA
2075645 TAAGGAGCTA
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
117 1 0.01
118 82 0.95
119 3 0.03
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (118 bp):
AACATTTCCAATGAGAGAGTTAATAATGAAAAGAACTCATCCGATGAGGAAGAAGAACTTTATAA
TGAGAAGAACTTCATCAACCTTGCTTCAATTCCATCACAGAATTAGGTGAATC
Found at i:2075844 original size:78 final size:78
Alignment explanation
Indices: 2075715--2075858 Score: 218
Period size: 78 Copynumber: 1.8 Consensus size: 78
2075705 TCATTAGTTT
*
2075715 GTTCGATTCCATCATAGAAAGAGCATGATCAACATTTCTAGTGAAGAGTTCATAATAAGAAGAAC
1 GTTCGATTCCATCATAGAAAGAGCATGATCAACATTTATAGTGAAGAGTTCATAATAAGAAGAAC
2075780 TTTTCCAACCTTG
66 TTTTCCAACCTTG
* * * * *
2075793 GTTCGATTCCATCATAGAAGGA-CGTGGATTAACATTTATAGTGGAGAGTTCATAATGAGAAGAA
1 GTTCGATTCCATCATAGAAAGAGCAT-GATCAACATTTATAGTGAAGAGTTCATAATAAGAAGAA
2075857 CT
65 CT
2075859 CTTCTGATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
77 2 0.03
78 57 0.97
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.29
Consensus pattern (78 bp):
GTTCGATTCCATCATAGAAAGAGCATGATCAACATTTATAGTGAAGAGTTCATAATAAGAAGAAC
TTTTCCAACCTTG
Found at i:2076046 original size:40 final size:40
Alignment explanation
Indices: 2075917--2076143 Score: 220
Period size: 40 Copynumber: 5.6 Consensus size: 40
2075907 TTAGTTCGAT
* * * * * * **
2075917 TCCATCACATAAGGAGTTAGAACCGCACCGACCTTGGCTTA
1 TCCATCACATAAGGAGTTGGATCAGCATC-ACTTTCGCTCG
*
2075958 TCCATCACATAAGGAGTTGGATCAGCATTATCATTTCGCTCG
1 TCCATCACATAAGGAGTTGGATCAGCATCA-C-TTTCGCTCG
*
2076000 TCCATCACATAAGGAGTTGGATCAGCATTACTTTCGCTCG
1 TCCATCACATAAGGAGTTGGATCAGCATCACTTTCGCTCG
* * * * * *
2076040 TCCATCACATAAGGAGTTGTATTAACATCATTTTTGTTCG
1 TCCATCACATAAGGAGTTGGATCAGCATCACTTTCGCTCG
* * * * **
2076080 TCCATCACATAAGGAGTTGGATTAGAATCACCTTGGCTTA
1 TCCATCACATAAGGAGTTGGATCAGCATCACTTTCGCTCG
*
2076120 TCGATCACATAAGGAGTTGGATCA
1 TCCATCACATAAGGAGTTGGATCA
2076144 ATATCACCTT
Statistics
Matches: 157, Mismatches: 27, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
40 96 0.61
41 26 0.17
42 35 0.22
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (40 bp):
TCCATCACATAAGGAGTTGGATCAGCATCACTTTCGCTCG
Found at i:2076165 original size:80 final size:79
Alignment explanation
Indices: 2075917--2076149 Score: 259
Period size: 80 Copynumber: 2.9 Consensus size: 79
2075907 TTAGTTCGAT
* * * * *
2075917 TCCATCACATAAGGAGTTAGAACCGCACCGACCTTGGCTTATCCATCACATAAGGAGTTGGATCA
1 TCCATCACATAAGGAGTTGGATCAGAATC-ACCTTGGCTTATCCATCACATAAGGAGTTGGATCA
2075982 GCATTATCATTTCGCTCG
65 --A-TATCATTTCGCTCG
* * * * ** * *
2076000 TCCATCACATAAGGAGTTGGATCAGCATTACTTTCGCTCGTCCATCACATAAGGAGTTGTATTAA
1 TCCATCACATAAGGAGTTGGATCAGAATCACCTTGGCTTATCCATCACATAAGGAGTTGGATCAA
* * *
2076065 CATCATTTTTGTTCG
66 TATCA-TTTCGCTCG
* *
2076080 TCCATCACATAAGGAGTTGGATTAGAATCACCTTGGCTTATCGATCACATAAGGAGTTGGATCAA
1 TCCATCACATAAGGAGTTGGATCAGAATCACCTTGGCTTATCCATCACATAAGGAGTTGGATCAA
2076145 TATCA
66 TATCA
2076150 CCTTGGGTCA
Statistics
Matches: 124, Mismatches: 25, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
79 4 0.03
80 67 0.54
82 29 0.23
83 24 0.19
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (79 bp):
TCCATCACATAAGGAGTTGGATCAGAATCACCTTGGCTTATCCATCACATAAGGAGTTGGATCAA
TATCATTTCGCTCG
Found at i:2078446 original size:2 final size:2
Alignment explanation
Indices: 2078439--2078472 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2078429 CAAATGGAAT
2078439 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
2078473 AACATACATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2080161 original size:12 final size:13
Alignment explanation
Indices: 2080135--2080180 Score: 60
Period size: 12 Copynumber: 3.7 Consensus size: 13
2080125 TCCTTTGATA
*
2080135 TTATATAATATAT
1 TTATATTATATAT
2080148 TTATATTATA-AT
1 TTATATTATATAT
2080160 TTATATTATATA-
1 TTATATTATATAT
*
2080172 ATATATTAT
1 TTATATTAT
2080181 TCATTTCTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
12 20 0.67
13 10 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATATTATATAT
Found at i:2081481 original size:15 final size:16
Alignment explanation
Indices: 2081458--2081493 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
2081448 TTTAATTATC
*
2081458 ATTTTTTATTTAT-TT
1 ATTTATTATTTATATT
2081473 ATTTATTATTTATATT
1 ATTTATTATTTATATT
2081489 ATTTA
1 ATTTA
2081494 ATAAGTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTATTATTTATATT
Found at i:2081828 original size:17 final size:18
Alignment explanation
Indices: 2081786--2081834 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 18
2081776 ATTTTGTTAT
2081786 TATTATTATTATTCTTTA
1 TATTATTATTATTCTTTA
* *
2081804 T-TTCTTATTATTCTTTC
1 TATTATTATTATTCTTTA
2081821 TATT-TTA-TATTCTT
1 TATTATTATTATTCTT
2081835 CACGTCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 7 0.25
17 18 0.64
18 3 0.11
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.69
Consensus pattern (18 bp):
TATTATTATTATTCTTTA
Found at i:2081831 original size:26 final size:26
Alignment explanation
Indices: 2081768--2081831 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 26
2081758 CTTCTTCCCT
*
2081768 TTATGTTTAT-TTTGTTATTATTATTA
1 TTAT-TTTATATTTCTTATTATTATTA
*
2081794 TTATTCTT-TATTTCTTATTATTCTT-
1 TTATT-TTATATTTCTTATTATTATTA
2081819 TCTATTTTATATT
1 T-TATTTTATATT
2081832 CTTCACGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
25 5 0.16
26 27 0.84
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.70
Consensus pattern (26 bp):
TTATTTTATATTTCTTATTATTATTA
Found at i:2086193 original size:21 final size:22
Alignment explanation
Indices: 2086176--2086237 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 22
2086166 AACAAAAAGG
2086176 GCAAAAAGAAAAAG-AAAAGAA
1 GCAAAAAGAAAAAGAAAAAGAA
2086197 GCAAAAAGAAAAAGAAGCAAA-AA
1 GCAAAAAGAAAAAGAA--AAAGAA
2086220 G-AAAAA-ACAAAAGAAAAA
1 GCAAAAAGA-AAAAGAAAAA
2086238 AGAAAGAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
20 3 0.08
21 15 0.41
22 13 0.35
23 3 0.08
24 3 0.08
ACGTcount: A:0.77, C:0.06, G:0.16, T:0.00
Consensus pattern (22 bp):
GCAAAAAGAAAAAGAAAAAGAA
Found at i:2086203 original size:16 final size:15
Alignment explanation
Indices: 2086184--2086236 Score: 76
Period size: 16 Copynumber: 3.7 Consensus size: 15
2086174 GGGCAAAAAG
2086184 AAAAAGAAAAGAAGC
1 AAAAAGAAAAGAAGC
2086199 AAAAAGAAAAAGAAGC
1 AAAAAG-AAAAGAAGC
2086215 AAAAAGAAAA-AA-C
1 AAAAAGAAAAGAAGC
2086228 -AAAAGAAAA
1 AAAAAGAAAA
2086237 AAGAAAGAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.24
13 1 0.03
14 2 0.05
15 10 0.27
16 15 0.41
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAGAAGC
Done.