Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008041.1 Hibiscus syriacus cultivar Beakdansim tig00110528_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: 4970990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 21
Found at i:1884142 original size:3 final size:3
Alignment explanation
Indices: 1884125--1884172 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
1884115 TATAAAAATG
1884125 TAA T-A TAA TAA -AA TAA TAA TAA TAA TAA TAAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
1884168 TAA TA
1 TAA TA
1884173 TATTATTATC
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
2 6 0.15
3 32 0.78
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1884157 original size:19 final size:18
Alignment explanation
Indices: 1884125--1884172 Score: 78
Period size: 19 Copynumber: 2.6 Consensus size: 18
1884115 TATAAAAATG
1884125 TAATATAATAAAATAATAA
1 TAATATAAT-AAATAATAA
1884144 TAATAATAATAAATAATAA
1 TAAT-ATAATAAATAATAA
1884163 TAATATAATA
1 TAATATAATA
1884173 TATTATTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.21
19 17 0.61
20 5 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAATATAATAAATAATAA
Found at i:1884723 original size:40 final size:41
Alignment explanation
Indices: 1884636--1884729 Score: 120
Period size: 40 Copynumber: 2.3 Consensus size: 41
1884626 AAACATCCTA
* * * * *
1884636 CTCGAAGGTCTTACGGATGGCCCAAATGACTTATCATCTTG
1 CTCGAAAGACTTACAGATGACCCAAATGACTTATCATCATG
1884677 CTCGAAAGACTTACAGATGACCCAAA-GA-TTAATCATCATG
1 CTCGAAAGACTTACAGATGACCCAAATGACTT-ATCATCATG
1884717 CTCGAAAGACTTA
1 CTCGAAAGACTTA
1884730 GTGATGGCTC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
39 2 0.04
40 23 0.49
41 22 0.47
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (41 bp):
CTCGAAAGACTTACAGATGACCCAAATGACTTATCATCATG
Found at i:1884972 original size:41 final size:40
Alignment explanation
Indices: 1884895--1884999 Score: 138
Period size: 41 Copynumber: 2.6 Consensus size: 40
1884885 TACCAAATGT
* * *
1884895 CTTACGGATGGCCCGAAGGACTTATCATCTGTTCGAAAGA
1 CTTACAGATGGCCCGAAGGACTTATCATCAGCTCGAAAGA
* * *
1884935 CTTACAGATGACCCGACGGATTTAATCATCAGCTCGAAAGA
1 CTTACAGATGGCCCGAAGGACTT-ATCATCAGCTCGAAAGA
*
1884976 CTTACTGATGGCCCGAAGGACTTA
1 CTTACAGATGGCCCGAAGGACTTA
1885000 CCAATTTAGG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 20 0.37
41 34 0.63
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTACAGATGGCCCGAAGGACTTATCATCAGCTCGAAAGA
Found at i:1884973 original size:250 final size:245
Alignment explanation
Indices: 1884617--1885109 Score: 699
Period size: 250 Copynumber: 2.0 Consensus size: 245
1884607 ATCGTTTCTC
* *
1884617 ATTCATGTGAAACATCCTACTCGAAGGTCTTACGGATGGCCCAAATGACTTATCATCTTGCTCGA
1 ATTCATGTGAAACATCCTACTCAAAGGTCTTACGGATGGCCCAAAGGACTTATCATCTTGCTCGA
* *
1884682 AAGACTTACAGATGACCCAAAGATTAATCATCATGCTCGAAAGACTTAGTGATGGCTCGAAGGAC
66 AAGACTTACAGATGACCCAAAGATTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGAC
* * * * *
1884747 TTA-CAATTTCGGAAATAATTTATTGGGTAAGAAACTTTGGTAATCACTTTTTTACTTTTCAAAA
131 TTACCAATTTAGG-AAT-AGTTACTGGGT-AGAAACTTTGGAAATCACTTTCTTACTTTTCAAAA
*
1884811 ATTTCA-TTTTAAGAAAATATTAAATGAAACTTTAGAAATCGCTTTCTCACTTTTAA
193 A-TTCATTTTTAAGAAAATATTAAAGGAAA-TTTA-AAATCGCTTTCTCA-TTTTAA
* * *
1884867 ATTCATGTGAAAACATCCTAC-CAAATGTCTTACGGATGGCCCGAAGGACTTATCATC-TGTTCG
1 ATTCATGTG-AAACATCCTACTCAAAGGTCTTACGGATGGCCCAAAGGACTTATCATCTTGCTCG
**
1884930 AAAGACTTACAGATGACCCGACGGATTTAATCATCA-GCTCGAAAGACTTACTGATGGCCCGAAG
65 AAAGACTTACAGATGACCC-AAAGA-TTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAG
*
1884994 GACTTACCAATTTAGGAATAGTTACTGGGTAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAA
128 GACTTACCAATTTAGGAATAGTTACTGGGTAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAA
* *
1885059 ATTCATTTTTCAGAAAATATTAAAGGAAATTTATAATCGCTTTCTCATTTT
193 ATTCATTTTTAAGAAAATATTAAAGGAAATTTAAAATCGCTTTCTCATTTT
1885110 GAAACACTTA
Statistics
Matches: 220, Mismatches: 18, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
245 4 0.02
246 13 0.06
247 8 0.04
248 54 0.25
249 33 0.15
250 79 0.36
251 29 0.13
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Consensus pattern (245 bp):
ATTCATGTGAAACATCCTACTCAAAGGTCTTACGGATGGCCCAAAGGACTTATCATCTTGCTCGA
AAGACTTACAGATGACCCAAAGATTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGAC
TTACCAATTTAGGAATAGTTACTGGGTAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATT
CATTTTTAAGAAAATATTAAAGGAAATTTAAAATCGCTTTCTCATTTTAA
Found at i:1904151 original size:31 final size:31
Alignment explanation
Indices: 1904113--1904235 Score: 158
Period size: 31 Copynumber: 4.0 Consensus size: 31
1904103 CCTCGACAAC
* *
1904113 TGTCCATAGGTCCCGAAGAACCTAGGTAAAA
1 TGTCCATATGTCCCGAAGAACATAGGTAAAA
* **
1904144 TGTCCATATGTTCCTTAGAACATAGGTAAAA
1 TGTCCATATGTCCCGAAGAACATAGGTAAAA
* *
1904175 TGTCCATATGTCTCGAA-AGACATAGGTAAAT
1 TGTCCATATGTCCCGAAGA-ACATAGGTAAAA
*
1904206 TGTCCATATGTCCTGAAGAACATAGGTAAA
1 TGTCCATATGTCCCGAAGAACATAGGTAAA
1904236 CCCTCGACTC
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
30 1 0.01
31 76 0.97
32 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Consensus pattern (31 bp):
TGTCCATATGTCCCGAAGAACATAGGTAAAA
Found at i:1906023 original size:18 final size:16
Alignment explanation
Indices: 1905980--1906016 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1905970 TTCATTTTTG
*
1905980 ATATCGAGTGTGTATA
1 ATATTGAGTGTGTATA
1905996 ATATTGAGTGTGTATA
1 ATATTGAGTGTGTATA
1906012 ATATT
1 ATATT
1906017 TGAAGTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.03, G:0.22, T:0.43
Consensus pattern (16 bp):
ATATTGAGTGTGTATA
Found at i:1906261 original size:67 final size:68
Alignment explanation
Indices: 1906177--1906312 Score: 247
Period size: 68 Copynumber: 2.0 Consensus size: 68
1906167 ATCTAGAATT
*
1906177 GTTCATTAAATAATTTTTAGCATAATC-TTTTTACATCTACCTAACATAATTTAATATATTAACA
1 GTTCATTAAATAATTTTTAGCATAATCTTTTTTACATCTACCTAACATAATTTAACATATTAACA
1906241 CTG
66 CTG
*
1906244 GTTCATTAAATAATTTTTAGCATCATCTTTTTTACATCTACCTAACATAATTTAACATATTAACA
1 GTTCATTAAATAATTTTTAGCATAATCTTTTTTACATCTACCTAACATAATTTAACATATTAACA
1906309 CTG
66 CTG
1906312 G
1 G
1906313 CAAGTCATTT
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
67 26 0.39
68 40 0.61
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (68 bp):
GTTCATTAAATAATTTTTAGCATAATCTTTTTTACATCTACCTAACATAATTTAACATATTAACA
CTG
Found at i:1906783 original size:18 final size:17
Alignment explanation
Indices: 1906734--1906783 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
1906724 TTTATGTTAT
* *
1906734 TCTTTGTTGAGTTATTTA
1 TCTTT-TTGAGTTGTTCA
1906752 TCTTCTTTGAGTTGTTCA
1 TCTT-TTTGAGTTGTTCA
1906770 TCTTTATTGAGTTG
1 TCTTT-TTGAGTTG
1906784 ATCACTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 26 0.93
19 1 0.04
ACGTcount: A:0.14, C:0.10, G:0.18, T:0.58
Consensus pattern (17 bp):
TCTTTTTGAGTTGTTCA
Found at i:1906982 original size:17 final size:18
Alignment explanation
Indices: 1906956--1906993 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1906946 ATTTTTAAAT
*
1906956 TTTATTTTTAT-ATTTAA
1 TTTATATTTATGATTTAA
*
1906973 TTTATATTTATGATTTTA
1 TTTATATTTATGATTTAA
1906991 TTT
1 TTT
1906994 TAAATATCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTATATTTATGATTTAA
Found at i:1909007 original size:21 final size:22
Alignment explanation
Indices: 1908982--1909031 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1908972 ATATAACAAG
1908982 AATCATTTTGAC-AAAAAATTA
1 AATCATTTTGACAAAAAAATTA
1909003 AATCATTTTGACAAAAAAATTA
1 AATCATTTTGACAAAAAAATTA
*
1909025 AAACATT
1 AATCATT
1909032 AAGGATTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.32
Consensus pattern (22 bp):
AATCATTTTGACAAAAAAATTA
Found at i:1909787 original size:25 final size:25
Alignment explanation
Indices: 1909750--1909806 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
1909740 TGATTCGTTA
*
1909750 AGGTGAAAGTGGTGAAGGATTTTGT
1 AGGTGAAACTGGTGAAGGATTTTGT
* ** *
1909775 AGGTTAAACTGGTTTAGGATTTTTT
1 AGGTGAAACTGGTGAAGGATTTTGT
1909800 AAGGTGA
1 -AGGTGA
1909807 GAGTGATCAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.28, C:0.02, G:0.33, T:0.37
Consensus pattern (25 bp):
AGGTGAAACTGGTGAAGGATTTTGT
Found at i:1909802 original size:51 final size:51
Alignment explanation
Indices: 1909723--1909845 Score: 138
Period size: 51 Copynumber: 2.4 Consensus size: 51
1909713 GGAGTGATTT
* * * * *
1909723 TAGGTTAAAGTGGTATATGATTCGTTAAGGTGAAAGTGGTGAAGGATTTTG
1 TAGGTTAAAGTGGTTTAGGATTCGTTAAGGTGAAAGTGATCAAGGATTGTG
* ** * *
1909774 TAGGTTAAACTGGTTTAGGATTTTTTAAGGTGAGAGTGATCAAGGGTTGTG
1 TAGGTTAAAGTGGTTTAGGATTCGTTAAGGTGAAAGTGATCAAGGATTGTG
* *
1909825 TAGATTAAAGTGATTTAGGAT
1 TAGGTTAAAGTGGTTTAGGAT
1909846 AAGGTTCAAT
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.29, C:0.02, G:0.32, T:0.37
Consensus pattern (51 bp):
TAGGTTAAAGTGGTTTAGGATTCGTTAAGGTGAAAGTGATCAAGGATTGTG
Found at i:1910003 original size:23 final size:25
Alignment explanation
Indices: 1909929--1910003 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 25
1909919 TACACATTGA
1909929 GAAATTATAGAAAATGCAATTACATT
1 GAAA-TATAGAAAATGCAATTACATT
*
1909955 GAAATATTAGAAGCAAAG-ACA-TACATT
1 GAAATA-TAGAA--AATGCA-ATTACATT
1909982 G-AA-ATAGAAAATGCAATTACAT
1 GAAATATAGAAAATGCAATTACAT
1910004 AAGTAAGGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 15
0.71 0.03 0.26
Matches are distributed among these distances:
22 4 0.10
23 6 0.15
24 5 0.12
25 3 0.07
26 11 0.27
27 8 0.20
28 4 0.10
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.25
Consensus pattern (25 bp):
GAAATATAGAAAATGCAATTACATT
Found at i:1922210 original size:23 final size:23
Alignment explanation
Indices: 1922179--1922225 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1922169 AGTCTCTCAC
1922179 AGTATGATTCTATTAAATACCAAA
1 AGTATGATTCTATTAAAT-CCAAA
* *
1922203 AGTA-GATTTTCTTAAATCCAAA
1 AGTATGATTCTATTAAATCCAAA
1922225 A
1 A
1922226 TATATGTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 11 0.52
24 4 0.19
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.34
Consensus pattern (23 bp):
AGTATGATTCTATTAAATCCAAA
Found at i:1923013 original size:23 final size:23
Alignment explanation
Indices: 1922987--1923039 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
1922977 CTCTCTAACT
1922987 GACCAGAAGAATCAGCGTGTCTA
1 GACCAGAAGAATCAGCGTGTCTA
1923010 GACCAGAAGAATCAGCGTGTCTA
1 GACCAGAAGAATCAGCGTGTCTA
1923033 GACCAGA
1 GACCAGA
1923040 TTCAAATCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.36, C:0.23, G:0.26, T:0.15
Consensus pattern (23 bp):
GACCAGAAGAATCAGCGTGTCTA
Found at i:1926318 original size:3 final size:3
Alignment explanation
Indices: 1926310--1926388 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
1926300 GTCAAGCACA
1926310 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1926358 TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1926389 CTATATATAT
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 73 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1928791 original size:130 final size:131
Alignment explanation
Indices: 1928469--1928851 Score: 509
Period size: 130 Copynumber: 2.9 Consensus size: 131
1928459 CGAATTTTAA
* *
1928469 GAGAGAAAACGATAATATATAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAAAGACCTCTCATGCCTTAAAGCA
* * * *
1928534 ATCATTTATTACTCCAATCT-AAATGAAGAGATATTACTATTTCATTCTAATATTCAATATCGTT
66 ATCATTTATTACTCCAAT-TGAAATGAAGAGATATTACTATTTTATCCTAAAATTCAATATCGAT
1928598 TC
130 TC
* * *
1928600 GAGAGAAAACGATAATATCTAATTACTTCCAATCGAGAATAAAAGACCTCTCATGCATTAAAGGA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAAAGACCTCTCATGCCTTAAAGCA
* * * * *
1928665 GTCACTTATTACTCCAATTGAAATGAAGAGATATTATTATTTTATCCTAAAATTTAAT-TTGATT
66 ATCATTTATTACTCCAATTGAAATGAAGAGATATTACTATTTTATCCTAAAATTCAATATCGATT
1928729 C
131 C
* * * *
1928730 GAGAAAAAACGATAATACCTAAATATTTCCAATCGAGAATAAAAGACCTCACATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAAAGACCTCTCATGCCTTAAAGCA
* * * * * * **
1928795 TTCATTTATTACTTCAATCGAAATAAAGAAATGTTACTATTTTGGCCTAAAATTCAA
66 ATCATTTATTACTCCAATTGAAATGAAGAGATATTACTATTTTATCCTAAAATTCAA
1928852 AATTAATTCC
Statistics
Matches: 219, Mismatches: 32, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
130 110 0.50
131 109 0.50
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAAAGACCTCTCATGCCTTAAAGCA
ATCATTTATTACTCCAATTGAAATGAAGAGATATTACTATTTTATCCTAAAATTCAATATCGATT
C
Found at i:1929197 original size:3 final size:3
Alignment explanation
Indices: 1929111--1929185 Score: 125
Period size: 3 Copynumber: 25.3 Consensus size: 3
1929101 TCATTATTAA
1929111 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
1929159 ATT ATC ATT ATT ATC A-T ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1929186 ATAAAATTAT
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
2 1 0.01
3 66 0.99
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1929409 original size:17 final size:18
Alignment explanation
Indices: 1929389--1929427 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1929379 CCACCGACGT
1929389 CGAGCCA-CCACCAACAC
1 CGAGCCACCCACCAACAC
*
1929406 CGAGCCATCCCACCAACGC
1 CGAGCCA-CCCACCAACAC
1929425 CGA
1 CGA
1929428 TGAGTCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
19 12 0.63
ACGTcount: A:0.31, C:0.51, G:0.15, T:0.03
Consensus pattern (18 bp):
CGAGCCACCCACCAACAC
Found at i:1939044 original size:90 final size:90
Alignment explanation
Indices: 1938891--1939084 Score: 309
Period size: 90 Copynumber: 2.2 Consensus size: 90
1938881 GAGCTTTCAA
* * * *
1938891 AGAAACTAAGCCTTCGGGGGTTTCTTAATTTGTAAGTCCTTCGGGCCATCTATAAGACCTTCAGT
1 AGAAACTAAGCCTTCAGAGGTTTCTTAATTTGTAAGTCATTCGGGCCATCCATAAGACCTTCAGT
*
1938956 GCAGGTTGTTTTCAAAAT-AGATTTT
66 GCAGGATGTTTTC-AAATGAGATTTT
*
1938981 AGAAACTAAGCCTTCAGAGGTTTCTTGATTTGTAAGTCATTCGGGCCATCCATAAGACCTTCAGT
1 AGAAACTAAGCCTTCAGAGGTTTCTTAATTTGTAAGTCATTCGGGCCATCCATAAGACCTTCAGT
*
1939046 GCATGATGTTTTCAAATGAGATTTT
66 GCAGGATGTTTTCAAATGAGATTTT
1939071 AGAAACTAAGCCTT
1 AGAAACTAAGCCTT
1939085 TTAGGGGTTT
Statistics
Matches: 96, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 4 0.04
90 92 0.96
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (90 bp):
AGAAACTAAGCCTTCAGAGGTTTCTTAATTTGTAAGTCATTCGGGCCATCCATAAGACCTTCAGT
GCAGGATGTTTTCAAATGAGATTTT
Found at i:1939248 original size:42 final size:42
Alignment explanation
Indices: 1939189--1939271 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
1939179 TTCTTGATTT
* *
1939189 TTAAATCCTTCGGGTCATCAATAAGTCTTTCGAGCATGATGC
1 TTAAATCCTTCGGGTCATCAATAAGCCTTTCGAGCAAGATGC
* **
1939231 TTAAATTCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATG
1 TTAAATCCTTCGGGTCATCAATAAGCCTTTCGAGCAAGATG
1939272 ATAAGACCTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (42 bp):
TTAAATCCTTCGGGTCATCAATAAGCCTTTCGAGCAAGATGC
Found at i:1939354 original size:23 final size:22
Alignment explanation
Indices: 1939324--1939394 Score: 62
Period size: 23 Copynumber: 3.4 Consensus size: 22
1939314 AGTTCATAAT
1939324 GAGAAGAACTCATCCGATAGAGG
1 GAGAAGAACTCAT-CGATAGAGG
* *
1939347 GAGAAGAAGT--TC-ATA-A-T
1 GAGAAGAACTCATCGATAGAGG
*
1939364 GAGAAGAACTCATTCGACAGAGG
1 GAGAAGAACTCA-TCGATAGAGG
1939387 GAGAAGAA
1 GAGAAGAA
1939395 GTTCATAATG
Statistics
Matches: 37, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
17 9 0.24
18 1 0.03
19 3 0.08
20 3 0.08
21 3 0.08
22 1 0.03
23 17 0.46
ACGTcount: A:0.44, C:0.13, G:0.30, T:0.14
Consensus pattern (22 bp):
GAGAAGAACTCATCGATAGAGG
Found at i:1939421 original size:40 final size:40
Alignment explanation
Indices: 1939314--1939408 Score: 172
Period size: 40 Copynumber: 2.4 Consensus size: 40
1939304 TCCAATGGAG
* *
1939314 AGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGA
1 AGTTCATAATGAGAAGAACTCATTCGACAGAGGGAGAAGA
1939354 AGTTCATAATGAGAAGAACTCATTCGACAGAGGGAGAAGA
1 AGTTCATAATGAGAAGAACTCATTCGACAGAGGGAGAAGA
1939394 AGTTCATAATGAGAA
1 AGTTCATAATGAGAA
1939409 AAGCTTGTTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.43, C:0.12, G:0.26, T:0.19
Consensus pattern (40 bp):
AGTTCATAATGAGAAGAACTCATTCGACAGAGGGAGAAGA
Found at i:1939552 original size:134 final size:132
Alignment explanation
Indices: 1939348--1939679 Score: 436
Period size: 134 Copynumber: 2.5 Consensus size: 132
1939338 CGATAGAGGG
* *
1939348 AGAAGAAGTTCATAATGAGAAGAACTCATTCGACAGAGGGAGAAGAAGTTCATAATGAGAAAAGC
1 AGAAG-AGTTCATAATGAGAAGAACTCATCCGACA-A-GGAGAAGAAGTTCATAATGAGAAGAGC
* * **
1939413 TTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACGCCTTTCTTGAGGGATTAACA
63 TTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGGGATTAACA
*
1939478 TTTTCC
128 -CTTCC
* *
1939484 ATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAGGAGAAGAAGTTCATAATGTGAAGAGCTT
1 A-GAAGAGTTCATAATGAGAAGAACTCATCCGACAAGGAGAAGAAGTTCATAATGAGAAGAGCTT
** * * *
1939549 GTTCGACCTATCACTCGATTCACGGTATTTTGAATCATTGACACCTCGCTTGAGGGATTGACACT
65 GTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGGGATTAACACT
1939614 TCC
130 TCC
* * * *
1939617 AGAAGAGTTCATAATGAGAAGAACACGTCCTA-AAGGAG-A-AAGTTCATAATGAGAAGAACTTG
1 AGAAGAGTTCATAATGAGAAGAACTCATCCGACAAGGAGAAGAAGTTCATAATGAGAAGAGCTTG
1939679 T
66 T
1939680 CCTTTCAAAT
Statistics
Matches: 175, Mismatches: 20, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
129 22 0.13
130 1 0.01
131 6 0.03
132 27 0.15
133 5 0.03
134 81 0.46
135 1 0.01
136 29 0.17
137 3 0.02
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (132 bp):
AGAAGAGTTCATAATGAGAAGAACTCATCCGACAAGGAGAAGAAGTTCATAATGAGAAGAGCTTG
TTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGGGATTAACACTT
CC
Found at i:1940099 original size:89 final size:91
Alignment explanation
Indices: 1939926--1940127 Score: 345
Period size: 89 Copynumber: 2.2 Consensus size: 91
1939916 TATTTCCAGA
*
1939926 AGAGTTCATAATGAGAAGAACTTATCCAACAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCAACAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
1939991 TAACCTTGCATCAACATTTCCAATGG
66 CAACCTTGCATCAACATTTCCAATGG
* *
1940017 AGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAA-AAGTTCATAATGAGAAG-ACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCAACAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
1940080 CAACCTTGCATCAACATTTCCAGTGG
66 CAACCTTGCATCAACATTTCCAATGG
1940106 AGAGTTCATAATGAGAAGAACT
1 AGAGTTCATAATGAGAAGAACT
1940128 TGTTCAACCT
Statistics
Matches: 106, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
89 53 0.50
90 17 0.16
91 36 0.34
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (91 bp):
AGAGTTCATAATGAGAAGAACTCATCCAACAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTGCATCAACATTTCCAATGG
Found at i:1940145 original size:52 final size:52
Alignment explanation
Indices: 1940055--1940179 Score: 207
Period size: 52 Copynumber: 2.4 Consensus size: 52
1940045 ACGAGGAAGA
*
1940055 AAAGTTCATAATGAGAAG-ACTTGTTCAACCTTGCATCAACATTTCCAGTGG
1 AAAGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAACATTTCCAATGG
* * *
1940106 AGAGTTCATAATGAGAAGAACTTGTTCAACCTTGTATCAACATTTTCAATGG
1 AAAGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAACATTTCCAATGG
1940158 AAAGTTCATAATGAGAAGAACT
1 AAAGTTCATAATGAGAAGAACT
1940180 CATCCAACGA
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
51 17 0.25
52 51 0.75
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (52 bp):
AAAGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAACATTTCCAATGG
Found at i:1940263 original size:91 final size:90
Alignment explanation
Indices: 1940108--1940314 Score: 283
Period size: 91 Copynumber: 2.3 Consensus size: 90
1940098 TCCAGTGGAG
* *
1940108 AGTTCATAATGAGAAGAACTTGTTCAACCTTGTATCAACATTTTCAATGGAAAGTTCATAATGAG
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAACATTTCCAATGGAAAGTTCATAATGAG
*
1940173 AAGAACTCATCCA-ACGAGGAAGAAGA
66 AAGAACTCATCCACAAGA-G-AGAAGA
*** *
1940199 AGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAGTGTTTCCAGT-GAAGAGTTCATAATGA
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAACATTTCCAATGGAA-AGTTCATAATGA
1940263 GAAGAACTCATCCACAAGAGAGAAGA
65 GAAGAACTCATCCACAAGAGAGAAGA
* * *
1940289 AGTTCATAATGAAAAGAGCTAGTTCA
1 AGTTCATAATGAGAAGAACTTGTTCA
1940315 TTCTAACAAT
Statistics
Matches: 104, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
90 32 0.31
91 69 0.66
92 3 0.03
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (90 bp):
AGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAACATTTCCAATGGAAAGTTCATAATGAG
AAGAACTCATCCACAAGAGAGAAGA
Found at i:1940537 original size:3 final size:3
Alignment explanation
Indices: 1940478--1940525 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
1940468 AAATTATTAA
* *
1940478 ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATC A-T ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1940525 A
1 A
1940526 ATAAAATTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 1 0.03
3 39 0.98
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1940750 original size:17 final size:17
Alignment explanation
Indices: 1940719--1940752 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1940709 CAGCTCTTCA
* *
1940719 CCACCACCGATGCCGAG
1 CCACCACCAACGCCGAG
1940736 CCACCACCAACGCCGAG
1 CCACCACCAACGCCGAG
1940753 TCATCCCACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.50, G:0.21, T:0.03
Consensus pattern (17 bp):
CCACCACCAACGCCGAG
Found at i:1946391 original size:7 final size:7
Alignment explanation
Indices: 1946381--1946462 Score: 66
Period size: 7 Copynumber: 11.9 Consensus size: 7
1946371 TTTTTTTGCT
1946381 TTTCTTC
1 TTTCTTC
1946388 TTTCTTC
1 TTTCTTC
1946395 TTTCTTC
1 TTTCTTC
1946402 TTTCTT-
1 TTTCTTC
*
1946408 TTTCTTTT
1 TTTC-TTC
*
1946416 TTTCATTT
1 TTTC-TTC
*
1946424 TTTCATC
1 TTTCTTC
1946431 ATTT-TTC
1 -TTTCTTC
1946438 TTTCTT-
1 TTTCTTC
1946444 TTT-TT-
1 TTTCTTC
1946449 TATTCTTC
1 T-TTCTTC
1946457 TTTCTT
1 TTTCTT
1946463 GAGGCGAAGT
Statistics
Matches: 64, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
5 3 0.05
6 12 0.19
7 34 0.53
8 15 0.23
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTCTTC
Found at i:1946402 original size:10 final size:9
Alignment explanation
Indices: 1946382--1946446 Score: 53
Period size: 10 Copynumber: 6.9 Consensus size: 9
1946372 TTTTTTGCTT
1946382 TTCTTCTTTC
1 TTCTT-TTTC
1946392 TTCTTTCTTC
1 TTCTTT-TTC
1946402 TTTCTTTTTC
1 -TTCTTTTTC
1946412 TT-TTTTTC
1 TTCTTTTTC
*
1946420 AT-TTTTTC
1 TTCTTTTTC
*
1946428 ATCATTTTTC
1 TTC-TTTTTC
1946438 TTTCTTTTT
1 -TTCTTTTT
1946447 TTTATTCTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
8 15 0.31
9 3 0.06
10 22 0.46
11 8 0.17
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:1950309 original size:44 final size:44
Alignment explanation
Indices: 1950253--1950349 Score: 185
Period size: 44 Copynumber: 2.2 Consensus size: 44
1950243 ACCATATCAA
*
1950253 CATTCGATGATCACGATTTTAGAGGCTAAACTTCTACCATAAAC
1 CATTCGAAGATCACGATTTTAGAGGCTAAACTTCTACCATAAAC
1950297 CATTCGAAGATCACGATTTTAGAGGCTAAACTTCTACCATAAAC
1 CATTCGAAGATCACGATTTTAGAGGCTAAACTTCTACCATAAAC
1950341 CATTCGAAG
1 CATTCGAAG
1950350 CAAATAGATA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (44 bp):
CATTCGAAGATCACGATTTTAGAGGCTAAACTTCTACCATAAAC
Found at i:1951611 original size:2 final size:2
Alignment explanation
Indices: 1951604--1951638 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
1951594 TCAAGTTCTT
1951604 TA TA TA TA CT- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA T
1951639 CGCATAGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.94
3 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1951771 original size:2 final size:2
Alignment explanation
Indices: 1951764--1951799 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
1951754 CAAGTTCTTT
1951764 TA TA TA TA CT- 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
1951800 AGTTATTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.94
3 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1951788 original size:160 final size:156
Alignment explanation
Indices: 1951482--1951798 Score: 541
Period size: 160 Copynumber: 2.0 Consensus size: 156
1951472 TTGTTAAATG
1951482 CGCATAGGTTGTAAATACATTAAAATATGTATTTAGTGTGTTGTGTGATATGTTTATATTATTTA
1 CGCATAGGTTGTAAATACATTAAAATATGTATTTAGTGTGTTGTGTGATATGTTTATATTATTTA
1951547 TATTAACTTTTATCTCTTATATGTGATATGATGTTGATTGTCGATTATCAAGTTCTTTATATATA
66 TATTAACTTTTA-CTCTTATATGTGATATGATGTTGATTGTCGATTATCAAGTTCTTTATATATA
1951612 CTTATATATATATATATATATATATAT
130 CTTATATATATATATATATATATATAT
1951639 CGCATAGGTTGTAAATACATTAAAATATGTATTTAGTGTGTTGTGTGATATGTTTGTATATTATA
1 CGCATAGGTTGTAAATACATTAAAATATGTATTTAGTGTGTTGTGTGATATG-TT-TATA-T-TA
1951704 TTTAATATTAACTTTTA-TCTTATATGTGATATGATGTTGATTGTCTGA-T-TCAAGTTCTTTTA
62 TTT-ATATTAACTTTTACTCTTATATGTGATATGATGTTGATTGTC-GATTATCAAGTTC-TTTA
1951766 TATATACTTATATATATATATATATATATATAT
124 TATATACTTATATATATATATATATATATATAT
1951799 AAGTTATTTG
Statistics
Matches: 153, Mismatches: 0, Indels: 11
0.93 0.00 0.07
Matches are distributed among these distances:
157 52 0.34
158 2 0.01
159 12 0.08
160 67 0.44
161 7 0.05
162 13 0.08
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (156 bp):
CGCATAGGTTGTAAATACATTAAAATATGTATTTAGTGTGTTGTGTGATATGTTTATATTATTTA
TATTAACTTTTACTCTTATATGTGATATGATGTTGATTGTCGATTATCAAGTTCTTTATATATAC
TTATATATATATATATATATATATAT
Found at i:1964998 original size:3 final size:3
Alignment explanation
Indices: 1964990--1965024 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1964980 TATATTATAT
1964990 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1965025 CTAATAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1965007 original size:23 final size:23
Alignment explanation
Indices: 1964980--1965024 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1964970 AAAATATATA
1964980 TATATTA-TATTTATTATTATTAT
1 TATATTATTA-TTATTATTATTAT
1965003 TATATTATTATTATTATTATTA
1 TATATTATTATTATTATTATTA
1965025 CTAATAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TATATTATTATTATTATTATTAT
Found at i:1967098 original size:2 final size:2
Alignment explanation
Indices: 1967091--1967164 Score: 114
Period size: 2 Copynumber: 37.0 Consensus size: 2
1967081 CAAGTTCTTT
*
1967091 TA TA TA TA TA CT- TT 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
*
1967133 TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1967165 AAAGTTATTT
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
1 1 0.01
2 65 0.97
3 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1975864 original size:131 final size:131
Alignment explanation
Indices: 1975644--1976041 Score: 625
Period size: 131 Copynumber: 3.0 Consensus size: 131
1975634 TGAATTTTAA
*
1975644 GAGAGAAATCGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * * * *
1975709 GTCATTTATTACTCCAATCAAAATGAAGAAATATTACTATTTCCTCCTAAATTTCAATATTGATT
66 GTCACTTATTACTCCAATCGAAATGAAGAGATGTTACTATTTCATCCTAAAATTCAATATTGATT
1975774 C
131 C
* * * *
1975775 GAGAGAAAATGGTAATATCTAATTACTTCAAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1975840 GTCACTTATTACTCCAATCGAAATGAAGAGATGTTACTATTTCATCCTAAAATTCAATATTGATT
66 GTCACTTATTACTCCAATCGAAATGAAGAGATGTTACTATTTCATCCTAAAATTCAATATTGATT
1975905 C
131 C
* * *
1975906 GAGAGAAAACGATAATATCTAATTATTTCCAATCGATAATAAAAGACCTCTCATGCCTTAAAACA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * * *
1975971 ATCACTTATTACTCCAATCGAAATGAAGAGATGTTACGATTTCGTCCTAAAATTCAAAATTAATT
66 GTCACTTATTACTCCAATCGAAATGAAGAGATGTTACTATTTCATCCTAAAATTCAATATTGATT
1976036 C
131 C
1976037 GAGAG
1 GAGAG
1976042 TTATTTATTT
Statistics
Matches: 244, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
131 244 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
GTCACTTATTACTCCAATCGAAATGAAGAGATGTTACTATTTCATCCTAAAATTCAATATTGATT
C
Found at i:1978471 original size:14 final size:14
Alignment explanation
Indices: 1978452--1978478 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1978442 TACTTTAAAG
1978452 TATTTATTTATTTT
1 TATTTATTTATTTT
1978466 TATTTATTTATTT
1 TATTTATTTATTT
1978479 ATAGTGTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TATTTATTTATTTT
Found at i:1980002 original size:3 final size:3
Alignment explanation
Indices: 1979987--1980048 Score: 67
Period size: 3 Copynumber: 21.3 Consensus size: 3
1979977 TATTTATATA
* * *
1979987 AAT AAT AAA AAT AAT AAT AAT GA- AAT AAT AATT AA- AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
1980031 AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
1980049 TTGCAAATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
2 4 0.08
3 42 0.86
4 3 0.06
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1981318 original size:3 final size:3
Alignment explanation
Indices: 1981310--1981372 Score: 96
Period size: 3 Copynumber: 21.7 Consensus size: 3
1981300 TAAAATTATT
1981310 TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1981357 TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA T-AA TAA TA
1981373 TTCAAATGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
2 6 0.11
3 48 0.86
4 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1981851 original size:113 final size:112
Alignment explanation
Indices: 1981710--1982460 Score: 978
Period size: 113 Copynumber: 6.7 Consensus size: 112
1981700 ATAGAGTCAT
* * *
1981710 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * *
1981775 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAA
66 ATTATGAACTCTC-CTGGCAATGCTGATCCATCAAGTGATGAATTCAA
* * * * *
1981823 ACAAAAGGTTGAACAAATTTTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * * * *
1981888 ATTATGAACTTTAACTGGCACTGCTGATTCACCGAGTGATGAATTCGA
66 ATTATGAACTCT-CCTGGCAATGCTGATCCATCAAGTGATGAATTCAA
*
1981936 GCAAAAGGTTGAACAAGTTCTTCTCATTTTGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
1982001 ATTATGAACTCTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAA
66 ATTATGAACTCTC-CTGGCAATGCTGATCCATCAAGTGATGAATTCAA
* * *
1982049 ACAAAAGGTTGAACAATTTCTTTTCATTATGAA--T-TTCTT-CTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * * *
1982110 ATTATGAACTCTAACTGGCACTGCTGATTCACCGAGTGATGAATTCGA
66 ATTATGAACTCT-CCTGGCAATGCTGATCCATCAAGTGATGAATTCAA
*
1982158 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
1982223 ATTATGAACTCGACCTGGCAATGCTGATCCATCGAA-TGATAAATTCAA
66 ATTATGAACTC-TCCTGGCAATGCTGATCCATC-AAGTGATGAATTCAA
1982271 GCGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GC-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
1982335 CATTAGGAACTCGACCTGGCAATGCTGATCCATCGAA-TGATAAATTCAA
65 CATTATGAACTC-TCCTGGCAATGCTGATCCATC-AAGTGATGAATTCAA
* *
1982384 GCGAAAA-GTTGAACAAGTTTTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCT
1 GC-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1982448 CATTATGAACTCT
65 CATTATGAACTCT
1982461 TACAGAAATG
Statistics
Matches: 562, Mismatches: 66, Indels: 21
0.87 0.10 0.03
Matches are distributed among these distances:
109 89 0.16
110 5 0.01
111 2 0.00
112 5 0.01
113 456 0.81
114 5 0.01
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (112 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTCCTGGCAATGCTGATCCATCAAGTGATGAATTCAA
Found at i:1982018 original size:226 final size:225
Alignment explanation
Indices: 1981710--1982460 Score: 1122
Period size: 226 Copynumber: 3.3 Consensus size: 225
1981700 ATAGAGTCAT
* * *
1981710 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
1981775 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAA
66 ATTATGAACTCTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAA
*
1981840 TTTTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAACTG
131 TTTTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTG
1981905 GCACTGCTGATTCACCGAGTGATGAATTCGA
195 GCACTGCTGATTCACCGAGTGATGAATTCGA
*
1981936 GCAAAAGGTTGAACAAGTTCTTCTCATTTTGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1982001 ATTATGAACTCTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAAC-AA
66 ATTATGAACTCTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAA
*
1982065 TTTCTTTTCATTATGAA-T-TTC-TTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTG
131 TTT-TTCTCATTATGAATTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTG
1982127 GCACTGCTGATTCACCGAGTGATGAATTCGA
195 GCACTGCTGATTCACCGAGTGATGAATTCGA
*
1982158 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * * * *
1982223 ATTATGAACTCGAC-CTGGCAATGCTGATCCATCGAA-TGATAAATTCAAGCGAAAA-GTTGAAC
66 ATTATGAACTC-TCTCTGGAAAAGTTGATCCATC-AAGTGATGAATTTAAAC-AAAAGGTTGAAC
* * * * * *
1982285 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAGGAACTCGAC
128 AAATTTTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAA
* * * * * *
1982350 CTGGCAATGCTGATCCATCGAATGATAAATTCAA
192 CTGGCACTGCTGATTCACCGAGTGATGAATTCGA
* *
1982384 GCGAAAA-GTTGAACAAGTTTTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCT
1 GC-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1982448 CATTATGAACTCT
65 CATTATGAACTCT
1982461 TACAGAAATG
Statistics
Matches: 482, Mismatches: 33, Indels: 21
0.90 0.06 0.04
Matches are distributed among these distances:
222 191 0.40
223 13 0.03
224 2 0.00
225 8 0.02
226 264 0.55
227 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (225 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAA
TTTTTCTCATTATGAATTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGG
CACTGCTGATTCACCGAGTGATGAATTCGA
Found at i:1982119 original size:335 final size:338
Alignment explanation
Indices: 1981711--1982460 Score: 1021
Period size: 335 Copynumber: 2.2 Consensus size: 338
1981701 TAGAGTCATG
* ** *
1981711 CAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCA
1 CAAAAGGTTGAACAATTTCTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** * * *
1981776 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAAT
65 TTATGAACTCTAACTGGAAAAGCTGATCCACCAAGTGATGAATTCAAACAAAAGGTTGAACAAAT
* * * **
1981841 TTTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAACTGG
130 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
* * * * * *
1981906 CACTGCTGATTCACCGAGTGATGAATTCGAGC-AAAAGGTTGAACAAGTTCTTCTCATTTTGAAC
195 CAATGCTGATCCACCGAATGATAAATTCAAGCGAAAA-GTTGAACAAGTTCTTCTCATTATGAAC
* * *
1981970 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC-TCTCTGGAAAAGTTGATCCATC
259 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAGGAACTCGAC-CTGGAAAAGCTGATCCATC
* *
1982034 -AAGTGATGAATTTAAA
323 GAA-TGATAAATTCAAA
*
1982050 CAAAAGGTTGAACAATTTCTTTTCATTATGAA-T-TTCTT-CTTCTTCAGATGAGTTCTTCTCAT
1 CAAAAGGTTGAACAATTTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* ** * * * *
1982112 TATGAACTCTAACTGGCACTGCTGATTCACCGAGTGATGAATTCGAGCAAAAGGTTGAACAAATT
66 TATGAACTCTAACTGGAAAAGCTGATCCACCAAGTGATGAATTCAAACAAAAGGTTGAACAAATT
*
1982177 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGC
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGC
*
1982242 AATGCTGATCCATCGAATGATAAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
196 AATGCTGATCCACCGAATGATAAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
* *
1982307 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAGGAACTCGACCTGGCAATGCTGATCCATCGAA
261 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAGGAACTCGACCTGGAAAAGCTGATCCATCGAA
*
1982372 TGATAAATTCAAG
326 TGATAAATTCAAA
*
1982385 CGAAAA-GTTGAACAAGTTT-TTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCT
1 C-AAAAGGTTGAACAA-TTTCTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCT
1982448 CATTATGAACTCT
63 CATTATGAACTCT
1982461 TACAGAAATG
Statistics
Matches: 361, Mismatches: 41, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
335 274 0.76
336 19 0.05
337 2 0.01
338 5 0.01
339 61 0.17
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (338 bp):
CAAAAGGTTGAACAATTTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTAACTGGAAAAGCTGATCCACCAAGTGATGAATTCAAACAAAAGGTTGAACAAATT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGC
AATGCTGATCCACCGAATGATAAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAGGAACTCGACCTGGAAAAGCTGATCCATCGAA
TGATAAATTCAAA
Found at i:1982923 original size:22 final size:22
Alignment explanation
Indices: 1982897--1982949 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1982887 TAAAGCTTTT
* *
1982897 ATCTTTGAAAAGATAATATGTC
1 ATCTTTGAAAAGAGAATATATC
* * *
1982919 ATCTTTAAAAAGGGAATCTATC
1 ATCTTTGAAAAGAGAATATATC
1982941 ATCTTTGAA
1 ATCTTTGAA
1982950 GAGTGTAGAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (22 bp):
ATCTTTGAAAAGAGAATATATC
Found at i:1983404 original size:50 final size:50
Alignment explanation
Indices: 1983319--1983418 Score: 137
Period size: 50 Copynumber: 2.0 Consensus size: 50
1983309 TAACTGGTTC
* * *
1983319 ATAAAACATTTGACAACACATGCATCATCTCATGTGGTTTTTGCTCAGAT
1 ATAAAACAATTGACAACACATGCATCATCTCATGTGGTTTCTACTCAGAT
* * * *
1983369 ATAAAACAATTGACAACACATTCATCCTTTTATGTGGTTTCTACTCAGAT
1 ATAAAACAATTGACAACACATGCATCATCTCATGTGGTTTCTACTCAGAT
1983419 GTTCGTAAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (50 bp):
ATAAAACAATTGACAACACATGCATCATCTCATGTGGTTTCTACTCAGAT
Found at i:1985763 original size:114 final size:114
Alignment explanation
Indices: 1985563--1985786 Score: 358
Period size: 114 Copynumber: 2.0 Consensus size: 114
1985553 GATCATGCAG
* * * *
1985563 TTCATCTTTCAATTCCAATGATTGGTTTTAGAGTTCCTACCGAACCAGATCATATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTAGAGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
1985628 ACACTTCCAGAAGATGCTATTGGGCCTCTTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACTATGAGCAAA
* * *
1985677 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTAGAGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
1985742 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTATTATGAG
66 ACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACTATGAG
1985787 AACGTGGCAC
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 100 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTAGAGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACTATGAGCAAA
Found at i:1986615 original size:23 final size:23
Alignment explanation
Indices: 1986585--1986645 Score: 122
Period size: 23 Copynumber: 2.7 Consensus size: 23
1986575 CATGGAACAG
1986585 ATGTAGAATTTGTTCGCATACAA
1 ATGTAGAATTTGTTCGCATACAA
1986608 ATGTAGAATTTGTTCGCATACAA
1 ATGTAGAATTTGTTCGCATACAA
1986631 ATGTAGAATTTGTTC
1 ATGTAGAATTTGTTC
1986646 CAATGTCTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (23 bp):
ATGTAGAATTTGTTCGCATACAA
Found at i:1989956 original size:7 final size:7
Alignment explanation
Indices: 1989922--1989963 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
1989912 ATAAGAGTAT
1989922 AAATGCA
1 AAATGCA
* *
1989929 CAATGAA
1 AAATGCA
1989936 AAATGCA
1 AAATGCA
1989943 AAGATGCA
1 AA-ATGCA
1989951 AAATGC-
1 AAATGCA
1989957 AAATGCA
1 AAATGCA
1989964 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:1992314 original size:3 final size:3
Alignment explanation
Indices: 1992299--1992357 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
1992289 TATTTATATA
* * **
1992299 AAT AAT AAA AAT AAT AAT AAT GA- AAT AAT AATT AA- AGC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
1992343 AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT A
1992358 TTGCAAATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:1992366 original size:26 final size:28
Alignment explanation
Indices: 1992307--1992368 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
1992297 TAAATAATAA
*
1992307 AAATAATAATAATGAAATAATAATTAAAGC
1 AAATAATAATAATAAAATAATAATT--AGC
1992337 -AATAATAATAATAAAATAAT-ATT-GC
1 AAATAATAATAATAAAATAATAATTAGC
1992362 AAATAAT
1 AAATAAT
1992369 GATTAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 2 0.07
26 6 0.20
28 3 0.10
29 19 0.63
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (28 bp):
AAATAATAATAATAAAATAATAATTAGC
Found at i:1993629 original size:3 final size:3
Alignment explanation
Indices: 1993621--1993695 Score: 102
Period size: 3 Copynumber: 25.7 Consensus size: 3
1993611 TAAAATTATT
* *
1993621 TAA TAA TAA TAA TAA T-A TAA TAA TTA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1993668 TAA TAA TAA TAA TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
1993696 TTCAAATGAG
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 6 0.09
3 56 0.88
4 2 0.03
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1999040 original size:19 final size:19
Alignment explanation
Indices: 1999012--1999051 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
1999002 TAACTCACTC
1999012 AAATTAAAAAAT-AAATTT
1 AAATTAAAAAATAAAATTT
1999030 AAATCTAAAAAATAAAATTT
1 AAAT-TAAAAAATAAAATTT
1999050 AA
1 AA
1999052 CTTTATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 8 0.40
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATTAAAAAATAAAATTT
Found at i:1999902 original size:21 final size:22
Alignment explanation
Indices: 1999873--1999917 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
1999863 TATAAAAATA
*
1999873 AAAATATT-AT-ATTATATTTT
1 AAAATATTAATAAATATATTTT
1999893 AAAATCATTAATAAATATATTTT
1 AAAAT-ATTAATAAATATATTTT
1999916 AA
1 AA
1999918 GGAATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 3 0.14
22 2 0.10
23 11 0.52
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AAAATATTAATAAATATATTTT
Found at i:1999909 original size:37 final size:36
Alignment explanation
Indices: 1999798--1999890 Score: 104
Period size: 37 Copynumber: 2.7 Consensus size: 36
1999788 ATAATTTTAT
* * * *
1999798 AAATAAAAATAT-T-AACTATAATATAT-TCTATTA
1 AAATAAAAATATATAAATTATATTAAATATCTATAA
1999831 AAATAAAAATATAATAAATTATATTAAATATCTATAA
1 AAATAAAAATAT-ATAAATTATATTAAATATCTATAA
*
1999868 AAATAAAAATAT-TATATTATATT
1 AAATAAAAATATATAAATTATATT
1999891 TTAAAATCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
33 12 0.24
35 11 0.22
36 10 0.20
37 18 0.35
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (36 bp):
AAATAAAAATATATAAATTATATTAAATATCTATAA
Found at i:2000015 original size:27 final size:29
Alignment explanation
Indices: 1999985--2000046 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
1999975 ATTCACTATT
* *
1999985 AATTATTTAATAATA-ATATTTT-TTAAA
1 AATTATTAAATAATATAAATTTTATTAAA
* *
2000012 AATTAATAAATAATATAAATTTTATTAAT
1 AATTATTAAATAATATAAATTTTATTAAA
2000041 AATTAT
1 AATTAT
2000047 ACATAGATGA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 13 0.46
28 6 0.21
29 9 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
AATTATTAAATAATATAAATTTTATTAAA
Found at i:2003357 original size:4 final size:4
Alignment explanation
Indices: 2003348--2003399 Score: 97
Period size: 4 Copynumber: 13.2 Consensus size: 4
2003338 ACGGTCATTT
2003348 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA -AAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
2003395 TAAA T
1 TAAA T
2003400 TTTGGAGTCG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 3 0.06
4 44 0.94
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:2005485 original size:3 final size:3
Alignment explanation
Indices: 2005479--2005562 Score: 118
Period size: 3 Copynumber: 28.0 Consensus size: 3
2005469 AAAAAAATTG
*
2005479 TAA TAA TAA TAA TAA -ATA TAA TAA TAA TAA TAA TAA T-C TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2005523 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
2005563 CCCATAAAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.03
3 67 0.92
4 4 0.05
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:2005951 original size:41 final size:42
Alignment explanation
Indices: 2005906--2005985 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
2005896 AAGGTCTAAT
* * * *
2005906 AGATGGCCTGAAGGACTTAA-CATCTTGCTCGAAAGACTGAC
1 AGATGACCCGAAGGACTTAACCAACCTGCTCGAAAGACTGAC
*
2005947 AGATGACCCGAAGGATTTAACCAACCTGCTCGAAAGACT
1 AGATGACCCGAAGGACTTAACCAACCTGCTCGAAAGACT
2005986 TACTGATAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
41 17 0.52
42 16 0.48
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.20
Consensus pattern (42 bp):
AGATGACCCGAAGGACTTAACCAACCTGCTCGAAAGACTGAC
Found at i:2016356 original size:18 final size:18
Alignment explanation
Indices: 2016333--2016391 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 18
2016323 ACTTGATTTG
2016333 TTTTCTTTCTTTCTTCTT
1 TTTTCTTTCTTTCTTCTT
*
2016351 TTTTCTTTCTTT-TTTTT
1 TTTTCTTTCTTTCTTCTT
2016368 GTTTTCTCTT-TTTCTTCTCT
1 -TTTTCT-TTCTTTCTTCT-T
2016388 TTTT
1 TTTT
2016392 ATTTGTTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
17 4 0.11
18 21 0.60
19 9 0.26
20 1 0.03
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTCTTTCTTTCTTCTT
Found at i:2016357 original size:14 final size:14
Alignment explanation
Indices: 2016338--2016391 Score: 55
Period size: 13 Copynumber: 4.1 Consensus size: 14
2016328 ATTTGTTTTC
2016338 TTTCTTTCTTCTTT
1 TTTCTTTCTTCTTT
2016352 TTTCTTTCTT-TTT
1 TTTCTTTCTTCTTT
*
2016365 TTT-GTT-TTCTCTT
1 TTTCTTTCTTCT-TT
2016378 TTTC-TTC-TCTTT
1 TTTCTTTCTTCTTT
2016390 TT
1 TT
2016392 ATTTGTTATC
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
11 2 0.06
12 7 0.20
13 16 0.46
14 10 0.29
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (14 bp):
TTTCTTTCTTCTTT
Found at i:2016363 original size:11 final size:11
Alignment explanation
Indices: 2016333--2016391 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 11
2016323 ACTTGATTTG
2016333 TTTTCTTTCTT
1 TTTTCTTTCTT
*
2016344 TCTTCTTT-TT
1 TTTTCTTTCTT
2016354 TCTTTCTTT-TT
1 T-TTTCTTTCTT
2016365 TTTGT-TTTCTCT
1 TTT-TCTTTCT-T
2016377 TTTTCTTCTCTT
1 TTTTCTT-TCTT
2016389 TTT
1 TTT
2016392 ATTTGTTATC
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
10 8 0.20
11 19 0.47
12 10 0.25
13 3 0.08
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:2016373 original size:28 final size:28
Alignment explanation
Indices: 2016346--2016420 Score: 93
Period size: 30 Copynumber: 2.7 Consensus size: 28
2016336 TCTTTCTTTC
2016346 TTCT-TTTTTCTT-TCTTTTT-TTTGTT
1 TTCTCTTTTTCTTCTCTTTTTATTTGTT
2016371 TTCTCTTTTTCTTCTCTTTTTATTTGTT
1 TTCTCTTTTTCTTCTCTTTTTATTTGTT
* *
2016399 ATCTCTATATTTGTTCTCTTTT
1 TTCTCT-T-TTTCTTCTCTTTT
2016421 ATCTCTCTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
25 4 0.09
26 8 0.19
27 7 0.16
28 11 0.26
29 1 0.02
30 12 0.28
ACGTcount: A:0.05, C:0.16, G:0.04, T:0.75
Consensus pattern (28 bp):
TTCTCTTTTTCTTCTCTTTTTATTTGTT
Found at i:2016377 original size:27 final size:29
Alignment explanation
Indices: 2016342--2016420 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 29
2016332 GTTTTCTTTC
2016342 TTTCTTCTTTTTTCTT-TCTTTTT-TTTGT
1 TTTC-TCTTTTTTCTTCTCTTTTTATTTGT
2016370 TTTCTC-TTTTTCTTCTCTTTTTATTTGT
1 TTTCTCTTTTTTCTTCTCTTTTTATTTGT
* * *
2016398 TATCTCTATATTTGTTCTCTTTT
1 TTTCTCT-TTTTTCTTCTCTTTT
2016421 ATCTCTCTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
26 8 0.18
27 9 0.20
28 14 0.32
30 13 0.30
ACGTcount: A:0.05, C:0.16, G:0.04, T:0.75
Consensus pattern (29 bp):
TTTCTCTTTTTTCTTCTCTTTTTATTTGT
Found at i:2025658 original size:20 final size:21
Alignment explanation
Indices: 2025612--2025672 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
2025602 TTCCCCTGTG
2025612 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
2025635 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
2025655 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
2025673 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:2030349 original size:275 final size:275
Alignment explanation
Indices: 2029850--2030399 Score: 1068
Period size: 275 Copynumber: 2.0 Consensus size: 275
2029840 TCATCTTCGA
2029850 GCATCATTTATGAGTGAGGAGCGACCCAATTAGCTCTTCAAGAGTTAAGGATGTTAAGTCCTTAG
1 GCATCATTTATGAGTGAGGAGCGACCCAATTAGCTCTTCAAGAGTTAAGGATGTTAAGTCCTTAG
2029915 ACTCGATGATTGCCGTCTTCTTTGATTGCCACGATTTTGGGAGGAGTAGACTAACTTCCTCACAA
66 ACTCGATGATTGCCGTCTTCTTTGATTGCCACGATTTTGGGAGGAGTAGACTAACTTCCTCACAA
2029980 GCTTTTCATTTGAATGATCTCCATATGATTTGAGACCATTGAAAATCATTGAAAATTTATCCTTC
131 GCTTTTCATTTGAATGATCTCCATATGATTTGAGACCATTGAAAATCATTGAAAATTTATCCTTC
2030045 ATAGCTTTGATATCTTCATTTGGTTTCATCCT-AAATTTTCATAGCTATACGTTAGAATACTAA-
196 ATAGCTTTGATATCTTCATTTGGTTTCATCCTAAAATTTTCATAGCTATACGTTAGAATACTAAT
2030108 TTTAGATTTCTTTAC
261 TTTAGATTTCTTTAC
2030123 GCATCATTTCATGAGTGAGGAGCGACCCAATTAGCTCTTCAAGAGTTAAGGATGTTAAGTCCTTA
1 GCATCATTT-ATGAGTGAGGAGCGACCCAATTAGCTCTTCAAGAGTTAAGGATGTTAAGTCCTTA
2030188 GACTCGATGATTGCCGTCTTCTTTGATTGCCACGATTTTGGGAGGGAGTAGACTAACTTCCTCAC
65 GACTCGATGATTGCCGTCTTCTTTGATTGCCACGATTTTGGGA-GGAGTAGACTAACTTCCTCAC
2030253 AAGCTTTTCATTTGAATGATCTCCATATGATTTGAGACCATTGAAAATCATTGAAAATTTATCCT
129 AAGCTTTTCATTTGAATGATCTCCATATGATTTGAGACCATTGAAAATCATTGAAAATTTATCCT
2030318 TCATAGCTTTGATATCTTCATTTGGTTTCATCCTAAAATTTTCATAGCTATACGTTAGAATACTA
194 TCATAGCTTTGATATCTTCATTTGGTTTCATCCTAAAATTTTCATAGCTATACGTTAGAATACTA
2030383 ATTTTAGATTTCTTTAC
259 ATTTTAGATTTCTTTAC
2030400 CTCATCGGTA
Statistics
Matches: 273, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
273 9 0.03
274 98 0.36
275 120 0.44
276 31 0.11
277 15 0.05
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (275 bp):
GCATCATTTATGAGTGAGGAGCGACCCAATTAGCTCTTCAAGAGTTAAGGATGTTAAGTCCTTAG
ACTCGATGATTGCCGTCTTCTTTGATTGCCACGATTTTGGGAGGAGTAGACTAACTTCCTCACAA
GCTTTTCATTTGAATGATCTCCATATGATTTGAGACCATTGAAAATCATTGAAAATTTATCCTTC
ATAGCTTTGATATCTTCATTTGGTTTCATCCTAAAATTTTCATAGCTATACGTTAGAATACTAAT
TTTAGATTTCTTTAC
Found at i:2034818 original size:31 final size:31
Alignment explanation
Indices: 2034783--2034846 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
2034773 TAACTATATC
* * *
2034783 TTAATTAAATGAAAATGAAAGTAATCAAATA
1 TTAATTAAATAAAAACGAAAGTAACCAAATA
*
2034814 TTAATTAAATAAAAACGAAAGTGACCAAATA
1 TTAATTAAATAAAAACGAAAGTAACCAAATA
2034845 TT
1 TT
2034847 GTAGTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.28
Consensus pattern (31 bp):
TTAATTAAATAAAAACGAAAGTAACCAAATA
Found at i:2035924 original size:31 final size:31
Alignment explanation
Indices: 2035861--2035925 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
2035851 TGGCTACATC
*
2035861 TTAATTAAATAAAAATAAAAGTAACCACATA
1 TTAATTAAATAAAAATAAAAGTAACCAAATA
* * **
2035892 TTAATTAAATAGAAATTAAAGTGGCCAAATA
1 TTAATTAAATAAAAATAAAAGTAACCAAATA
2035923 TTA
1 TTA
2035926 TATTTTTACA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (31 bp):
TTAATTAAATAAAAATAAAAGTAACCAAATA
Found at i:2037641 original size:43 final size:43
Alignment explanation
Indices: 2037575--2037718 Score: 168
Period size: 43 Copynumber: 3.3 Consensus size: 43
2037565 GTAGCGTTAG
*
2037575 GTTATGATATTTAGCGGCG-TTTTTTCATAAACGTCGCAACAT
1 GTTATGATATTTAGCGGCGTTTTTTTTATAAACGTCGCAACAT
* *
2037617 GTTATGATATTTTAGTGG-GTTTTTTTTATAAACGTTGCAACAT
1 GTTATGATA-TTTAGCGGCGTTTTTTTTATAAACGTCGCAACAT
* * * *
2037660 GTTATTACATTTAGCGGCCTTTTTTTGGTATAAATG-CTGCAACAT
1 GTTATGATATTTAGCGGCGTTTTTTT--TATAAACGTC-GCAACAT
2037705 GTTATGATATTTAG
1 GTTATGATATTTAG
2037719 TGATGTTTCT
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
42 17 0.20
43 42 0.49
45 26 0.31
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.44
Consensus pattern (43 bp):
GTTATGATATTTAGCGGCGTTTTTTTTATAAACGTCGCAACAT
Found at i:2037701 original size:45 final size:43
Alignment explanation
Indices: 2037575--2037765 Score: 136
Period size: 43 Copynumber: 4.3 Consensus size: 43
2037565 GTAGCGTTAG
* * * * *
2037575 GTTATGATATTTAGCGGCGTTTTTT-CATAAACG-TCGCAACAT
1 GTTATGACATTTAGTGGCTTTTTTTGTATAAATGCT-GCAACAT
* * * *
2037617 GTTATGATATTTTAGTGGGTTTTTTT-TATAAACGTTGCAACAT
1 GTTATGACA-TTTAGTGGCTTTTTTTGTATAAATGCTGCAACAT
* *
2037660 GTTATTACATTTAGCGGCCTTTTTTTGGTATAAATGCTGCAACAT
1 GTTATGACATTTAGTGG-CTTTTTTT-GTATAAATGCTGCAACAT
* * *
2037705 GTTATGATATTTAGTGATGTTTCTTTTTTTTGTATAAATGCCGCAACAA
1 GTTATGACATTTAGTG--G---C-TTTTTTTGTATAAATGCTGCAACAT
*
2037754 GTTATTACATTT
1 GTTATGACATTT
2037766 TATGATATTT
Statistics
Matches: 121, Mismatches: 18, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
42 16 0.13
43 41 0.34
44 1 0.01
45 28 0.23
47 1 0.01
49 27 0.22
50 7 0.06
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (43 bp):
GTTATGACATTTAGTGGCTTTTTTTGTATAAATGCTGCAACAT
Found at i:2038089 original size:27 final size:27
Alignment explanation
Indices: 2038035--2038096 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
2038025 TCAAGCAATG
*
2038035 TAGTTCAACATTAAGTGAAATGTAATA
1 TAGTTCAAAATTAAGTGAAATGTAATA
2038062 TAGTTCAATAATTAAGTGAAATGT-ATA
1 TAGTTCAA-AATTAAGTGAAATGTAATA
2038089 TAGTTCAA
1 TAGTTCAA
2038097 CAAGTATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
27 19 0.58
28 14 0.42
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (27 bp):
TAGTTCAAAATTAAGTGAAATGTAATA
Found at i:2041549 original size:24 final size:24
Alignment explanation
Indices: 2041473--2041566 Score: 75
Period size: 24 Copynumber: 4.0 Consensus size: 24
2041463 TTCAATTTGA
* * * *
2041473 ATTCTGTTATGATACCTGACTTGG
1 ATTCTGATCTGATACTTGACCTGG
* * * **
2041497 ATTCTAATTTGAGAC-TGATATGG
1 ATTCTGATCTGATACTTGACCTGG
*
2041520 ATTCTGATCTTATA-TATGACCTGG
1 ATTCTGATCTGATACT-TGACCTGG
2041544 ATTCTGATCTGATACTTGACCTG
1 ATTCTGATCTGATACTTGACCTG
2041567 AATTATGTTT
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
23 16 0.30
24 37 0.69
25 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACCTGG
Found at i:2041772 original size:14 final size:15
Alignment explanation
Indices: 2041753--2041781 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2041743 AGTGTTTATA
2041753 TTTTAAAAA-ATATG
1 TTTTAAAAAGATATG
2041767 TTTTAAAAAGATATG
1 TTTTAAAAAGATATG
2041782 AAAAGTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.41
Consensus pattern (15 bp):
TTTTAAAAAGATATG
Found at i:2049380 original size:3 final size:3
Alignment explanation
Indices: 2049372--2049427 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
2049362 GGGTTTGTAT
*
2049372 TAA TAA TAA TAGA -AA TAA TAA TAA CAA T-A TAA T-A TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2049415 CAA CAA TAA TAA T
1 TAA TAA TAA TAA T
2049428 TATGGGTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 5 0.11
3 39 0.87
4 1 0.02
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:2049410 original size:19 final size:18
Alignment explanation
Indices: 2049372--2049417 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
2049362 GGGTTTGTAT
*
2049372 TAATAATAATAGAAATAA
1 TAATAACAATAGAAATAA
*
2049390 TAATAACAATATAATATAA
1 TAATAACAATAGAA-ATAA
2049409 TAATAACAA
1 TAATAACAA
2049418 CAATAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.28
Consensus pattern (18 bp):
TAATAACAATAGAAATAA
Found at i:2049413 original size:22 final size:23
Alignment explanation
Indices: 2049373--2049427 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
2049363 GGTTTGTATT
* *
2049373 AATAATAATAGAAATAATAATAAC
1 AATAATAATA-TAATAATAACAAC
2049397 AAT-ATAATATAATAATAACAAC
1 AATAATAATATAATAATAACAAC
2049419 AATAATAAT
1 AATAATAAT
2049428 TATGGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 14 0.50
23 11 0.39
24 3 0.11
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.27
Consensus pattern (23 bp):
AATAATAATATAATAATAACAAC
Found at i:2049746 original size:40 final size:42
Alignment explanation
Indices: 2049669--2049770 Score: 97
Period size: 40 Copynumber: 2.5 Consensus size: 42
2049659 ATGGTTGACC
* * ** *
2049669 CAAGGTGATGCTAATCCTACTCCTTATGTAATCGACGA-C-A
1 CAAGGTGATGCTGATCCAACTCCCAATATAATCGACGAGCGA
* *
2049709 CAAGGTGATGCTGATCCAACTCCCAATATGATGGACGAGCGA
1 CAAGGTGATGCTGATCCAACTCCCAATATAATCGACGAGCGA
*
2049751 -AA--TGATGATGATCCAACTCC
1 CAAGGTGATGCTGATCCAACTCC
2049771 TTATGTGACG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
39 17 0.33
40 31 0.60
41 3 0.06
42 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (42 bp):
CAAGGTGATGCTGATCCAACTCCCAATATAATCGACGAGCGA
Found at i:2051901 original size:54 final size:54
Alignment explanation
Indices: 2051830--2052540 Score: 403
Period size: 55 Copynumber: 13.1 Consensus size: 54
2051820 TTTCAGTTAT
* * * **
2051830 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAGC
1 CATCAAGAAAACCCTAAAAATCAGGCTTAGCTTCTTTGAAAATTCATTTGAAAA
* * * *
2051884 CATCAAGAAAACCCTAAAAATCATGCTTAGCTTCTTTCAAAA-TCCTTTTAAAGA
1 CATCAAGAAAACCCTAAAAATCAGGCTTAGCTTCTTTGAAAATTCATTTGAAA-A
* * * *
2051938 CAT-AA-AAAACCCCTAAAAATTAGGATTAGCTTCGTTT-AGAA-TCTATTTGAATA
1 CATCAAGAAAA-CCCTAAAAATCAGGCTTAGCTTC-TTTGAAAATTC-ATTTGAAAA
* * * * * *
2051991 CATCAAGAAACCCCTAAAAA-CTAGGCTTAACATATTTCAAAA-TCTATTTGAATA
1 CATCAAGAAAACCCTAAAAATC-AGGCTTAGCTTCTTTGAAAATTC-ATTTGAAAA
* * * *
2052045 TATCAAG-AAACTCCTGAAAATCAGACTTAGCTTCTTTGAAAACTCATTT-ATAAA
1 CATCAAGAAAAC-CCTAAAAATCAGGCTTAGCTTCTTTGAAAATTCATTTGA-AAA
* * * ** * *
2052099 TAATCCAG-AAA-CTTATGAAAATCAAACCTAGTTTCTTTGAAAATTCATTTGAAAA
1 -CATCAAGAAAACCCTA--AAAATCAGGCTTAGCTTCTTTGAAAATTCATTTGAAAA
* * * * * *
2052154 CATCAAGAAACCCCTGAAAATTAGGTTTAGCTTCTTTGAAAACTCATTTAAAAA
1 CATCAAGAAAACCCTAAAAATCAGGCTTAGCTTCTTTGAAAATTCATTTGAAAA
* * *
2052208 TCATCAAG-AAACTTCTAAAAATCAGTCTTAGTTTCTTTGAAAATTCATTTGAAAA
1 -CATCAAGAAAAC-CCTAAAAATCAGGCTTAGCTTCTTTGAAAATTCATTTGAAAA
* * * * * * *
2052263 CATCAAGAAACCCCTGAAAATCAGGTTTTGCTTATTTGAAAACTCATTTAAAAA
1 CATCAAGAAAACCCTAAAAATCAGGCTTAGCTTCTTTGAAAATTCATTTGAAAA
* ** * * * *
2052317 TCATCAA-TAAACTTTTGAAAACCAGGCTTAGTTTCTTTGAAAATTCATTTAAAAA
1 -CATCAAGAAAAC-CCTAAAAATCAGGCTTAGCTTCTTTGAAAATTCATTTGAAAA
****** * * * * * * *
2052372 TCATCAAGATTTTTTTGAAAATCAGACTTAGTTTCTTTAAAAACTCGTTTAAAAA
1 -CATCAAGAAAACCCTAAAAATCAGGCTTAGCTTCTTTGAAAATTCATTTGAAAA
* * * ** * *
2052427 TCATCAAG-AAACTTCTGAAAACCATACTTAGTTTCTTTGAAAACTCATTT-ATAAA
1 -CATCAAGAAAAC-CCTAAAAATCAGGCTTAGCTTCTTTGAAAATTCATTTGA-AAA
** * * * *
2052482 TCATCAAG-AAACTTTCAAAAATCAGACTTAGCTACTTT-CAAAGTCATTTGAAAA
1 -CATCAAGAAAACCCT-AAAAATCAGGCTTAGCTTCTTTGAAAATTCATTTGAAAA
2052536 CATCA
1 CATCA
2052541 TATTGTTTGG
Statistics
Matches: 521, Mismatches: 108, Indels: 57
0.76 0.16 0.08
Matches are distributed among these distances:
52 4 0.01
53 52 0.10
54 213 0.41
55 249 0.48
56 3 0.01
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (54 bp):
CATCAAGAAAACCCTAAAAATCAGGCTTAGCTTCTTTGAAAATTCATTTGAAAA
Found at i:2051970 original size:53 final size:54
Alignment explanation
Indices: 2051830--2052283 Score: 238
Period size: 54 Copynumber: 8.4 Consensus size: 54
2051820 TTTCAGTTAT
* * * * *
2051830 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAGC
1 CATCAAAAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATCCTTTTGAAGA
* * *
2051884 CATCAAGAAAA-CCCTAAAAATCATGCTTAGCTTCTTTCAAAATCCTTTTAAAGA
1 CATCAA-AAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATCCTTTTGAAGA
* * *
2051938 CAT-AAAAAACCCCTAAAAATTAGGATTAGCTTCGTTT-AGAAT-CTATTTGAATA
1 CATCAAAAAACCCCTAAAAATTAGGCTTAGCTTC-TTTCAAAATCCT-TTTGAAGA
* * * * * *
2051991 CATCAAGAAACCCCTAAAAACTAGGCTTAACATATTTCAAAAT-CTATTTGAATA
1 CATCAAAAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATCCT-TTTGAAGA
* * * * * * * * * *
2052045 TATCAAGAAACTCCTGAAAATCAGACTTAGCTTCTTTGAAAACTCATTTATAAATA
1 CATCAAAAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAA-TCCTTT-TGAAGA
* * *** * * ** * * * * * *
2052101 -ATCCAGAAACTTATGAAAATCAAACCTAGTTTCTTTGAAAATTCATTTGAAAA
1 CATCAAAAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATCCTTTTGAAGA
* * * * * * *
2052154 CATCAAGAAACCCCTGAAAATTAGGTTTAGCTTCTTTGAAAA-CTCATTTAAAAA
1 CATCAAAAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATC-CTTTTGAAGA
* ** * * * * * * *
2052208 TCATCAAGAAACTTCTAAAAATCAGTCTTAGTTTCTTTGAAAATTCATTTGAAAA
1 -CATCAAAAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATCCTTTTGAAGA
* *
2052263 CATCAAGAAACCCCTGAAAAT
1 CATCAAAAAACCCCTAAAAAT
2052284 CAGGTTTTGC
Statistics
Matches: 319, Mismatches: 68, Indels: 26
0.77 0.16 0.06
Matches are distributed among these distances:
52 6 0.02
53 42 0.13
54 180 0.56
55 85 0.27
56 6 0.02
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (54 bp):
CATCAAAAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATCCTTTTGAAGA
Found at i:2052029 original size:107 final size:107
Alignment explanation
Indices: 2051837--2052034 Score: 267
Period size: 107 Copynumber: 1.9 Consensus size: 107
2051827 TATCATCAAG
* *
2051837 AAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAGCCATCAAGAAAACCCTAAA
1 AAACCCCTAAAAATTAGGATTAGCTTCTTTAAAAATTCATTTGAAGACATCAAGAAAACCCTAAA
* * * *
2051902 AATCATGCTTAGCTTCTTTCAAAATCCTTTTAAAGACATAAA
66 AATCAGGCTTAACATATTTCAAAATCCTTTTAAAGACATAAA
* * *
2051944 AAACCCCTAAAAATTAGGATTAGCTTCGTTT-AGAA-TCTATTTGAATACATCAAGAAACCCCTA
1 AAACCCCTAAAAATTAGGATTAGCTTC-TTTAAAAATTC-ATTTGAAGACATCAAGAAAACCCTA
2052007 AAAA-CTAGGCTTAACATATTTCAAAATC
64 AAAATC-AGGCTTAACATATTTCAAAATC
2052035 TATTTGAATA
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
106 3 0.04
107 73 0.92
108 3 0.04
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.29
Consensus pattern (107 bp):
AAACCCCTAAAAATTAGGATTAGCTTCTTTAAAAATTCATTTGAAGACATCAAGAAAACCCTAAA
AATCAGGCTTAACATATTTCAAAATCCTTTTAAAGACATAAA
Found at i:2052135 original size:55 final size:55
Alignment explanation
Indices: 2052046--2052512 Score: 526
Period size: 55 Copynumber: 8.5 Consensus size: 55
2052036 ATTTGAATAT
* * * *
2052046 ATCAAGAAACTCCTGAAAATCAGACTTAGCTTCTTTGAAAACTCATTTATAAATA
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATC
* * * * * *
2052101 ATCCAGAAACTTATGAAAATCAAACCTAGTTTCTTTGAAAATTCATTTGAAAA-C
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATC
** * ** *
2052155 ATCAAGAAACCCCTGAAAATTAGGTTTAGCTTCTTTGAAAACTCATTTAAAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATC
* * * *
2052210 ATCAAGAAACTTCTAAAAATCAGTCTTAGTTTCTTTGAAAATTCATTTGAAAA-C
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATC
** ** * * *
2052264 ATCAAGAAACCCCTGAAAATCAGGTTTTGCTTATTTGAAAACTCATTTAAAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATC
* * * * *
2052319 ATCAATAAACTTTTGAAAACCAGGCTTAGTTTCTTTGAAAATTCATTTAAAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATC
*** * * *
2052374 ATCAAGATTTTTTTGAAAATCAGACTTAGTTTCTTTAAAAACTCGTTTAAAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATC
* * *
2052429 ATCAAGAAACTTCTGAAAACCATACTTAGTTTCTTTGAAAACTCATTTATAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATC
*
2052484 ATCAAGAAACTT-TCAAAAATCAGACTTAG
1 ATCAAGAAACTTCT-GAAAATCAGACTTAG
2052513 CTACTTTCAA
Statistics
Matches: 337, Mismatches: 72, Indels: 6
0.81 0.17 0.01
Matches are distributed among these distances:
54 86 0.26
55 251 0.74
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.33
Consensus pattern (55 bp):
ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATC
Found at i:2052170 original size:109 final size:109
Alignment explanation
Indices: 2051830--2052541 Score: 568
Period size: 109 Copynumber: 6.5 Consensus size: 109
2051820 TTTCAGTTAT
* * * * * * **
2051830 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTT-GAAGCCATCAAGAAA
1 CATCAAGAAACCCCTGAAAATCAGACTTAGCTTCTTTGAAAACTCATTTAAAAATCATCAAG-AA
* * * * * * *
2051894 AC-CCTAAAAATCATG-CTTAGCTTCTTTCAAAA-TCCTTTTAAAGA
65 ACTTCTGAAAACCA-GACTTAGTTTCTTTGAAAATTCATTTGAAA-A
* * * * * *
2051938 CAT-AAAAAACCCCTAAAAATTAGGA-TTAGCTTCGTTT-AGAA-TCTATTTGAATA-CATCAAG
1 CATCAAGAAACCCCTGAAAATCA-GACTTAGCTTC-TTTGAAAACTC-ATTTAAAAATCATCAAG
** * * * *** * * *
2051998 AAACCCCTAAAAACTAGGCTTAACATATTTCAAAA-TCTATTTGAATA
63 AAACTTCTGAAAACCAGACTTAGTTTCTTTGAAAATTC-ATTTGAAAA
* * * * *
2052045 TATCAAGAAACTCCTGAAAATCAGACTTAGCTTCTTTGAAAACTCATTTATAAATAATCCAGAAA
1 CATCAAGAAACCCCTGAAAATCAGACTTAGCTTCTTTGAAAACTCATTTAAAAATCATCAAGAAA
* * * *
2052110 CTTATGAAAATCAAACCTAGTTTCTTTGAAAATTCATTTGAAAA
66 CTTCTGAAAACCAGACTTAGTTTCTTTGAAAATTCATTTGAAAA
* **
2052154 CATCAAGAAACCCCTGAAAATTAGGTTTAGCTTCTTTGAAAACTCATTTAAAAATCATCAAGAAA
1 CATCAAGAAACCCCTGAAAATCAGACTTAGCTTCTTTGAAAACTCATTTAAAAATCATCAAGAAA
* * *
2052219 CTTCTAAAAATCAGTCTTAGTTTCTTTGAAAATTCATTTGAAAA
66 CTTCTGAAAACCAGACTTAGTTTCTTTGAAAATTCATTTGAAAA
** * * *
2052263 CATCAAGAAACCCCTGAAAATCAGGTTTTGCTTATTTGAAAACTCATTTAAAAATCATCAATAAA
1 CATCAAGAAACCCCTGAAAATCAGACTTAGCTTCTTTGAAAACTCATTTAAAAATCATCAAGAAA
* * *
2052328 CTTTTGAAAACCAGGCTTAGTTTCTTTGAAAATTCATTTAAAAA
66 CTTCTGAAAACCAGACTTAGTTTCTTTGAAAATTCATTTGAAAA
****** * * *
2052372 TCATCAAGATTTTTTTGAAAATCAGACTTAGTTTCTTTAAAAACTCGTTTAAAAATCATCAAGAA
1 -CATCAAGAAACCCCTGAAAATCAGACTTAGCTTCTTTGAAAACTCATTTAAAAATCATCAAGAA
* *
2052437 ACTTCTGAAAACCATACTTAGTTTCTTTGAAAACTCATTT-ATAAA
65 ACTTCTGAAAACCAGACTTAGTTTCTTTGAAAATTCATTTGA-AAA
** * * * *
2052482 TCATCAAGAAA-CTTTCAAAAATCAGACTTAGCTACTTT-CAAAGTCATTTGAAAACATCAT
1 -CATCAAGAAACCCCT-GAAAATCAGACTTAGCTTCTTTGAAAACTCATTT-AAAA-ATCAT
2052542 ATTGTTTGGG
Statistics
Matches: 497, Mismatches: 89, Indels: 33
0.80 0.14 0.05
Matches are distributed among these distances:
106 7 0.01
107 73 0.15
108 45 0.09
109 244 0.49
110 123 0.25
111 5 0.01
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (109 bp):
CATCAAGAAACCCCTGAAAATCAGACTTAGCTTCTTTGAAAACTCATTTAAAAATCATCAAGAAA
CTTCTGAAAACCAGACTTAGTTTCTTTGAAAATTCATTTGAAAA
Found at i:2058949 original size:20 final size:19
Alignment explanation
Indices: 2058922--2058982 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 19
2058912 CATTTTTGTG
2058922 CAGAGGGAATCGATCCCCC
1 CAGAGGGAATCGATCCCCC
*
2058941 CATGAGGGAACCGATTCCCCC
1 CA-GAGGGAATCGA-TCCCCC
*
2058962 CACAGGGGAATCGATACCCCC
1 CAGA-GGGAATCGAT-CCCCC
2058983 TGGGGTTCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 2 0.06
20 12 0.34
21 21 0.60
ACGTcount: A:0.26, C:0.38, G:0.25, T:0.11
Consensus pattern (19 bp):
CAGAGGGAATCGATCCCCC
Found at i:2058961 original size:21 final size:20
Alignment explanation
Indices: 2058924--2058963 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2058914 TTTTTGTGCA
*
2058924 GAGGGAATCGATCCCCCCAT
1 GAGGGAACCGATCCCCCCAT
2058944 GAGGGAACCGATTCCCCCCA
1 GAGGGAACCGA-TCCCCCCA
2058964 CAGGGGAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCAT
Found at i:2063046 original size:17 final size:17
Alignment explanation
Indices: 2063024--2063058 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2063014 CTTCAAACCT
2063024 TCTGATCTCTCAGACTA
1 TCTGATCTCTCAGACTA
2063041 TCTGATCTCTCAGACTA
1 TCTGATCTCTCAGACTA
2063058 T
1 T
2063059 TTGCTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.29, G:0.11, T:0.37
Consensus pattern (17 bp):
TCTGATCTCTCAGACTA
Found at i:2063476 original size:28 final size:29
Alignment explanation
Indices: 2063394--2063469 Score: 118
Period size: 29 Copynumber: 2.7 Consensus size: 29
2063384 TTAGGCTGAC
*
2063394 TTGGGAAGGTAATGTGTTTCAGGTTAATT
1 TTGGGGAGGTAATGTGTTTCAGGTTAATT
*
2063423 TTGAGGAGGTAATGTGTTTCAGGTTAA-T
1 TTGGGGAGGTAATGTGTTTCAGGTTAATT
*
2063451 TTGGGGAGGTAATATGTTT
1 TTGGGGAGGTAATGTGTTT
2063470 TGGGTTAGCT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 18 0.42
29 25 0.58
ACGTcount: A:0.24, C:0.03, G:0.33, T:0.41
Consensus pattern (29 bp):
TTGGGGAGGTAATGTGTTTCAGGTTAATT
Found at i:2064831 original size:85 final size:85
Alignment explanation
Indices: 2064688--2064859 Score: 283
Period size: 85 Copynumber: 2.0 Consensus size: 85
2064678 ATACAATCAC
* *
2064688 GACACACGAATGTGTGTCATTTTCATTTATGACAGGGGCTTCAATGACACGCAATGTAAGTTATA
1 GACACACAAATGTGTGTCATTTTCATTTATGACAGGGGCTTCAATGACACGCAATGTAAGTCATA
*
2064753 AATGCGTGTCATAAATTTAT
66 AATGCGCGTCATAAATTTAT
* *
2064773 GACACACAAATGTGTGTCATCTTT-ATTTATGACGGGGGCTTCAATGACGCGCAATGTAAGTCAT
1 GACACACAAATGTGTGTCAT-TTTCATTTATGACAGGGGCTTCAATGACACGCAATGTAAGTCAT
2064837 AAATGCGCGTCATAAATTTAT
65 AAATGCGCGTCATAAATTTAT
2064858 GA
1 GA
2064860 TGCACAGTTG
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
85 78 0.96
86 3 0.04
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATTTTCATTTATGACAGGGGCTTCAATGACACGCAATGTAAGTCATA
AATGCGCGTCATAAATTTAT
Found at i:2064877 original size:85 final size:86
Alignment explanation
Indices: 2064688--2064880 Score: 255
Period size: 85 Copynumber: 2.3 Consensus size: 86
2064678 ATACAATCAC
* * * *
2064688 GACACACGAATGTGTGTCAT-TTTCATTTATGACAGGGGCTTCAATGACACGCAATGTAAGTTAT
1 GACACACAAATGCGCGTCATCTTTCATTTATGACAGGGGCTTCAATGACACGCAATGTAAGTCAT
*
2064752 AAATGCGTGTCATAAATTTAT
66 AAATGCGCGTCATAAATTTAT
* * * *
2064773 GACACACAAATGTGTGTCATCTTT-ATTTATGACGGGGGCTTCAATGACGCGCAATGTAAGTCAT
1 GACACACAAATGCGCGTCATCTTTCATTTATGACAGGGGCTTCAATGACACGCAATGTAAGTCAT
2064837 AAATGCGCGTCATAAATTTAT
66 AAATGCGCGTCATAAATTTAT
** **
2064858 GATGCACAGTTGCGCGTCATCTT
1 GACACACAAATGCGCGTCATCTT
2064881 AAATTCATGT
Statistics
Matches: 96, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
85 93 0.97
86 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (86 bp):
GACACACAAATGCGCGTCATCTTTCATTTATGACAGGGGCTTCAATGACACGCAATGTAAGTCAT
AAATGCGCGTCATAAATTTAT
Found at i:2065115 original size:19 final size:20
Alignment explanation
Indices: 2065078--2065115 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2065068 TTTAATATGC
*
2065078 TTATGTTTCTTTTATTTTTT
1 TTATGTTTCTTTTAGTTTTT
*
2065098 TTAT-TTTCTTTTGGTTTT
1 TTATGTTTCTTTTAGTTTT
2065116 CCATGATCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.08, C:0.05, G:0.08, T:0.79
Consensus pattern (20 bp):
TTATGTTTCTTTTAGTTTTT
Found at i:2065198 original size:9 final size:9
Alignment explanation
Indices: 2065184--2065282 Score: 84
Period size: 9 Copynumber: 11.1 Consensus size: 9
2065174 ATATGTTTTA
2065184 TTTCTTCTT
1 TTTCTTCTT
2065193 TTTCTTCTT
1 TTTCTTCTT
2065202 TTTCCTTC-T
1 TTT-CTTCTT
2065211 TTTCTCTCTTT
1 TTTCT-TC-TT
*
2065222 TTTATTCTT
1 TTTCTTCTT
*
2065231 CTT-TTCTT
1 TTTCTTCTT
2065239 TTT-TTCTT
1 TTTCTTCTT
2065247 TTT-TTC-T
1 TTTCTTCTT
2065254 TTTC-TCTAT
1 TTTCTTCT-T
*
2065263 TTTCTATGTT
1 TTTCT-TCTT
2065273 TTTCTTCTT
1 TTTCTTCTT
2065282 T
1 T
2065283 ATGCCATATA
Statistics
Matches: 76, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
7 6 0.08
8 20 0.26
9 31 0.41
10 12 0.16
11 7 0.09
ACGTcount: A:0.03, C:0.20, G:0.01, T:0.76
Consensus pattern (9 bp):
TTTCTTCTT
Found at i:2065211 original size:19 final size:17
Alignment explanation
Indices: 2065184--2065282 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
2065174 ATATGTTTTA
2065184 TTTCTTCTTTTTCTTCTT
1 TTTCTTCTTTTT-TTCTT
*
2065202 TTTCCTTCTTTTCTCTCTTT
1 TTT-CTTCTTTT-TTTC-TT
* *
2065222 TTTATTCTTCTTTTCTT
1 TTTCTTCTTTTTTTCTT
2065239 TTT-TTCTTTTTTTC-T
1 TTTCTTCTTTTTTTCTT
*
2065254 TTTC-TCTATTTTCTATGTT
1 TTTCTTCT-TTTT-T-TCTT
2065273 TTTCTTCTTT
1 TTTCTTCTTT
2065283 ATGCCATATA
Statistics
Matches: 66, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
15 7 0.11
16 14 0.21
17 6 0.09
18 7 0.11
19 23 0.35
20 9 0.14
ACGTcount: A:0.03, C:0.20, G:0.01, T:0.76
Consensus pattern (17 bp):
TTTCTTCTTTTTTTCTT
Found at i:2065235 original size:13 final size:12
Alignment explanation
Indices: 2065179--2065251 Score: 56
Period size: 13 Copynumber: 5.6 Consensus size: 12
2065169 ATTTGATATG
*
2065179 TTTTATTTCTTC
1 TTTTTTTTCTTC
* *
2065191 TTTTTCTTCTTT
1 TTTTTTTTCTTC
2065203 TTCCTTCTTTTCTCTC
1 TT--TT-TTTTCT-TC
2065219 TTTTTTATTCTTC
1 TTTTTT-TTCTTC
*
2065232 TTTTCTTTTTTTC
1 TTTT-TTTTCTTC
2065245 TTTTTTT
1 TTTTTTT
2065252 CTTTTCTCTA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
12 14 0.29
13 17 0.35
14 10 0.20
15 5 0.10
16 3 0.06
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTTTTCTTC
Found at i:2065243 original size:8 final size:8
Alignment explanation
Indices: 2065188--2065256 Score: 66
Period size: 8 Copynumber: 7.9 Consensus size: 8
2065178 GTTTTATTTC
2065188 TTCTTTTT
1 TTCTTTTT
2065196 CTTCTTTTT
1 -TTCTTTTT
2065205 CCTTCTTTTCT
1 --TTCTTTT-T
*
2065216 CTCTTTTTT
1 TTC-TTTTT
*
2065225 ATTCTTCTT
1 -TTCTTTTT
2065234 TTCTTTTT
1 TTCTTTTT
2065242 TTCTTTTT
1 TTCTTTTT
2065250 TTCTTTT
1 TTCTTTT
2065257 CTCTATTTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
8 22 0.42
9 15 0.29
10 14 0.27
11 1 0.02
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.78
Consensus pattern (8 bp):
TTCTTTTT
Found at i:2065256 original size:13 final size:13
Alignment explanation
Indices: 2065192--2065258 Score: 50
Period size: 13 Copynumber: 5.1 Consensus size: 13
2065182 TATTTCTTCT
2065192 TTTTCTTCTTTTTC
1 TTTTCTT-TTTTTC
* *
2065206 -CTTCTTTTCTCTC
1 TTTTCTTTT-TTTC
*
2065219 TTTT-TTATTCTTC
1 TTTTCTT-TTTTTC
2065232 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
2065245 TTTT-TTTCTTTTC
1 TTTTCTTT-TTTTC
2065258 T
1 T
2065259 CTATTTTCTA
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
12 5 0.12
13 31 0.74
14 6 0.14
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:2070348 original size:3 final size:3
Alignment explanation
Indices: 2070340--2070454 Score: 173
Period size: 3 Copynumber: 39.3 Consensus size: 3
2070330 TTTGGGTTTG
* * *
2070340 TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA CAA TAA CAA T-A TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2070386 TAA T-A TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2070433 TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
2070455 GGGTTGACAA
Statistics
Matches: 101, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
2 6 0.06
3 95 0.94
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:2070695 original size:42 final size:41
Alignment explanation
Indices: 2070541--2070789 Score: 201
Period size: 41 Copynumber: 6.0 Consensus size: 41
2070531 ATTGAAATAA
* * * *
2070541 CGGTGTTTGTTAAAAAAGCGCCACAAATTATGTATCATATTG
1 CGGTGTTCGTTAAAAAA-AGCCACAAACTATGTATCCTATTG
* * * *
2070583 CGGCGTTCTTTAAAAAAAGTCACAAACTATGTATCGTATTG
1 CGGTGTTCGTTAAAAAAAGCCACAAACTATGTATCCTATTG
* * *
2070624 TGGTGTTTGTTAAAAAAAGCCACAAACTATGCATCCTATTG
1 CGGTGTTCGTTAAAAAAAGCCACAAACTATGTATCCTATTG
*** * *
2070665 CGGTGTTCGTTAAAAAAATGCCATGTACTATGTACCCTATTA
1 CGGTGTTCGTTAAAAAAA-GCCACAAACTATGTATCCTATTG
* ** * * * * *
2070707 CCGCATTTGTTTAAAAAAGCCAGAAACTATGTACCCTATTA
1 CGGTGTTCGTTAAAAAAAGCCACAAACTATGTATCCTATTG
*** * * * *
2070748 CAAAGTTTGTTAAAAAAAGCAACAAACTATGTAACCAATTG
1 CGGTGTTCGTTAAAAAAAGCCACAAACTATGTATCCTATTG
2070789 C
1 C
2070790 AACGTTTATT
Statistics
Matches: 166, Mismatches: 40, Indels: 3
0.79 0.19 0.01
Matches are distributed among these distances:
41 122 0.73
42 44 0.27
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (41 bp):
CGGTGTTCGTTAAAAAAAGCCACAAACTATGTATCCTATTG
Found at i:2070802 original size:41 final size:41
Alignment explanation
Indices: 2070719--2070806 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
2070709 GCATTTGTTT
* * * * *
2070719 AAAAAAGCCAGAAACTATGTACCCTATTACAAAGTTTGTTA
1 AAAAAAGCAACAAACTATGTAACCAATTACAAAGTTTATTA
* *
2070760 AAAAAAGCAACAAACTATGTAACCAATTGCAACGTTTATTA
1 AAAAAAGCAACAAACTATGTAACCAATTACAAAGTTTATTA
2070801 AAAAAA
1 AAAAAA
2070807 CACCACAAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.50, C:0.16, G:0.10, T:0.24
Consensus pattern (41 bp):
AAAAAAGCAACAAACTATGTAACCAATTACAAAGTTTATTA
Found at i:2072612 original size:74 final size:73
Alignment explanation
Indices: 2072491--2072631 Score: 264
Period size: 74 Copynumber: 1.9 Consensus size: 73
2072481 TCGTCATTTT
*
2072491 GATCTTTTTGAAATATTTTAGCTTCTAACGTTTGGCTAGATAATCATTTTAATTTTTTTTAAAAG
1 GATCTTTTTGAAATATTTTAGCTTCTAACATTTGGCTAGATAATCATTTTAA-TTTTTTTAAAAG
2072556 TATAATGAC
65 TATAATGAC
2072565 GATCTTTTTGAAATATTTTAGCTTCTAACATTTGGCTAGATAATCATTTTAATTTTTTTAAAAGT
1 GATCTTTTTGAAATATTTTAGCTTCTAACATTTGGCTAGATAATCATTTTAATTTTTTTAAAAGT
2072630 AT
66 AT
2072632 TTTGGCCCCC
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
73 15 0.23
74 51 0.77
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.48
Consensus pattern (73 bp):
GATCTTTTTGAAATATTTTAGCTTCTAACATTTGGCTAGATAATCATTTTAATTTTTTTAAAAGT
ATAATGAC
Found at i:2080312 original size:23 final size:23
Alignment explanation
Indices: 2080268--2080312 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2080258 AAAGAAAACT
**
2080268 AATAAAATAACAAAATCTAAAAG
1 AATAAAATAACAAAATAAAAAAG
2080291 AATAAAGATAA-AAAATAAAAAA
1 AATAAA-ATAACAAAATAAAAAA
2080313 ATATAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (23 bp):
AATAAAATAACAAAATAAAAAAG
Found at i:2081640 original size:32 final size:33
Alignment explanation
Indices: 2081603--2081664 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
2081593 TTATTGTTGT
*
2081603 GGCTATGCAACTTGTT-TCGTGTCTGATGTCAG
1 GGCTATGCAACTTGTTGTCGTGACTGATGTCAG
* *
2081635 GGCTATGCTACTTGTTGTTGTGACTGATGT
1 GGCTATGCAACTTGTTGTCGTGACTGATGT
2081665 AGAGGCATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 15 0.58
33 11 0.42
ACGTcount: A:0.15, C:0.16, G:0.29, T:0.40
Consensus pattern (33 bp):
GGCTATGCAACTTGTTGTCGTGACTGATGTCAG
Found at i:2097940 original size:17 final size:17
Alignment explanation
Indices: 2097918--2097961 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
2097908 TATACCCTTG
2097918 GTATTGATACCCAATGA
1 GTATTGATACCCAATGA
2097935 GTATTGATACCCAATGA
1 GTATTGATACCCAATGA
*
2097952 GTATCGATAC
1 GTATTGATAC
2097962 AAATTTGGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (17 bp):
GTATTGATACCCAATGA
Found at i:2098022 original size:20 final size:20
Alignment explanation
Indices: 2097997--2098046 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2097987 CTGAACTTGG
2097997 TATCGATACCTC-CCTACGAC
1 TATCGATACCTCACCTAC-AC
*
2098017 TATCGATACCTCACCTACAG
1 TATCGATACCTCACCTACAC
2098037 TATCGATACC
1 TATCGATACC
2098047 CATTGCATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 23 0.82
21 5 0.18
ACGTcount: A:0.28, C:0.36, G:0.10, T:0.26
Consensus pattern (20 bp):
TATCGATACCTCACCTACAC
Found at i:2109996 original size:22 final size:20
Alignment explanation
Indices: 2109959--2110010 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
2109949 CATCCAAATG
*
2109959 AACTATGCAAATATCCATCA
1 AACTATGCAAATATCCAACA
2109979 AACTATGCATCAATATCCAACA
1 AACTATGCA--AATATCCAACA
*
2110001 AAATATGCAA
1 AACTATGCAA
2110011 GTAGTATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 10 0.36
22 18 0.64
ACGTcount: A:0.48, C:0.23, G:0.06, T:0.23
Consensus pattern (20 bp):
AACTATGCAAATATCCAACA
Found at i:2112088 original size:24 final size:22
Alignment explanation
Indices: 2112033--2112090 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
2112023 CCATAGTAGT
* *
2112033 CCATCATCATCAACTCCATATA
1 CCATCATCATCAACACCATAGA
* *
2112055 CCATCTTCATCAACACTATTAAGA
1 CCATCATCATCAACACCA-T-AGA
2112079 CCATCATCATCA
1 CCATCATCATCA
2112091 TCATATTTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 15 0.52
23 1 0.03
24 13 0.45
ACGTcount: A:0.36, C:0.34, G:0.02, T:0.28
Consensus pattern (22 bp):
CCATCATCATCAACACCATAGA
Found at i:2116451 original size:17 final size:17
Alignment explanation
Indices: 2116431--2116477 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
2116421 AGTCTTTCAT
2116431 TACTTCATTTCTATTTC
1 TACTTCATTTCTATTTC
* *
2116448 TACTTAAGTTTTTATTTC
1 TACTTCA-TTTCTATTTC
2116466 -ACTTCAATTTCT
1 TACTTC-ATTTCT
2116478 CATATTCCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.21, C:0.19, G:0.02, T:0.57
Consensus pattern (17 bp):
TACTTCATTTCTATTTC
Found at i:2138038 original size:21 final size:20
Alignment explanation
Indices: 2138010--2138048 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
2138000 ATTGCTCAGA
2138010 GGGAACCGATTCCCCCCTAG
1 GGGAACCGATTCCCCCCTAG
2138030 GGGATACCGATTCCCCCCT
1 GGGA-ACCGATTCCCCCCT
2138049 GAATAGTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.18, C:0.41, G:0.23, T:0.18
Consensus pattern (20 bp):
GGGAACCGATTCCCCCCTAG
Found at i:2143667 original size:23 final size:20
Alignment explanation
Indices: 2143616--2143676 Score: 70
Period size: 19 Copynumber: 2.9 Consensus size: 20
2143606 TTTTGGTGCA
*
2143616 GAGGGAATCGA-TCCCCCTT
1 GAGGGAACCGATTCCCCCTT
2143635 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC-TT
2143656 GAAGGGGAACCGATTTCCCCC
1 G-A-GGGAACCGA-TTCCCCC
2143677 ATAGGGGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
19 10 0.28
20 6 0.17
21 3 0.08
22 1 0.03
23 9 0.25
24 7 0.19
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.20
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCTT
Found at i:2144104 original size:26 final size:24
Alignment explanation
Indices: 2144062--2144112 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
2144052 AGCATTTTCA
2144062 AAAAAAAAATTAAATTTTCGAAATT
1 AAAAAAAAATTAAATTTTC-AAATT
**
2144087 AAAAAAAAATGTTCATTTTCAAATT
1 AAAAAAAAAT-TAAATTTTCAAATT
2144112 A
1 A
2144113 TTGTGTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (24 bp):
AAAAAAAAATTAAATTTTCAAATT
Found at i:2150434 original size:21 final size:19
Alignment explanation
Indices: 2150391--2150435 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
2150381 CTACCAACTC
*
2150391 TTTCATTACTTCATTTCTA
1 TTTCATTACTTAATTTCTA
*
2150410 TTTCATTTACTTAAGTTTTTA
1 TTTCA-TTACTTAA-TTTCTA
2150431 TTTCA
1 TTTCA
2150436 CTTCTATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 7 0.32
21 10 0.45
ACGTcount: A:0.22, C:0.16, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTCATTACTTAATTTCTA
Found at i:2152878 original size:60 final size:60
Alignment explanation
Indices: 2152775--2153077 Score: 410
Period size: 60 Copynumber: 5.0 Consensus size: 60
2152765 TCTAAAATCG
* * *
2152775 AAGTTAAACGCCTAACGGTGCATTTTGGTAGAAAGGTGTCACTAATGCAAGTTAGATGAA
1 AAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAA
** *
2152835 AAGTTAAATGCCTAATAGTGCATTTTGGCA-AAAGGGTGCCACTAATGCAAGTTATATGAA
1 AAGTTAAATGCCTAACGGTGCATTTTGGCAGAAA-GGTGCCACTAATGCAAGTTAGATGAA
* * *
2152895 AAGTTAAACGCCTAACAGTGCATTTTGGTAGAAAGGTGCCACTAATGCAAGTTAGATGAA
1 AAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAA
* * *
2152955 AAGTTAAATTCCTAACGGTGCATTTTGGCAGAAAGGTTCCACTAATGCAAGTTAGTTGAA
1 AAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAA
* * * * * * *
2153015 AAGTTAAATGTCTAACGGTGCATTTTTAGCAGAAAAGTGCCACTATTTCCATTTAGATGAA
1 AAGTTAAATGCCTAACGGTGCA-TTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAA
2153076 AA
1 AA
2153078 ACAGTGAATT
Statistics
Matches: 214, Mismatches: 26, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
59 3 0.01
60 176 0.82
61 35 0.16
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (60 bp):
AAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAA
Found at i:2153688 original size:21 final size:22
Alignment explanation
Indices: 2153664--2153704 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2153654 AAATTTAAAT
*
2153664 TGAGGG-TTTTAAAACCTTTTA
1 TGAGGGATTTCAAAACCTTTTA
*
2153685 TGAGGGATTTCGAAACCTTT
1 TGAGGGATTTCAAAACCTTT
2153705 GGACCCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (22 bp):
TGAGGGATTTCAAAACCTTTTA
Found at i:2158779 original size:7 final size:7
Alignment explanation
Indices: 2158770--2158801 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
2158760 TTAAAACATA
2158770 AAAATA-
1 AAAATAG
2158776 AAAATAG
1 AAAATAG
2158783 AAAATAG
1 AAAATAG
2158790 AAAATAG
1 AAAATAG
2158797 AAAAT
1 AAAAT
2158802 TAAGGACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (7 bp):
AAAATAG
Found at i:2158801 original size:14 final size:13
Alignment explanation
Indices: 2158761--2158801 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
2158751 AAACCAATAT
2158761 TAAAACATA-AAAA
1 TAAAA-ATAGAAAA
2158774 TAAAAATAGAAAA
1 TAAAAATAGAAAA
2158787 TAGAAAATAGAAAA
1 TA-AAAATAGAAAA
2158801 T
1 T
2158802 TAAGGACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 3 0.12
13 11 0.42
14 12 0.46
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.17
Consensus pattern (13 bp):
TAAAAATAGAAAA
Found at i:2159463 original size:16 final size:16
Alignment explanation
Indices: 2159442--2159475 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2159432 TGTTGCATAC
2159442 TTTTCCATTTTTCTCT
1 TTTTCCATTTTTCTCT
2159458 TTTTCCATTTTTCTCT
1 TTTTCCATTTTTCTCT
2159474 TT
1 TT
2159476 GCAACCTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTCCATTTTTCTCT
Found at i:2163844 original size:3 final size:3
Alignment explanation
Indices: 2163831--2163887 Score: 105
Period size: 3 Copynumber: 18.7 Consensus size: 3
2163821 GGGTTGGGTA
2163831 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2163877 AAT AAT AAT AA
1 AAT AAT AAT AA
2163888 GATATATATA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2163896 original size:2 final size:2
Alignment explanation
Indices: 2163889--2163914 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2163879 TAATAATAAG
2163889 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
2163915 CCCGAAAAAT
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:2170125 original size:23 final size:23
Alignment explanation
Indices: 2170090--2170134 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2170080 TTATCAGACG
* * *
2170090 GTGGTCGGCGAGTGACGCCGACA
1 GTGGCCGGAGAGTGACGACGACA
2170113 GTGGCCGGAGAGTGACGACGAC
1 GTGGCCGGAGAGTGACGACGAC
2170135 CGAGCAACAA
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:0.20, C:0.24, G:0.44, T:0.11
Consensus pattern (23 bp):
GTGGCCGGAGAGTGACGACGACA
Found at i:2172046 original size:24 final size:24
Alignment explanation
Indices: 2171978--2172048 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
2171968 AAACGGAGAT
* *
2171978 ATCAGTAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATCCAG
* * *
2172002 ATAAGATAT-AAGAATAGAATCCAG
1 ATCAGAAATCAA-AACAGAATCCAG
*
2172026 ATCAGAAATCAAAACATAATCCA
1 ATCAGAAATCAAAACAGAATCCA
2172049 AGTCAAGTAT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
23 2 0.06
24 32 0.89
25 2 0.06
ACGTcount: A:0.54, C:0.15, G:0.11, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATCCAG
Done.