Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008091.1 Hibiscus syriacus cultivar Beakdansim tig00110602_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: 2471235
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:1297047 original size:21 final size:21
Alignment explanation
Indices: 1297023--1297260 Score: 123
Period size: 21 Copynumber: 11.2 Consensus size: 21
1297013 ATCGCAATGT
*
1297023 GATTTTCCAAATTCGCGTTGC
1 GATTTTCCAAGTTCGCGTTGC
1297044 GATTTATTCCAAGTT--CGTTGC
1 GA-TT-TTCCAAGTTCGCGTTGC
** * *
1297065 GATAGTCGAAGTTTGCGTTGC
1 GATTTTCCAAGTTCGCGTTGC
* *
1297086 GATTTATTCCAAATTTGCGTTGC
1 GA-TT-TTCCAAGTTCGCGTTGC
** *
1297109 GATAGTCGAAGTTCGCGTTGC
1 GATTTTCCAAGTTCGCGTTGC
*
1297130 GATTTATTTCAAGTT--CGTTGC
1 GA-TT-TTCCAAGTTCGCGTTGC
** *
1297151 GATAGTCGAAGTTCGCGTTGC
1 GATTTTCCAAGTTCGCGTTGC
1297172 GATTTATTCCAAGTT--CGTTGC
1 GA-TT-TTCCAAGTTCGCGTTGC
** * *
1297193 GATAGTCGAAGTTCTCGTTGC
1 GATTTTCCAAGTTCGCGTTGC
*
1297214 GATTTATTCCAAGTT--TGTTGC
1 GA-TT-TTCCAAGTTCGCGTTGC
** * *
1297235 GATAGTCGAAGTTCGCGTTAC
1 GATTTTCCAAGTTCGCGTTGC
1297256 GATTT
1 GATTT
1297261 ATTCGTTGCG
Statistics
Matches: 161, Mismatches: 38, Indels: 36
0.69 0.16 0.15
Matches are distributed among these distances:
19 27 0.17
20 4 0.02
21 79 0.49
22 7 0.04
23 44 0.27
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (21 bp):
GATTTTCCAAGTTCGCGTTGC
Found at i:1297096 original size:42 final size:42
Alignment explanation
Indices: 1297034--1297264 Score: 390
Period size: 42 Copynumber: 5.5 Consensus size: 42
1297024 ATTTTCCAAA
1297034 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
* *
1297076 TTTGCGTTGCGATTTATTCCAAATTTGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCC-AAGTT-CGTTGCGATAGTCGAAG
*
1297120 TTCGCGTTGCGATTTATTTCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1297162 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
* *
1297204 TTCTCGTTGCGATTTATTCCAAGTTTGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
*
1297246 TTCGCGTTACGATTTATTC
1 TTCGCGTTGCGATTTATTC
1297265 GTTGCGGTAG
Statistics
Matches: 177, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
42 134 0.76
43 8 0.05
44 35 0.20
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (42 bp):
TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
Found at i:1298198 original size:42 final size:42
Alignment explanation
Indices: 1298139--1298319 Score: 292
Period size: 42 Copynumber: 4.3 Consensus size: 42
1298129 TACGATTTTG
*
1298139 GACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
1298181 GACTATCGCAACGAATTTGTAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1298223 GACTATCGCAACGAATTTGTAATAAATCGCAACGCGAACTT-
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
1298264 GAACTATTGCAACAAATTTGGAATAAATCGCAACGCGAACTTC
1 G-ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1298307 GACTATCGCAACG
1 GACTATCGCAACG
1298320 CGAACTTGGA
Statistics
Matches: 129, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
41 1 0.01
42 127 0.98
43 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.23
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:1298314 original size:21 final size:21
Alignment explanation
Indices: 1298136--1298344 Score: 137
Period size: 21 Copynumber: 10.0 Consensus size: 21
1298126 CGTTACGATT
*
1298136 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
1298155 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
1298178 TTCGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
1298197 TTGTAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
1298220 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
1298239 TTGTAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* * * *
1298262 TTGAACTATTGCAA--CAAAT
1 TTGGACTATCGCAACGCGAAC
*
1298281 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
1298304 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
1298325 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAACGCGAA
1298345 TATGTAAATC
Statistics
Matches: 145, Mismatches: 29, Indels: 30
0.71 0.14 0.15
Matches are distributed among these distances:
19 31 0.21
21 79 0.54
23 35 0.24
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:1298336 original size:84 final size:83
Alignment explanation
Indices: 1298139--1298344 Score: 281
Period size: 84 Copynumber: 2.4 Consensus size: 83
1298129 TACGATTTTG
* *
1298139 GACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGACTATCGCAACGAATTTGTAAT
1 GACTATCGCAACGAATTTGGAAT-AATCGCAATGCGAACTTCGACTATCGCAACAAATTTGGAAT
*
1298204 AAATCGCAACGCGAACTTG
65 AAATCGCAACGCGAACTTC
* * *
1298223 GACTATCGCAACGAATTTGTAATAAATCGCAACGCGAACTT-GAACTATTGCAACAAATTTGGAA
1 GACTATCGCAACGAATTTGGAAT-AATCGCAATGCGAACTTCG-ACTATCGCAACAAATTTGGAA
1298287 TAAATCGCAACGCGAACTTC
64 TAAATCGCAACGCGAACTTC
* *
1298307 GACTATCGCAACGCGAACTTGGACT-ATCGCAATGCGAA
1 GACTATCGCAA--CGAATTTGGAATAATCGCAATGCGAA
1298345 TATGTAAATC
Statistics
Matches: 109, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
83 1 0.01
84 99 0.91
86 9 0.08
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (83 bp):
GACTATCGCAACGAATTTGGAATAATCGCAATGCGAACTTCGACTATCGCAACAAATTTGGAATA
AATCGCAACGCGAACTTC
Found at i:1299515 original size:35 final size:35
Alignment explanation
Indices: 1299464--1299537 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
1299454 AACAATCCTA
* *
1299464 AATTTCATTCTAAACCCCAATTTCCAAAGTAATTC
1 AATTTCATTCTAAACCCCAAATTCCAAAATAATTC
* *
1299499 AATTTCATTCTCAACCCTAAATTCCAAAATAATTC
1 AATTTCATTCTAAACCCCAAATTCCAAAATAATTC
1299534 AATT
1 AATT
1299538 AAATTCAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.35
Consensus pattern (35 bp):
AATTTCATTCTAAACCCCAAATTCCAAAATAATTC
Found at i:1299925 original size:21 final size:22
Alignment explanation
Indices: 1299901--1299941 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1299891 AGGAATTGAC
*
1299901 ATTA-TTATACATTCAATTTTT
1 ATTATTTATACAATCAATTTTT
*
1299922 ATTATTTATATAATCAATTT
1 ATTATTTATACAATCAATTT
1299942 GGTCCTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTATTTATACAATCAATTTTT
Found at i:1300080 original size:130 final size:130
Alignment explanation
Indices: 1299934--1300181 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
1299924 TATTTATATA
* ** *
1299934 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* * *
1299999 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCGCCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
1300064 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* * *
1300129 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
1300182 GAAGAAAATT
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:1300154 original size:23 final size:21
Alignment explanation
Indices: 1300108--1300154 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
1300098 AATTAATCAT
1300108 TTAACCAGGATCTGACATATG
1 TTAACCAGGATCTGACATATG
* *
1300129 TTAACACATGATCATGATATATG
1 TTAAC-CAGGATC-TGACATATG
1300152 TTA
1 TTA
1300155 TTGGTGACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (21 bp):
TTAACCAGGATCTGACATATG
Found at i:1300212 original size:130 final size:129
Alignment explanation
Indices: 1299948--1300212 Score: 291
Period size: 130 Copynumber: 2.0 Consensus size: 129
1299938 ATTTGGTCCT
* ** * *
1299948 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
* * *** * * **** *
1300013 TGACACGTGTCATTGGTGACACATGTCACCGCCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
1300078 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
* * * *
1300143 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
1300207 -A
128 CA
1300208 AAATT
1 AAATT
1300213 TGGGTCTTGG
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
130 98 0.88
132 8 0.07
133 5 0.05
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:1300538 original size:28 final size:27
Alignment explanation
Indices: 1300507--1300569 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
1300497 AGTTGATACA
1300507 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGATTT
** * *
1300535 ATATATTTTTAAACTAAATTTAATATTT
1 ATAT-TTTAAAAAATAAATTTAAGATTT
1300563 ATATTTT
1 ATATTTT
1300570 TCATATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 3 0.10
28 22 0.73
29 5 0.17
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGATTT
Found at i:1300670 original size:16 final size:18
Alignment explanation
Indices: 1300649--1300682 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1300639 ATTTCTTATT
1300649 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
1300665 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
1300683 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:1310860 original size:20 final size:19
Alignment explanation
Indices: 1310835--1310920 Score: 82
Period size: 20 Copynumber: 4.3 Consensus size: 19
1310825 TTTTAGTGCA
*
1310835 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCC-T
*
1310855 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC--T
*
1310876 GAAGGGAAACCGATTCCCCCT
1 G-AGGG-AACCGATACCCCCT
* *
1310897 AAGGGAATCGATACCCCCT
1 GAGGGAACCGATACCCCCT
1310916 GAGGG
1 GAGGG
1310921 TTCTGGTTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
19 16 0.29
20 20 0.36
21 3 0.05
22 4 0.07
23 13 0.23
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (19 bp):
GAGGGAACCGATACCCCCT
Found at i:1316507 original size:40 final size:40
Alignment explanation
Indices: 1316463--1316542 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
1316453 AATTCATGCC
1316463 ATACCTTTCATATCACCACAAGCATATGCATCTTATATAT
1 ATACCTTTCATATCACCACAAGCATATGCATCTTATATAT
1316503 ATACCTTTCATATCACCACAAGCATATGCATCTTATATAT
1 ATACCTTTCATATCACCACAAGCATATGCATCTTATATAT
1316543 TGTATTTGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (40 bp):
ATACCTTTCATATCACCACAAGCATATGCATCTTATATAT
Found at i:1316727 original size:22 final size:21
Alignment explanation
Indices: 1316673--1316728 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
1316663 CATATGAAAT
*
1316673 TTGTCCCAAAAGACCTATGTA
1 TTGTCCCAAAGGACCTATGTA
*
1316694 TTGTCCCGAAGGACC-ACTGTA
1 TTGTCCCAAAGGACCTA-TGTA
1316715 TATGTCCCAAAGGA
1 T-TGTCCCAAAGGA
1316729 GTAGACCCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 18 0.60
22 11 0.37
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
TTGTCCCAAAGGACCTATGTA
Found at i:1322064 original size:22 final size:22
Alignment explanation
Indices: 1322039--1322086 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
1322029 CAGATTTCAA
1322039 ACAGGGAACCGATTCCCCTACT
1 ACAGGGAACCGATTCCCCTACT
*
1322061 ACAGGGAACCGATTCCCCTGCT
1 ACAGGGAACCGATTCCCCTACT
1322083 ACAG
1 ACAG
1322087 TACTGCTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.27, C:0.35, G:0.21, T:0.17
Consensus pattern (22 bp):
ACAGGGAACCGATTCCCCTACT
Found at i:1322868 original size:22 final size:21
Alignment explanation
Indices: 1322816--1322873 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
1322806 CATATGAAAT
1322816 TTGTCCCGAATGACCTATGTA
1 TTGTCCCGAATGACCTATGTA
*
1322837 TTATCCCGAATGACC-ACTGTA
1 TTGTCCCGAATGACCTA-TGTA
*
1322858 TATGTCCCGAAGGACC
1 T-TGTCCCGAATGACC
1322874 GCGTAGACCC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 19 0.59
22 12 0.38
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (21 bp):
TTGTCCCGAATGACCTATGTA
Found at i:1324240 original size:17 final size:17
Alignment explanation
Indices: 1324218--1324251 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1324208 AGCTCTTACG
*
1324218 GGAAGAGGAAGAAGAAA
1 GGAAGAAGAAGAAGAAA
*
1324235 GGAAGAAGAAGATGAAA
1 GGAAGAAGAAGAAGAAA
1324252 TAATTTCATC
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:0.59, C:0.00, G:0.38, T:0.03
Consensus pattern (17 bp):
GGAAGAAGAAGAAGAAA
Found at i:1333377 original size:6 final size:6
Alignment explanation
Indices: 1333366--1333390 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1333356 ACACCCGGCT
1333366 CCGTCC CCGTCC CCGTCC CCGTCC C
1 CCGTCC CCGTCC CCGTCC CCGTCC C
1333391 GTTGCCATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.68, G:0.16, T:0.16
Consensus pattern (6 bp):
CCGTCC
Found at i:1347378 original size:2 final size:2
Alignment explanation
Indices: 1347371--1347395 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1347361 CTATTCTATC
1347371 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1347396 ATAATGAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1349543 original size:57 final size:57
Alignment explanation
Indices: 1349455--1349573 Score: 238
Period size: 57 Copynumber: 2.1 Consensus size: 57
1349445 GATAAAAGTA
1349455 ATTTATAGGAATATATAGATATTGTGATAGCCGGGAACCCAAGTATTGCTACCTGAG
1 ATTTATAGGAATATATAGATATTGTGATAGCCGGGAACCCAAGTATTGCTACCTGAG
1349512 ATTTATAGGAATATATAGATATTGTGATAGCCGGGAACCCAAGTATTGCTACCTGAG
1 ATTTATAGGAATATATAGATATTGTGATAGCCGGGAACCCAAGTATTGCTACCTGAG
1349569 ATTTA
1 ATTTA
1349574 GGGGAAGGGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (57 bp):
ATTTATAGGAATATATAGATATTGTGATAGCCGGGAACCCAAGTATTGCTACCTGAG
Found at i:1352989 original size:23 final size:24
Alignment explanation
Indices: 1352936--1352997 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 24
1352926 ATATTTTAAA
1352936 ATTAAGTTAATATTAAAATATATTT
1 ATTAAGTTAATA-TAAAATATATTT
*
1352961 AATAAGTTAATATAAAAGTAT-TTT
1 ATTAAGTTAATATAAAA-TATATTT
1352985 -TTAAGTTAATATA
1 ATTAAGTTAATATA
1352998 TATATAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 12 0.35
24 8 0.24
25 14 0.41
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
ATTAAGTTAATATAAAATATATTT
Found at i:1356943 original size:2 final size:2
Alignment explanation
Indices: 1356936--1356974 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1356926 ATGAACAATC
1356936 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1356975 GACCTCACGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1359958 original size:21 final size:21
Alignment explanation
Indices: 1359932--1359990 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
1359922 AGGTTATGGG
*
1359932 CATAGTGCATCGATGCACATT
1 CATAGTGCACCGATGCACATT
1359953 CATAGTGCACCGATGCACATT
1 CATAGTGCACCGATGCACATT
1359974 CATAGTGCACCGATGCA
1 CATAGTGCACCGATGCA
1359991 TCAAGGTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (21 bp):
CATAGTGCACCGATGCACATT
Found at i:1361209 original size:30 final size:30
Alignment explanation
Indices: 1361175--1361306 Score: 212
Period size: 30 Copynumber: 4.4 Consensus size: 30
1361165 GGTTCTTCGG
*
1361175 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
1361205 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
1361235 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* *
1361265 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1361294 GACCTCTGGATAG
1 GACCTCTGGATAG
1361307 GTCCTTTGGG
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 21 0.22
30 76 0.78
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:1366971 original size:7 final size:7
Alignment explanation
Indices: 1366959--1366986 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1366949 AAACTAATCA
1366959 CACATCC
1 CACATCC
1366966 CACATCC
1 CACATCC
1366973 CACATCC
1 CACATCC
1366980 CACATCC
1 CACATCC
1366987 AAAAGTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.57, G:0.00, T:0.14
Consensus pattern (7 bp):
CACATCC
Found at i:1375632 original size:61 final size:61
Alignment explanation
Indices: 1375537--1375659 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
1375527 AAAGAATTAC
1375537 AAAGTAACCACCCCCAATGATCTCGTTAAAAAATCTCTCTAAGCCTAAACGGAGGAAAAAG
1 AAAGTAACCACCCCCAATGATCTCGTTAAAAAATCTCTCTAAGCCTAAACGGAGGAAAAAG
1375598 AAAGTAACCACCCCCAATGATCTCGTTAAAAAATCTCTCTAAGCCTAAACGGAGGAAAAAG
1 AAAGTAACCACCCCCAATGATCTCGTTAAAAAATCTCTCTAAGCCTAAACGGAGGAAAAAG
1375659 A
1 A
1375660 GTACATCATG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.18
Consensus pattern (61 bp):
AAAGTAACCACCCCCAATGATCTCGTTAAAAAATCTCTCTAAGCCTAAACGGAGGAAAAAG
Found at i:1381334 original size:12 final size:13
Alignment explanation
Indices: 1381317--1381346 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1381307 GAATTATCAA
1381317 ATATAAATTCT-T
1 ATATAAATTCTAT
1381329 ATATAAATTCTAT
1 ATATAAATTCTAT
1381342 ATATA
1 ATATA
1381347 TATATAGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATAAATTCTAT
Found at i:1384469 original size:25 final size:25
Alignment explanation
Indices: 1384415--1384463 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
1384405 GCAGGGAAAG
*
1384415 CTGGTGACGATAAAGAAGTCATCGC
1 CTGGTGACGATAAAAAAGTCATCGC
*
1384440 CTGGTGACGCTAAAAAAGTCATCG
1 CTGGTGACGATAAAAAAGTCATCG
1384464 GGTGGTCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (25 bp):
CTGGTGACGATAAAAAAGTCATCGC
Found at i:1389035 original size:13 final size:13
Alignment explanation
Indices: 1389017--1389041 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1389007 ATCCACATTA
1389017 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
1389030 TTTTCTTTTTTT
1 TTTTCTTTTTTT
1389042 TAATTTTATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:1389770 original size:2 final size:2
Alignment explanation
Indices: 1389763--1389794 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1389753 ATAATTAATC
*
1389763 AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1389795 GGTCGAGCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1392587 original size:3 final size:3
Alignment explanation
Indices: 1392579--1392606 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1392569 GAATTGGGTT
1392579 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1392607 ATATATGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:1395119 original size:27 final size:27
Alignment explanation
Indices: 1395089--1395142 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1395079 CAAGTCGTAT
1395089 ATCATCTTCTTTAACTCACTGAAACCA
1 ATCATCTTCTTTAACTCACTGAAACCA
*
1395116 ATCATCTTCTTTAACTCATTGAAACCA
1 ATCATCTTCTTTAACTCACTGAAACCA
1395143 CGTAGTTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (27 bp):
ATCATCTTCTTTAACTCACTGAAACCA
Found at i:1395446 original size:2 final size:2
Alignment explanation
Indices: 1395435--1395486 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1395425 TATCGTTGCT
1395435 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1395476 TA TA TA TA TA T
1 TA TA TA TA TA T
1395487 GGCTATCCAT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1395885 original size:12 final size:12
Alignment explanation
Indices: 1395868--1395895 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1395858 ACCGTTAATA
1395868 AATTAAATTTAT
1 AATTAAATTTAT
1395880 AATTAAATTTAT
1 AATTAAATTTAT
1395892 AATT
1 AATT
1395896 TATTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTAAATTTAT
Found at i:1396167 original size:51 final size:50
Alignment explanation
Indices: 1396101--1396294 Score: 210
Period size: 51 Copynumber: 3.8 Consensus size: 50
1396091 AGATATATAT
* * *
1396101 ACTTACAACGGTGTAAGTATGTGTTAAGTGCTACATTTTTTTATTTTATTT
1 ACTTAC-ACGTTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
* * * *
1396152 ACTTGCATCGTTGTAAATATGTGTTAAGTGATACACTTTTTTGTTTTATTC
1 ACTTACA-CGTTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
* * *
1396203 ATTTACAC-TGTGTAAGTATGTGTTAAGTACTACACTTATTTATTTTATTC
1 ACTTACACGT-TGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
* ** * *
1396253 ACTTACACCGGTGTAAGTACATGTTAAGTGCTATATTTTTTT
1 ACTTACA-CGTTGTAAGTATGTGTTAAGTGCTACACTTTTTT
1396295 GTAGTATGAA
Statistics
Matches: 117, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
49 1 0.01
50 43 0.37
51 73 0.62
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (50 bp):
ACTTACACGTTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
Found at i:1396293 original size:101 final size:101
Alignment explanation
Indices: 1396111--1396296 Score: 255
Period size: 101 Copynumber: 1.8 Consensus size: 101
1396101 ACTTACAACG
* * * * * * * **
1396111 GTGTAAGTATGTGTTAAGTGCTACATTTTTTTATTTTATTTACTTGCATCGTTGTAAATATGTGT
1 GTGTAAGTATGTGTTAAGTACTACACTTATTTATTTTATTCACTTACACCGGTGTAAATACATGT
1396176 TAAGTGATACACTTTTTTGTTTTATTCATTTACACT
66 TAAGTGATACACTTTTTTGTTTTATTCATTTACACT
*
1396212 GTGTAAGTATGTGTTAAGTACTACACTTATTTATTTTATTCACTTACACCGGTGTAAGTACATGT
1 GTGTAAGTATGTGTTAAGTACTACACTTATTTATTTTATTCACTTACACCGGTGTAAATACATGT
* * *
1396277 TAAGTGCTATATTTTTTTGT
66 TAAGTGATACACTTTTTTGT
1396297 AGTATGAATT
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
101 72 1.00
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.49
Consensus pattern (101 bp):
GTGTAAGTATGTGTTAAGTACTACACTTATTTATTTTATTCACTTACACCGGTGTAAATACATGT
TAAGTGATACACTTTTTTGTTTTATTCATTTACACT
Found at i:1396577 original size:14 final size:14
Alignment explanation
Indices: 1396560--1396606 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1396550 AATTATTTAA
1396560 TAATTTTTTTTATT
1 TAATTTTTTTTATT
* * *
1396574 TAATTGTATTTATA
1 TAATTTTTTTTATT
*
1396588 TAAATTTTTTTA-T
1 TAATTTTTTTTATT
1396601 TAATTT
1 TAATTT
1396607 AGGATAAGTA
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
13 5 0.20
14 20 0.80
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (14 bp):
TAATTTTTTTTATT
Found at i:1396583 original size:27 final size:27
Alignment explanation
Indices: 1396553--1396605 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1396543 TAATAAAAAT
*
1396553 TATTTA-ATAATTTTTTTTATTTAATTG
1 TATTTATATAAATTTTTTTA-TTAATTG
1396580 TATTTATATAAATTTTTTTATTAATT
1 TATTTATATAAATTTTTTTATTAATT
1396606 TAGGATAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (27 bp):
TATTTATATAAATTTTTTTATTAATTG
Found at i:1397579 original size:28 final size:28
Alignment explanation
Indices: 1397548--1397605 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
1397538 TAAAATTATC
* * *
1397548 TTTTTTGTCACAATAAATACCTAAAGTA
1 TTTTATGTCAAAATAAATACCTAAACTA
**
1397576 TTTTATGTCAAAATAGGTACCTAAACTA
1 TTTTATGTCAAAATAAATACCTAAACTA
1397604 TT
1 TT
1397606 CAAACTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.40
Consensus pattern (28 bp):
TTTTATGTCAAAATAAATACCTAAACTA
Found at i:1397797 original size:30 final size:30
Alignment explanation
Indices: 1397756--1397816 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
1397746 GGGCAGTGCG
1397756 AGAAAAATTATTTT-GAGGTGTCAAATTTAA
1 AGAAAAATTATTTTAG-GGTGTCAAATTTAA
*
1397786 AGAAAATTTATTTTAGGGTGTCAAATTTAA
1 AGAAAAATTATTTTAGGGTGTCAAATTTAA
1397816 A
1 A
1397817 AATGGTGAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (30 bp):
AGAAAAATTATTTTAGGGTGTCAAATTTAA
Found at i:1397887 original size:20 final size:20
Alignment explanation
Indices: 1397862--1397899 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1397852 TGATTAATGT
1397862 GTGTCAAT-TTATGTTTAAGG
1 GTGTCAATATTAT-TTTAAGG
1397882 GTGTCAATATTATTTTAA
1 GTGTCAATATTATTTTAA
1397900 AATATGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.47
Consensus pattern (20 bp):
GTGTCAATATTATTTTAAGG
Found at i:1411288 original size:24 final size:24
Alignment explanation
Indices: 1411214--1411288 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
1411204 AGCACTTCCA
1411214 CTTCACCAGGGGAAGCAATCCCAT
1 CTTCACCAGGGGAAGCAATCCCAT
* * * **
1411238 CTT--CCAGCAGCAAGCGATAGGCA-
1 CTTCACCAG-GGGAAGCAAT-CCCAT
1411261 CTTCACCAGGGGAAGCAATCCCAT
1 CTTCACCAGGGGAAGCAATCCCAT
1411285 CTTC
1 CTTC
1411289 CAAAAGCCCT
Statistics
Matches: 36, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
22 4 0.11
23 12 0.33
24 16 0.44
25 4 0.11
ACGTcount: A:0.28, C:0.33, G:0.21, T:0.17
Consensus pattern (24 bp):
CTTCACCAGGGGAAGCAATCCCAT
Found at i:1413277 original size:19 final size:20
Alignment explanation
Indices: 1413253--1413327 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 20
1413243 GACCCGACTC
1413253 AAAATAATATATTTATT-AA
1 AAAATAATATATTTATTAAA
*
1413272 AAAATATTAT-TTATATTCAATA
1 AAAATAATATATT-TATT-AA-A
1413294 AAAATAA-ATATTTAATTGAAA
1 AAAATAATATATTT-ATT-AAA
1413315 TAAAATAATATAT
1 -AAAATAATATAT
1413328 AGAGGGGTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
18 2 0.04
19 13 0.29
21 5 0.11
22 21 0.47
23 4 0.09
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (20 bp):
AAAATAATATATTTATTAAA
Found at i:1413282 original size:17 final size:17
Alignment explanation
Indices: 1413253--1413285 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1413243 GACCCGACTC
1413253 AAAATAATATATTTATT
1 AAAATAATATATTTATT
1413270 AAAA-AATATTATTTAT
1 AAAATAATA-TATTTAT
1413286 ATTCAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATAATATATTTATT
Found at i:1432475 original size:58 final size:60
Alignment explanation
Indices: 1432400--1432516 Score: 150
Period size: 58 Copynumber: 2.0 Consensus size: 60
1432390 TTGAAGATTA
**
1432400 ATTTGGAATATTCAAAAGTTTGGGGACCAACATAGAATGA-G-TCATAGCTTAGGGATGG
1 ATTTGGAATATTCAAAAGTTTGAAGACCAACATAGAATGAGGATCATAGCTTAGGGATGG
** * *
1432458 ATTTGGAATA-TCTAAAAGTTTGAAGACCAATTTAGAATTAGGATCATAGTTTAGGGATG
1 ATTTGGAATATTC-AAAAGTTTGAAGACCAACATAGAATGAGGATCATAGCTTAGGGATG
1432517 TGTGGTTCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
57 2 0.04
58 32 0.64
59 1 0.02
60 15 0.30
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.31
Consensus pattern (60 bp):
ATTTGGAATATTCAAAAGTTTGAAGACCAACATAGAATGAGGATCATAGCTTAGGGATGG
Found at i:1448084 original size:319 final size:315
Alignment explanation
Indices: 1447567--1448169 Score: 918
Period size: 319 Copynumber: 1.9 Consensus size: 315
1447557 TAAAAATAAA
* * * * *
1447567 AAAATATTAAAATAAACTTTTACTTATAATTGATAGATTAAATAAATTATTATTTATTTTTTAAA
1 AAAATATAAAAATAAACTTTTAATTACAATTGATAGATCAAATAAATTATTATTCATTTTTTAAA
* ***
1447632 AAAGCAATAAAAATTAAATTTGAATAAAATTCAATAAAAAAGAATATAAAACTAAAAAATATCAC
66 AAAGCAATAAAAATGAAATAAAAATAAAATTCAATAAAAAAGAATATAAAACTAAAAAATATCAC
* * *
1447697 CTCTTTATTTAAAATATTCTTTATAATATTAATTTTAAAAAATATAACATAAATATTAAATTCTA
131 CTCTTTATTTAAAATATTCTTTATAATATTAATTTTAAAAAATATAAAACAAATATAAAATTCTA
** *
1447762 ATTTTATTAAAAATTAATAAACATTATTAACTGTTGTTAAAAAATTTAAAAGTTTATCTTAATAT
196 ATTTTATTAAAAACGAATAAACATTATTAACTGCTGTTAAAAAATTTAAAAGTTTATCTTAATAT
*
1447827 TTTTTATATTTTTAAACAATTAATAATGTTTATTTACTTTTAATATTAATTATTT
261 TTTTTATATTTTTAAAAAATTAATAATGTTTATTTACTTTTAATATTAATTATTT
*
1447882 AAAATATAAAAATAAACTTTTAATTACAATTGATAGATCAAATGAATTATTATTCACTTTTTTAA
1 AAAATATAAAAATAAACTTTTAATTACAATTGATAGATCAAATAAATTATTATTCA-TTTTTTAA
* * * * *
1447947 AAAATCAATAAAAATGCAATAAAAAGTTAAAATTCAATAAAAAAATAATATAAATCTAAAACATA
65 AAAAGCAATAAAAATGAAATAAAAA--TAAAATTCAAT-AAAAAAGAATATAAAACTAAAAAATA
* * * *
1448012 TCCCCTCTTTTTTTAAAATATTTTTTATAATATTAATTTTTAAAAATATAAAACAAATATAAAAT
127 TCACCTCTTTATTTAAAATATTCTTTATAATATTAATTTTAAAAAATATAAAACAAATATAAAAT
* *
1448077 TCTAATTTTATTAAAAACGAATAAACATTATTAACTGCTGTTAAAAATTTTAAAAGTTTATTTTA
192 TCTAATTTTATTAAAAACGAATAAACATTATTAACTGCTGTTAAAAAATTTAAAAGTTTATCTTA
1448142 ATATTTTTTATATTTTTAAAAAATTAAT
257 ATATTTTTTATATTTTTAAAAAATTAAT
1448170 TTTAAAAGTA
Statistics
Matches: 256, Mismatches: 28, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
315 50 0.20
316 27 0.11
318 11 0.04
319 168 0.66
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (315 bp):
AAAATATAAAAATAAACTTTTAATTACAATTGATAGATCAAATAAATTATTATTCATTTTTTAAA
AAAGCAATAAAAATGAAATAAAAATAAAATTCAATAAAAAAGAATATAAAACTAAAAAATATCAC
CTCTTTATTTAAAATATTCTTTATAATATTAATTTTAAAAAATATAAAACAAATATAAAATTCTA
ATTTTATTAAAAACGAATAAACATTATTAACTGCTGTTAAAAAATTTAAAAGTTTATCTTAATAT
TTTTTATATTTTTAAAAAATTAATAATGTTTATTTACTTTTAATATTAATTATTT
Found at i:1452911 original size:26 final size:26
Alignment explanation
Indices: 1452882--1452934 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
1452872 AATACAATGT
1452882 AAAAAAA-TATTCAAATGGAGTGGTGG
1 AAAAAAAGT-TTCAAATGGAGTGGTGG
*
1452908 AAAAAAAGTTTCAAATGGGGTGGTGG
1 AAAAAAAGTTTCAAATGGAGTGGTGG
1452934 A
1 A
1452935 GACGTATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.43, C:0.04, G:0.30, T:0.23
Consensus pattern (26 bp):
AAAAAAAGTTTCAAATGGAGTGGTGG
Found at i:1456275 original size:23 final size:23
Alignment explanation
Indices: 1456240--1456289 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1456230 GTTATGTTCA
*
1456240 ATTTAGTTCATACATTTATCAAT
1 ATTTAGTTCATACATTTACCAAT
* *
1456263 ATTTGGTTTATACATTTACCAAT
1 ATTTAGTTCATACATTTACCAAT
1456286 ATTT
1 ATTT
1456290 CAAATGGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.12, G:0.06, T:0.50
Consensus pattern (23 bp):
ATTTAGTTCATACATTTACCAAT
Found at i:1457665 original size:6 final size:6
Alignment explanation
Indices: 1457581--1457662 Score: 121
Period size: 6 Copynumber: 13.8 Consensus size: 6
1457571 CGGTGAAGAA
*
1457581 GAAAGA GAAAGG G-AAGG GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG
1 GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG
* * *
1457628 GAAAGA GAAAGA GAAAGG GAAAGG GAAAGA GAAAG
1 GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG GAAAG
1457663 AGAGGGAAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
5 5 0.07
6 66 0.93
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (6 bp):
GAAAGG
Found at i:1459325 original size:17 final size:16
Alignment explanation
Indices: 1459279--1459329 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
1459269 CTCGTGTCAC
*
1459279 ATTTATATATTTTTTAAA
1 ATTTAT-TA-TTTTAAAA
*
1459297 ATTTTTTA-TTTAAAA
1 ATTTATTATTTTAAAA
1459312 ATATTATTATTTTAAAA
1 AT-TTATTATTTTAAAA
1459329 A
1 A
1459330 ACTCAAATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 8 0.29
16 5 0.18
17 10 0.36
18 5 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTATTATTTTAAAA
Found at i:1460781 original size:22 final size:23
Alignment explanation
Indices: 1460756--1460806 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1460746 TATATTTTAG
1460756 AAAAATTATAT-GA-AATAATTAT
1 AAAAATTATATCGATAAT-ATTAT
* *
1460778 AAAAAATATATCTATAATATTAT
1 AAAAATTATATCGATAATATTAT
1460801 AAAAAT
1 AAAAAT
1460807 ATTTATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 10 0.42
23 11 0.46
24 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
AAAAATTATATCGATAATATTAT
Found at i:1460817 original size:22 final size:21
Alignment explanation
Indices: 1460773--1460842 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 21
1460763 ATATGAAATA
*
1460773 ATTATAAAAAATATATCTATAAT
1 ATTATAAAAAATTTAT-T-TAAT
1460796 ATTATAAAAATATTTATTTAAT
1 ATTATAAAAA-ATTTATTTAAT
* *
1460818 TTTA-AAATAAAATTATTT-AT
1 ATTATAAA-AAATTTATTTAAT
1460838 ATTAT
1 ATTAT
1460843 TTTTAAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 5 0.12
21 10 0.25
22 9 0.22
23 11 0.28
24 5 0.12
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTATAAAAAATTTATTTAAT
Found at i:1460834 original size:25 final size:26
Alignment explanation
Indices: 1460799--1460849 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
1460789 CTATAATATT
1460799 ATAAAAATATTTAT-TTAATTTTAAA
1 ATAAAAATATTTATATTAATTTTAAA
* *
1460824 ATAAAATTATTTATATTATTTTTAAA
1 ATAAAAATATTTATATTAATTTTAAA
1460850 TTATCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATAAAAATATTTATATTAATTTTAAA
Found at i:1460852 original size:20 final size:19
Alignment explanation
Indices: 1460827--1460874 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1460817 TTTTAAAATA
*
1460827 AAATTATTTATATTATTTTT
1 AAATTATTTAT-TTAATTTT
*
1460847 AAATTATCTATTTAATTTT
1 AAATTATTTATTTAATTTT
*
1460866 AAATAATTT
1 AAATTATTT
1460875 TAAGTTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
AAATTATTTATTTAATTTT
Found at i:1460867 original size:19 final size:20
Alignment explanation
Indices: 1460827--1460869 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1460817 TTTTAAAATA
* *
1460827 AAATTATTTATATTATTTTT
1 AAATTATCTATATTAATTTT
1460847 AAATTATCTAT-TTAATTTT
1 AAATTATCTATATTAATTTT
1460866 AAAT
1 AAAT
1460870 AATTTTAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
AAATTATCTATATTAATTTT
Found at i:1460989 original size:23 final size:23
Alignment explanation
Indices: 1460963--1461007 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1460953 AGTTTTAAAA
1460963 TAATATTATATAAAATAAATAAT
1 TAATATTATATAAAATAAATAAT
* *
1460986 TAATATTATTTCAAATAAATAA
1 TAATATTATATAAAATAAATAA
1461008 CCAATGTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TAATATTATATAAAATAAATAAT
Found at i:1461019 original size:23 final size:23
Alignment explanation
Indices: 1460975--1461019 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1460965 ATATTATATA
** *
1460975 AAATAAATAATTAATATTATTTC
1 AAATAAATAACCAATATGATTTC
*
1460998 AAATAAATAACCAATGTGATTT
1 AAATAAATAACCAATATGATTT
1461020 TAAAAATTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (23 bp):
AAATAAATAACCAATATGATTTC
Found at i:1461084 original size:21 final size:25
Alignment explanation
Indices: 1461030--1461111 Score: 67
Period size: 21 Copynumber: 3.7 Consensus size: 25
1461020 TAAAAATTAA
* *
1461030 ATAAATAT-TTTAAA-AT-AATTTC
1 ATAAATATATATAAATATAAATTTT
*
1461052 AT-AATAT-TATAAATAT-ACTTTT
1 ATAAATATATATAAATATAAATTTT
1461074 -TAAA-ATA-AT-AATATAAATTTT
1 ATAAATATATATAAATATAAATTTT
1461095 ATAAATATATATAAATA
1 ATAAATATATATAAATA
1461112 ATTATTTAGT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
20 5 0.10
21 20 0.42
22 14 0.29
23 3 0.06
24 2 0.04
25 4 0.08
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
ATAAATATATATAAATATAAATTTT
Found at i:1461108 original size:19 final size:20
Alignment explanation
Indices: 1461071--1461110 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
1461061 TAAATATACT
1461071 TTTTAAAATAATAATATAAA
1 TTTTAAAATAATAATATAAA
1461091 TTTTATAAAT-AT-ATATAAA
1 TTTTA-AAATAATAATATAAA
1461110 T
1 T
1461111 AATTATTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 7 0.37
21 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTTAAAATAATAATATAAA
Found at i:1461904 original size:7 final size:7
Alignment explanation
Indices: 1461892--1461919 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1461882 CGACCATGAC
1461892 GATTCAG
1 GATTCAG
1461899 GATTCAG
1 GATTCAG
1461906 GATTCAG
1 GATTCAG
1461913 GATTCAG
1 GATTCAG
1461920 AATGGAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (7 bp):
GATTCAG
Found at i:1462144 original size:19 final size:19
Alignment explanation
Indices: 1462120--1462159 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1462110 GGTAATTTGT
1462120 TTTATTT-TGGAATATCCAA
1 TTTATTTGT-GAATATCCAA
*
1462139 TTTATTTGTGAATATTCAA
1 TTTATTTGTGAATATCCAA
1462158 TT
1 TT
1462160 AAAATTAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (19 bp):
TTTATTTGTGAATATCCAA
Found at i:1463867 original size:19 final size:19
Alignment explanation
Indices: 1463843--1463882 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1463833 GGTAATTTGT
1463843 TTTATTT-TGTAATATCCAA
1 TTTATTTGTG-AATATCCAA
*
1463862 TTTATTTGTGAATATTCAA
1 TTTATTTGTGAATATCCAA
1463881 TT
1 TT
1463883 AAAATTAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (19 bp):
TTTATTTGTGAATATCCAA
Found at i:1465595 original size:19 final size:19
Alignment explanation
Indices: 1465571--1465610 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1465561 GGTAATTTGT
1465571 TTTATTT-TGGAATATCCAA
1 TTTATTTGT-GAATATCCAA
*
1465590 TTTATTTGTGAATATTCAA
1 TTTATTTGTGAATATCCAA
1465609 TT
1 TT
1465611 AAAATTAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (19 bp):
TTTATTTGTGAATATCCAA
Found at i:1465847 original size:13 final size:13
Alignment explanation
Indices: 1465829--1465854 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1465819 TATATTGCTC
1465829 CGTGGAATGTTGA
1 CGTGGAATGTTGA
1465842 CGTGGAATGTTGA
1 CGTGGAATGTTGA
1465855 TGGAAGGGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.38, T:0.31
Consensus pattern (13 bp):
CGTGGAATGTTGA
Found at i:1467327 original size:19 final size:19
Alignment explanation
Indices: 1467303--1467342 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1467293 GGTAATTTGT
1467303 TTTATTT-TGGAATATCCAA
1 TTTATTTGT-GAATATCCAA
*
1467322 TTTATTTGTGAATATTCAA
1 TTTATTTGTGAATATCCAA
1467341 TT
1 TT
1467343 AAAATTAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (19 bp):
TTTATTTGTGAATATCCAA
Found at i:1483257 original size:20 final size:20
Alignment explanation
Indices: 1483246--1483372 Score: 211
Period size: 20 Copynumber: 6.4 Consensus size: 20
1483236 GCAACACAGA
1483246 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
* *
1483266 AGTCAAATTCGCAACAC-AA
1 AGTCAAATTCGCAACGCGAT
1483285 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
*
1483305 AGTCAAATTCGTAACGCGAT
1 AGTCAAATTCGCAACGCGAT
1483325 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
*
1483345 AGTCAAATTCGCAACGCGAA
1 AGTCAAATTCGCAACGCGAT
1483365 AGTCAAAT
1 AGTCAAAT
1483373 GTTTTTACGC
Statistics
Matches: 99, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
19 17 0.17
20 82 0.83
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAT
Found at i:1483637 original size:16 final size:18
Alignment explanation
Indices: 1483618--1483652 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1483608 TAATCTATTA
1483618 TTTTTATT-TT-GATTTT
1 TTTTTATTATTAGATTTT
1483634 TTTTTATTATTAGATTTT
1 TTTTTATTATTAGATTTT
1483652 T
1 T
1483653 CTTATATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 2 0.12
18 7 0.41
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (18 bp):
TTTTTATTATTAGATTTT
Found at i:1483902 original size:20 final size:20
Alignment explanation
Indices: 1483852--1483902 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1483842 TCGCAACGCG
* *
1483852 ATTTTAGTTTCGCGTTGTGA
1 ATTTAAGTTTCGCGTTGCGA
* * *
1483872 TTTTCATTTTCGCGTTGCGA
1 ATTTAAGTTTCGCGTTGCGA
1483892 ATTTAAGTTTC
1 ATTTAAGTTTC
1483903 AGAAACTTCT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.51
Consensus pattern (20 bp):
ATTTAAGTTTCGCGTTGCGA
Found at i:1484319 original size:23 final size:23
Alignment explanation
Indices: 1484276--1484388 Score: 83
Period size: 22 Copynumber: 4.8 Consensus size: 23
1484266 TAATTATTAA
* *
1484276 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
1484297 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
1484320 -ATATTTTTAATATTATATAAATAATC
1 AATATTTATAATA--ATAT-AAT-ATT
1484346 AATTATATTATAATAATATAAGATATT
1 AA-TAT-TTATAATAATAT-A-ATATT
1484373 -ATATTT-TAATAATATA
1 AATATTTATAATAATATA
1484389 TAATAAATTT
Statistics
Matches: 76, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
21 11 0.14
22 16 0.21
23 13 0.17
24 6 0.08
25 6 0.08
26 3 0.04
27 9 0.12
28 5 0.07
29 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:1484351 original size:30 final size:32
Alignment explanation
Indices: 1484287--1484364 Score: 92
Period size: 30 Copynumber: 2.5 Consensus size: 32
1484277 ATATTTAAAA
1484287 TATATTTATTAATATTTATAATAATATAATAT
1 TATATTTATTAATATTTATAATAATATAATAT
1484319 TATATTT-TTAATA-TTAT-ATAA-ATAATCAAT
1 TATATTTATTAATATTTATAATAATATAAT--AT
*
1484349 TATATTATAATAATAT
1 TATATT-TATTAATAT
1484365 AAGATATTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
28 5 0.12
29 4 0.10
30 12 0.30
31 7 0.17
32 12 0.30
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAATATAATAT
Found at i:1484363 original size:32 final size:31
Alignment explanation
Indices: 1484287--1484364 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 31
1484277 ATATTTAAAA
1484287 TATATTTATTAATATTTATAATAATATAATAT
1 TATATTTATTAATA-TTATAATAATATAATAT
1484319 TATATTT-TTAATATTAT-ATAA-ATAATCAAT
1 TATATTTATTAATATTATAATAATATAAT--AT
*
1484349 TATATTATAATAATAT
1 TATATT-TATTAATAT
1484365 AAGATATTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
28 5 0.12
29 4 0.10
30 12 0.29
31 7 0.17
32 13 0.32
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (31 bp):
TATATTTATTAATATTATAATAATATAATAT
Found at i:1484413 original size:51 final size:53
Alignment explanation
Indices: 1484298--1484444 Score: 142
Period size: 52 Copynumber: 2.7 Consensus size: 53
1484288 ATATTTATTA
*
1484298 ATAT-TTATAATAATATAATATTATATTTTTAATATTATATAAATAATCAA-T
1 ATATATTATAATAATATAATATTATATTTTTAATAATATATAAATAATCAATT
***
1484349 -TATATTATAATAATATAAGATATTATA-TTTTAATAATATAT-AATAAATTTTTT
1 ATATATTATAATAATAT-A-ATATTATATTTTTAATAATATATAAAT-AATCAATT
* *
1484402 ATATATTATAATGAATAATATTATTTATATATTTCAATAATAT
1 ATATATTATAAT-AAT-ATAATA-TTATAT-TTTTAATAATAT
1484445 TTTAGTAAAG
Statistics
Matches: 79, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
50 3 0.04
51 15 0.19
52 17 0.22
53 9 0.11
54 13 0.16
55 9 0.11
56 2 0.03
57 11 0.14
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (53 bp):
ATATATTATAATAATATAATATTATATTTTTAATAATATATAAATAATCAATT
Found at i:1484688 original size:20 final size:20
Alignment explanation
Indices: 1484610--1484679 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
1484600 TTTCCAGATG
1484610 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1484630 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
1484650 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1484670 TTTTCCAGAA
1 TTTTCCAGAA
1484680 TTCAAATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:1484688 original size:40 final size:40
Alignment explanation
Indices: 1484610--1484688 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
1484600 TTTCCAGATG
* **
1484610 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
1484650 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
1484689 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:1484698 original size:15 final size:15
Alignment explanation
Indices: 1484662--1484728 Score: 82
Period size: 15 Copynumber: 4.5 Consensus size: 15
1484652 TTACAGAAAT
**
1484662 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
1484677 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
** *
1484691 GTAATTCATTTTTCA
1 GTAATTCAAATTCCA
1484706 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
1484721 GTAATTCA
1 GTAATTCA
1484729 TTTTCTGGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
14 12 0.28
15 31 0.72
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.40
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:1484712 original size:30 final size:29
Alignment explanation
Indices: 1484662--1484733 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 29
1484652 TTACAGAAAT
1484662 GTAATTCATTTTCCAGAATTCAAATTCCA
1 GTAATTCATTTTCCAGAATTCAAATTCCA
*
1484691 GTAATTCATTTTTCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAG-AATTCAAATTCCA
1484721 GTAATTCATTTTC
1 GTAATTCATTTTC
1484734 TGGAAAACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 15 0.38
30 25 0.62
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (29 bp):
GTAATTCATTTTCCAGAATTCAAATTCCA
Found at i:1484746 original size:29 final size:30
Alignment explanation
Indices: 1484662--1484746 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 30
1484652 TTACAGAAAT
* **
1484662 GTAATTCATTTTCCA-GAATTCAAATTCCA
1 GTAATTCATTTTTCAGGAAAACAAATTCCA
* **
1484691 GTAATTCATTTTTCAGTAATTCAAATTCCA
1 GTAATTCATTTTTCAGGAAAACAAATTCCA
* *
1484721 GTAATTCA-TTTTCTGGAAAACCAATT
1 GTAATTCATTTTTCAGGAAAACAAATT
1484747 ACAGCTAAAC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 27 0.56
30 21 0.44
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.40
Consensus pattern (30 bp):
GTAATTCATTTTTCAGGAAAACAAATTCCA
Found at i:1486842 original size:42 final size:42
Alignment explanation
Indices: 1486795--1486893 Score: 126
Period size: 42 Copynumber: 2.4 Consensus size: 42
1486785 GATGCACCTA
* * *
1486795 TCATCATTCAAGAGGCGCCTCCTATCGTTCAAGAGGCCCCTC
1 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
* * *
1486837 TCATCATTGAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
* *
1486879 TCATCGTTTAAGAGG
1 TCATCATTCAAGAGG
1486894 TCATGCCCTC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.23
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
Found at i:1486886 original size:21 final size:21
Alignment explanation
Indices: 1486795--1486893 Score: 101
Period size: 21 Copynumber: 4.7 Consensus size: 21
1486785 GATGCACCTA
* *
1486795 TCATCATTCAAGAGGCGCCTC
1 TCATCGTTCAAGAGGCCCCTC
1486816 -CTATCGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
* * *
1486837 TCATCATTGAAGAAGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
1486858 CCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
*
1486879 TCATCGTTTAAGAGG
1 TCATCGTTCAAGAGG
1486894 TCATGCCCTC
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
20 1 0.02
21 60 0.97
22 1 0.02
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1488333 original size:14 final size:14
Alignment explanation
Indices: 1488314--1488343 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1488304 TTTTGATTAA
1488314 TTGATTTATAAAAG
1 TTGATTTATAAAAG
*
1488328 TTGATTTGTAAAAG
1 TTGATTTATAAAAG
1488342 TT
1 TT
1488344 TGATGTGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.47
Consensus pattern (14 bp):
TTGATTTATAAAAG
Found at i:1488358 original size:62 final size:63
Alignment explanation
Indices: 1488264--1488402 Score: 167
Period size: 66 Copynumber: 2.2 Consensus size: 63
1488254 TTTTACATTG
**
1488264 AAAGTTGATTTGTTTAATTGATGAGGAAATAAG-ATT-TATTTT-TTGATTAATTGATTTATA
1 AAAGTTGATTTGTAAAATTGATGAGGAAATAAGAATTATATTTTCTTGATTAATTGATTTATA
* * * * *
1488324 AAAGTTGATTTGTAAAAGTTTGATGTGTAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTAAAA--TTGATGAGGAAATAAGAATTATATTTT-CTTGATTAATTGATTTAT
1488389 A
63 A
1488390 AAAGTTGATTTGT
1 AAAGTTGATTTGT
1488403 TGTTTCTAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
60 15 0.23
62 14 0.21
63 3 0.05
64 5 0.08
66 29 0.44
ACGTcount: A:0.33, C:0.01, G:0.18, T:0.48
Consensus pattern (63 bp):
AAAGTTGATTTGTAAAATTGATGAGGAAATAAGAATTATATTTTCTTGATTAATTGATTTATA
Found at i:1488742 original size:39 final size:39
Alignment explanation
Indices: 1488685--1488771 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
1488675 TCAAGTTGTA
*
1488685 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCGTTTGCTTGGCACCATATGAGATTTG
*
1488724 GATTTTGATTTCCGTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCGTTTGCTTGGCACCATATGAGATTTG
1488763 GATTTTGAT
1 GATTTTGAT
1488772 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.15, G:0.22, T:0.46
Consensus pattern (39 bp):
GATTTTGATTTCCGTTTGCTTGGCACCATATGAGATTTG
Found at i:1489104 original size:18 final size:18
Alignment explanation
Indices: 1489081--1489117 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1489071 CGAAATTTAT
1489081 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1489099 ATTGAAATTGAAATTCAA
1 ATTGAAATTCAAACTCAA
1489117 A
1 A
1489118 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1489627 original size:20 final size:20
Alignment explanation
Indices: 1489602--1489651 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1489592 GCAACGCTTA
*
1489602 TTTCGCGTTGCGAATTTAAC
1 TTTCGCGTTGCCAATTTAAC
*
1489622 TTTCGCGTTGCCAATTTGAC
1 TTTCGCGTTGCCAATTTAAC
1489642 TTTCGCGTTG
1 TTTCGCGTTG
1489652 ATCGCAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.42
Consensus pattern (20 bp):
TTTCGCGTTGCCAATTTAAC
Found at i:1492240 original size:24 final size:24
Alignment explanation
Indices: 1492213--1492266 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1492203 CCATCACATC
*
1492213 ATCAAAATCCGAGTATTCCCCAAG
1 ATCAAAATCCGAGTATTCACCAAG
* * * *
1492237 ATCAAAGTTCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTCACCAAG
1492261 ATCAAA
1 ATCAAA
1492267 TTTCGAATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTCACCAAG
Found at i:1492280 original size:24 final size:24
Alignment explanation
Indices: 1492232--1492280 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1492222 CGAGTATTCC
** *
1492232 CCAAGATCAAAGTTCGGGTATTGA
1 CCAAGATCAAAGTTCGAATACTGA
*
1492256 CCAAGATCAAATTTCGAATACTGA
1 CCAAGATCAAAGTTCGAATACTGA
1492280 C
1 C
1492281 TAGTACTCAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.24
Consensus pattern (24 bp):
CCAAGATCAAAGTTCGAATACTGA
Found at i:1493563 original size:64 final size:65
Alignment explanation
Indices: 1493416--1493571 Score: 178
Period size: 64 Copynumber: 2.4 Consensus size: 65
1493406 GAAGGTGTAT
** *
1493416 CGATGCACAAGTAGTGCATCGATGCA-CTCTTTTAAAATAAAAAAGATCGAATGCAATTAGTGCA
1 CGATGCACAAGTAGTGCATCGATGCATCTCCATTAAAAT-AAAAACATCGAATGCAATTAGTGCA
*
1493480 T
65 C
* * *
1493481 CGATGCATAAGGCA-TGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCATTTTA-TG
1 CGATGCACAA-GTAGTGCATCGATGCATCTCCATTAA-AATAAAAACATCGAATGCA-ATTAGTG
1493542 CAC
63 CAC
1493545 CGATGCACAAGTAGTGCATCGATGCAT
1 CGATGCACAAGTAGTGCATCGATGCAT
1493572 ACCTTCATTA
Statistics
Matches: 77, Mismatches: 9, Indels: 11
0.79 0.09 0.11
Matches are distributed among these distances:
63 2 0.03
64 40 0.52
65 29 0.38
66 6 0.08
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (65 bp):
CGATGCACAAGTAGTGCATCGATGCATCTCCATTAAAATAAAAACATCGAATGCAATTAGTGCAC
Found at i:1493988 original size:29 final size:29
Alignment explanation
Indices: 1493949--1494058 Score: 195
Period size: 29 Copynumber: 3.8 Consensus size: 29
1493939 TATGTGATAT
1493949 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
1493979 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
1494008 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
1494037 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
1494059 ACATATAAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
28 7 0.09
29 66 0.85
30 5 0.06
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:1494175 original size:15 final size:15
Alignment explanation
Indices: 1494143--1494176 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1494133 GAGGGTATAA
*
1494143 TAGTCCTTCGGGACG
1 TAGTCCTTCGAGACG
*
1494158 TAGTCCTTCGAGATG
1 TAGTCCTTCGAGACG
1494173 TAGT
1 TAGT
1494177 GGTCCTACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCGAGACG
Found at i:1495220 original size:14 final size:15
Alignment explanation
Indices: 1495184--1495221 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1495174 GAAATCATTG
1495184 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
1495199 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
1495214 AAAAATTA
1 AAAAATTA
1495222 GAAATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:1495384 original size:19 final size:19
Alignment explanation
Indices: 1495360--1495429 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
1495350 AAACATTTGT
*
1495360 GTTGCGATTTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
1495379 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
** **
1495398 GTTGCGAATTTGATTTTGT
1 GTTGCGAATTTGAAATTCA
1495417 GTTGCGAATTTGA
1 GTTGCGAATTTGA
1495430 CTATCGCGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:1495442 original size:20 final size:20
Alignment explanation
Indices: 1495398--1495504 Score: 105
Period size: 20 Copynumber: 5.4 Consensus size: 20
1495388 TTGAAATTCA
* * *
1495398 GTTGCGAATTTGA-TTTTGT
1 GTTGCGAATTTGACTATCGC
1495417 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
*
1495437 GTTGCGAATTTGAATATCGC
1 GTTGCGAATTTGACTATCGC
* *
1495457 GTTGCGAATTTAACTTAT-GT
1 GTTGCGAATTTGAC-TATCGC
1495477 GTTGCG-ATTT-ACATATTCGC
1 GTTGCGAATTTGAC-TA-TCGC
1495497 GTTGCGAA
1 GTTGCGAA
1495505 ATTGGAAACT
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
18 4 0.05
19 18 0.24
20 48 0.65
21 4 0.05
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.40
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:1495524 original size:60 final size:59
Alignment explanation
Indices: 1495398--1495511 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 59
1495388 TTGAAATTCA
* * *
1495398 GTTGCGAATTTGATTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGAATATCGC
1 GTTGCGAATTTAATTATGTGTTGCGAATTTGACTATCGCGTTGCGAATTGGAATATCGC
1495457 GTTGCGAATTTAACTTATGTGTTGCG-ATTT-ACATATTCGCGTTGCGAAATTGGAA
1 GTTGCGAATTTAA-TTATGTGTTGCGAATTTGAC-TA-TCGCGTTGCG-AATTGGAA
1495512 ACTGGGTTGC
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
58 2 0.04
59 18 0.38
60 21 0.44
61 7 0.15
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.39
Consensus pattern (59 bp):
GTTGCGAATTTAATTATGTGTTGCGAATTTGACTATCGCGTTGCGAATTGGAATATCGC
Found at i:1495540 original size:20 final size:20
Alignment explanation
Indices: 1495495--1495544 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1495485 TTACATATTC
1495495 GCGTTGCGAAATTGGAAACT
1 GCGTTGCGAAATTGGAAACT
* ***
1495515 GGGTTGCGAAATTGGAGTTT
1 GCGTTGCGAAATTGGAAACT
1495535 GCGTTGCGAA
1 GCGTTGCGAA
1495545 TTTGTTGGTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.36, T:0.28
Consensus pattern (20 bp):
GCGTTGCGAAATTGGAAACT
Found at i:1500082 original size:20 final size:20
Alignment explanation
Indices: 1500046--1500083 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1500036 ATCCTATTCC
**
1500046 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1500066 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1500084 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1500826 original size:216 final size:218
Alignment explanation
Indices: 1500437--1500872 Score: 671
Period size: 221 Copynumber: 2.0 Consensus size: 218
1500427 TATTTTGGTC
* * * *
1500437 GGGTTCGGGTTTAGGGTGAAAAAATCGGACCGACCTGAAAATATATATAATTCAGGTCGGGTTGG
1 GGGTTCGGGTTTAGGGTGAAAAAACCAGACCGACCCGAAAATATATATAATTCAGGTCGGGATGG
* * *
1500502 ATTAAGTCATTGTTTTTATTAAATAAAAAATAATTTTTTATTATTTCGGGTTGGGTCGGGTTGGA
66 ATTAAGTCACTGTTTGTATTAAATAAAAAATAATTTTTTATTATTTC--G--GGGTCGGGTCGGA
1500567 TTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGT-TCGGGTCAGGTTTTTTA
127 TTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTGTCGGGTCAGGTTTTTTA
*
1500631 AGTGTGATATTTGGGTCGGGTCGGGTT
192 AGTGTGATATTCGGGTCGGGTCGGGTT
1500658 GGGTTCGGGTTTAGGGTGAAAAAAACCAGACCGACCCGAAAATATATATAATTCAGGTCGGGATG
1 GGGTTCGGGTTTAGGGTG-AAAAAACCAGACCGACCCGAAAATATATATAATTCAGGTCGGGATG
*
1500723 GATTAAGTCACTGTTTGTATTAAAT-AAAAATATTTTTTTATTATTTC-GGGTCGGGTCGGATTT
65 GATTAAGTCACTGTTTGTATTAAATAAAAAATAATTTTTTATTATTTCGGGGTCGGGTCGGATTT
* *
1500786 CTAATTCATATATTCGGGTCGGGTCGGATGAGACTTTATTTTGTCCGGGTCGGGTCGGGTTTTTT
130 CTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGT----GTCGGGTCAGGTTTTTT
1500851 AAGTGTGATATTCGGGTCGGGT
191 AAGTGTGATATTCGGGTCGGGT
1500873 TTTTTTAAGT
Statistics
Matches: 198, Mismatches: 11, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
216 58 0.29
221 75 0.38
222 65 0.33
ACGTcount: A:0.24, C:0.11, G:0.28, T:0.37
Consensus pattern (218 bp):
GGGTTCGGGTTTAGGGTGAAAAAACCAGACCGACCCGAAAATATATATAATTCAGGTCGGGATGG
ATTAAGTCACTGTTTGTATTAAATAAAAAATAATTTTTTATTATTTCGGGGTCGGGTCGGATTTC
TAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTGTCGGGTCAGGTTTTTTAAGTG
TGATATTCGGGTCGGGTCGGGTT
Found at i:1500865 original size:27 final size:28
Alignment explanation
Indices: 1500835--1500896 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
1500825 TTTGTCCGGG
1500835 TCGGGTCGGG-TTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1500862 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1500890 TCGGGTC
1 TCGGGTC
1500897 AGTTCGGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 10 0.29
28 24 0.71
ACGTcount: A:0.13, C:0.10, G:0.34, T:0.44
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATAT
Found at i:1501488 original size:18 final size:18
Alignment explanation
Indices: 1501465--1501524 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
1501455 CCTACATATC
1501465 CCAATTCTTTCACAGATT
1 CCAATTCTTTCACAGATT
*
1501483 CCAATTCCTTCACAGATT
1 CCAATTCTTTCACAGATT
*
1501501 TCAATTCCTTT-ACAGATT
1 CCAATT-CTTTCACAGATT
*
1501519 TCAATT
1 CCAATT
1501525 TCCTCATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
18 35 0.92
19 3 0.08
ACGTcount: A:0.28, C:0.27, G:0.05, T:0.40
Consensus pattern (18 bp):
CCAATTCTTTCACAGATT
Found at i:1501516 original size:36 final size:34
Alignment explanation
Indices: 1501445--1501524 Score: 90
Period size: 36 Copynumber: 2.3 Consensus size: 34
1501435 TATGGAATTG
*
1501445 GATTCCAATTCCTACATATCCCAATTCTTTCACA
1 GATTCCAATTCCTACAGATCCCAATTCTTTCACA
**
1501479 GATTCCAATTCCTTCACAGATTTCAATTCCTTT-ACA
1 GATTCCAATTCC-T-ACAGATCCCAATT-CTTTCACA
*
1501515 GATTTCAATT
1 GATTCCAATT
1501525 TCCTCATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
34 12 0.31
35 1 0.03
36 22 0.56
37 4 0.10
ACGTcount: A:0.29, C:0.28, G:0.05, T:0.39
Consensus pattern (34 bp):
GATTCCAATTCCTACAGATCCCAATTCTTTCACA
Found at i:1501823 original size:21 final size:23
Alignment explanation
Indices: 1501799--1501840 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
1501789 AAAAAACTTC
*
1501799 TTTAGGCACC-AAAA-TATATAA
1 TTTAAGCACCTAAAAGTATATAA
1501820 TTTAAGCACCTAAAAGTATAT
1 TTTAAGCACCTAAAAGTATAT
1501841 TAAGTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 4 0.22
23 5 0.28
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (23 bp):
TTTAAGCACCTAAAAGTATATAA
Found at i:1501997 original size:15 final size:15
Alignment explanation
Indices: 1501977--1502007 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1501967 AGCACTAAAA
1501977 ATCAATTTAAAATAT
1 ATCAATTTAAAATAT
*
1501992 ATCAATTTGAAATAT
1 ATCAATTTAAAATAT
1502007 A
1 A
1502008 ATTTAGACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (15 bp):
ATCAATTTAAAATAT
Found at i:1502353 original size:27 final size:27
Alignment explanation
Indices: 1502322--1502390 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
1502312 CACATCCACC
1502322 TTAAATTCATAATATTTTTTTGATTAA
1 TTAAATTCATAATATTTTTTTGATTAA
1502349 TTAAATTCATAATATTTTTTTGATTAA
1 TTAAATTCATAATATTTTTTTGATTAA
*
1502376 TTAAAGTCATAATAT
1 TTAAATTCATAATAT
1502391 ATCTAAATTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (27 bp):
TTAAATTCATAATATTTTTTTGATTAA
Found at i:1502946 original size:25 final size:25
Alignment explanation
Indices: 1502918--1502970 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
1502908 GAAAAATGTA
1502918 AGAAAAATTCAGATCTAGAAACAAT
1 AGAAAAATTCAGATCTAGAAACAAT
1502943 AGAAAAATTCAGATCTAGAAACAAT
1 AGAAAAATTCAGATCTAGAAACAAT
1502968 AGA
1 AGA
1502971 TTGAAGCAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.57, C:0.11, G:0.13, T:0.19
Consensus pattern (25 bp):
AGAAAAATTCAGATCTAGAAACAAT
Found at i:1519933 original size:2 final size:2
Alignment explanation
Indices: 1519926--1519955 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1519916 TATATCGTTA
1519926 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1519956 TAATGATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1531670 original size:16 final size:18
Alignment explanation
Indices: 1531649--1531685 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1531639 TGAATTTTTC
1531649 TATT-AATTAT-TTATTT
1 TATTAAATTATATTATTT
1531665 TATTAAATTATACTTATTT
1 TATTAAATTATA-TTATTT
1531684 TA
1 TA
1531686 AATTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
17 6 0.33
19 8 0.44
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTAAATTATATTATTT
Found at i:1533107 original size:37 final size:36
Alignment explanation
Indices: 1533036--1533107 Score: 83
Period size: 37 Copynumber: 2.0 Consensus size: 36
1533026 CTATAATTAG
* **
1533036 TTTATATATTTTTTTTAAAATTTTAAATTCATAAAA
1 TTTATATATTTTTTTTAAAATATTAAAAACATAAAA
*
1533072 TTTATATAATTTTTTTTACAAA-ATTAAAAAGATAAA
1 TTTATAT-ATTTTTTTTA-AAATATTAAAAACATAAA
1533108 TAGGTTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
36 7 0.23
37 20 0.67
38 3 0.10
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (36 bp):
TTTATATATTTTTTTTAAAATATTAAAAACATAAAA
Found at i:1533825 original size:24 final size:23
Alignment explanation
Indices: 1533797--1533915 Score: 80
Period size: 24 Copynumber: 4.8 Consensus size: 23
1533787 AATTAAATGT
*
1533797 ATATATAATATTATTAATAATTAA
1 ATATATAATAATA-TAATAATTAA
* *
1533821 ATATATAATACTAGAAT-ATTATTA
1 ATATATAATAATATAATAATTA--A
1533845 ATA-ATTAATAATATAATAATATTTAA
1 ATATA-TAATAATATAAT-A-A-TTAA
* *
1533871 TATATAAAATATATTAATAGTAATTAA
1 -ATATATAATA-A-T-ATAATAATTAA
1533898 ATATATAATAATATAATA
1 ATATATAATAATATAATA
1533916 TTATTTTATA
Statistics
Matches: 75, Mismatches: 8, Indels: 25
0.69 0.07 0.23
Matches are distributed among these distances:
22 4 0.05
23 9 0.12
24 27 0.36
25 1 0.01
26 10 0.13
27 12 0.16
28 6 0.08
29 2 0.03
30 4 0.05
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (23 bp):
ATATATAATAATATAATAATTAA
Found at i:1533871 original size:15 final size:16
Alignment explanation
Indices: 1533797--1533917 Score: 63
Period size: 16 Copynumber: 7.3 Consensus size: 16
1533787 AATTAAATGT
*
1533797 ATATATAATAT-TATTA
1 ATATTTAATATATA-TA
*
1533813 ATAATTAA-ATATATA
1 ATATTTAATATATATA
**
1533828 ATACTAGAATAT-TATTA
1 ATA-TTTAATATATA-TA
*
1533845 ATAATTAATAATATAATA
1 ATATTTAAT-ATAT-ATA
*
1533863 ATATTTAATATATAAA
1 ATATTTAATATATATA
1533879 ATATATTAATAGTA-ATTAA
1 ATAT-TTAATA-TATA-T-A
*
1533898 ATATATAATA-ATATA
1 ATATTTAATATATATA
1533913 ATATT
1 ATATT
1533918 ATTTTATATA
Statistics
Matches: 80, Mismatches: 13, Indels: 25
0.68 0.11 0.21
Matches are distributed among these distances:
15 12 0.15
16 23 0.29
17 21 0.26
18 18 0.22
19 6 0.08
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.43
Consensus pattern (16 bp):
ATATTTAATATATATA
Found at i:1533921 original size:53 final size:55
Alignment explanation
Indices: 1533799--1533932 Score: 152
Period size: 53 Copynumber: 2.5 Consensus size: 55
1533789 TTAAATGTAT
*
1533799 ATATAATATTA-TTAATA-ATTAAATATATAATACTAGAATATTATTAATAATTAATA
1 ATATAATATTATTTAATATA-TAAA-ATATAATAATAGAATATTA-TAATAATTAATA
* * *
1533855 ATATAATAATATTTAATATATAAAATATATTAATAGTA-ATTA-AAT-ATATAATA
1 ATATAATATTATTTAATATATAAAATATAATAATAGAATATTATAATAAT-TAATA
*
1533908 ATATAATATTATTTTATATATAAAA
1 ATATAATATTATTTAATATATAAAA
1533933 ACTCACTAAC
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
52 2 0.03
53 31 0.45
55 4 0.06
56 21 0.30
57 10 0.14
58 1 0.01
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (55 bp):
ATATAATATTATTTAATATATAAAATATAATAATAGAATATTATAATAATTAATA
Found at i:1533928 original size:27 final size:26
Alignment explanation
Indices: 1533796--1533930 Score: 113
Period size: 25 Copynumber: 5.3 Consensus size: 26
1533786 AAATTAAATG
* * *
1533796 TATATATAATATTATTA-ATAATTAA
1 TATATATAATAATATAATATTATTAA
* *
1533821 -ATATATAATACTAGAATATTATTAA
1 TATATATAATAATATAATATTATTAA
*
1533846 TA-AT-TAATAATATAATAATATTTAA
1 TATATATAATAATATAATATTA-TTAA
* *
1533871 TATATAAAAT-ATATTAATAGTAATTAA
1 TATATATAATAATA-TAATA-TTATTAA
*
1533898 -ATATATAATAATATAATATTATT-T
1 TATATATAATAATATAATATTATTAA
1533922 TATATATAA
1 TATATATAA
1533931 AAACTCACTA
Statistics
Matches: 88, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
24 26 0.30
25 27 0.31
26 19 0.22
27 15 0.17
28 1 0.01
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (26 bp):
TATATATAATAATATAATATTATTAA
Found at i:1534411 original size:23 final size:23
Alignment explanation
Indices: 1534385--1534438 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
1534375 TAACATGTTT
1534385 TCTGTCTTTATGACATGTTTATC
1 TCTGTCTTTATGACATGTTTATC
* * ** *
1534408 TCTGTTTTTGTGGTATGTTTTTC
1 TCTGTCTTTATGACATGTTTATC
1534431 TCTG-CTTT
1 TCTGTCTTT
1534439 TTGGTAACTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.09, C:0.15, G:0.17, T:0.59
Consensus pattern (23 bp):
TCTGTCTTTATGACATGTTTATC
Found at i:1534439 original size:23 final size:22
Alignment explanation
Indices: 1534399--1534444 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1534389 TCTTTATGAC
*
1534399 ATGTTTATCTCTGTTTTTGTGGT
1 ATGTTTATCTCTGCTTTT-TGGT
*
1534422 ATGTTTTTCTCTGCTTTTTGGT
1 ATGTTTATCTCTGCTTTTTGGT
1534444 A
1 A
1534445 ACTTACGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.09, C:0.11, G:0.20, T:0.61
Consensus pattern (22 bp):
ATGTTTATCTCTGCTTTTTGGT
Found at i:1548220 original size:2 final size:2
Alignment explanation
Indices: 1548209--1548243 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1548199 GCACTTGCAC
1548209 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1548244 GAGAGAGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1548740 original size:2 final size:2
Alignment explanation
Indices: 1548733--1548774 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1548723 AACCATCTAC
1548733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1548775 GGAACGCGGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1551783 original size:38 final size:38
Alignment explanation
Indices: 1551741--1551852 Score: 170
Period size: 38 Copynumber: 2.9 Consensus size: 38
1551731 CAGCTGAAGC
*
1551741 AGAGGTGTTGGGTTTTGCCATCACAGATGACATGTCTA
1 AGAGGTGTCGGGTTTTGCCATCACAGATGACATGTCTA
*
1551779 AGAGGTGTCGGGTTTTGCCATCACAGATGACATGTCTG
1 AGAGGTGTCGGGTTTTGCCATCACAGATGACATGTCTA
* * * *
1551817 AGAGGTATCGTGTTTTTCCATCACAGACGACATGTC
1 AGAGGTGTCGGGTTTTGCCATCACAGATGACATGTC
1551853 GGACATATAT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 68 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (38 bp):
AGAGGTGTCGGGTTTTGCCATCACAGATGACATGTCTA
Found at i:1554401 original size:2 final size:2
Alignment explanation
Indices: 1554394--1554419 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1554384 TCAAATATTA
1554394 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
1554420 GAATTTTTAA
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:1555031 original size:39 final size:39
Alignment explanation
Indices: 1554945--1555031 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
1554935 TCCGATGCTC
* *
1554945 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATTCAAAGCTCATATGGTGCCAAACAAAAGGAA
*
1554984 ATCAAAATTCAAATCTCATATGGTGCCAAACAAAAGGAA
1 ATCAAAATTCAAAGCTCATATGGTGCCAAACAAAAGGAA
1555023 ATCAAAATT
1 ATCAAAATT
1555032 TACAACTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (39 bp):
ATCAAAATTCAAAGCTCATATGGTGCCAAACAAAAGGAA
Found at i:1555230 original size:20 final size:20
Alignment explanation
Indices: 1555205--1555244 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1555195 ATGTTGCGAT
1555205 CAACGCAAAAGTCAAATTCG
1 CAACGCAAAAGTCAAATTCG
**
1555225 CAACGCGGAAGTCAAATTCG
1 CAACGCAAAAGTCAAATTCG
1555245 TAAACCGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.15
Consensus pattern (20 bp):
CAACGCAAAAGTCAAATTCG
Found at i:1555483 original size:62 final size:65
Alignment explanation
Indices: 1555350--1555492 Score: 195
Period size: 66 Copynumber: 2.2 Consensus size: 65
1555340 TTTTTAGAAA
1555350 TAACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAAT
1 TAACAAATCAACTTTTACAAATCAATTAAACAA-CAAAAAAATAATTCTTATTTACAAATCAAAT
1555415 T
65 T
* * * **
1555416 AAACAAACCAACTTTTACAAATCAATTAATCAA-AAAAAAA-AA-TCTTATTTACTCATC-AATT
1 TAACAAATCAACTTTTACAAATCAATTAAACAACAAAAAAATAATTCTTATTTACAAATCAAATT
1555477 GTAACAAATCAACTTT
1 -TAACAAATCAACTTT
1555493 CAATGTAAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
61 4 0.06
62 26 0.38
63 2 0.03
64 7 0.10
66 30 0.43
ACGTcount: A:0.52, C:0.17, G:0.01, T:0.30
Consensus pattern (65 bp):
TAACAAATCAACTTTTACAAATCAATTAAACAACAAAAAAATAATTCTTATTTACAAATCAAATT
Done.