Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008523.1 Hibiscus syriacus cultivar Beakdansim tig00111392_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: 4657139
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 18
Found at i:1119815 original size:2 final size:2
Alignment explanation
Indices: 1119810--1119853 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1119800 TTCATATGTG
1119810 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
1119852 AT
1 AT
1119854 CATACATAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1131001 original size:24 final size:23
Alignment explanation
Indices: 1130973--1131019 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
1130963 AATAATATAT
1130973 TTTTAT-CTTCAAAATTTTTATAAA
1 TTTTATACTT-AAAA-TTTTATAAA
1130997 TTTTATCACTTAAAATTTTATAA
1 TTTTAT-ACTTAAAATTTTATAA
1131020 GGTCACATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 14 0.67
25 4 0.19
26 3 0.14
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTATACTTAAAATTTTATAAA
Found at i:1131412 original size:26 final size:25
Alignment explanation
Indices: 1131379--1131432 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 25
1131369 ATAATTGTTT
1131379 TTCGTTCCCTCTAAAATTTTATAGG
1 TTCGTTCCCTCTAAAATTTTATAGG
1131404 TTCGCTTCCCTCTAAAATTTTATAGG
1 TTCG-TTCCCTCTAAAATTTTATAGG
1131430 TTC
1 TTC
1131433 ACCCAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (25 bp):
TTCGTTCCCTCTAAAATTTTATAGG
Found at i:1132807 original size:34 final size:35
Alignment explanation
Indices: 1132764--1132842 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
1132754 AACATAGTCA
* *
1132764 TCAATTACATTCTAAACCC-C-AATTTCAAAATGCT
1 TCAATTACATTCT-AACCCTCAAATTCCAAAATACT
*
1132798 TCAATTACATTCTAACCCTCAAATTCCAAAATATT
1 TCAATTACATTCTAACCCTCAAATTCCAAAATACT
1132833 TCAATTACAT
1 TCAATTACAT
1132843 GGCCAACCCT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
33 5 0.12
34 14 0.35
35 21 0.52
ACGTcount: A:0.39, C:0.25, G:0.01, T:0.34
Consensus pattern (35 bp):
TCAATTACATTCTAACCCTCAAATTCCAAAATACT
Found at i:1133287 original size:147 final size:149
Alignment explanation
Indices: 1133013--1133297 Score: 457
Period size: 147 Copynumber: 1.9 Consensus size: 149
1133003 AAATGCTCAA
*
1133013 TTCAATTTATAAAATAGACGACTCAAAATTTTTTCGATTTTAGTTTTATAAAATTTAAATCAAGT
1 TTCAATTTATAAAATAGACGACTCAAAATTTTTTCGATTTGAGTTTTATAAAATTTAAATCAAGT
* * *
1133078 CGAATTGAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTATAATA
66 CGAATTGAATTGAATTTTCAAGTTTATGTTTAAATTTAATTATAAATATTTATAATACTATAATA
1133143 TTATTTGATTATAATTCAG
131 TTATTTGATTATAATTCAG
** **
1133162 TTCAATTTATAAAATAGTTGACTTGAAATTTTTTCGATTTGAG-TTTATAAAATTTAAATCAAGT
1 TTCAATTTATAAAATAGACGACTCAAAATTTTTTCGATTTGAGTTTTATAAAATTTAAATCAAGT
** *
1133226 CGAATTGAATT-AATTTTTGAGTTTATGTTTAATTTTAATTATAAATATTTATAATACTATAATA
66 CGAATTGAATTGAATTTTCAAGTTTATGTTTAAATTTAATTATAAATATTTATAATACTATAATA
1133290 TTATTTGA
131 TTATTTGA
1133298 ATCTAATTTA
Statistics
Matches: 125, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
147 55 0.44
148 32 0.26
149 38 0.30
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (149 bp):
TTCAATTTATAAAATAGACGACTCAAAATTTTTTCGATTTGAGTTTTATAAAATTTAAATCAAGT
CGAATTGAATTGAATTTTCAAGTTTATGTTTAAATTTAATTATAAATATTTATAATACTATAATA
TTATTTGATTATAATTCAG
Found at i:1137090 original size:20 final size:20
Alignment explanation
Indices: 1137065--1137114 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1137055 TTATGTGTGG
1137065 ATGGATGATATGGAAAGATA
1 ATGGATGATATGGAAAGATA
1137085 ATGGATGATATGGAAAGATA
1 ATGGATGATATGGAAAGATA
*
1137105 ATGCATGATA
1 ATGGATGATA
1137115 ATGCCAGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.02, G:0.28, T:0.26
Consensus pattern (20 bp):
ATGGATGATATGGAAAGATA
Found at i:1141176 original size:22 final size:22
Alignment explanation
Indices: 1141140--1141182 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1141130 CTGTTAATAT
** *
1141140 CATGAGTTATTTGATTTAATTC
1 CATGAGTTACATGATATAATTC
1141162 CATGAGTTACATGATATAATT
1 CATGAGTTACATGATATAATT
1141183 TCGGGAGTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (22 bp):
CATGAGTTACATGATATAATTC
Found at i:1141831 original size:3 final size:3
Alignment explanation
Indices: 1141823--1141859 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1141813 TTTTATACTT
1141823 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1141860 TGTTTGTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1142465 original size:2 final size:2
Alignment explanation
Indices: 1142458--1142498 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1142448 TGGAAAATTT
1142458 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1142499 ATATATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1142503 original size:2 final size:2
Alignment explanation
Indices: 1142498--1142582 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
1142488 TCTCTCTCTC
1142498 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1142540 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1142582 T
1 T
1142583 CCCACAAACA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1143458 original size:2 final size:2
Alignment explanation
Indices: 1143451--1143501 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1143441 CCCACACTCA
1143451 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
1143493 AT AT AT AT A
1 AT AT AT AT A
1143502 ATTTCTTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1177908 original size:2 final size:2
Alignment explanation
Indices: 1177901--1177943 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1177891 TCCGATGTTT
1177901 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1177943 T
1 T
1177944 GTTGGATAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1178978 original size:70 final size:70
Alignment explanation
Indices: 1178892--1179038 Score: 197
Period size: 70 Copynumber: 2.1 Consensus size: 70
1178882 AAAACAGTCC
* * * * * *
1178892 TCAATTTCATTTTAAACCC-CAATTTCCAAAGTAATTCAATTTCATTCTAAACCCTAATTTCTAA
1 TCAATTTCATTCTAAACCCTAAATTT-CAAAATAATTCAATTTAATTCTAAACCCCAAATTCTAA
*
1178956 AGTAAT
65 AATAAT
*
1178962 TCAATTTCATTCTAAACCCTAAATTTCAAAATAATTCAATTTAATTTTAAACCCCAAATTCTAAA
1 TCAATTTCATTCTAAACCCTAAATTTCAAAATAATTCAATTTAATTCTAAACCCCAAATTCTAAA
*
1179027 ATACT
66 ATAAT
1179032 TCAATTT
1 TCAATTT
1179039 AAGGTTTAGA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
70 62 0.93
71 5 0.07
ACGTcount: A:0.39, C:0.20, G:0.01, T:0.39
Consensus pattern (70 bp):
TCAATTTCATTCTAAACCCTAAATTTCAAAATAATTCAATTTAATTCTAAACCCCAAATTCTAAA
ATAAT
Found at i:1179040 original size:35 final size:35
Alignment explanation
Indices: 1178892--1179038 Score: 179
Period size: 35 Copynumber: 4.2 Consensus size: 35
1178882 AAAACAGTCC
* * * *
1178892 TCAATTTCATTTTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
* * *
1178927 TCAATTTCATTCTAAACCCTAATTTCTAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
*
1178962 TCAATTTCATTCTAAACCCTAAATT-TCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCT-AAAATAAT
* * *
1178997 TCAATTTAATTTTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
1179032 TCAATTT
1 TCAATTT
1179039 AAGGTTTAGA
Statistics
Matches: 101, Mismatches: 9, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
34 1 0.01
35 99 0.98
36 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.01, T:0.39
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
Found at i:1180094 original size:21 final size:21
Alignment explanation
Indices: 1180070--1180109 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1180060 GTTTACCCTT
*
1180070 AAATTTAATATAAAT-TTAAAA
1 AAATTGAATA-AAATATTAAAA
1180091 AAATTGAATAAAATATTAA
1 AAATTGAATAAAATATTAA
1180110 TATATTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
AAATTGAATAAAATATTAAAA
Found at i:1180735 original size:19 final size:19
Alignment explanation
Indices: 1180711--1180748 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1180701 GGTTACACTG
1180711 GTCGTTAAGGTCCCGTGAA
1 GTCGTTAAGGTCCCGTGAA
1180730 GTCGTTAAGGTCCCGTGAA
1 GTCGTTAAGGTCCCGTGAA
1180749 TAAACTGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (19 bp):
GTCGTTAAGGTCCCGTGAA
Found at i:1180928 original size:12 final size:12
Alignment explanation
Indices: 1180911--1180935 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1180901 TAAGAGGAGA
1180911 GTCATAATCAAT
1 GTCATAATCAAT
1180923 GTCATAATCAAT
1 GTCATAATCAAT
1180935 G
1 G
1180936 AGAAAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (12 bp):
GTCATAATCAAT
Found at i:1207189 original size:24 final size:24
Alignment explanation
Indices: 1207157--1207207 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
1207147 TAAAGCAACC
1207157 AAATATATATACATCATTCAGATA
1 AAATATATATACATCATTCAGATA
1207181 AAATATATATACATCATTCAGATA
1 AAATATATATACATCATTCAGATA
1207205 AAA
1 AAA
1207208 AAAAGGCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.53, C:0.12, G:0.04, T:0.31
Consensus pattern (24 bp):
AAATATATATACATCATTCAGATA
Found at i:1216539 original size:2 final size:2
Alignment explanation
Indices: 1216532--1216588 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1216522 ATTGGATAAT
1216532 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1216574 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1216589 TCAGACTTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1220379 original size:21 final size:22
Alignment explanation
Indices: 1220353--1220394 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1220343 AATTAGAGTT
1220353 TTCAA-TTTGGATTTGTTATCC
1 TTCAATTTTGGATTTGTTATCC
1220374 TTCAATTTTGGATTTGTTATC
1 TTCAATTTTGGATTTGTTATC
1220395 TCAAAACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.19, C:0.12, G:0.14, T:0.55
Consensus pattern (22 bp):
TTCAATTTTGGATTTGTTATCC
Found at i:1222052 original size:2 final size:2
Alignment explanation
Indices: 1222045--1222076 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1222035 ATTACTCCCT
1222045 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
1222077 AATGGTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1224799 original size:41 final size:41
Alignment explanation
Indices: 1224748--1224988 Score: 286
Period size: 41 Copynumber: 5.9 Consensus size: 41
1224738 CATCGATAGC
*
1224748 GGCGTTTTTATACAAACGCCGCTATAGACTTGTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGT
* * * *
1224789 GGCGTTTTTATACACAACGCCGTTATACACTTGTACTATAGT
1 GGCGTTTTTATACA-AACGCCGCTATAGACTCGTACTTTAGT
* * * *
1224831 GGCGTTTTTATATAAACGCCGTTAAAGACTCGTACTTTACT
1 GGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGT
* * * *
1224872 GGCATTTTTATATAAACGTCGCTAAAGACTCGTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGT
* *
1224913 GGCG-TTTTAGTACAAATGCCGCTATACACTCGTACTTTAGT
1 GGCGTTTTTA-TACAAACGCCGCTATAGACTCGTACTTTAGT
* * * *
1224954 GACGTTTTTATTCAAACGTCGCTATATACTCGTAC
1 GGCGTTTTTATACAAACGCCGCTATAGACTCGTAC
1224989 AAATTTTAAG
Statistics
Matches: 173, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
40 5 0.03
41 126 0.73
42 42 0.24
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36
Consensus pattern (41 bp):
GGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGT
Found at i:1224985 original size:123 final size:124
Alignment explanation
Indices: 1224752--1224988 Score: 318
Period size: 123 Copynumber: 1.9 Consensus size: 124
1224742 GATAGCGGCG
* * *
1224752 TTTTTATACAAACGCCGCTATAGACTTGTACTTTAGTGGCGTTTTTATACACAACGCCGTTATAC
1 TTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACACAACGCCGCTATAC
* * *
1224817 ACTTGTACTATAGTGGCGTTTTTATATAAACGCCGTTAAAGACTCGTACTTTACTGGCA
66 ACTCGTACTATAGTGACGTTTTTATATAAACGCCGCTAAAGACTCGTACTTTACTGGCA
* * *
1224876 TTTTTATATAAACGTCGCTAAAGACTCGTACTTTAGTGGCG-TTTTAGTACA-AATGCCGCTATA
1 TTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTA-TACACAACGCCGCTATA
* * * *
1224939 CACTCGTACTTTAGTGACGTTTTTAT-TCAAACGTCGCTATATACTCGTAC
65 CACTCGTACTATAGTGACGTTTTTATAT-AAACGCCGCTAAAGACTCGTAC
1224989 AAATTTTAAG
Statistics
Matches: 98, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
122 1 0.01
123 56 0.57
124 41 0.42
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (124 bp):
TTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACACAACGCCGCTATAC
ACTCGTACTATAGTGACGTTTTTATATAAACGCCGCTAAAGACTCGTACTTTACTGGCA
Found at i:1228750 original size:43 final size:42
Alignment explanation
Indices: 1228681--1228987 Score: 273
Period size: 43 Copynumber: 7.2 Consensus size: 42
1228671 ATTGAAATTA
*
1228681 GCGGCGTTT-TTATCAAAATA--CCGCTATAGATATGACCTTTT
1 GCGGCGTTTGTTA-CAAAA-ACGCCGCTATAGATCTGACCTTTT
* * *
1228722 GTGGCGTTTGTATCCAAAAACGCCGCTATAAATCTGACCTTTT
1 GCGGCGTTTGT-TACAAAAACGCCGCTATAGATCTGACCTTTT
* * ** * *
1228765 ACGGCGTTCGTATACAAAAATACCGTTATAGATCTGACATTTT
1 GCGGCGTTTGT-TACAAAAACGCCGCTATAGATCTGACCTTTT
*
1228808 GCGGTGTTTGTATACAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGT-TACAAAAACGCCGCTATAGATCTGACCTTTT
* * * *
1228851 GCGACGTTTGTTGCAAAAATGCCGCTATAGATCTTGACTTTTT
1 GCGGCGTTTGTTACAAAAACGCCGCTATAGATC-TGACCTTTT
*** * *
1228894 ATTGCGTTTTTTGA-ACAAACGCCGCTATAGATCTCGACCTTTT
1 GCGGCGTTTGTT-ACAAAAACGCCGCTATAGATCT-GACCTTTT
* * * * *
1228937 GTGGCGTTTGTT-CAATAACGCCGCAATAGATATTGACCTATT
1 GCGGCGTTTGTTACAAAAACGCCGCTATAGAT-CTGACCTTTT
1228979 GCGGCGTTT
1 GCGGCGTTT
1228988 TTTGTTCTCA
Statistics
Matches: 214, Mismatches: 43, Indels: 17
0.78 0.16 0.06
Matches are distributed among these distances:
41 9 0.04
42 57 0.27
43 148 0.69
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.35
Consensus pattern (42 bp):
GCGGCGTTTGTTACAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:1228988 original size:85 final size:85
Alignment explanation
Indices: 1228825--1228991 Score: 219
Period size: 85 Copynumber: 2.0 Consensus size: 85
1228815 TTGTATACAA
* * * *
1228825 AAACGCCGCTATAGATCTGACCTTTTGCGACGTTTGTTGCAAAAATGCCGCTATAGATCTTGACT
1 AAACGCCGCTATAGATCTGACCTTTTGCGACGTTTGTTGCAAAAACGCCGCAATAGATATTGACC
* **
1228890 TTTTATTGCGTTTTTTGAAC
66 TATTACGGCGTTTTTTGAAC
* * *
1228910 AAACGCCGCTATAGATCTCGACCTTTTGTGGCGTTTGTT-CAATAACGCCGCAATAGATATTGAC
1 AAACGCCGCTATAGATCT-GACCTTTTGCGACGTTTGTTGCAAAAACGCCGCAATAGATATTGAC
*
1228974 CTATTGCGGCGTTTTTTG
65 CTATTACGGCGTTTTTTG
1228992 TTCTCAAACG
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
85 52 0.74
86 18 0.26
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (85 bp):
AAACGCCGCTATAGATCTGACCTTTTGCGACGTTTGTTGCAAAAACGCCGCAATAGATATTGACC
TATTACGGCGTTTTTTGAAC
Found at i:1230169 original size:20 final size:21
Alignment explanation
Indices: 1230134--1230172 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1230124 TAATCAAATT
1230134 TTAAATATTATAAAATAATCA
1 TTAAATATTATAAAATAATCA
*
1230155 TTAAA-ATTTTAAAATAAT
1 TTAAATATTATAAAATAAT
1230173 TATAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAAATATTATAAAATAATCA
Found at i:1230178 original size:31 final size:30
Alignment explanation
Indices: 1230129--1230270 Score: 119
Period size: 31 Copynumber: 4.7 Consensus size: 30
1230119 TTAATTAATC
*
1230129 AAATTTTAAAT-ATTATAAAATAATCATTA
1 AAATTTTAAATAATTATAAAATGATCATTA
*
1230158 AAATTTTAAAATAATTATAAAATGATCACTAA
1 AAATTTT-AAATAATTATAAAATGATCA-TTA
* * *
1230190 AAATTATCAAA-AGTTATAGAATGATCATTA
1 AAATT-TTAAATAATTATAAAATGATCATTA
* * * *
1230220 AACTTATTGAATTATTATAAAATGATCCTT-
1 AAATT-TTAAATAATTATAAAATGATCATTA
* *
1230250 AAATTTATAACTATTTATAAA
1 AAATTT-TAAATAATTATAAA
1230271 GTCACATAAT
Statistics
Matches: 89, Mismatches: 18, Indels: 11
0.75 0.15 0.09
Matches are distributed among these distances:
29 8 0.09
30 28 0.31
31 42 0.47
32 10 0.11
33 1 0.01
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (30 bp):
AAATTTTAAATAATTATAAAATGATCATTA
Found at i:1233531 original size:14 final size:14
Alignment explanation
Indices: 1233514--1233562 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
1233504 TAAAATTAAA
1233514 AAATATATATGGTT
1 AAATATATATGGTT
* * *
1233528 AAATTTAAAAGGTT
1 AAATATATATGGTT
1233542 AAA-ATATATGGATT
1 AAATATATATGG-TT
1233556 AAATATA
1 AAATATA
1233563 CATAGAACAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
13 5 0.19
14 19 0.70
15 3 0.11
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (14 bp):
AAATATATATGGTT
Found at i:1235983 original size:30 final size:30
Alignment explanation
Indices: 1235947--1236012 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
1235937 TGCGACGTTC
1235947 GAAGCACATGACCGACAAAAACCGAAATGG
1 GAAGCACATGACCGACAAAAACCGAAATGG
1235977 GAAGCACATGACCGACAAAAACCGAAATGG
1 GAAGCACATGACCGACAAAAACCGAAATGG
*
1236007 TAAGCA
1 GAAGCA
1236013 ACAATTTCAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.47, C:0.23, G:0.23, T:0.08
Consensus pattern (30 bp):
GAAGCACATGACCGACAAAAACCGAAATGG
Found at i:1239661 original size:14 final size:14
Alignment explanation
Indices: 1239642--1239672 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1239632 GATAAGATTC
*
1239642 AAACTTAACTTTAT
1 AAACTTAAATTTAT
1239656 AAACTTAAATTTAT
1 AAACTTAAATTTAT
1239670 AAA
1 AAA
1239673 TCTCATACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (14 bp):
AAACTTAAATTTAT
Found at i:1240295 original size:20 final size:21
Alignment explanation
Indices: 1240270--1240321 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
1240260 TTTTCCCAAT
*
1240270 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGAAAAA
* **
1240290 TCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAGAAAAA
1240311 TCGCAATGCGA
1 TCGCAATGCGA
1240322 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATAAGAAAAA
Found at i:1240335 original size:20 final size:20
Alignment explanation
Indices: 1240310--1240423 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
1240300 AATTGGAAAA
*
1240310 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1240330 ATCGCAATGCAATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
1240350 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1240371 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1240391 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1240411 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1240424 TTACATAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 62 0.78
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1240354 original size:61 final size:61
Alignment explanation
Indices: 1240307--1240423 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
1240297 GCGAATTGGA
* * * * *
1240307 AAAATCGCAATGCGATACTGACTATCGCAATGCAATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCAATACTGACTATCGCAACGCGATAATAC
* * * *
1240368 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCAATACTGACTATCGCAACGCGAT
1240424 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCAATACTGACTATCGCAACGCGATAATAC
Found at i:1241007 original size:19 final size:19
Alignment explanation
Indices: 1240979--1241015 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1240969 ACGAGAGAAT
* *
1240979 CGCAATGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
1240998 CGCAACGCGAAACAAAAA
1 CGCAACGCGAAACAAAAA
1241016 TCGTATTGCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.22, G:0.16, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:1241072 original size:33 final size:33
Alignment explanation
Indices: 1241030--1241117 Score: 133
Period size: 33 Copynumber: 2.6 Consensus size: 33
1241020 ATTGCGATTT
1241030 TCATTTCGCGTTGCGATTCTCTCG-TCCTGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTTCC-GATAG
* *
1241063 TCATTTCGCGTTGCAATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTTCCGATAG
1241096 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
1241118 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
33 34 0.68
34 16 0.32
ACGTcount: A:0.12, C:0.27, G:0.20, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTTCCGATAG
Found at i:1241119 original size:20 final size:20
Alignment explanation
Indices: 1241085--1241142 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1241075 GCAATTCTCT
**
1241085 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
1241105 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
1241125 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1241143 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:1243219 original size:21 final size:21
Alignment explanation
Indices: 1243195--1243264 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
1243185 TCATTCCTCG
1243195 AGAGCCCCCTCCCACCGTTCA
1 AGAGCCCCCTCCCACCGTTCA
* * ** * *
1243216 AGAGGCCACTGTCATCGTTGA
1 AGAGCCCCCTCCCACCGTTCA
** *
1243237 AGAGGTCCCTCCCACCATTCA
1 AGAGCCCCCTCCCACCGTTCA
1243258 AGAGCCC
1 AGAGCCC
1243265 GATTCACATG
Statistics
Matches: 34, Mismatches: 15, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.23, C:0.40, G:0.20, T:0.17
Consensus pattern (21 bp):
AGAGCCCCCTCCCACCGTTCA
Found at i:1244637 original size:14 final size:14
Alignment explanation
Indices: 1244618--1244653 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1244608 ATTGTTTAAT
*
1244618 TGATTTGTAAACGG
1 TGATTTGTAAAAGG
*
1244632 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1244646 TGATTTGT
1 TGATTTGT
1244654 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.28, C:0.03, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1244834 original size:19 final size:19
Alignment explanation
Indices: 1244812--1244962 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
1244802 CGAAATTAAA
1244812 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1244831 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1244846 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1244864 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
1244878 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1244897 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1244912 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * ** *
1244930 TTCTCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1244949 TTCTGCGTTGCGAT
1 TTC-GCGTTGCGAT
1244963 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 47 0.49
20 8 0.08
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1244858 original size:33 final size:32
Alignment explanation
Indices: 1244816--1244942 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
1244806 ATTAAATTCG
1244816 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
1244849 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1244882 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
1244915 CGTTGCGATTTTCATTTCTCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1244943 AGTAATTTCT
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1244899 original size:66 final size:66
Alignment explanation
Indices: 1244809--1244941 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
1244799 ACGCGAAATT
*
1244809 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1244874 G
66 G
* *
1244875 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCTCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1244940 G
66 G
1244941 A
1 A
1244942 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1247469 original size:24 final size:24
Alignment explanation
Indices: 1247435--1247488 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1247425 CTGAAACATC
* *
1247435 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
1247459 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
1247483 ATCAAA
1 ATCAAA
1247489 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:1248574 original size:20 final size:20
Alignment explanation
Indices: 1248545--1248602 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
1248535 ATTCATTTGA
*
1248545 CTATCACAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1248565 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
1248585 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1248603 CTCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1248643 original size:19 final size:18
Alignment explanation
Indices: 1248621--1248688 Score: 81
Period size: 19 Copynumber: 3.9 Consensus size: 18
1248611 GAAATGAAAA
1248621 TTGCATTGCGATTTTC--
1 TTGCATTGCGATTTTCAT
*
1248637 -T-CGTTGCGATTTTCAT
1 TTGCATTGCGATTTTCAT
1248653 TTCGCATTGCGATTTTCAT
1 TT-GCATTGCGATTTTCAT
1248672 TTCGCATTGCGATTTTC
1 TT-GCATTGCGATTTTC
1248689 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 12 0.27
15 1 0.02
17 1 0.02
19 31 0.69
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (18 bp):
TTGCATTGCGATTTTCAT
Found at i:1248645 original size:14 final size:16
Alignment explanation
Indices: 1248625--1248698 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
1248615 TGAAAATTGC
1248625 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
1248640 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
1248657 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
1248676 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
1248692 -TTGCGAT
1 ATTGCGAT
1248699 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:1248824 original size:14 final size:14
Alignment explanation
Indices: 1248805--1248841 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1248795 CATCAATTAA
1248805 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1248819 ACAAATCATCTTTT
1 ACAAATCAACATTT
1248833 ACAAATCAA
1 ACAAATCAA
1248842 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1250732 original size:20 final size:20
Alignment explanation
Indices: 1250709--1250762 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1250699 GAAACTTAAA
*
1250709 ATCGCAATGCGAAAATGTCT
1 ATCGCAATGCGAAAATGGCT
** *
1250729 ATCGCAACACGGAAATGGCT
1 ATCGCAATGCGAAAATGGCT
1250749 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
1250763 TGAAAATCGC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGGCT
Found at i:1250843 original size:14 final size:14
Alignment explanation
Indices: 1250824--1250881 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1250814 TTTCATTTCA
1250824 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1250838 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1250854 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1250870 CGTTGCGATTTT
1 CGTTGCGATTTT
1250882 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1250888 original size:33 final size:33
Alignment explanation
Indices: 1250807--1250897 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1250797 ATAAATCGCA
* *
1250807 TTGCGATTTTCATTTCACGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1250840 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1250872 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1250898 AGCCATTTAT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1250904 original size:19 final size:20
Alignment explanation
Indices: 1250882--1250925 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1250872 TTGCGATTTT
1250882 CATTT-CGCATTGCGATAGC
1 CATTTACGCATTGCGATAGC
* * *
1250901 CATTTATGCGTTGCGATAGT
1 CATTTACGCATTGCGATAGC
1250921 CATTT
1 CATTT
1250926 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
CATTTACGCATTGCGATAGC
Found at i:1251443 original size:18 final size:18
Alignment explanation
Indices: 1251417--1251461 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1251407 GTCGATCAGA
*
1251417 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1251435 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1251453 TGATGGCTC
1 TGATGGCTC
1251462 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1252835 original size:20 final size:20
Alignment explanation
Indices: 1252783--1252841 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
1252773 AATAGTTTCT
** *
1252783 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
1252803 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
** *
1252823 GAATTTGATTATCGCAACG
1 GAAAATGACTATCGCAACG
1252842 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:1253133 original size:22 final size:22
Alignment explanation
Indices: 1253106--1253149 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1253096 GATGGAGATA
1253106 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1253128 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1253150 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1253362 original size:20 final size:20
Alignment explanation
Indices: 1253337--1253430 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1253327 GATTATGTAT
1253337 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1253357 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
1253377 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
1253398 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1253418 TATCGCATTGCGA
1 TATCGCGTTGCGA
1253431 TTTTCCCAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 45 0.73
21 12 0.19
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1253402 original size:41 final size:41
Alignment explanation
Indices: 1253357--1253434 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
1253347 CGAAAGTCAG
* * *
1253357 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTAT
* *
1253398 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
1253435 CCCAATTTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTAT
Found at i:1253431 original size:20 final size:19
Alignment explanation
Indices: 1253317--1253431 Score: 86
Period size: 20 Copynumber: 5.7 Consensus size: 19
1253307 CGCTTTGAAA
*
1253317 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGA-TA-GTAGT
* *
1253338 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGT-AGT
* *
1253358 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGT-AGT
* * * *
1253378 ATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGA--TAGTAGT
1253399 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGT-AGT
1253419 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1253432 TTTCCCAATT
Statistics
Matches: 78, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
19 5 0.06
20 48 0.62
21 23 0.29
22 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (19 bp):
ATCGCATTGCGATAGTAGT
Found at i:1254236 original size:39 final size:39
Alignment explanation
Indices: 1254193--1254271 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
1254183 TAGTATAATC
*
1254193 TTAACCTATTACGTAGAATGAGAGATAAACACTAACATA
1 TTAACCTATTACGTAGAATGAGAGATAAACACGAACATA
1254232 TTAACCTATTACGTAGAATGAGAGATAAACACGAACATA
1 TTAACCTATTACGTAGAATGAGAGATAAACACGAACATA
1254271 T
1 T
1254272 ATTACTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (39 bp):
TTAACCTATTACGTAGAATGAGAGATAAACACGAACATA
Found at i:1259547 original size:60 final size:60
Alignment explanation
Indices: 1259465--1259579 Score: 131
Period size: 60 Copynumber: 1.9 Consensus size: 60
1259455 AATTTGGTCC
* * * * * *
1259465 TTAAACTTTTAAATATTCCAATTACATCCCTAAATTATGACTATGATTCTAAATTAGTCA
1 TTAAACTTCTAAACATTCCAATTACACCCCCAAACTATGACTATCATTCTAAATTAGTCA
* * * * *
1259525 TTAAACTTCTGAACATTTCAATTTCACCCCCGAACTATGACTTTCATTCTAAATT
1 TTAAACTTCTAAACATTCCAATTACACCCCCAAACTATGACTATCATTCTAAATT
1259580 GGTCCCCAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (60 bp):
TTAAACTTCTAAACATTCCAATTACACCCCCAAACTATGACTATCATTCTAAATTAGTCA
Found at i:1259927 original size:60 final size:60
Alignment explanation
Indices: 1259778--1259908 Score: 172
Period size: 60 Copynumber: 2.2 Consensus size: 60
1259768 AAGAGTTTGG
* * * * * *
1259778 GGACTAATTTAGAAAGAAAGTCATAGTTTAAGGATGAAATTAGAATGTTCAAAAGTTTAA
1 GGACTAATTTAGAATGAGAGACATAGTTTGAGGATGAAATTAGAATATTCAAAAGATTAA
* * * *
1259838 GGATTAATTTAGAATGAGAGACATAGTTTGGGGATGAAATTGGAATATTTAAAAGATTAA
1 GGACTAATTTAGAATGAGAGACATAGTTTGAGGATGAAATTAGAATATTCAAAAGATTAA
1259898 GGACTAATTTA
1 GGACTAATTTA
1259909 AGATGAAGAT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.31
Consensus pattern (60 bp):
GGACTAATTTAGAATGAGAGACATAGTTTGAGGATGAAATTAGAATATTCAAAAGATTAA
Found at i:1264996 original size:2 final size:2
Alignment explanation
Indices: 1264989--1265016 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1264979 ACCCAAGATT
1264989 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
1265017 ACTCAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1278311 original size:2 final size:2
Alignment explanation
Indices: 1278304--1278347 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1278294 AGATATTAGA
1278304 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
1278346 AT
1 AT
1278348 TGATATACAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1278466 original size:2 final size:2
Alignment explanation
Indices: 1278461--1278486 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1278451 ACAATATTAA
1278461 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
1278487 GACATACCAA
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:1280174 original size:11 final size:11
Alignment explanation
Indices: 1280158--1280196 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1280148 ACATATGTTT
1280158 TATTTTATTAA
1 TATTTTATTAA
*
1280169 TATTTTATGACA
1 TATTTTATTA-A
*
1280181 TATTCTATTAA
1 TATTTTATTAA
1280192 TATTT
1 TATTT
1280197 ACATATGACG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:1284868 original size:2 final size:2
Alignment explanation
Indices: 1284863--1284902 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1284853 CTATTTTTTA
1284863 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
1284903 TAACCTAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1286421 original size:2 final size:2
Alignment explanation
Indices: 1286414--1286446 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1286404 AATCCAACAC
1286414 AT AT AT AT 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 AT AT AT AT A
1286447 ATGTTATTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1287956 original size:17 final size:18
Alignment explanation
Indices: 1287923--1287955 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1287913 TTATTTTTTA
1287923 AAATTTAATAAATAAAAC
1 AAATTTAATAAATAAAAC
1287941 AAATTT-AT-AATAAAA
1 AAATTTAATAAATAAAA
1287956 AATGAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
AAATTTAATAAATAAAAC
Found at i:1292137 original size:7 final size:7
Alignment explanation
Indices: 1292125--1292149 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1292115 TTAATCTGAA
1292125 TTTAAGG
1 TTTAAGG
1292132 TTTAAGG
1 TTTAAGG
1292139 TTTAAGG
1 TTTAAGG
1292146 TTTA
1 TTTA
1292150 GAGTATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (7 bp):
TTTAAGG
Found at i:1298610 original size:2 final size:2
Alignment explanation
Indices: 1298599--1298647 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1298589 ACATGTAAGA
1298599 AT AT -T 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
1298640 AT AT AT AT
1 AT AT AT AT
1298648 TTGAAAGAGG
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1324236 original size:60 final size:60
Alignment explanation
Indices: 1324122--1324237 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
1324112 AATGATCCCT
* * * * * *
1324122 TAACTATAGGGTACTATTTTATTGAGTCACTCGATTATTAAAAGTTATACAATAGTTATC
1 TAACTATAGGGTAATATTTTATTGAATCACTCGACTATTAAAACTTACAAAATAGTTATC
* * *
1324182 TAACTATAGGG-AATTTCTTTATTGAATCCCTTGACTATTAAAACTTACAAAATAGT
1 TAACTATAGGGTAATAT-TTTATTGAATCACTCGACTATTAAAACTTACAAAATAGT
1324238 CACCCGACTA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
59 3 0.07
60 43 0.93
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (60 bp):
TAACTATAGGGTAATATTTTATTGAATCACTCGACTATTAAAACTTACAAAATAGTTATC
Found at i:1325719 original size:19 final size:19
Alignment explanation
Indices: 1325695--1325733 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1325685 TTAGTTCTTT
*
1325695 GCCAAGCTTTGTTTTAAAG
1 GCCAAGCATTGTTTTAAAG
1325714 GCCAAGCATTGTTTTAAAG
1 GCCAAGCATTGTTTTAAAG
1325733 G
1 G
1325734 TTTTACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.33
Consensus pattern (19 bp):
GCCAAGCATTGTTTTAAAG
Found at i:1337167 original size:6 final size:6
Alignment explanation
Indices: 1337153--1337182 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1337143 ACCAAGACAC
*
1337153 ACATAT ACATGT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT
1337183 GTATGTATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (6 bp):
ACATAT
Found at i:1338641 original size:20 final size:20
Alignment explanation
Indices: 1338547--1338915 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
1338537 GATTTTCCAT
* ** *
1338547 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1338567 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1338587 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1338607 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1338627 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1338647 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1338667 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1338687 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1338707 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1338727 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1338747 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1338767 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1338787 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1338807 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1338827 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1338847 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1338867 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1338887 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1338907 AATCACAAC
1 AATCGCAAC
1338916 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1339628 original size:24 final size:24
Alignment explanation
Indices: 1339589--1339635 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1339579 AAATTTGGTC
1339589 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1339613 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1339636 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1339827 original size:12 final size:12
Alignment explanation
Indices: 1339810--1339834 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1339800 ATATAATCCT
1339810 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1339822 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1339834 G
1 G
1339835 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1342156 original size:19 final size:19
Alignment explanation
Indices: 1342134--1342402 Score: 309
Period size: 19 Copynumber: 15.4 Consensus size: 19
1342124 CGGAAAATAC
*
1342134 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1342153 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1342167 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1342187 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1342201 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1342220 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1342239 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1342253 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1342272 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1342291 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1342305 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1342324 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1342343 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1342357 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1342376 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1342395 AATCGCAA
1 AATCGCAA
1342403 CGAGATGATC
Statistics
Matches: 216, Mismatches: 8, Indels: 52
0.78 0.03 0.19
Matches are distributed among these distances:
14 50 0.23
15 3 0.01
16 13 0.06
17 12 0.06
18 4 0.02
19 121 0.56
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1342221 original size:33 final size:34
Alignment explanation
Indices: 1342134--1342424 Score: 268
Period size: 33 Copynumber: 8.5 Consensus size: 34
1342124 CGGAAAATAC
* *
1342134 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
1342167 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
1342201 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
1342239 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
1342272 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
1342305 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
1342343 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
1342376 AATCGCAATGCGAAATGAAAATCGCAACGA-GAT
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
1342409 GATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
1342425 TATAAACGCA
Statistics
Matches: 226, Mismatches: 10, Indels: 44
0.81 0.04 0.16
Matches are distributed among these distances:
33 128 0.57
34 32 0.14
35 13 0.06
36 12 0.05
37 3 0.01
38 38 0.17
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:1342440 original size:52 final size:52
Alignment explanation
Indices: 1342162--1342424 Score: 492
Period size: 52 Copynumber: 5.0 Consensus size: 52
1342152 AAATCCCAAC
1342162 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1342215 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1342267 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1342319 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1342371 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATG-ATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA-GAATCGCAATGCGAA
1342423 AT
1 AT
1342425 TATAAACGCA
Statistics
Matches: 207, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
52 190 0.92
53 17 0.08
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1342539 original size:19 final size:19
Alignment explanation
Indices: 1342431--1342531 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
1342421 AAATTATAAA
1342431 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1342450 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1342470 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1342486 CG--TTGCGA-TTTCATTT
1 CGCATTGCGATTTTCATTT
1342502 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1342521 CGCATTGCGAT
1 CGCATTGCGAT
1342532 AGTCATTTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
15 3 0.04
16 8 0.11
17 3 0.04
18 6 0.08
19 29 0.39
20 19 0.26
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1342657 original size:14 final size:14
Alignment explanation
Indices: 1342638--1342674 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1342628 CATCAATTAC
1342638 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1342652 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1342666 ACAAATCAA
1 ACAAATCAA
1342675 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1342703 original size:38 final size:38
Alignment explanation
Indices: 1342655--1342727 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
1342645 AACTTTTACA
*
1342655 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
1342693 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1342728 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:1344612 original size:14 final size:14
Alignment explanation
Indices: 1344593--1344649 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1344583 GCGAAATGAA
*
1344593 AATCGCAACGACAG
1 AATCGCAACGAAAG
1344607 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1344624 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1344640 AATCGCAACG
1 AATCGCAACG
1344650 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1344620 original size:33 final size:33
Alignment explanation
Indices: 1344574--1344666 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1344564 GCGAAACCAA
*
1344574 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1344607 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1344640 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1344667 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1344631 original size:19 final size:19
Alignment explanation
Indices: 1344537--1344671 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1344527 AAATTTACTT
* *
1344537 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1344557 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1344576 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1344595 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1344609 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1344628 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1344642 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1344661 TCGCAATGCGA
1 TCGCAACGCGA
1344672 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1344689 original size:19 final size:19
Alignment explanation
Indices: 1344667--1344795 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1344657 AAAATCGCAA
1344667 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1344686 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1344700 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1344719 TGCGA--TT-CTTT--CGT
1 TGCGATTTTGGTTTCGCGT
**
1344733 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1344752 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1344771 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1344791 TGCGA
1 TGCGA
1344796 AAGTAAACTA
Statistics
Matches: 91, Mismatches: 8, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
14 19 0.21
15 1 0.01
16 6 0.07
17 6 0.07
18 1 0.01
19 45 0.49
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1344758 original size:33 final size:34
Alignment explanation
Indices: 1344667--1344758 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 34
1344657 AAAATCGCAA
1344667 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
1344700 TGCGATTTTGGTTTCGCGTTGCGATTCTT-TCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
**
1344733 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1344759 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 52 0.93
34 4 0.07
ACGTcount: A:0.08, C:0.18, G:0.27, T:0.47
Consensus pattern (34 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
Found at i:1344998 original size:93 final size:93
Alignment explanation
Indices: 1344839--1345218 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
1344829 TTGAATGGAT
1344839 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1344904 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1344932 AAATTTACTTTCAAGCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1344997 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1345025 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1345089 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1345117 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1345182 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1345210 AAATTTACT
1 AAATTTACT
1345219 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
92 92 0.32
93 192 0.68
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1345152 original size:185 final size:186
Alignment explanation
Indices: 1344839--1345218 Score: 744
Period size: 185 Copynumber: 2.0 Consensus size: 186
1344829 TTGAATGGAT
1344839 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1344904 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAAGCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1344969 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1345025 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1345089 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1345154 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1345210 AAATTTACT
1 AAATTTACT
1345219 AAGCAATCTA
Statistics
Matches: 193, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
185 154 0.80
186 39 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1346943 original size:14 final size:14
Alignment explanation
Indices: 1346924--1347013 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1346914 TTGAAATGAA
1346924 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1346938 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1346955 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1346971 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1346990 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1347004 AATCGCAACG
1 AATCGCAACG
1347014 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1346961 original size:33 final size:33
Alignment explanation
Indices: 1346916--1347030 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1346906 TCTTTTGGTT
1346916 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1346949 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1346982 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1347015 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1347031 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1346962 original size:19 final size:18
Alignment explanation
Indices: 1346923--1347035 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1346913 GTTGAAATGA
1346923 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1346938 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1346955 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1346971 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1346988 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1347004 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1347021 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1347036 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1347066 original size:14 final size:14
Alignment explanation
Indices: 1347047--1347102 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
1347037 TTTGGTTTCG
1347047 CGTTGCGATTCTAT
1 CGTTGCGATTCTAT
*
1347061 CGTTGCGATTTCATTT
1 CGTTGCGA-TTC-TAT
*
1347077 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTAT
1347093 CGTTGCGATT
1 CGTTGCGATT
1347103 GTCATCTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 18 0.50
15 3 0.08
16 4 0.11
17 3 0.08
18 8 0.22
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTAT
Found at i:1347081 original size:32 final size:33
Alignment explanation
Indices: 1347042--1347121 Score: 117
Period size: 32 Copynumber: 2.4 Consensus size: 33
1347032 GCGATTTTGG
1347042 TTTCGCGTTGCGATTCTATCGTTGCGATT-TCA
1 TTTCGCGTTGCGATTCTATCGTTGCGATTGTCA
*
1347074 TTTCGCGTTGCGATTCTCTCGTTGCGATTGTCA
1 TTTCGCGTTGCGATTCTATCGTTGCGATTGTCA
*
1347107 TCTCTCTCGTTGCGA
1 T-T-TCGCGTTGCGA
1347122 CAGTCATTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
32 28 0.65
33 4 0.09
34 1 0.02
35 10 0.23
ACGTcount: A:0.10, C:0.25, G:0.23, T:0.42
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTATCGTTGCGATTGTCA
Found at i:1347084 original size:18 final size:17
Alignment explanation
Indices: 1347042--1347088 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
1347032 GCGATTTTGG
1347042 TTTCGCGTTGCGA-TTC
1 TTTCGCGTTGCGATTTC
*
1347058 TAT--CGTTGCGATTTC
1 TTTCGCGTTGCGATTTC
1347073 ATTTCGCGTTGCGATT
1 -TTTCGCGTTGCGATT
1347089 CTCTCGTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 8 0.32
15 3 0.12
16 4 0.16
18 10 0.40
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (17 bp):
TTTCGCGTTGCGATTTC
Found at i:1347143 original size:41 final size:41
Alignment explanation
Indices: 1347086--1347163 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
1347076 TCGCGTTGCG
*
1347086 ATTCTCTCGTTGCGATTGTCATCTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTGTCATCTATCTCGTTGCGACAGTC
* *
1347127 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTGTCATCTATCTCGTTGCGAC
1347164 TCTTCTGCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.13, C:0.27, G:0.18, T:0.42
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTGTCATCTATCTCGTTGCGACAGTC
Found at i:1347148 original size:20 final size:20
Alignment explanation
Indices: 1347086--1347162 Score: 100
Period size: 21 Copynumber: 3.8 Consensus size: 20
1347076 TCGCGTTGCG
1347086 ATTCTCTCGTTGCGATTGTC
1 ATTCTCTCGTTGCGATTGTC
**
1347106 ATCTCTCTCGTTGCGACAGTC
1 AT-TCTCTCGTTGCGATTGTC
*
1347127 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTGTC
*
1347147 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1347163 CTCTTCTGCA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
20 18 0.37
21 31 0.63
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.43
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTGTC
Found at i:1347288 original size:33 final size:33
Alignment explanation
Indices: 1347244--1347311 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
1347234 TACTAACTTG
* *
1347244 AAATCGGAACGAGAGAATAGCAACGCGAAATGA
1 AAATCGCAACGACAGAATAGCAACGCGAAATGA
* *
1347277 AAATCGCAACGACAGAATCGTAACGCGAAATGA
1 AAATCGCAACGACAGAATAGCAACGCGAAATGA
1347310 AA
1 AA
1347312 TCTAAGTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.49, C:0.18, G:0.24, T:0.10
Consensus pattern (33 bp):
AAATCGCAACGACAGAATAGCAACGCGAAATGA
Found at i:1347544 original size:22 final size:22
Alignment explanation
Indices: 1347492--1347546 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1347482 TGGTTGTGAG
**
1347492 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1347514 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1347536 GGATTTCTTCG
1 GGATTTCTTCG
1347547 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1347717 original size:20 final size:20
Alignment explanation
Indices: 1347692--1347885 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1347682 CTTTAAATAT
1347692 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1347712 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1347734 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1347753 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1347773 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1347793 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1347813 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1347833 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1347853 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1347873 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1347886 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1347879 original size:60 final size:60
Alignment explanation
Indices: 1347692--1347885 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1347682 CTTTAAATAT
**
1347692 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1347753 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1347813 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1347873 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1347886 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1347902 original size:21 final size:20
Alignment explanation
Indices: 1347878--1347954 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
1347868 ATATTCGCGT
1347878 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
1347899 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
1347919 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
1347941 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
1347955 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:1347965 original size:20 final size:20
Alignment explanation
Indices: 1347940--1347991 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1347930 AAGAATCGCG
*
1347940 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1347960 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1347980 TTGCGATTCTGG
1 TTGCGATTCTGG
1347992 GGGATCGCGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:1349494 original size:31 final size:32
Alignment explanation
Indices: 1349437--1349496 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
1349427 TAAAATTTTT
*
1349437 AAAAATTTAGAGATTTAAATTAAAATTTTGAA
1 AAAAATTAAGAGATTTAAATTAAAATTTTGAA
*
1349469 AAAAATTGAAGAG-TTT-AATTGAAATTTT
1 AAAAATT-AAGAGATTTAAATTAAAATTTT
1349497 TTGTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 11 0.44
32 10 0.40
33 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (32 bp):
AAAAATTAAGAGATTTAAATTAAAATTTTGAA
Found at i:1351185 original size:35 final size:35
Alignment explanation
Indices: 1351140--1351259 Score: 107
Period size: 35 Copynumber: 3.4 Consensus size: 35
1351130 TTAAGCCTGC
* * *
1351140 TGCTCATTAAGTTCGATGCTCGTTG-CTCGCCTCAT
1 TGCTCATTAAGCTCAATGCTCATTGTC-CGCCTCAT
*
1351175 TGCTCCTTAAGCTCAATGCTCATTGTCCGCCTCAT
1 TGCTCATTAAGCTCAATGCTCATTGTCCGCCTCAT
* ** * ** **
1351210 TGCACATTAAGGACAATGCTCGTTGTTTGCCTTGT
1 TGCTCATTAAGCTCAATGCTCATTGTCCGCCTCAT
*
1351245 TGCTCGTTAAGCTCA
1 TGCTCATTAAGCTCA
1351260 TTGAAATTTT
Statistics
Matches: 67, Mismatches: 17, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
35 66 0.99
36 1 0.01
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (35 bp):
TGCTCATTAAGCTCAATGCTCATTGTCCGCCTCAT
Found at i:1351990 original size:21 final size:23
Alignment explanation
Indices: 1351947--1351999 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 23
1351937 AATTTTGTAC
* *
1351947 TCTCTAAAATTTTATTATTTATA
1 TCTCTAAAATTTTATAATATATA
1351970 TCTCT-AAA-TTTATAATATATA
1 TCTCTAAAATTTTATAATATATA
1351991 T-TCTTAAAA
1 TCTC-TAAAA
1352000 AAACAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 2 0.08
21 13 0.50
22 6 0.23
23 5 0.19
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (23 bp):
TCTCTAAAATTTTATAATATATA
Found at i:1353190 original size:31 final size:31
Alignment explanation
Indices: 1353133--1353191 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1353123 AAATAGGGTA
* * *
1353133 AATTTTTTATTTGGTCATTCATCTATTACTT
1 AATTTTTTATTTGGTAACTCAACTATTACTT
1353164 AATTTTTTATTTGGTAACTCAACTATTA
1 AATTTTTTATTTGGTAACTCAACTATTA
1353192 TTTTTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.54
Consensus pattern (31 bp):
AATTTTTTATTTGGTAACTCAACTATTACTT
Found at i:1353210 original size:25 final size:26
Alignment explanation
Indices: 1353182--1353249 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 26
1353172 ATTTGGTAAC
* *
1353182 TCAACTATT-ATTTTTTTAAATCATA
1 TCAAATATTAATTTTTTTAAATAATA
*
1353207 TCAAATGTTACATTTTTTTAAATAATA
1 TCAAATATTA-ATTTTTTTAAATAATA
*
1353234 TCAAATGTTACATTTT
1 TCAAATATTA-ATTTT
1353250 GGTTATGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 7 0.18
27 31 0.82
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.50
Consensus pattern (26 bp):
TCAAATATTAATTTTTTTAAATAATA
Found at i:1353222 original size:26 final size:27
Alignment explanation
Indices: 1353191--1353249 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
1353181 CTCAACTATT
*
1353191 ATTTTTTTAAATCATATCAAATGTTAC
1 ATTTTTTTAAATAATATCAAATGTTAC
1353218 ATTTTTTTAAATAATATCAAATGTTAC
1 ATTTTTTTAAATAATATCAAATGTTAC
1353245 ATTTT
1 ATTTT
1353250 GGTTATGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.51
Consensus pattern (27 bp):
ATTTTTTTAAATAATATCAAATGTTAC
Found at i:1358965 original size:29 final size:29
Alignment explanation
Indices: 1358910--1358965 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1358900 CCAAAATTTA
** *
1358910 TTCGGTTCGGTTAATATTTTTAAAAAATG
1 TTCGGTTCGGTTAATAGGTTAAAAAAATG
1358939 TTCGGTTCGGTTAAT-GGTTAAAGAAAA
1 TTCGGTTCGGTTAATAGGTTAAA-AAAA
1358966 AAAAAATCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.39
Consensus pattern (29 bp):
TTCGGTTCGGTTAATAGGTTAAAAAAATG
Found at i:1362847 original size:177 final size:174
Alignment explanation
Indices: 1362554--1362901 Score: 588
Period size: 177 Copynumber: 2.0 Consensus size: 174
1362544 TTTTTAAATT
** *
1362554 TTACATAGATTTAAGACCGTTAAATTAGTAAAATAAAATGAGATTAACAGTAGAAAATTATAAGA
1 TTACATAGATTTAAGACCACTAAATTAGTAAAATAAAATAAGATTAACAGTAGAAAATTATAAGA
* *
1362619 TATTCAGTGAAAAAATGACTTAATCTTAACTTTCTATTTTCACTCATCCAACTGTCTTAAATCTA
66 TATTCAATGAAAAAATGACTTAATCTTAACTTTATATTTTCACTCATCCAACTGTCTTAAATCTA
*
1362684 TGTAAACTGAAAACTATTTTACACTGTATAAATGAATCTTATAA
131 TGTAAACTGAAAACTATTTTACACAGTATAAATGAATCTTATAA
*
1362728 TTACATAGATTTAAGACCACTAAATTAGTAAAATATAAAATTAAGATTAACCGTAGAAAATTATA
1 TTACATAGATTTAAGACCACTAAATTAGT-AAA-ATAAAA-TAAGATTAACAGTAGAAAATTATA
*
1362793 AGATATTCAATGAAAAAATGACTTAATCTTAGCTTTATATTTTCACTCATCCAACTGTCTTAAAT
63 AGATATTCAATGAAAAAATGACTTAATCTTAACTTTATATTTTCACTCATCCAACTGTCTTAAAT
*
1362858 CTATGTAAACTGAAAATTATTTTACACAGTATAAATGAATCTTA
128 CTATGTAAACTGAAAACTATTTTACACAGTATAAATGAATCTTA
1362902 ACCTATATAT
Statistics
Matches: 162, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
174 27 0.17
175 3 0.02
176 6 0.04
177 126 0.78
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (174 bp):
TTACATAGATTTAAGACCACTAAATTAGTAAAATAAAATAAGATTAACAGTAGAAAATTATAAGA
TATTCAATGAAAAAATGACTTAATCTTAACTTTATATTTTCACTCATCCAACTGTCTTAAATCTA
TGTAAACTGAAAACTATTTTACACAGTATAAATGAATCTTATAA
Found at i:1383595 original size:49 final size:49
Alignment explanation
Indices: 1383522--1383615 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
1383512 TTTTGTTGAA
** *
1383522 TAATGCTAAGGTGCAGGCGTGCCTAGGTGAACGCCTTGACAACACTGGT
1 TAATGCTAAGGTGCAGGCACGCCTAGGTGAACACCTTGACAACACTGGT
*
1383571 TAATGCTAAGGTGCAGGCACGCCTAGGTGCACACCTTGACAACAC
1 TAATGCTAAGGTGCAGGCACGCCTAGGTGAACACCTTGACAACAC
1383616 AGATTACAGC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.27, C:0.26, G:0.28, T:0.20
Consensus pattern (49 bp):
TAATGCTAAGGTGCAGGCACGCCTAGGTGAACACCTTGACAACACTGGT
Found at i:1393784 original size:24 final size:24
Alignment explanation
Indices: 1393757--1393816 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
1393747 GAACGCAGAG
*
1393757 GTCTACGAATTGGAGAACGGCTCC
1 GTCTACGAATTGGAGAACGGCTAC
* *
1393781 GTCTACGAATCGGAGAAGGGCTAC
1 GTCTACGAATTGGAGAACGGCTAC
1393805 GTCTACG-ATTGG
1 GTCTACGAATTGG
1393817 TGGGAGACCT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 4 0.12
24 28 0.88
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.22
Consensus pattern (24 bp):
GTCTACGAATTGGAGAACGGCTAC
Found at i:1398818 original size:70 final size:70
Alignment explanation
Indices: 1398705--1398849 Score: 281
Period size: 70 Copynumber: 2.1 Consensus size: 70
1398695 ATTAGTCACA
1398705 TTTGTATATATTGATACGAGAATATTGACATATATTTGTATGTGTGTGAATACATGTACGTCACT
1 TTTGTATATATTGATACGAGAATATTGACATATATTTGTATGTGTGTGAATACATGTACGTCACT
1398770 CATAT
66 CATAT
*
1398775 TTTGTATATATTGATACGAGAATGTTGACATATATTTGTATGTGTGTGAATACATGTACGTCACT
1 TTTGTATATATTGATACGAGAATATTGACATATATTTGTATGTGTGTGAATACATGTACGTCACT
1398840 CATAT
66 CATAT
1398845 TTTGT
1 TTTGT
1398850 TACGTCATTC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 74 1.00
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.43
Consensus pattern (70 bp):
TTTGTATATATTGATACGAGAATATTGACATATATTTGTATGTGTGTGAATACATGTACGTCACT
CATAT
Found at i:1398845 original size:35 final size:35
Alignment explanation
Indices: 1398736--1398846 Score: 113
Period size: 35 Copynumber: 3.2 Consensus size: 35
1398726 ATATTGACAT
1398736 ATATTTGTATGTGTGTGAATACATGTACGTCACTC
1 ATATTTGTATGTGTGTGAATACATGTACGTCACTC
* * * * *
1398771 ATATTTTGTATATAT-TG-ATACGA-GAATGTTGACAT-
1 ATA-TTTGTATGTGTGTGAATAC-ATGTACG-TCAC-TC
1398806 ATATTTGTATGTGTGTGAATACATGTACGTCACTC
1 ATATTTGTATGTGTGTGAATACATGTACGTCACTC
1398841 ATATTT
1 ATATTT
1398847 TGTTACGTCA
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
34 17 0.29
35 24 0.41
36 17 0.29
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (35 bp):
ATATTTGTATGTGTGTGAATACATGTACGTCACTC
Found at i:1401502 original size:128 final size:128
Alignment explanation
Indices: 1401274--1401658 Score: 770
Period size: 128 Copynumber: 3.0 Consensus size: 128
1401264 AGTTTCAATC
1401274 AGATTCGCTAAATTTATTTCATGCTTTAATGCTGCTTATGCTAGCAGATGGTACATATATAAAGA
1 AGATTCGCTAAATTTATTTCATGCTTTAATGCTGCTTATGCTAGCAGATGGTACATATATAAAGA
1401339 GTTTTGGATTATGTTAACTACTATAAAGGAATCCATTTCCTCCATAAAAATAAAAAGGGACAA
66 GTTTTGGATTATGTTAACTACTATAAAGGAATCCATTTCCTCCATAAAAATAAAAAGGGACAA
1401402 AGATTCGCTAAATTTATTTCATGCTTTAATGCTGCTTATGCTAGCAGATGGTACATATATAAAGA
1 AGATTCGCTAAATTTATTTCATGCTTTAATGCTGCTTATGCTAGCAGATGGTACATATATAAAGA
1401467 GTTTTGGATTATGTTAACTACTATAAAGGAATCCATTTCCTCCATAAAAATAAAAAGGGACAA
66 GTTTTGGATTATGTTAACTACTATAAAGGAATCCATTTCCTCCATAAAAATAAAAAGGGACAA
1401530 AGATTCGCTAAATTTATTTCATGCTTTAATGCTGCTTATGCTAGCAGATGGTACATATATAAAGA
1 AGATTCGCTAAATTTATTTCATGCTTTAATGCTGCTTATGCTAGCAGATGGTACATATATAAAGA
1401595 GTTTTGGATTATGTTAACTACTATAAAGGAATCCATTTCCTCCATAAAAATAAAAAGGGACAA
66 GTTTTGGATTATGTTAACTACTATAAAGGAATCCATTTCCTCCATAAAAATAAAAAGGGACAA
1401658 A
1 A
1401659 CGTACCAAAG
Statistics
Matches: 257, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 257 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.34
Consensus pattern (128 bp):
AGATTCGCTAAATTTATTTCATGCTTTAATGCTGCTTATGCTAGCAGATGGTACATATATAAAGA
GTTTTGGATTATGTTAACTACTATAAAGGAATCCATTTCCTCCATAAAAATAAAAAGGGACAA
Found at i:1409569 original size:280 final size:280
Alignment explanation
Indices: 1409068--1409909 Score: 1648
Period size: 280 Copynumber: 3.0 Consensus size: 280
1409058 GCAGTCATGA
1409068 TACATAAGCAGTACCTAGGAGAAGTTCTAATACAAATGTGTTCGAGACAGCAACAATTGAAGTAC
1 TACATAAGCAGTACCTAGGAGAAGTTCTAATACAAATGTGTTCGAGACAGCAACAATTGAAGTAC
1409133 ACAATAAGGTGCAAATGATGCCAAGGCTGAAAGGAATTCAATTAGCTATACCGTTCCACACAAAT
66 ACAATAAGGTGCAAATGATGCCAAGGCTGAAAGGAATTCAATTAGCTATACCGTTCCACACAAAT
1409198 GTGGCTATGATGGAGCGTCAACTGTGGTTCAGGTGAAACACCAAAGATAACTTTTTAAGTAAAGG
131 GTGGCTATGATGGAGCGTCAACTGTGGTTCAGGTGAAACACCAAAGATAACTTTTTAAGTAAAGG
1409263 CCAATTTCCTTTGAGATTTTAGTTTTATTACCTGTGTTTTCACTTTCATCCCTTGTTTTTGCAAA
196 CCAATTTCCTTTGAGATTTTAGTTTTATTACCTGTGTTTTCACTTTCATCCCTTGTTTTTGCAAA
1409328 ACATTGAAGTGGCTTATGTG
261 ACATTGAAGTGGCTTATGTG
1409348 TACATAAGCAGTACCTAGGAGAAGTTCTAATACAAATGTGTTCGAGACAGCAACAATTGAAGTAC
1 TACATAAGCAGTACCTAGGAGAAGTTCTAATACAAATGTGTTCGAGACAGCAACAATTGAAGTAC
1409413 ACAATAAGGTGCAAATGATGCCAAGGCTGAAAGGAATTCAATTAGCTATACCGTTCCACACAAAT
66 ACAATAAGGTGCAAATGATGCCAAGGCTGAAAGGAATTCAATTAGCTATACCGTTCCACACAAAT
1409478 GTGGCTATGATGGAGCGTCAACTGTGGTTCAGGTGAAACACCAAAGATAACTTTTTAAGTAAAGG
131 GTGGCTATGATGGAGCGTCAACTGTGGTTCAGGTGAAACACCAAAGATAACTTTTTAAGTAAAGG
1409543 CCAATTTCCTTTGAGATTTTAGTTTTATTACCTGTGTTTTCACTTTCATCCCTTGTTTTTGCAAA
196 CCAATTTCCTTTGAGATTTTAGTTTTATTACCTGTGTTTTCACTTTCATCCCTTGTTTTTGCAAA
1409608 ACATTGAAGTGGCTTATGTG
261 ACATTGAAGTGGCTTATGTG
* *
1409628 TACATAAGAAGTACCTAGGAGAAGTTCTAATAAAAATGTGTTCGAGACAGCAACAATTGAAGTAC
1 TACATAAGCAGTACCTAGGAGAAGTTCTAATACAAATGTGTTCGAGACAGCAACAATTGAAGTAC
1409693 ACAATAAGGTGCAAATGATGCCAAGGCTGAAAGGAATTCAATTAGCTATACCGTTCCACACAAAT
66 ACAATAAGGTGCAAATGATGCCAAGGCTGAAAGGAATTCAATTAGCTATACCGTTCCACACAAAT
1409758 GTGGCTATGATGGAGCGTCAACTGTGGTTCAGGTGAAACACCAAAGATAACTTTTTAAGTAAAGG
131 GTGGCTATGATGGAGCGTCAACTGTGGTTCAGGTGAAACACCAAAGATAACTTTTTAAGTAAAGG
* *
1409823 CCAATTTCCTTTGAGATTTTAGTTTTATTACCTGTGTTTTCACTTTCATCCATTCTTTTTGCAAA
196 CCAATTTCCTTTGAGATTTTAGTTTTATTACCTGTGTTTTCACTTTCATCCCTTGTTTTTGCAAA
1409888 ACATTGAAGTGGCTTATGTG
261 ACATTGAAGTGGCTTATGTG
1409908 TA
1 TA
1409910 TAGAAACTTG
Statistics
Matches: 558, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
280 558 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Consensus pattern (280 bp):
TACATAAGCAGTACCTAGGAGAAGTTCTAATACAAATGTGTTCGAGACAGCAACAATTGAAGTAC
ACAATAAGGTGCAAATGATGCCAAGGCTGAAAGGAATTCAATTAGCTATACCGTTCCACACAAAT
GTGGCTATGATGGAGCGTCAACTGTGGTTCAGGTGAAACACCAAAGATAACTTTTTAAGTAAAGG
CCAATTTCCTTTGAGATTTTAGTTTTATTACCTGTGTTTTCACTTTCATCCCTTGTTTTTGCAAA
ACATTGAAGTGGCTTATGTG
Found at i:1411278 original size:20 final size:20
Alignment explanation
Indices: 1411255--1411306 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1411245 AACGCGATCC
1411255 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
1411275 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
1411295 CCAAAATCGCAA
1 CCAGAATCGCAA
1411307 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:1411456 original size:20 final size:20
Alignment explanation
Indices: 1411362--1411730 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
1411352 GATTTTCCAT
* ** *
1411362 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1411382 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1411402 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1411422 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1411442 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1411462 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1411482 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1411502 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1411522 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1411542 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1411562 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1411582 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1411602 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1411622 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1411642 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1411662 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1411682 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1411702 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1411722 AATCACAAC
1 AATCGCAAC
1411731 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1412452 original size:24 final size:24
Alignment explanation
Indices: 1412413--1412459 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1412403 AAATTTGGTC
1412413 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1412437 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1412460 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1412651 original size:12 final size:12
Alignment explanation
Indices: 1412634--1412658 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1412624 ATATAATCCT
1412634 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1412646 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1412658 G
1 G
1412659 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1414962 original size:19 final size:19
Alignment explanation
Indices: 1414940--1415246 Score: 376
Period size: 19 Copynumber: 17.4 Consensus size: 19
1414930 CGGAAAATAC
*
1414940 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1414959 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1414973 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1414993 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1415007 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1415026 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1415045 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1415059 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1415078 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1415097 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
1415111 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
1415130 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1415149 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1415168 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1415187 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1415201 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1415220 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1415239 AATCGCAA
1 AATCGCAA
1415247 CGAGATAATC
Statistics
Matches: 252, Mismatches: 10, Indels: 52
0.80 0.03 0.17
Matches are distributed among these distances:
14 48 0.19
15 2 0.01
16 16 0.06
17 14 0.06
18 3 0.01
19 156 0.62
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Done.