Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 129 of 170
Found at i:39248159 original size:3 final size:3
Alignment explanation
Indices: 39248153--39248188 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
39248143 ATAATAATAA
* *
39248153 TAT TAT TAT TGT TAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39248189 AATTGCCCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:39248222 original size:20 final size:21
Alignment explanation
Indices: 39248197--39248245 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
39248187 ATAATTGCCC
*
39248197 TTATATATATACGT-TTTTTT
1 TTATATATATACATATTTTTT
39248217 TTATATATATACATATTTTTT
1 TTATATATATACATATTTTTT
39248238 TT-TATATA
1 TTATATATA
39248246 CTTACACACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (21 bp):
TTATATATATACATATTTTTT
Found at i:39248226 original size:22 final size:22
Alignment explanation
Indices: 39248198--39248253 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
39248188 TAATTGCCCT
* *
39248198 TATATATATACGTTTTTTTTTA
1 TATATATACACATTTTTTTTTA
*
39248220 TATATATACATATTTTTTTTTA
1 TATATATACACATTTTTTTTTA
39248242 TATACT-TACACA
1 TATA-TATACACA
39248254 CATACTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (22 bp):
TATATATACACATTTTTTTTTA
Found at i:39248538 original size:18 final size:17
Alignment explanation
Indices: 39248515--39248550 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
39248505 TTTAATTTTA
*
39248515 TATTTGTTTATTTACTTT
1 TATTTGTTGATTT-CTTT
39248533 TATTTGTTGATTTCTTT
1 TATTTGTTGATTTCTTT
39248550 T
1 T
39248551 CATTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (17 bp):
TATTTGTTGATTTCTTT
Found at i:39248851 original size:110 final size:110
Alignment explanation
Indices: 39248658--39249314 Score: 1095
Period size: 110 Copynumber: 6.0 Consensus size: 110
39248648 TATCAAAAAC
39248658 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* *
39248723 AGGTGTCGATTGTTCTCATTCAACCAAATGGCTAAATATCCTTTT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
39248768 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
*
39248833 GGGTGTTGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
*
39248878 AAAAATTTTCAAATAAGGCAATGTATTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
*
39248943 AGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
* *
39248988 AAAAATTTT-AAATTAAGGCAATGTTTTGCGTTTAGGAAATTCGAGAGAACGTGCCCTAAGGTGC
1 AAAAATTTTCAAA-TAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGC
*
39249052 TGGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTT
65 TGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
* *
39249098 AAAAAAATTTCGAAATAAGGCAATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTG
1 -AAAAATTTTC-AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTG
* *
39249163 CTGGGTGTTGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTT
64 CTGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
* * *
39249210 AAAAATTTTAAAATAAAGCAATGTTTTGCGTTT--GAAATTTGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* * * *
39249273 GGGTGTCGATTTTTCTCATTTAACCGAATAGCCAAATATCCT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCT
39249315 CTTGAATTTC
Statistics
Matches: 516, Mismatches: 27, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
108 65 0.13
109 3 0.01
110 336 0.65
111 16 0.03
112 93 0.18
113 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (110 bp):
AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
Found at i:39253377 original size:6 final size:6
Alignment explanation
Indices: 39253368--39253406 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
39253358 AAATCATAAG
39253368 AGAAAA AGAAAGA AGAAAA A-AGAAA AGAAAA AGAAAA AG
1 AGAAAA AGAAA-A AGAAAA AGA-AAA AGAAAA AGAAAA AG
39253407 GAGAAGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 1 0.03
6 22 0.73
7 7 0.23
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:39255688 original size:46 final size:46
Alignment explanation
Indices: 39255451--39255678 Score: 384
Period size: 46 Copynumber: 5.0 Consensus size: 46
39255441 AATGAAGTTA
*
39255451 CAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
39255497 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
39255543 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
* * *
39255589 CAGATCTTGTCTTCCTGTATTTGGCAGCAGAAGAGATCGAAGATAA
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
* * * *
39255635 CAGATCTTGTCTTTCTGTATTTGGCAGCAGAGTAGCTCGAAGAT
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
39255679 GGTGAATCTT
Statistics
Matches: 174, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 174 1.00
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (46 bp):
CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
Found at i:39255822 original size:132 final size:132
Alignment explanation
Indices: 39255674--39255962 Score: 438
Period size: 132 Copynumber: 2.2 Consensus size: 132
39255664 GAGTAGCTCG
* *
39255674 AAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACT
1 AAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAACCATTAGTCCTATCACC
* * * * * *
39255739 CTAAGCAGTAGTGGAGTAGGTTGAA-GATTACAGATTCTGTCA-CCCTAAGCAGTAGTGGAGCAG
66 CTAAGCAGTAGTGGAATA-GATCAATGACTACAGATTCTGT-ATCCCTAAACAGTAGTGGAACAG
39255802 ATCA
129 ATCA
39255806 AAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAACCATTAGTCCTATCACC
1 AAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAACCATTAGTCCTATCACC
*
39255871 CTAAGCAGTAGTGGAATAGATCAATGACTATAGATTCTGTATCCCTAAACAGTAGTGGAACAGAT
66 CTAAGCAGTAGTGGAATAGATCAATGACTACAGATTCTGTATCCCTAAACAGTAGTGGAACAGAT
39255936 CA
131 CA
* * *
39255938 AAGACGGTGAATTTTACCTTCCCAA
1 AAGATGGTGAATCTTATCTTCCCAA
39255963 GATACTAGGG
Statistics
Matches: 143, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
131 5 0.03
132 138 0.97
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (132 bp):
AAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAACCATTAGTCCTATCACC
CTAAGCAGTAGTGGAATAGATCAATGACTACAGATTCTGTATCCCTAAACAGTAGTGGAACAGAT
CA
Found at i:39256303 original size:22 final size:22
Alignment explanation
Indices: 39256277--39256318 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39256267 CCTCAGCTAC
39256277 CCAAACACAACCAAACCCAAAT
1 CCAAACACAACCAAACCCAAAT
* *
39256299 CCAAACAGAACCAGACCCAA
1 CCAAACACAACCAAACCCAA
39256319 CTAGCCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.40, G:0.05, T:0.02
Consensus pattern (22 bp):
CCAAACACAACCAAACCCAAAT
Found at i:39257451 original size:3 final size:3
Alignment explanation
Indices: 39257445--39257480 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
39257435 TTAATAATAA
* *
39257445 TAT TAT TAT TGT TAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39257481 AATTTCCCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:39257678 original size:39 final size:39
Alignment explanation
Indices: 39257616--39257693 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
39257606 TATATGTGTT
* * *
39257616 CTTTATATTTTATGATTCATACATATATCTATATATATA
1 CTTTATATTTTATGATACATACATACATATATATATATA
* ** *
39257655 CTTTTTATTTTATGATAGTTACATACATATATATGTATA
1 CTTTATATTTTATGATACATACATACATATATATATATA
39257694 TGCTTACTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (39 bp):
CTTTATATTTTATGATACATACATACATATATATATATA
Found at i:39257874 original size:18 final size:17
Alignment explanation
Indices: 39257851--39257886 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
39257841 TTTAATTTTA
*
39257851 TATTTGTTTATTTACTTT
1 TATTTGTTGATTT-CTTT
39257869 TATTTGTTGATTTCTTT
1 TATTTGTTGATTTCTTT
39257886 T
1 T
39257887 CATTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (17 bp):
TATTTGTTGATTTCTTT
Found at i:39258187 original size:110 final size:110
Alignment explanation
Indices: 39257994--39258541 Score: 891
Period size: 110 Copynumber: 5.0 Consensus size: 110
39257984 TATCAAAAAC
39257994 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* *
39258059 AGGTGTCGATTGTTCTCATTCAACCAAATGGCTAAATATCCTTTT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
*
39258104 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTCGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
*
39258169 GGGTGTTGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
* *
39258214 AAAAATTTTCAAATAAGGCAATGTATTGCGTTTGGGAAATTCGAGAGAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* *
39258279 GGGTGTCGATTTGTCTCGTTCAACCAAATGGCTAAATATCCTTTT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
** *
39258324 AAAAAATTTTCGAAATAAGGCAATGTTTTGTATTTGGGAAATTCGAGAAAACGTGCCTTAAGGTG
1 -AAAAATTTTC-AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTG
* * *
39258389 CCGGGTGTTGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTT
64 CTGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
* *
39258436 AAAAATTTTAAAATAAGGCAATGTTTTGCGTTT-GAAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* * * *
39258500 GGGTGTCGATTTTTCTCATTTAACCGAATAGCCAAATATCCT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCT
39258542 CTTGAATTTC
Statistics
Matches: 406, Mismatches: 30, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
109 64 0.16
110 231 0.57
111 19 0.05
112 92 0.23
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (110 bp):
AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
Found at i:39258452 original size:222 final size:220
Alignment explanation
Indices: 39257994--39258541 Score: 902
Period size: 222 Copynumber: 2.5 Consensus size: 220
39257984 TATCAAAAAC
39257994 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
*
39258059 AGGTGTCGA-TTGTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTCAAATAAGGC
66 GGGTGTCGATTTG-TCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTCAAATAAGGC
* *
39258123 AATGTTTTGCGTTCGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTTGATTTTTCTCAT
130 AATGTTTTGCATTCGGGAAATTCGAGAAAACGTGCCCTAAGGTGCCGGGTGTTGATTTTTCTCAT
39258188 TCAACCAAATGGCTAAATATCCTTTT
195 TCAACCAAATGGCTAAATATCCTTTT
* *
39258214 AAAAATTTTCAAATAAGGCAATGTATTGCGTTTGGGAAATTCGAGAGAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
*
39258279 GGGTGTCGATTTGTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAAATTTTCGAAATAAGG
66 GGGTGTCGATTTGTCTCATTCAACCAAATGGCTAAATATCCTTTT-AAAAATTTTC-AAATAAGG
* * * *
39258344 CAATGTTTTGTATTTGGGAAATTCGAGAAAACGTGCCTTAAGGTGCCGGGTGTTGATTTTTCTCG
129 CAATGTTTTGCATTCGGGAAATTCGAGAAAACGTGCCCTAAGGTGCCGGGTGTTGATTTTTCTCA
39258409 TTCAACCAAATGGCTAAATATCCTTTT
194 TTCAACCAAATGGCTAAATATCCTTTT
* *
39258436 AAAAATTTTAAAATAAGGCAATGTTTTGCGTTT-GAAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* * * * *
39258500 GGGTGTCGATTTTTCTCATTTAACCGAATAGCCAAATATCCT
66 GGGTGTCGATTTGTCTCATTCAACCAAATGGCTAAATATCCT
39258542 CTTGAATTTC
Statistics
Matches: 305, Mismatches: 20, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
220 102 0.33
221 78 0.26
222 125 0.41
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (220 bp):
AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
GGGTGTCGATTTGTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTCAAATAAGGCA
ATGTTTTGCATTCGGGAAATTCGAGAAAACGTGCCCTAAGGTGCCGGGTGTTGATTTTTCTCATT
CAACCAAATGGCTAAATATCCTTTT
Found at i:39260093 original size:63 final size:63
Alignment explanation
Indices: 39260008--39260130 Score: 174
Period size: 63 Copynumber: 2.0 Consensus size: 63
39259998 TAATCACACG
* *
39260008 CACGCACACACACACAAAGACATACTTTTTTCAACCCAAACTCTCAATTTGCATAAGTCCACA
1 CACGCACACACACACAAAGACATACTTCTTTCAACCCAAACTATCAATTTGCATAAGTCCACA
* * * * * *
39260071 CACGCACGCACACACAATGACATACTTCTTTCGATCCACACTATGAATTTGCATAAGTCC
1 CACGCACACACACACAAAGACATACTTCTTTCAACCCAAACTATCAATTTGCATAAGTCC
39260131 TATCAAATCC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.35, C:0.33, G:0.09, T:0.24
Consensus pattern (63 bp):
CACGCACACACACACAAAGACATACTTCTTTCAACCCAAACTATCAATTTGCATAAGTCCACA
Found at i:39261821 original size:38 final size:37
Alignment explanation
Indices: 39261769--39261918 Score: 196
Period size: 38 Copynumber: 4.0 Consensus size: 37
39261759 AGAAGCATAA
39261769 TGTTATTC-GAGCTCTGTGCCTAGCAGGCTTTGTGCCAG
1 TGTTATTCAG-GCTCTGTGCCTAGCAGGCTTTGTGCC-G
**
39261807 TGTTATTTGGGCTCTGTGCCTAGCAGGCTTTGTGCCG
1 TGTTATTCAGGCTCTGTGCCTAGCAGGCTTTGTGCCG
*
39261844 ATGTTATTCAGGCTCTGTGCCTAGTAGGCTTTGTGCCGG
1 -TGTTATTCAGGCTCTGTGCCTAGCAGGCTTTGTGCC-G
* * *
39261883 TGTTATTCATGCTTTGTGCCTAGTAGGC-TTGTGCCG
1 TGTTATTCAGGCTCTGTGCCTAGCAGGCTTTGTGCCG
39261919 ATATATTGAA
Statistics
Matches: 103, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
36 1 0.01
37 8 0.08
38 92 0.89
39 2 0.02
ACGTcount: A:0.11, C:0.21, G:0.30, T:0.37
Consensus pattern (37 bp):
TGTTATTCAGGCTCTGTGCCTAGCAGGCTTTGTGCCG
Found at i:39261855 original size:22 final size:21
Alignment explanation
Indices: 39261830--39261902 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 21
39261820 CTGTGCCTAG
39261830 CAGGCTTTGTGCCGATGTTATT
1 CAGGCTTTGTGCCG-TGTTATT
* *
39261852 CAGGCTCTGTGCC----TAGT
1 CAGGCTTTGTGCCGTGTTATT
39261869 -AGGCTTTGTGCCGGTGTTATT
1 CAGGCTTTGTGCC-GTGTTATT
*
39261890 CATGCTTTGTGCC
1 CAGGCTTTGTGCC
39261903 TAGTAGGCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
16 11 0.28
17 3 0.08
21 3 0.08
22 23 0.57
ACGTcount: A:0.11, C:0.22, G:0.29, T:0.38
Consensus pattern (21 bp):
CAGGCTTTGTGCCGTGTTATT
Found at i:39261901 original size:76 final size:75
Alignment explanation
Indices: 39261768--39261920 Score: 218
Period size: 76 Copynumber: 2.0 Consensus size: 75
39261758 TAGAAGCATA
**
39261768 ATGTTATTCGAGCTCTGTGCCTAGCAGGCTTTGTGCCAGTGTTATTTGGGCTCTGTGCCTAGCAG
1 ATGTTATTCGAGCTCTGTGCCTAGCAGGCTTTGTGCCAGTGTTATTCAGGCTCTGTGCCTAGCAG
39261833 GCTTTGTGCCG
66 GC-TTGTGCCG
* * * * *
39261844 ATGTTATTC-AGGCTCTGTGCCTAGTAGGCTTTGTGCCGGTGTTATTCATGCTTTGTGCCTAGTA
1 ATGTTATTCGA-GCTCTGTGCCTAGCAGGCTTTGTGCCAGTGTTATTCAGGCTCTGTGCCTAGCA
39261908 GGCTTGTGCCG
65 GGCTTGTGCCG
39261919 AT
1 AT
39261921 ATATTGAAAG
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
75 11 0.16
76 58 0.84
ACGTcount: A:0.12, C:0.21, G:0.29, T:0.37
Consensus pattern (75 bp):
ATGTTATTCGAGCTCTGTGCCTAGCAGGCTTTGTGCCAGTGTTATTCAGGCTCTGTGCCTAGCAG
GCTTGTGCCG
Found at i:39263840 original size:50 final size:50
Alignment explanation
Indices: 39263765--39263957 Score: 269
Period size: 50 Copynumber: 3.8 Consensus size: 50
39263755 ATTTGGGTAA
*
39263765 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
*
39263815 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * * *
39263865 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACTGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * *
39263915 AGAACATCCCATGTAAGACCACGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
39263958 TGTTATTATT
Statistics
Matches: 128, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
50 95 0.74
51 33 0.26
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:39268695 original size:38 final size:38
Alignment explanation
Indices: 39268643--39268759 Score: 146
Period size: 38 Copynumber: 3.1 Consensus size: 38
39268633 TAGAAGCATA
* * * *
39268643 ATGTTATTCCGGCTCTATACCTAGCAGGCTTTGTGTCG
1 ATGTTATTCAGGCTCTGTGCCTAGCAGGCTTTGTGCCG
* *
39268681 ATGTTATTCGGGCTCTGTGCCTAGCAGGTTTTGTGCCG
1 ATGTTATTCAGGCTCTGTGCCTAGCAGGCTTTGTGCCG
* * *
39268719 GTGTTATTCAGGCTCTGTGCCTAGTAGGC-TTGTTCCG
1 ATGTTATTCAGGCTCTGTGCCTAGCAGGCTTTGTGCCG
39268756 ATGT
1 ATGT
39268760 ATTGAAAGTT
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
37 10 0.15
38 58 0.85
ACGTcount: A:0.13, C:0.21, G:0.28, T:0.38
Consensus pattern (38 bp):
ATGTTATTCAGGCTCTGTGCCTAGCAGGCTTTGTGCCG
Found at i:39270247 original size:55 final size:55
Alignment explanation
Indices: 39270163--39270269 Score: 178
Period size: 55 Copynumber: 1.9 Consensus size: 55
39270153 TTATAGATTA
* * *
39270163 CAAATTAATTATTCATGAGCCCTATTCAAATTAAAAGTGATGATTTATCATCTTG
1 CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATAATTTATCATCTTG
*
39270218 CAAATTAATTATTCATAAGTACTATTCAAATTAAAAGTGATAATTTATCATC
1 CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATAATTTATCATC
39270270 CAATGGATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.38
Consensus pattern (55 bp):
CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATAATTTATCATCTTG
Found at i:39273597 original size:55 final size:55
Alignment explanation
Indices: 39273513--39273622 Score: 184
Period size: 55 Copynumber: 2.0 Consensus size: 55
39273503 AAATTATAGA
* * *
39273513 TTGCAAATTAATTATTCATGAGTACTATTCAAATTAAAAGTGATGATTTATCATC
1 TTGCAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATGATCTATCATC
*
39273568 TTGCAAATTAATTATTCATAAGCACTATTCAAATTAAAATTGATGATCTATCATC
1 TTGCAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATGATCTATCATC
39273623 CAATGGATAC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (55 bp):
TTGCAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATGATCTATCATC
Found at i:39278802 original size:32 final size:31
Alignment explanation
Indices: 39278736--39278812 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
39278726 ATAAACCTAG
*
39278736 AAAAATATTTTTTAAGATTTGTTATCTGTTA
1 AAAAATATTTTTTAAGATTTGTTATCTATTA
*
39278767 AAAAATATTTTTTAAGATTTTTTATCTATTA
1 AAAAATATTTTTTAAGATTTGTTATCTATTA
39278798 AAAAATATTTGTTTA
1 AAAAATATTT-TTTA
39278813 CTTAACATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
31 39 0.91
32 4 0.09
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (31 bp):
AAAAATATTTTTTAAGATTTGTTATCTATTA
Found at i:39284118 original size:192 final size:189
Alignment explanation
Indices: 39283774--39284137 Score: 496
Period size: 192 Copynumber: 1.9 Consensus size: 189
39283764 TCAATGTTGG
* *** * *
39283774 TTTTTTACTTTGATATTCTTGAAATTTTTATTATTTGTTAAATTTTATTTACTTAATTTTTTTTC
1 TTTTTTACTTTGATATTCTTGAAAATTTTATTATTTGTTAAAACATATTTACTAAATTTATTTTC
* * * * *
39283839 GAAATATATTTTTAAGGTTAATTTGACACTTTTGAGTATTGAGTACAGTGCATTATCAAATCATT
66 AAAATATATTTTTAAGGTTAACTCGACACCTTTGAGTATTGAGTACAATGCATTATCAAATCATT
* * *
39283904 ATAAGAATGCATCCATTATATGTCAAGAGAAAAGGATTGTTGTAACGTCCCAATTTTTT
131 ACAAGAACGCATCCACTATATGTCAAGAGAAAAGGATTGTTGTAACGTCCCAATTTTTT
* *
39283963 TTTTTTACTTTGATATTGTTGAAAATTTTATTATTTGTTAAAACATATTTGCTCAAAATTTATTT
1 TTTTTTACTTTGATATTCTTGAAAATTTTATTATTTGTTAAAACATATTTACT--AAATTTATTT
* * *
39284028 TCAAAATGCAT-TTTTTAAGGTTAACTCGACACCTTTGAGTGTTGAGTACAATGCGTTGTCAAAT
64 TCAAAAT--ATATTTTTAAGGTTAACTCGACACCTTTGAGTATTGAGTACAATGCATTATCAAAT
* *
39284092 CATTACAAGAGCGCATGCACTATATGTCAAGAGAAAAGGATTGTTG
127 CATTACAAGAACGCATCCACTATATGTCAAGAGAAAAGGATTGTTG
39284138 AAACACCCTA
Statistics
Matches: 150, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
189 47 0.31
191 14 0.09
192 87 0.58
193 2 0.01
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (189 bp):
TTTTTTACTTTGATATTCTTGAAAATTTTATTATTTGTTAAAACATATTTACTAAATTTATTTTC
AAAATATATTTTTAAGGTTAACTCGACACCTTTGAGTATTGAGTACAATGCATTATCAAATCATT
ACAAGAACGCATCCACTATATGTCAAGAGAAAAGGATTGTTGTAACGTCCCAATTTTTT
Found at i:39292301 original size:26 final size:27
Alignment explanation
Indices: 39292266--39292318 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
39292256 ACCATAGCAC
39292266 AAATCAGTCATTTACCC-TCGAGGGGCA
1 AAATCAGTCATTTACCCTTC-AGGGGCA
39292293 AAAT-AGTCATTTACCCTTCAGGGGCA
1 AAATCAGTCATTTACCCTTCAGGGGCA
39292319 TTATGGTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (27 bp):
AAATCAGTCATTTACCCTTCAGGGGCA
Found at i:39298818 original size:22 final size:22
Alignment explanation
Indices: 39298758--39298829 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
39298748 CCACTGATTC
* * *
39298758 GCACTACAGTGCCTACTGTTTA
1 GCACTTCAGTGCCTACTATCTA
* *
39298780 GCATTTC-GATGCTTACTATCTA
1 GCACTTCAG-TGCCTACTATCTA
39298802 GCACTTCAGTGCCTACTAATC-A
1 GCACTTCAGTGCCTACT-ATCTA
39298824 GCACTT
1 GCACTT
39298830 TGATGCCTAC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
21 1 0.03
22 35 0.88
23 4 0.10
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (22 bp):
GCACTTCAGTGCCTACTATCTA
Found at i:39307835 original size:44 final size:44
Alignment explanation
Indices: 39307789--39307936 Score: 178
Period size: 43 Copynumber: 3.4 Consensus size: 44
39307779 TGTGTTATCG
* * *
39307789 TGTAAGACCACATCTGGGACATTGGCATCGATTTGTGATTTACG
1 TGTAAGACCATATCTGGGACATTGGCATCGATATGTGATTTACA
* * *
39307833 TGTAAGACCATGTCTGGGACATCGGCATCG-TATATGATTT-CA
1 TGTAAGACCATATCTGGGACATTGGCATCGATATGTGATTTACA
* * *
39307875 TGTAAGACTC-TGTCTGGGACAGTGGCATCGATATGTGA-TAACA
1 TGTAAGAC-CATATCTGGGACATTGGCATCGATATGTGATTTACA
39307918 TGTAAGACCATATCTGGGA
1 TGTAAGACCATATCTGGGA
39307937 TATGGCGTTG
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
42 29 0.33
43 33 0.37
44 27 0.30
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (44 bp):
TGTAAGACCATATCTGGGACATTGGCATCGATATGTGATTTACA
Found at i:39310996 original size:9 final size:9
Alignment explanation
Indices: 39310972--39311014 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
39310962 AGCCACCCCT
39310972 TTTATTTTA
1 TTTATTTTA
39310981 TTTTATTTTA
1 -TTTATTTTA
39310991 TTTA--TTA
1 TTTATTTTA
*
39310998 TTTATATTA
1 TTTATTTTA
39311007 TTTATTTT
1 TTTATTTT
39311015 TGTTTTACTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
7 7 0.23
9 14 0.47
10 9 0.30
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATTTTA
Found at i:39311007 original size:16 final size:16
Alignment explanation
Indices: 39310982--39311012 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39310972 TTTATTTTAT
*
39310982 TTTATTTTATTTATTA
1 TTTATATTATTTATTA
39310998 TTTATATTATTTATT
1 TTTATATTATTTATT
39311013 TTTGTTTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTATATTATTTATTA
Found at i:39312204 original size:21 final size:21
Alignment explanation
Indices: 39312180--39312223 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
39312170 TCTTATTTTT
39312180 AAAAGAAGAAAA-AAATCGAAA
1 AAAAGAA-AAAAGAAATCGAAA
* *
39312201 AAAATAAAAAAGAAATTGAAA
1 AAAAGAAAAAAGAAATCGAAA
39312222 AA
1 AA
39312224 TATATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.77, C:0.02, G:0.11, T:0.09
Consensus pattern (21 bp):
AAAAGAAAAAAGAAATCGAAA
Found at i:39313117 original size:30 final size:30
Alignment explanation
Indices: 39313076--39313133 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
39313066 TTGGGCATTT
* * * *
39313076 CCACACGGGCTGGGCACACGCCCGTGTGAG
1 CCACACAGGCTGGCCACACACCCATGTGAG
39313106 CCACACAGGCTGGCCACACACCCATGTG
1 CCACACAGGCTGGCCACACACCCATGTG
39313134 CCAGCTTGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.21, C:0.40, G:0.29, T:0.10
Consensus pattern (30 bp):
CCACACAGGCTGGCCACACACCCATGTGAG
Found at i:39316009 original size:42 final size:42
Alignment explanation
Indices: 39315962--39316047 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
39315952 TCCTTCTTTT
* * *
39315962 GTGGAAAAAATGTTATAATT-TATGTGCTAATTTTGTATTTAA
1 GTGGAAAAAATGTAATAATTGTAAG-GCTAATTTTGTACTTAA
* *
39316004 GTGGAAATAATGTAATAGTTGTAAGGCTAATTTTGTACTTAA
1 GTGGAAAAAATGTAATAATTGTAAGGCTAATTTTGTACTTAA
39316046 GT
1 GT
39316048 CTACAATAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
42 35 0.92
43 3 0.08
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.42
Consensus pattern (42 bp):
GTGGAAAAAATGTAATAATTGTAAGGCTAATTTTGTACTTAA
Found at i:39316617 original size:45 final size:45
Alignment explanation
Indices: 39316522--39316609 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
39316512 TACAAGAAGC
** **
39316522 GAAGACTTATTAAACAATGGAAAACAAACAAAAACTTCTAAAAGT
1 GAAGACTTATTAAACAATGGAAAACAAACAAAAAAATAGAAAAGT
39316567 GAAGACTTATTAAACAATGGAAAACAAACAAAAAAATAGAAAA
1 GAAGACTTATTAAACAATGGAAAACAAACAAAAAAATAGAAAA
39316610 TTTAAGACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.60, C:0.11, G:0.11, T:0.17
Consensus pattern (45 bp):
GAAGACTTATTAAACAATGGAAAACAAACAAAAAAATAGAAAAGT
Found at i:39327918 original size:22 final size:22
Alignment explanation
Indices: 39327871--39327919 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
39327861 TAAATATTTT
* * *
39327871 TAAATAAATTTTTATTTTTATT
1 TAAATAAATGTTTATTTTGATA
39327893 TAAATAAATGTTTATATTTGA-A
1 TAAATAAATGTTTAT-TTTGATA
39327915 TAAAT
1 TAAAT
39327920 TAAAACTCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (22 bp):
TAAATAAATGTTTATTTTGATA
Found at i:39330908 original size:30 final size:30
Alignment explanation
Indices: 39330874--39330931 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
39330864 AAACCTTTTA
* *
39330874 TTTTCCCCCAAAATTTTTACTCCCTTCCAC
1 TTTTCCCCCAAAACTTTTACTCCATTCCAC
* * *
39330904 TTTTCTCCTAAAACTTTTATTCCATTCC
1 TTTTCCCCCAAAACTTTTACTCCATTCC
39330932 CATCTCACCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.21, C:0.34, G:0.00, T:0.45
Consensus pattern (30 bp):
TTTTCCCCCAAAACTTTTACTCCATTCCAC
Found at i:39333351 original size:19 final size:18
Alignment explanation
Indices: 39333329--39333371 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
39333319 AACATAAGTT
39333329 TTAAAA-AATTAATATAATA
1 TTAAAATAATTAA-ATAA-A
39333348 TTAAAATTAATTAAATAAA
1 TTAAAA-TAATTAAATAAA
39333367 TTAAA
1 TTAAA
39333372 CATGTGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.55
20 4 0.18
21 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TTAAAATAATTAAATAAA
Found at i:39334043 original size:22 final size:21
Alignment explanation
Indices: 39334008--39334103 Score: 74
Period size: 19 Copynumber: 4.7 Consensus size: 21
39333998 AAAGGGTATC
* *
39334008 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
39334029 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
39334052 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
39334071 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
39334090 TGCATATCATATCT
1 TACAAATCATATCT
39334104 AAGATTGCAT
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
19 34 0.54
21 4 0.06
22 15 0.24
23 10 0.16
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:39334051 original size:23 final size:22
Alignment explanation
Indices: 39334008--39334065 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
39333998 AAAGGGTATC
* *
39334008 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
39334029 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
39334052 TGCATATCATATCT
1 TACAAATCATATCT
39334066 AAGATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:39334068 original size:19 final size:19
Alignment explanation
Indices: 39334044--39334116 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
39334034 AATCATATCT
39334044 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
39334063 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
39334082 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
39334101 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
39334117 CCTGAAGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:39334756 original size:43 final size:42
Alignment explanation
Indices: 39334708--39334857 Score: 119
Period size: 43 Copynumber: 3.5 Consensus size: 42
39334698 GATCTGAAAT
*
39334708 CTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTATTGG
1 CTTCAATCTACTCCACTGTTGTCCAGAAAAGTAGAATTA-TGG
* *** *
39334751 CTTCAATGTACTCCACTGTAACCACAGGGAGATAAGATCTGAA--AT--
1 CTTCAATCTACTCCACTGTTGTC-CA--GA-A-AAG-T-AGAATTATGG
*
39334796 CTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGG
1 CTTCAATCTACTCCACTGTTGTCCAGAAAAGTAGAATTA-TGG
*
39334839 CTTCAATGTACTCCACTGT
1 CTTCAATCTACTCCACTGT
39334858 AACCACAGGG
Statistics
Matches: 81, Mismatches: 14, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
38 3 0.04
39 1 0.01
40 4 0.05
41 2 0.02
42 2 0.02
43 35 0.43
44 4 0.05
45 18 0.22
46 2 0.02
47 2 0.02
48 4 0.05
49 1 0.01
50 3 0.04
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (42 bp):
CTTCAATCTACTCCACTGTTGTCCAGAAAAGTAGAATTATGG
Found at i:39334790 original size:88 final size:88
Alignment explanation
Indices: 39334690--39334869 Score: 351
Period size: 88 Copynumber: 2.0 Consensus size: 88
39334680 TACTGCTTAA
*
39334690 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTATTGGCTTC
1 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGGCTTC
39334755 AATGTACTCCACTGTAACCACAG
66 AATGTACTCCACTGTAACCACAG
39334778 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGGCTTC
1 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGGCTTC
39334843 AATGTACTCCACTGTAACCACAG
66 AATGTACTCCACTGTAACCACAG
39334866 GGAG
1 GGAG
39334870 GTAAAATCCG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 91 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (88 bp):
GGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGGCTTC
AATGTACTCCACTGTAACCACAG
Found at i:39334812 original size:132 final size:132
Alignment explanation
Indices: 39334479--39334804 Score: 526
Period size: 132 Copynumber: 2.5 Consensus size: 132
39334469 AAGGAGATAT
* * *
39334479 ATTACTAGCTTCAATGTACTCCATTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATTTGCT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATCTGCT
* **
39334544 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
66 CCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTA
39334609 GA
131 GA
* *
39334611 ATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATCTGCT
39334676 CCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTA
66 CCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTA
39334741 GA
131 GA
* * * * **
39334743 ATTATTGGCTTCAATGTACTCCACTGTAACCACAGGGAGATAAGATCTGAAATCTTCAATCT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATCT
39334805 ATTCCACTGT
Statistics
Matches: 178, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 178 1.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (132 bp):
ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATCTGCT
CCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTA
GA
Found at i:39334816 original size:220 final size:220
Alignment explanation
Indices: 39334556--39335011 Score: 804
Period size: 220 Copynumber: 2.1 Consensus size: 220
39334546 ACTACTGCTT
**
39334556 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGGCT
39334621 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
* *
39334686 TTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTATTGG
131 TTAAGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGG
39334751 CTTCAATGTACTCCACTGTAACCAC
196 CTTCAATGTACTCCACTGTAACCAC
39334776 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGGCT
* *
39334841 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGTTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
* * **
39334906 TTAGGGAGATAATACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGG
131 TTAAGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGG
39334971 CTTCAATGTACTCCACTGTAACCAC
196 CTTCAATGTACTCCACTGTAACCAC
* *
39334996 AGGGAGGTAAAATCTG
1 AGGGAGATAAGATCTG
39335012 CCATTTTCGA
Statistics
Matches: 224, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
220 224 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (220 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGGCT
TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
TTAAGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGG
CTTCAATGTACTCCACTGTAACCAC
Found at i:39334886 original size:88 final size:88
Alignment explanation
Indices: 39334690--39334900 Score: 332
Period size: 88 Copynumber: 2.4 Consensus size: 88
39334680 TACTGCTTAA
* * *
39334690 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTATTGGCTTC
1 GGAGATAAAATCCGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGGCTTC
39334755 AATGTACTCCACTGTAACCACAG
66 AATGTACTCCACTGTAACCACAG
* *
39334778 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGGCTTC
1 GGAGATAAAATCCGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGGCTTC
39334843 AATGTACTCCACTGTAACCACAG
66 AATGTACTCCACTGTAACCACAG
* ** * *
39334866 GGAGGTAAAATCCGCCATCTTCGATCTGTTCCACT
1 GGAGATAAAATCCGAAATCTTCAATCTATTCCACT
39334901 ACTGCTTAGG
Statistics
Matches: 115, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 115 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (88 bp):
GGAGATAAAATCCGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGGCTTC
AATGTACTCCACTGTAACCACAG
Found at i:39334912 original size:132 final size:132
Alignment explanation
Indices: 39334776--39335555 Score: 1353
Period size: 132 Copynumber: 5.9 Consensus size: 132
39334766 CTGTAACCAC
* **
39334776 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAGTAGAATTACTGGCT
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
*
39334841 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGTTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
39334906 TT
131 TT
*
39334908 AGGGAGATAATACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* *
39334973 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
39335038 TT
131 TT
* *
39335040 AGGGAGATAAGACCTGAAATCTTCAATTTATTCCACTGATGTCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
*
39335105 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGTTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
39335170 TT
131 TT
* *
39335172 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGATGTCCAAGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
*
39335237 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTACTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
39335302 TT
131 TT
* * *
39335304 AAGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGTT
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* *
39335369 TTAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
39335434 TT
131 TT
* *
39335436 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* * *
39335501 TCAATGTACTCCACTGTAACCACATGGAGGTAAAATTCGCTATCTTCGATCTGCT
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
39335556 TCGCTGTCAA
Statistics
Matches: 613, Mismatches: 35, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 613 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (132 bp):
AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
TT
Found at i:39335048 original size:352 final size:352
Alignment explanation
Indices: 39334479--39335133 Score: 1157
Period size: 352 Copynumber: 1.9 Consensus size: 352
39334469 AAGGAGATAT
* *
39334479 ATTACTAGCTTCAATGTACTCCATTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATTTGCT
1 ATTACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATCTGCT
*
39334544 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
66 CCACTACTGCTTAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
39334609 GAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTG
131 GAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTG
* *
39334674 CTCCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGAAAAG
196 CTCCACTACTGCTTAAGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGATGTCCAGAAAAG
*
39334739 TAGAATTATTGGCTTCAATGTACTCCACTGTAACCACAGGGAGATAAGATCTGAAATCTTCAATC
261 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGATAAGATCTGAAATCTTCAATC
39334804 TATTCCACTGTTGTCCAGAAAAGTAGA
326 TATTCCACTGTTGTCCAGAAAAGTAGA
* * *
39334831 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGTT
1 ATTACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATCTGCT
*
39334896 CCACTACTGCTTAGGGAGATAATACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
66 CCACTACTGCTTAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
* * *
39334961 GAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTCGATCTG
131 GAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTG
* * **
39335026 CTCCACTACTGCTTAGGGAGATAAGACCTGAAATCTTCAATTTATTCCACTGATGTCCAGGGAAG
196 CTCCACTACTGCTTAAGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGATGTCCAGAAAAG
39335091 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAG
261 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAG
39335134 GTAAAATCCG
Statistics
Matches: 286, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
352 286 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (352 bp):
ATTACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCAATCTGCT
CCACTACTGCTTAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
GAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTG
CTCCACTACTGCTTAAGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGATGTCCAGAAAAG
TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGATAAGATCTGAAATCTTCAATC
TATTCCACTGTTGTCCAGAAAAGTAGA
Found at i:39336980 original size:14 final size:15
Alignment explanation
Indices: 39336957--39336989 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
39336947 GTTGATGCTT
*
39336957 TTCCAGATAAGG-CC
1 TTCCAAATAAGGTCC
39336971 TTCCAAATAAGGTCC
1 TTCCAAATAAGGTCC
39336986 TTCC
1 TTCC
39336990 TAGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.27
Consensus pattern (15 bp):
TTCCAAATAAGGTCC
Found at i:39344669 original size:16 final size:17
Alignment explanation
Indices: 39344636--39344670 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
39344626 ATCCAGTTCT
*
39344636 TTCTTCTCAATCCTTTC
1 TTCTTCTAAATCCTTTC
39344653 TTCTTCTAAAT-CTTTC
1 TTCTTCTAAATCCTTTC
39344669 TT
1 TT
39344671 TTCAACCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (17 bp):
TTCTTCTAAATCCTTTC
Found at i:39345268 original size:22 final size:22
Alignment explanation
Indices: 39345243--39345285 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
39345233 AAGTCTGTAA
*
39345243 AAATGAA-ATAGAAATACTATTG
1 AAATGAATATAAAAATA-TATTG
*
39345265 AAATTAATATAAAAATATATT
1 AAATGAATATAAAAATATATT
39345286 AAAGATCGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (22 bp):
AAATGAATATAAAAATATATTG
Found at i:39345529 original size:4 final size:4
Alignment explanation
Indices: 39345520--39345579 Score: 66
Period size: 4 Copynumber: 13.8 Consensus size: 4
39345510 AAAATAAGGA
*
39345520 TAAT TAAT TAAG TAAT TAAT TAAT TAATT TAAT TAAGTT TAAT TAAT TAAGTT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAA-T TAAT TAA--T TAAT TAAT TAA--T
39345573 TAAT TAA
1 TAAT TAA
39345580 ACATTAAACT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
4 37 0.76
5 4 0.08
6 8 0.16
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:39345567 original size:14 final size:13
Alignment explanation
Indices: 39345520--39345579 Score: 79
Period size: 14 Copynumber: 4.5 Consensus size: 13
39345510 AAAATAAGGA
39345520 TAATTAATTAAG-
1 TAATTAATTAAGT
39345532 TAATTAATTAA-T
1 TAATTAATTAAGT
39345544 TAATTTAATTAAGTT
1 TAA-TTAATTAAG-T
39345559 TAATTAATTAAGTT
1 TAATTAATTAAG-T
39345573 TAATTAA
1 TAATTAA
39345580 ACATTAAACT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
12 14 0.32
13 8 0.18
14 18 0.41
15 4 0.09
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (13 bp):
TAATTAATTAAGT
Found at i:39346947 original size:23 final size:23
Alignment explanation
Indices: 39346921--39346971 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
39346911 CTACTGATTT
39346921 GCAATTCTAAGAATCTAACCCTA
1 GCAATTCTAAGAATCTAACCCTA
39346944 GCAATTCTAAGAATCTAACCCTA
1 GCAATTCTAAGAATCTAACCCTA
*
39346967 CCAAT
1 GCAAT
39346972 ATGAGCTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.25
Consensus pattern (23 bp):
GCAATTCTAAGAATCTAACCCTA
Found at i:39348047 original size:19 final size:19
Alignment explanation
Indices: 39348023--39348133 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
39348013 AATCTTCAGG
39348023 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
39348042 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
39348061 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
39348080 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
39348099 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
39348118 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
39348134 AGATATGATT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 80 1.00
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:39348073 original size:38 final size:38
Alignment explanation
Indices: 39348030--39348133 Score: 208
Period size: 38 Copynumber: 2.7 Consensus size: 38
39348020 AGGGATATGC
39348030 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
39348068 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
39348106 AATCTTAGATATGATATGCAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
39348134 AGATATGATT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 66 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:39348159 original size:22 final size:21
Alignment explanation
Indices: 39348023--39348159 Score: 105
Period size: 19 Copynumber: 6.9 Consensus size: 21
39348013 AATCTTCAGG
*
39348023 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
39348042 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
* *
39348061 AATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
39348080 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
* *
39348099 AATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
39348118 GATATGCAATCTTAGAAGATAT
1 GATATGTAATCTTAG-AGATAT
*
39348140 GATTTTGTAATCTTAGAGAT
1 GA-TATGTAATCTTAGAGAT
39348160 TTAATTTGTA
Statistics
Matches: 100, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
19 77 0.77
22 12 0.12
23 11 0.11
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (21 bp):
GATATGTAATCTTAGAGATAT
Found at i:39351598 original size:24 final size:24
Alignment explanation
Indices: 39351554--39351599 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
39351544 TTTTATGTAC
* *
39351554 TTTTAACATTCTTTTTTTTTCTCA
1 TTTTAACATTCTTTCTGTTTCTCA
39351578 TTTT-ACATTCTCTTCTGTTTCT
1 TTTTAACATTCT-TTCTGTTTCT
39351600 TCCTCTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.13, C:0.20, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTTAACATTCTTTCTGTTTCTCA
Found at i:39354166 original size:27 final size:27
Alignment explanation
Indices: 39354135--39354192 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
39354125 ATAAATGAAG
*
39354135 AAGAG-AGGAAAACAAAGGGAGAAG-TAA
1 AAGAGAAGGAAAA-AAAAGGA-AAGTTAA
*
39354162 AAGAGAATGAAAAAAAAGGAAAGTTAA
1 AAGAGAAGGAAAAAAAAGGAAAGTTAA
39354189 AAGA
1 AAGA
39354193 ACATAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 3 0.11
27 18 0.67
28 6 0.22
ACGTcount: A:0.64, C:0.02, G:0.28, T:0.07
Consensus pattern (27 bp):
AAGAGAAGGAAAAAAAAGGAAAGTTAA
Found at i:39354579 original size:20 final size:21
Alignment explanation
Indices: 39354547--39354588 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
39354537 TATTATACTT
39354547 TATTTCATTTTTTCTT-AAAAA
1 TATTTCATTTTTT-TTCAAAAA
39354568 TATTTC-TTTTTTTTCAAAAA
1 TATTTCATTTTTTTTCAAAAA
39354588 T
1 T
39354589 TCCAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 2 0.10
20 12 0.60
21 6 0.30
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTCATTTTTTTTCAAAAA
Found at i:39365800 original size:17 final size:17
Alignment explanation
Indices: 39365778--39365811 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
39365768 TTGGGTTGGG
39365778 AGCTTAACTCAATTAAC
1 AGCTTAACTCAATTAAC
39365795 AGCTTAACTCAATTAAC
1 AGCTTAACTCAATTAAC
39365812 CTTTACACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.29
Consensus pattern (17 bp):
AGCTTAACTCAATTAAC
Found at i:39366161 original size:37 final size:37
Alignment explanation
Indices: 39366120--39366191 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
39366110 TTAACTCTGC
39366120 TAACTCAAAGAGATATAGGTTGCGATCTTAAATCAGT
1 TAACTCAAAGAGATATAGGTTGCGATCTTAAATCAGT
*
39366157 TAACTCAGAGAGATATAGGTTGCGATCTTAAATCA
1 TAACTCAAAGAGATATAGGTTGCGATCTTAAATCA
39366192 ACTAACCTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (37 bp):
TAACTCAAAGAGATATAGGTTGCGATCTTAAATCAGT
Found at i:39366445 original size:104 final size:104
Alignment explanation
Indices: 39366138--39366714 Score: 642
Period size: 104 Copynumber: 5.6 Consensus size: 104
39366128 AGAGATATAG
*
39366138 GTTGCGATCTTAAATCAGTTAACTCAGAGAGATATAGGTTGCGATCTTAAATCAACTAACC-TTA
1 GTTGCGATCTTAAATCAGCTAACTCAGAGAGATATAGGTTGCGATCTTAAATCAACTAACCTTTA
* * * *
39366202 AACATCAACTGGGAATGTAGGTCTGCGAGTTATTTGGGA
66 AACATCAACTGGGAACGTAGGTCCGCGAGCTGTTTGGGA
* * * * * * * *
39366241 GTTGCAATCTTAAATCAACT-ATTTAGAGAGATATAGGTTGCAATCTTAAGTCAAATAACTTTTA
1 GTTGCGATCTTAAATCAGCTAACTCAGAGAGATATAGGTTGCGATCTTAAATCAACTAACCTTTA
* * * *
39366305 AACATCAACTGAGAACATAGGTCTGCGAGTTGTTTGGGA
66 AACATCAACTGGGAACGTAGGTCCGCGAGCTGTTTGGGA
* * * *
39366344 GTTGCGATCTTAAATCAACTAACTCAGAGAGATATAAGTTGCGATATTAAATCAGCTAACCTTTA
1 GTTGCGATCTTAAATCAGCTAACTCAGAGAGATATAGGTTGCGATCTTAAATCAACTAACCTTTA
* * * * ** *
39366409 AACATCAGCTAGGAACATAGTTCCGTAAGCTATTTGGGA
66 AACATCAACTGGGAACGTAGGTCCGCGAGCTGTTTGGGA
* * * *
39366448 GTTGAGATCTTAATTCAGCTAACTCAGAGAGATTTAGGTTGCGATATTAAATCAACTAACCTTTA
1 GTTGCGATCTTAAATCAGCTAACTCAGAGAGATATAGGTTGCGATCTTAAATCAACTAACCTTTA
* * *
39366513 AATATCATCTGGGAACGTAGGTCCGCGAGCTGTTTAGGA
66 AACATCAACTGGGAACGTAGGTCCGCGAGCTGTTTGGGA
* * * * *
39366552 GTTGCGATCTTAAAT-ATGTTAACTCAAATAGATTTA-GTTGCGATCTTAAATCAACTAATCTTT
1 GTTGCGATCTTAAATCA-GCTAACTCAGAGAGATATAGGTTGCGATCTTAAATCAACTAACCTTT
** * * ** *
39366615 AAACATCAGTTGGAAACGTAAGTTTGCGAGCTGTTTAGGA
65 AAACATCAACTGGGAACGTAGGTCCGCGAGCTGTTTGGGA
* * * *
39366655 GTTGTGATCTTAAATCTG-TCAACTTAGAGAGATTTAGGTTGCGATCTTAAATCAACTAAC
1 GTTGCGATCTTAAATCAGCT-AACTCAGAGAGATATAGGTTGCGATCTTAAATCAACTAAC
39366715 TCGGAGAGAT
Statistics
Matches: 401, Mismatches: 67, Indels: 11
0.84 0.14 0.02
Matches are distributed among these distances:
102 35 0.09
103 161 0.40
104 205 0.51
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (104 bp):
GTTGCGATCTTAAATCAGCTAACTCAGAGAGATATAGGTTGCGATCTTAAATCAACTAACCTTTA
AACATCAACTGGGAACGTAGGTCCGCGAGCTGTTTGGGA
Found at i:39366603 original size:207 final size:205
Alignment explanation
Indices: 39366138--39366714 Score: 662
Period size: 207 Copynumber: 2.8 Consensus size: 205
39366128 AGAGATATAG
*
39366138 GTTGCGATCTTAAATCAGTTAACTCAGAGAGATATAGGTTGCGATCTTAAATCAACTAACC-TTA
1 GTTGCGATCTTAAATCAGTTAACTCAGAGAGATTTA-GTTGCGATCTTAAATCAACTAACCTTTA
* * * * * * *
39366202 AACATCAACTGGGAATGTAGGTCTGCGAGTTATTTGGGAGTTGCA-ATCTTAAATCAACT-ATTT
65 AACATCAGCTAGGAACGTA-GT-TCCGAGCTATTTGGGAGTTG-AGATCTTAAATCAGCTAACTT
* * * * * *
39366265 AGAGAGATATAGGTTGCAATCTTAAGTCAAATAACTTTTAAACATCAACTGAGAACATAGGTCTG
127 AGAGAGATTTAGGTTGCGATCTTAAATCAACTAACCTTTAAACATCAACTGAGAACATAGGTCCG
* *
39366330 CGAGTTGTTTGGGA
192 CGAGCTGTTTAGGA
** * * *
39366344 GTTGCGATCTTAAATCAACTAACTCAGAGAGATATAAGTTGCGATATTAAATCAGCTAACCTTTA
1 GTTGCGATCTTAAATCAGTTAACTCAGAGAGAT-TTAGTTGCGATCTTAAATCAACTAACCTTTA
* * *
39366409 AACATCAGCTAGGAACATAGTTCCGTAAGCTATTTGGGAGTTGAGATCTTAATTCAGCTAACTCA
65 AACATCAGCTAGGAACGTAGTTCCG--AGCTATTTGGGAGTTGAGATCTTAAATCAGCTAACTTA
* * * * *
39366474 GAGAGATTTAGGTTGCGATATTAAATCAACTAACCTTTAAATATCATCTGGGAACGTAGGTCCGC
128 GAGAGATTTAGGTTGCGATCTTAAATCAACTAACCTTTAAACATCAACTGAGAACATAGGTCCGC
39366539 GAGCTGTTTAGGA
193 GAGCTGTTTAGGA
* * *
39366552 GTTGCGATCTTAAAT-ATGTTAACTCAAATAGATTTAGTTGCGATCTTAAATCAACTAATCTTTA
1 GTTGCGATCTTAAATCA-GTTAACTCAGAGAGATTTAGTTGCGATCTTAAATCAACTAACCTTTA
* * * * * *
39366616 AACATCAG-TTGGAAACGTAAGTTTGCGAGCTGTTTAGGAGTTGTGATCTTAAATCTG-TCAACT
65 AACATCAGCTAGG-AACGT-AG-TTCCGAGCTATTTGGGAGTTGAGATCTTAAATCAGCT-AACT
39366679 TAGAGAGATTTAGGTTGCGATCTTAAATCAACTAAC
126 TAGAGAGATTTAGGTTGCGATCTTAAATCAACTAAC
39366715 TCGGAGAGAT
Statistics
Matches: 313, Mismatches: 47, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
205 3 0.01
206 60 0.19
207 149 0.48
208 97 0.31
209 4 0.01
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (205 bp):
GTTGCGATCTTAAATCAGTTAACTCAGAGAGATTTAGTTGCGATCTTAAATCAACTAACCTTTAA
ACATCAGCTAGGAACGTAGTTCCGAGCTATTTGGGAGTTGAGATCTTAAATCAGCTAACTTAGAG
AGATTTAGGTTGCGATCTTAAATCAACTAACCTTTAAACATCAACTGAGAACATAGGTCCGCGAG
CTGTTTAGGA
Found at i:39373039 original size:15 final size:16
Alignment explanation
Indices: 39373008--39373055 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
39372998 TACACTCAAT
*
39373008 TTTTCACATTCTTTTTC
1 TTTTCTCATT-TTTTTC
39373025 -TTTCTCATTTTTTTC
1 TTTTCTCATTTTTTTC
39373040 TTTTCTCACTTTTTTT
1 TTTTCTCA-TTTTTTT
39373056 TCATTTTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 6 0.21
16 15 0.54
17 7 0.25
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTCTCATTTTTTTC
Found at i:39375199 original size:16 final size:16
Alignment explanation
Indices: 39375179--39375216 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
39375169 TTTCTTTTTT
39375179 ATTTTTTTAATCACG-
1 ATTTTTTTAATCACGA
*
39375194 ATTTTTTTAATTACGA
1 ATTTTTTTAATCACGA
39375210 ATTTTTT
1 ATTTTTT
39375217 ATTTTGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.61
Consensus pattern (16 bp):
ATTTTTTTAATCACGA
Found at i:39376860 original size:20 final size:20
Alignment explanation
Indices: 39376800--39376861 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
39376790 TACTAATTAG
* * *
39376800 AACATATTTAATAGACTTAA
1 AACATATTTAACACACATAA
* **
39376820 GACATATTAATAACATGCATAA
1 AACATATT--TAACACACATAA
39376842 AACATATTTAACACACATAA
1 AACATATTTAACACACATAA
39376862 TTAAATTTGT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 17 0.53
22 15 0.47
ACGTcount: A:0.52, C:0.15, G:0.05, T:0.29
Consensus pattern (20 bp):
AACATATTTAACACACATAA
Found at i:39380447 original size:25 final size:23
Alignment explanation
Indices: 39380419--39380472 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 23
39380409 AAGAGAAGCG
39380419 AGAAAAATATGTTAAAGAATA-AAAT
1 AGAAAAA-AT-TTAAAGAA-ACAAAT
*
39380444 AGAAGAAAATTTGAAGAAACAAAT
1 AGAA-AAAATTTAAAGAAACAAAT
39380468 AGAAA
1 AGAAA
39380473 TGAATCATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 2 0.08
24 15 0.58
25 6 0.23
26 3 0.12
ACGTcount: A:0.65, C:0.02, G:0.15, T:0.19
Consensus pattern (23 bp):
AGAAAAAATTTAAAGAAACAAAT
Found at i:39384382 original size:20 final size:21
Alignment explanation
Indices: 39384359--39384410 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
39384349 AATCTTAGTT
39384359 TTATCGATACTT-A-ATAAAAA
1 TTATCGATACTTGACA-AAAAA
*
39384379 TTATTGATACTTGACAAAAAA
1 TTATCGATACTTGACAAAAAA
*
39384400 ATATCGATACT
1 TTATCGATACT
39384411 GGATCGGTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 11 0.41
21 15 0.56
22 1 0.04
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.35
Consensus pattern (21 bp):
TTATCGATACTTGACAAAAAA
Found at i:39391061 original size:13 final size:13
Alignment explanation
Indices: 39391043--39391069 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39391033 CAAGAATCAG
39391043 ATCATAATTTAAC
1 ATCATAATTTAAC
39391056 ATCATAATTTAAC
1 ATCATAATTTAAC
39391069 A
1 A
39391070 ACTTCAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
ATCATAATTTAAC
Found at i:39391974 original size:21 final size:21
Alignment explanation
Indices: 39391918--39391974 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
39391908 TTCGGTTTAA
*
39391918 TAATTGAAT-TTTATATTTTTT
1 TAATTTAATATTTA-ATTTTTT
** *
39391939 TAATTTGGTACTTAATTTTTT
1 TAATTTAATATTTAATTTTTT
39391960 TAATTTAATATTTAA
1 TAATTTAATATTTAA
39391975 ATCTATCAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (21 bp):
TAATTTAATATTTAATTTTTT
Found at i:39409438 original size:30 final size:31
Alignment explanation
Indices: 39409402--39409461 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
39409392 AAACCTTTTA
*
39409402 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
39409432 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
39409462 TCCCCCCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:39410115 original size:5 final size:5
Alignment explanation
Indices: 39410105--39410130 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
39410095 AAATAAATAT
39410105 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
39410131 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:39415379 original size:9 final size:8
Alignment explanation
Indices: 39415362--39415387 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
39415352 TTTAATTCTG
39415362 TTATTTTT
1 TTATTTTT
39415370 TTATTTTT
1 TTATTTTT
39415378 TTATTTTT
1 TTATTTTT
39415386 TT
1 TT
39415388 CCAGTAACGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTATTTTT
Found at i:39422054 original size:10 final size:10
Alignment explanation
Indices: 39422039--39422063 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
39422029 TAAAGTGATT
39422039 TTGATAGATA
1 TTGATAGATA
39422049 TTGATAGATA
1 TTGATAGATA
39422059 TTGAT
1 TTGAT
39422064 TTTAGGACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (10 bp):
TTGATAGATA
Found at i:39422759 original size:41 final size:42
Alignment explanation
Indices: 39422693--39422794 Score: 152
Period size: 41 Copynumber: 2.5 Consensus size: 42
39422683 TATGAGTTTT
* * *
39422693 CGTTCAACCCTAATGGGTTTTCGTTCAGCTCTTTTGAGC-TC
1 CGTTCAACCCTTATGGGTTTCCGTTCAGCTCTTATGAGCATC
* *
39422734 TGTTTAACCCTTATGGGTTTCCGTTCAGCTCTTATGAGCATC
1 CGTTCAACCCTTATGGGTTTCCGTTCAGCTCTTATGAGCATC
39422776 CGTTCAACCCTTATGGGTT
1 CGTTCAACCCTTATGGGTT
39422795 CCTGTTTAGC
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 34 0.64
42 19 0.36
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (42 bp):
CGTTCAACCCTTATGGGTTTCCGTTCAGCTCTTATGAGCATC
Found at i:39422769 original size:21 final size:21
Alignment explanation
Indices: 39422674--39422794 Score: 73
Period size: 21 Copynumber: 5.8 Consensus size: 21
39422664 CGAGCTTCTA
* * * *
39422674 TTCAACTCATATGAGTTTTCG
1 TTCAACCCTTATGGGTTTCCG
* *
39422695 TTCAACCCTAATGGGTTTTCG
1 TTCAACCCTTATGGGTTTCCG
* * * * * *
39422716 TTCAGCTCTTTTGAG-CTCTG
1 TTCAACCCTTATGGGTTTCCG
*
39422736 TTTAACCCTTATGGGTTTCCG
1 TTCAACCCTTATGGGTTTCCG
* * * **
39422757 TTCAGCTCTTATGAGCATCCG
1 TTCAACCCTTATGGGTTTCCG
39422778 TTCAACCCTTATGGGTT
1 TTCAACCCTTATGGGTT
39422795 CCTGTTTAGC
Statistics
Matches: 69, Mismatches: 30, Indels: 2
0.68 0.30 0.02
Matches are distributed among these distances:
20 12 0.17
21 57 0.83
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.40
Consensus pattern (21 bp):
TTCAACCCTTATGGGTTTCCG
Found at i:39422810 original size:42 final size:41
Alignment explanation
Indices: 39422693--39422810 Score: 132
Period size: 41 Copynumber: 2.9 Consensus size: 41
39422683 TATGAGTTTT
* * *
39422693 CGTTCAACCCTAATGGGTT-TTCGTTCAGCTCTTTTGAGCTC
1 CGTTCAACCCTTATGGGTTCCT-GTTCAGCTCTTATGAGCTC
* *
39422734 TGTTTAACCCTTATGGGTTTCC-GTTCAGCTCTTATGAGCATC
1 CGTTCAACCCTTATGGG-TTCCTGTTCAGCTCTTATGAGC-TC
* *
39422776 CGTTCAACCCTTATGGGTTCCTGTTTAGCACTTAT
1 CGTTCAACCCTTATGGGTTCCTGTTCAGCTCTTAT
39422811 ATGCTTCTGT
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
41 34 0.53
42 30 0.47
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.40
Consensus pattern (41 bp):
CGTTCAACCCTTATGGGTTCCTGTTCAGCTCTTATGAGCTC
Found at i:39432240 original size:16 final size:16
Alignment explanation
Indices: 39432218--39432261 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
39432208 CTAGCTTTTT
39432218 ATTTTTTTTTCACGAA
1 ATTTTTTTTTCACGAA
*
39432234 TTTTTTTTTTCACGAA
1 ATTTTTTTTTCACGAA
39432250 ATTTTTTTTTCA
1 ATTTTTTTTTCA
39432262 ACTTGATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.20, C:0.11, G:0.05, T:0.64
Consensus pattern (16 bp):
ATTTTTTTTTCACGAA
Found at i:39432318 original size:13 final size:13
Alignment explanation
Indices: 39432300--39432330 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
39432290 AGGAAACCAA
39432300 TTTTTTT-GAATT
1 TTTTTTTCGAATT
39432312 TTTTTTTCGAATT
1 TTTTTTTCGAATT
39432325 TTTTTT
1 TTTTTT
39432331 GAAGAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.13, C:0.03, G:0.06, T:0.77
Consensus pattern (13 bp):
TTTTTTTCGAATT
Found at i:39433371 original size:21 final size:23
Alignment explanation
Indices: 39433326--39433372 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
39433316 TCATCTGCAA
* *
39433326 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
39433349 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
39433370 TAA
1 TAA
39433373 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:39435693 original size:14 final size:14
Alignment explanation
Indices: 39435674--39435712 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
39435664 TGTTACTGTG
39435674 TTTTAGTTTTAGAC
1 TTTTAGTTTTAGAC
*
39435688 TTTTAGTTTTAGAT
1 TTTTAGTTTTAGAC
*
39435702 TTTTATTTTTA
1 TTTTAGTTTTA
39435713 TTTATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.21, C:0.03, G:0.10, T:0.67
Consensus pattern (14 bp):
TTTTAGTTTTAGAC
Found at i:39444946 original size:29 final size:29
Alignment explanation
Indices: 39444913--39444969 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
39444903 TTACTTTGTC
*
39444913 ATTTATGTTTGAAATATTACGTTCTAGTT
1 ATTTATGTTTCAAATATTACGTTCTAGTT
* *
39444942 ATTTATGTTTCAAATGTTACGTTTTAGT
1 ATTTATGTTTCAAATATTACGTTCTAGT
39444970 CACATATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.26, C:0.07, G:0.14, T:0.53
Consensus pattern (29 bp):
ATTTATGTTTCAAATATTACGTTCTAGTT
Found at i:39444977 original size:29 final size:29
Alignment explanation
Indices: 39444916--39444979 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
39444906 CTTTGTCATT
* * **
39444916 TATGTTTGAAATATTACGTTCTAGTTATT
1 TATGTTTCAAATATTACGTTCTAGTCACA
* *
39444945 TATGTTTCAAATGTTACGTTTTAGTCACA
1 TATGTTTCAAATATTACGTTCTAGTCACA
39444974 TATGTT
1 TATGTT
39444980 ATCGTGTTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (29 bp):
TATGTTTCAAATATTACGTTCTAGTCACA
Found at i:39455432 original size:14 final size:14
Alignment explanation
Indices: 39455413--39455444 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
39455403 ATGTGGAATG
39455413 ATTTTAGTTTTTGT
1 ATTTTAGTTTTTGT
39455427 ATTTTAGTTTTTGT
1 ATTTTAGTTTTTGT
39455441 ATTT
1 ATTT
39455445 CATTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (14 bp):
ATTTTAGTTTTTGT
Found at i:39455451 original size:14 final size:14
Alignment explanation
Indices: 39455413--39455451 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
39455403 ATGTGGAATG
*
39455413 ATTTTAGTTTTTGT
1 ATTTCAGTTTTTGT
*
39455427 ATTTTAGTTTTTGT
1 ATTTCAGTTTTTGT
39455441 ATTTCA-TTTTT
1 ATTTCAGTTTTT
39455452 ATTTGTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.15, C:0.03, G:0.10, T:0.72
Consensus pattern (14 bp):
ATTTCAGTTTTTGT
Found at i:39455525 original size:4 final size:4
Alignment explanation
Indices: 39455516--39455544 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
39455506 AATTTGTTAC
39455516 ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
39455545 AATCTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:39455915 original size:15 final size:15
Alignment explanation
Indices: 39455895--39455924 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39455885 CCCTAACCTG
*
39455895 ACCCTAAATCTCTAA
1 ACCCTAAATCACTAA
39455910 ACCCTAAATCACTAA
1 ACCCTAAATCACTAA
39455925 CTCTTAACCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.23
Consensus pattern (15 bp):
ACCCTAAATCACTAA
Found at i:39456223 original size:14 final size:15
Alignment explanation
Indices: 39456206--39456238 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
39456196 CTTAAATCAG
39456206 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
39456220 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
39456235 AATC
1 AATC
39456239 TATAAGCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:39456928 original size:30 final size:30
Alignment explanation
Indices: 39456894--39456956 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
39456884 ACTTAACAAG
* *
39456894 CAAATGCCTCTAAAATAATAACAATATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
*
39456924 CAAATACCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
39456954 CAA
1 CAA
39456957 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.25
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:39457011 original size:22 final size:22
Alignment explanation
Indices: 39456986--39457028 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
39456976 TATCCAAACA
39456986 ATAAAAATAAAATAGTAGCAAC
1 ATAAAAATAAAATAGTAGCAAC
* * *
39457008 ATAATAGTAAAATGGTAGCAA
1 ATAAAAATAAAATAGTAGCAA
39457029 AATAGGGAGA
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:0.58, C:0.07, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAAAAATAAAATAGTAGCAAC
Found at i:39457394 original size:58 final size:60
Alignment explanation
Indices: 39457323--39457438 Score: 182
Period size: 60 Copynumber: 2.0 Consensus size: 60
39457313 GTGATAGAAA
* *
39457323 TTCTAGTGGTTAATAAACAAG-TTGTTTTA-TTTTTCTATGCAATATTAGCCGTGGGAGT
1 TTCTAGTAGTTAATAAACAAGTTTGTTTTATTTTTTCTATACAATATTAGCCGTGGGAGT
* *
39457381 TTCTAGTAGTTAATAAACAAGTTTGTTTTATTTTTTTTATACAATATTAGCCTTGGGA
1 TTCTAGTAGTTAATAAACAAGTTTGTTTTATTTTTTCTATACAATATTAGCCGTGGGA
39457439 CTAGGGAATG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 20 0.38
59 8 0.15
60 24 0.46
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.46
Consensus pattern (60 bp):
TTCTAGTAGTTAATAAACAAGTTTGTTTTATTTTTTCTATACAATATTAGCCGTGGGAGT
Found at i:39459891 original size:19 final size:19
Alignment explanation
Indices: 39459867--39459904 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
39459857 CATGTATTTG
39459867 TGTGGTATGAATGGTGGTT
1 TGTGGTATGAATGGTGGTT
* *
39459886 TGTGGTGTGATTGGTGGTT
1 TGTGGTATGAATGGTGGTT
39459905 GGTAAGCAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.45, T:0.45
Consensus pattern (19 bp):
TGTGGTATGAATGGTGGTT
Found at i:39460145 original size:5 final size:5
Alignment explanation
Indices: 39460135--39460167 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
39460125 TGAACAATGT
39460135 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTA
39460168 TTTTTAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TTAAA
Found at i:39483612 original size:60 final size:60
Alignment explanation
Indices: 39483538--39483676 Score: 190
Period size: 60 Copynumber: 2.3 Consensus size: 60
39483528 TTTGAATATT
* * *
39483538 AAATTGATAGAATTTGTAAATGTGAAGTGTTAAATTTATT-AATTATTCAGAATTAGGATC
1 AAATTGATAAAATTTGTAAATGTGAAG-ATTAAATTTATTAAATTATTCAAAATTAGGATC
* * *
39483598 AAATTGATAAAATTTATGAATGTGAAGATTAAATTTATTAAATTATTTAAAATTAGGATC
1 AAATTGATAAAATTTGTAAATGTGAAGATTAAATTTATTAAATTATTCAAAATTAGGATC
* *
39483658 AAATTAATAAAATATGTAA
1 AAATTGATAAAATTTGTAA
39483677 GTATTGAGGG
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 11 0.16
60 57 0.84
ACGTcount: A:0.46, C:0.02, G:0.13, T:0.39
Consensus pattern (60 bp):
AAATTGATAAAATTTGTAAATGTGAAGATTAAATTTATTAAATTATTCAAAATTAGGATC
Found at i:39483662 original size:30 final size:30
Alignment explanation
Indices: 39483569--39483662 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
39483559 GTGAAGTGTT
*
39483569 AAATTTATT-AATTATTCAGAATTAGGATC
1 AAATTTATTAAATTATTTAGAATTAGGATC
* * *
39483598 AAATTGA-TAAA--ATTTATGAATGTGAAGATT
1 AAATTTATTAAATTATTTA-GAAT-T-AGGATC
*
39483628 AAATTTATTAAATTATTTAAAATTAGGATC
1 AAATTTATTAAATTATTTAGAATTAGGATC
39483658 AAATT
1 AAATT
39483663 AATAAAATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
27 4 0.08
28 5 0.10
29 9 0.18
30 19 0.38
31 5 0.10
32 3 0.06
33 5 0.10
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.40
Consensus pattern (30 bp):
AAATTTATTAAATTATTTAGAATTAGGATC
Found at i:39493902 original size:17 final size:16
Alignment explanation
Indices: 39493873--39493919 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
39493863 AAACAAGTGG
39493873 AAGTGAAGA-AAGTGACC
1 AAGTGAA-ATAAGTG-CC
*
39493890 AAGTGAAATAAGTGCT
1 AAGTGAAATAAGTGCC
*
39493906 AAGAGAAATAAGTG
1 AAGTGAAATAAGTG
39493920 GTAAGCAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.49, C:0.06, G:0.28, T:0.17
Consensus pattern (16 bp):
AAGTGAAATAAGTGCC
Found at i:39493915 original size:16 final size:16
Alignment explanation
Indices: 39493894--39493924 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39493884 GTGACCAAGT
39493894 GAAATAAGTGCTAAGA
1 GAAATAAGTGCTAAGA
*
39493910 GAAATAAGTGGTAAG
1 GAAATAAGTGCTAAG
39493925 CAAAGTAAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.29, T:0.19
Consensus pattern (16 bp):
GAAATAAGTGCTAAGA
Found at i:39497431 original size:18 final size:18
Alignment explanation
Indices: 39497398--39497451 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 18
39497388 GTTTCCTGCA
39497398 AAAATAAAA-A-TGAAAAT
1 AAAATAAAATAGT-AAAAT
39497415 AAAATAAAATAGTAAAA-
1 AAAATAAAATAGTAAAAT
*
39497432 ATAAATAATAATAGGAAAAT
1 A-AAATAA-AATAGTAAAAT
39497452 TTAAAATGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 10 0.32
18 11 0.35
19 10 0.32
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.20
Consensus pattern (18 bp):
AAAATAAAATAGTAAAAT
Found at i:39497434 original size:19 final size:19
Alignment explanation
Indices: 39497398--39497450 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
39497388 GTTTCCTGCA
*
39497398 AAAATAAAA-A-TGAAAAT
1 AAAATAAAATAGTAAAAAT
39497415 AAAATAAAATAGTAAAAAT
1 AAAATAAAATAGTAAAAAT
*
39497434 -AAATAATAATAGGAAAA
1 AAAATAA-AATAGTAAAA
39497451 TTTAAAATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 9 0.29
18 7 0.23
19 15 0.48
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.19
Consensus pattern (19 bp):
AAAATAAAATAGTAAAAAT
Found at i:39509089 original size:20 final size:20
Alignment explanation
Indices: 39509064--39509102 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
39509054 AAATATATAT
39509064 ATAATA-ATAATAAATAAAAA
1 ATAATATAT-ATAAATAAAAA
39509084 ATAATATATATAAATAAAA
1 ATAATATATATAAATAAAA
39509103 TGTCCAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
ATAATATATATAAATAAAAA
Found at i:39512720 original size:104 final size:104
Alignment explanation
Indices: 39512582--39513022 Score: 483
Period size: 104 Copynumber: 4.3 Consensus size: 104
39512572 GGCCAATAGT
* * * *** * *
39512582 AGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAGACTTAAGCTTGTAGCTCCCAGATAAC
1 AGAGTTAAGCTCGCAACCTCCGATCTTTTGAGTTAGCAAAGTTAAGCTCACAACTCCCAGACAAC
* *
39512647 TAGCGGACCTACGCTTCCAGCTGATTATTTAAGGTTAGC
66 TAGCGGACCTACACTTCCAGCTGATTATTAAAGGTTAGC
* * * *** *
39512686 AGAGTTAAGCTTGTAACCTCCGATCTTTTGAGTTAGCAAAGTTAAACTTGTAACTCCTAGACAAC
1 AGAGTTAAGCTCGCAACCTCCGATCTTTTGAGTTAGCAAAGTTAAGCTCACAACTCCCAGACAAC
* * *
39512751 TAGCGAACCTACAC-TCCAACTGATTATT-AAGGTTAGT
66 TAGCGGACCTACACTTCCAGCTGATTATTAAAGGTTAGC
* ** *
39512788 AGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAAAGTTAAGCTCACAACTCCTGGACAGC
1 AGAGTTAAGCTCGCAACCTCCGATCTTTTGAGTTAGCAAAGTTAAGCTCACAACTCCCAGACAAC
** * * *
39512853 TAGCGGACCTATGCTCCCAGCTGAGTATTAAAAGTTAGC
66 TAGCGGACCTACACTTCCAGCTGATTATTAAAGGTTAGC
* * * * * * *
39512892 AGAGTTAAGCTCGCAACCTCTGGTCTTTTGAGTTAGCAGAGTTAAGCTCACAGCTCTCATACAGC
1 AGAGTTAAGCTCGCAACCTCCGATCTTTTGAGTTAGCAAAGTTAAGCTCACAACTCCCAGACAAC
* * *
39512957 TCGTGGACCTACACTTCCATCTGATTATTAAAGGTTAGC
66 TAGCGGACCTACACTTCCAGCTGATTATTAAAGGTTAGC
* *
39512996 ATG-GTTAAGCTCGCAACCCCCAATCTT
1 A-GAGTTAAGCTCGCAACCTCCGATCTT
39513023 ATTTACAAAC
Statistics
Matches: 283, Mismatches: 51, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
102 75 0.27
103 24 0.08
104 183 0.65
105 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (104 bp):
AGAGTTAAGCTCGCAACCTCCGATCTTTTGAGTTAGCAAAGTTAAGCTCACAACTCCCAGACAAC
TAGCGGACCTACACTTCCAGCTGATTATTAAAGGTTAGC
Found at i:39512969 original size:206 final size:208
Alignment explanation
Indices: 39512578--39513022 Score: 538
Period size: 206 Copynumber: 2.1 Consensus size: 208
39512568 ACCAGGCCAA
* *** *
39512578 TAGTAGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAGACTTAAGCTTGTAGCTCCCAGA
1 TAGTAGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAAACTTAAGCTCACAACTCCCAGA
* * * * * * *
39512643 TAACTAGCGGACCTACGCTTCCAGCTGATTATTTAAGGTTAGCAGAGTTAAGCTTGTAACCTCCG
66 CAACTAGCGGACCTACGCTCCCAGCTGAGTATTAAAAGTTAGCAGAGTTAAGCTCGCAACCTCCG
***
39512708 ATCTTTTGAGTTAGCAAAGTTAAACTTGTAACTCCTAGACAACTAGCGAACCTACAC-TCCAACT
131 ATCTTTTGAGTTAGCAAAGTTAAACTCACAACTCCTAGACAACTAGCGAACCTACACTTCCAACT
39512772 GATTATT-AAGGT
196 GATTATTAAAGGT
* **
39512784 TAGTAGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAAAGTTAAGCTCACAACTCCTGGA
1 TAGTAGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAAACTTAAGCTCACAACTCCCAGA
* * *
39512849 CAGCTAGCGGACCTATGCTCCCAGCTGAGTATTAAAAGTTAGCAGAGTTAAGCTCGCAACCTCTG
66 CAACTAGCGGACCTACGCTCCCAGCTGAGTATTAAAAGTTAGCAGAGTTAAGCTCGCAACCTCCG
* * * * * * * * * *
39512914 GTCTTTTGAGTTAGCAGAGTTAAGCTCACAGCT-CTCATACAGCTCGTGGACCTACACTTCCATC
131 ATCTTTTGAGTTAGCAAAGTTAAACTCACAACTCCT-AGACAACTAGCGAACCTACACTTCCAAC
39512978 TGATTATTAAAGGT
195 TGATTATTAAAGGT
* * *
39512992 TAGCATG-GTTAAGCTCGCAACCCCCAATCTT
1 TAGTA-GAGTTAAGCTCGCAACCTCCTATCTT
39513023 ATTTACAAAC
Statistics
Matches: 201, Mismatches: 34, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
205 2 0.01
206 154 0.77
207 13 0.06
208 31 0.15
209 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (208 bp):
TAGTAGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAAACTTAAGCTCACAACTCCCAGA
CAACTAGCGGACCTACGCTCCCAGCTGAGTATTAAAAGTTAGCAGAGTTAAGCTCGCAACCTCCG
ATCTTTTGAGTTAGCAAAGTTAAACTCACAACTCCTAGACAACTAGCGAACCTACACTTCCAACT
GATTATTAAAGGT
Found at i:39521734 original size:42 final size:42
Alignment explanation
Indices: 39521675--39521756 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
39521665 GGAAGTTGAA
**
39521675 AATTCTTTAATTAAAATCTTTGGACTTCAAATAATGCTAGAC
1 AATTCTTTAAACAAAATCTTTGGACTTCAAATAATGCTAGAC
*
39521717 AATTCTTTAAACAAAATCTTTGGACTTCGAATAATGCTAG
1 AATTCTTTAAACAAAATCTTTGGACTTCAAATAATGCTAG
39521757 TACTATGGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.37
Consensus pattern (42 bp):
AATTCTTTAAACAAAATCTTTGGACTTCAAATAATGCTAGAC
Found at i:39521790 original size:14 final size:14
Alignment explanation
Indices: 39521771--39521797 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39521761 ATGGAAGTAT
39521771 GAAAGCTCATCTAC
1 GAAAGCTCATCTAC
39521785 GAAAGCTCATCTA
1 GAAAGCTCATCTA
39521798 TAAAGATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (14 bp):
GAAAGCTCATCTAC
Found at i:39521957 original size:20 final size:17
Alignment explanation
Indices: 39521918--39521961 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
39521908 TCAAATGATC
*
39521918 TATTTTATATTGATCTT
1 TATTTTATATTGATATT
39521935 TATTATTATATTGTATATGT
1 TATT-TTATATTG-ATAT-T
39521955 TATTTTA
1 TATTTTA
39521962 GATGTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 6 0.26
20 5 0.22
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (17 bp):
TATTTTATATTGATATT
Found at i:39524523 original size:2 final size:2
Alignment explanation
Indices: 39524516--39524549 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
39524506 CACTTACGTT
39524516 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
39524550 GAGAGAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39527332 original size:6 final size:6
Alignment explanation
Indices: 39527313--39527344 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
39527303 TCTAAATAAA
39527313 TTCATT TCTCATT TTCATT TTCATT TTCATT T
1 TTCATT T-TCATT TTCATT TTCATT TTCATT T
39527345 CCGTTTTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.66
Consensus pattern (6 bp):
TTCATT
Found at i:39527351 original size:12 final size:12
Alignment explanation
Indices: 39527313--39527351 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
39527303 TCTAAATAAA
39527313 TTCATTTCTCATT
1 TTCATTTC-CATT
*
39527326 TTCATTTTCATT
1 TTCATTTCCATT
*
39527338 TTCATTTCCGTT
1 TTCATTTCCATT
39527350 TT
1 TT
39527352 GAGAAAACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 16 0.70
13 7 0.30
ACGTcount: A:0.13, C:0.21, G:0.03, T:0.64
Consensus pattern (12 bp):
TTCATTTCCATT
Found at i:39530024 original size:29 final size:30
Alignment explanation
Indices: 39529965--39530022 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
39529955 TCCGAGCCTT
*
39529965 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
39529995 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
39530023 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:39530252 original size:13 final size:13
Alignment explanation
Indices: 39530234--39530265 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
39530224 TTTCCAGCAA
39530234 TTATGAATTTATT
1 TTATGAATTTATT
39530247 TTATGAATTTATT
1 TTATGAATTTATT
*
39530260 TGATGA
1 TTATGA
39530266 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:39530473 original size:50 final size:50
Alignment explanation
Indices: 39530360--39530601 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
39530350 ATTTGGGTAA
* * *
39530360 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
39530416 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
39530466 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
39530516 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
39530566 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
39530602 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:39530549 original size:100 final size:103
Alignment explanation
Indices: 39530360--39530609 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
39530350 ATTTGGGTAA
39530360 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
39530425 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
39530466 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
39530528 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
39530566 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
39530610 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:39537614 original size:16 final size:17
Alignment explanation
Indices: 39537592--39537636 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 17
39537582 CGAATATAAT
39537592 AATTTTTTTTATTTTT-
1 AATTTTTTTTATTTTTA
*
39537608 TATTTTTTTTAATTTTTA
1 AATTTTTTTT-ATTTTTA
39537626 AATTTTTTTTA
1 AATTTTTTTTA
39537637 AAATTTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 9 0.36
17 7 0.28
18 9 0.36
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
AATTTTTTTTATTTTTA
Found at i:39537636 original size:18 final size:17
Alignment explanation
Indices: 39537591--39537637 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 17
39537581 CCGAATATAA
39537591 TAATTTTTTTT-ATTTT
1 TAATTTTTTTTAATTTT
*
39537607 TTATTTTTTTTAATTTT
1 TAATTTTTTTTAATTTT
39537624 TAAATTTTTTTTAA
1 T-AATTTTTTTTAA
39537638 AATTTGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 10 0.37
17 6 0.22
18 11 0.41
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TAATTTTTTTTAATTTT
Found at i:39537663 original size:11 final size:11
Alignment explanation
Indices: 39537649--39537699 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
39537639 ATTTGTTTAA
39537649 TTTTAAAATAT
1 TTTTAAAATAT
39537660 TTTTAAAATAT
1 TTTTAAAATAT
***
39537671 TTTTTTTA-AT
1 TTTTAAAATAT
39537681 TTTT-AAA-AT
1 TTTTAAAATAT
39537690 TTTTAAAATA
1 TTTTAAAATA
39537700 AATTTTTGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
9 7 0.21
10 9 0.27
11 17 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:39537706 original size:30 final size:30
Alignment explanation
Indices: 39537612--39537706 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
39537602 ATTTTTTATT
***
39537612 TTTTTTAATTTTT-AAATTTTTTTTA-AAA
1 TTTTTTAATTTTTAAAATTTTTAAAATAAA
* **
39537640 TTTGTTTAATTTTAAAATATTTTTAAAATATT
1 TTT-TTTAATTTTTAAA-ATTTTTAAAATAAA
39537672 TTTTTTAATTTTTAAAATTTTTAAAATAAA
1 TTTTTTAATTTTTAAAATTTTTAAAATAAA
39537702 TTTTT
1 TTTTT
39537707 GGTGTTTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
28 3 0.06
29 9 0.17
30 19 0.35
31 19 0.35
32 4 0.07
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (30 bp):
TTTTTTAATTTTTAAAATTTTTAAAATAAA
Found at i:39543753 original size:6 final size:6
Alignment explanation
Indices: 39543737--39543771 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
39543727 TGGTTTTCTC
* *
39543737 AAAATA GAAATG AAAATA AAAATA AAAATA AAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT
39543772 GAGGAATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:39550679 original size:15 final size:16
Alignment explanation
Indices: 39550650--39550687 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
39550640 GCCATGCGTA
39550650 TTCTCTTCTTCTTTCT
1 TTCTCTTCTTCTTTCT
*
39550666 TTCT-TTCTTTTTTCT
1 TTCTCTTCTTCTTTCT
39550681 TTCTCTT
1 TTCTCTT
39550688 TTATTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TTCTCTTCTTCTTTCT
Found at i:39553739 original size:9 final size:9
Alignment explanation
Indices: 39553725--39553788 Score: 58
Period size: 9 Copynumber: 6.7 Consensus size: 9
39553715 GTGATTTCTA
39553725 TTTATTATT
1 TTTATTATT
39553734 TTTATTATT
1 TTTATTATT
39553743 TTT-TATATT
1 TTTAT-TATT
39553752 TTTATTTATT
1 TTTA-TTATT
**
39553762 TTTAAAATTT
1 TTTATTA-TT
39553772 TTTAATCTATT
1 TTT-AT-TATT
39553783 TTTATT
1 TTTATT
39553789 TTTATTTTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
8 1 0.02
9 21 0.47
10 15 0.33
11 7 0.16
12 1 0.02
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTATTATT
Found at i:39554177 original size:17 final size:16
Alignment explanation
Indices: 39554141--39554181 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
39554131 TATTTGATAA
*
39554141 ACTAAAAAATTAAGCT
1 ACTAAAAAATTAAGAT
39554157 -CTAAAAAATTAAGTAT
1 ACTAAAAAATTAAG-AT
39554173 ACTAAAAAA
1 ACTAAAAAA
39554182 ATATTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 13 0.59
16 1 0.05
17 8 0.36
ACGTcount: A:0.61, C:0.10, G:0.05, T:0.24
Consensus pattern (16 bp):
ACTAAAAAATTAAGAT
Found at i:39562276 original size:22 final size:22
Alignment explanation
Indices: 39562233--39562276 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
39562223 GGCTCGGCCT
**
39562233 ATTTTTTTAATAAATACCAAAA
1 ATTTTTTTAATAAATAAAAAAA
39562255 ATTTATTTTAA-AAATAAAAAAA
1 ATTT-TTTTAATAAATAAAAAAA
39562277 TAAAAAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTTTTTTAATAAATAAAAAAA
Done.