Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 144 of 150
Found at i:43449528 original size:15 final size:15
Alignment explanation
Indices: 43449508--43449543 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
43449498 AGAAACATTG
43449508 GATACTCTGTTGTTT
1 GATACTCTGTTGTTT
43449523 GATACTCTGTTGTTT
1 GATACTCTGTTGTTT
*
43449538 AATACT
1 GATACT
43449544 GCATATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (15 bp):
GATACTCTGTTGTTT
Found at i:43451639 original size:2 final size:2
Alignment explanation
Indices: 43451632--43451660 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43451622 ATAAAATAAC
43451632 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 A
43451661 CTATTTAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43457227 original size:13 final size:13
Alignment explanation
Indices: 43457209--43457236 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
43457199 TTAGAAAGAT
43457209 TAGTATAAATACA
1 TAGTATAAATACA
43457222 TAGTATAAATACA
1 TAGTATAAATACA
43457235 TA
1 TA
43457237 CACAAATTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (13 bp):
TAGTATAAATACA
Found at i:43465847 original size:32 final size:32
Alignment explanation
Indices: 43465806--43465870 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
43465796 AAGCCCTAAG
43465806 GATAATTTTCCTTTGCCACACATCGATACGTT
1 GATAATTTTCCTTTGCCACACATCGATACGTT
43465838 GATAATTTTCCTTTGCCACACATCGATACGTT
1 GATAATTTTCCTTTGCCACACATCGATACGTT
43465870 G
1 G
43465871 GTGGATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.37
Consensus pattern (32 bp):
GATAATTTTCCTTTGCCACACATCGATACGTT
Found at i:43467481 original size:32 final size:32
Alignment explanation
Indices: 43467440--43467505 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
43467430 TGGTTATAGA
*
43467440 TTACTTCATAAAATGGGTAGAAGCCTCTTCGT
1 TTACTTCATAAAATGGGTAGAAGCCACTTCGT
43467472 TTACTTCATAAAATGGGTAGAAGCCACTTCGT
1 TTACTTCATAAAATGGGTAGAAGCCACTTCGT
43467504 TT
1 TT
43467506 GCCCATGTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (32 bp):
TTACTTCATAAAATGGGTAGAAGCCACTTCGT
Found at i:43468266 original size:17 final size:17
Alignment explanation
Indices: 43468246--43468278 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43468236 ATATTTTGCC
43468246 TAAAAAAACAAAAAAAA
1 TAAAAAAACAAAAAAAA
*
43468263 TAAAAAAATAAAAAAA
1 TAAAAAAACAAAAAAA
43468279 TCAAGATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (17 bp):
TAAAAAAACAAAAAAAA
Found at i:43468267 original size:7 final size:8
Alignment explanation
Indices: 43468246--43468279 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
43468236 ATATTTTGCC
43468246 TAAAAAAA
1 TAAAAAAA
*
43468254 CAAAAAAAA
1 -TAAAAAAA
43468263 TAAAAAAA
1 TAAAAAAA
43468271 TAAAAAAA
1 TAAAAAAA
43468279 T
1 T
43468280 CAAGATGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (8 bp):
TAAAAAAA
Found at i:43468876 original size:20 final size:20
Alignment explanation
Indices: 43468837--43468880 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
43468827 GGGTTACTCG
* *
43468837 CAAAACTTGAGGAGAGAAGT
1 CAAAACTAGAGGAGAAAAGT
43468857 ACAAAACTAGA-GAGAAAAGT
1 -CAAAACTAGAGGAGAAAAGT
43468877 CAAA
1 CAAA
43468881 GATTGAAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 8 0.38
21 9 0.43
ACGTcount: A:0.55, C:0.11, G:0.23, T:0.11
Consensus pattern (20 bp):
CAAAACTAGAGGAGAAAAGT
Found at i:43469263 original size:77 final size:77
Alignment explanation
Indices: 43469139--43469351 Score: 297
Period size: 77 Copynumber: 2.8 Consensus size: 77
43469129 GAATTATTTG
* * *
43469139 TTTCAATTTCTTTTTTTTTCAAAAATAAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGCCAC
1 TTTCAATTT-TTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCCAC
43469204 ACGCCGAG-G-TA
65 ACGCCGAGCGTTA
* * *
43469215 TTTTCAATTTTTGTTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTGAGTCA
1 -TTTCAATTTTTGTTTTTTC-AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCCA
43469280 CACGCCGAGCGTTA
64 CACGCCGAGCGTTA
* * *
43469294 TTTCAATTTATG-TTTTTCAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCGG
1 TTTCAATTTTTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGG
43469352 ACANNNNNNN
Statistics
Matches: 122, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
76 45 0.37
77 63 0.52
78 12 0.10
79 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (77 bp):
TTTCAATTTTTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCCACA
CGCCGAGCGTTA
Found at i:43469702 original size:77 final size:77
Alignment explanation
Indices: 43469455--43470443 Score: 1016
Period size: 76 Copynumber: 13.0 Consensus size: 77
43469445 NNNNNNNNNN
* ** * * * *
43469455 ACTCATAATGCGAGAGGTGA-ATGAGCCTTTGGCCGCACGCCGAGGTATTTTCAA-TTCATGTTT
1 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTAATTTC-TGTTT
**** *
43469518 CAAAAAAAAAATTA
65 -TTTCAAAAAATCA
* * * *
43469532 ACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACACGCTGAGGTATTTTTTAA--T-T-TTT
1 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTA-TTTTTAATTTCTGTTT
*
43469593 TTTC-AGAAATCA
65 TTTCAAAAAATCA
* * *** *
43469605 ACTCATAATGCGAGATGTGAGTTGAGCCTCGGGCCACACAACGAGGTATTTTTAATTTTTGTTTT
1 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTAATTTCTGTTTT
43469670 TTCAAAAAATCA
66 TTCAAAAAATCA
* * *
43469682 ACTCATATTGCGAGAGGTGAGTTGA---TCGGG-CACATGCCAAGGTATTTTTTTAATTTTTG-T
1 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTA--TTTTTAATTTCTGTT
43469742 TTTTCAAAAAATCA
64 TTTTCAAAAAATCA
* ** * * *
43469756 ACTCATAATGCG-GAAGTGAGTTGAGCCTCGGGTTGCACGCCGAGGTATTTTCAATTTCTATTTT
1 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTAATTTCTGTTTT
43469820 TTCAAAAAAAATCA
66 TTC--AAAAAATCA
* * *
43469834 ACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATGCCGAGGTATTTTTTAACTTCTG-TT
1 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTA-TTTTTAATTTCTGTTT
43469898 TTTC-AAAAATCA
65 TTTCAAAAAATCA
* * * * *
43469910 ACTCATAATGCGAGAGGTGAGTTAAGCCTCGGGCCGCATGCCTAGGTATTTTCAATTTCTGTCTT
1 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTAATTTCTGT-TT
*
43469975 TTTGAAAAAATCA
65 TTTCAAAAAATCA
* * * ** *
43469988 ACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCACACGTTGAGGAATTTTTTAATTTCTG-TT
1 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTA-TTTTTAATTTCTGTTT
43470052 TTTC-AAAAATCA
65 TTTCAAAAAATCA
** * * * * *
43470064 ACTCATAATGCGAGAGGTGAGTTGAGCCTATGGCCGCATTCCGAGGTATTTTCAATTTTTGTTTT
1 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTAATTTCTGTTTT
43470129 TTCAAAAAATCA
66 TTCAAAAAATCA
* * * * * *
43470141 ACTCATATTGCAAGAGGTGAGTTAAGCCTCGGGTCACATGCCGAGTTCTTTTTCATTTCTGTTTT
1 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTAATTTCTG-TTT
43470206 TTTC-AAAAATCA
65 TTTCAAAAAATCA
* * * * *
43470218 ACTCATAATGCAAGAGGTGAGTTGAGCCCCGGGT-ACACGCTGAGGTATTTTTCAATTTTTGTTT
1 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTT-AATTTCTGTTT
43470282 TTTC-AAAAATCA
65 TTTCAAAAAATCA
** * *
43470294 ACTCATAATGTTAGAGGTGAGTTGAGCCTCGGGTCACATACCGAAGTATTTTTCAATTTCTG-TT
1 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTT-AATTTCTGTTT
*
43470358 TTTC-AAAAGTCA
65 TTTCAAAAAATCA
* * * * *
43470370 ACTCATAATGCGAGAGGTGAGTTAAGCCTCAGG-CACATGCCGATGTATCTTTCAATTTATGTTT
1 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTAT-TTTTAATTTCTGTTT
43470434 TTTCAAAAAA
65 TTTCAAAAAA
43470444 AAAAAAAGGA
Statistics
Matches: 763, Mismatches: 119, Indels: 60
0.81 0.13 0.06
Matches are distributed among these distances:
72 7 0.01
73 68 0.09
74 32 0.04
75 69 0.09
76 231 0.30
77 196 0.26
78 96 0.13
79 54 0.07
80 10 0.01
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (77 bp):
ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTAATTTCTGTTTT
TTCAAAAAATCA
Found at i:43470014 original size:154 final size:153
Alignment explanation
Indices: 43469455--43470443 Score: 1207
Period size: 154 Copynumber: 6.5 Consensus size: 153
43469445 NNNNNNNNNN
* **
43469455 ACTCATAATGCGAGAGGTGA-ATGAGCCTTTGGCCGCACGCCGAGGTATTTTCAA-TTCATGTTT
1 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCCGCACGCCGAGGTATTTTCAATTTC-TGTTT
**** * * * *
43469518 CAAAAAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACACGCTGAGGTATTT
65 -TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTT
*
43469583 TTTAA-TT-T-TTTTTCAGAAATCA
129 TTTAATTTCTGTTTTTCAAAAATCA
* * ** * *
43469605 ACTCATAATGCGAGATGTGAGTTGAGCCTCGGGCCACACAACGAGGTATTTTTAATTTTTGTTTT
1 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCCGCACGCCGAGGTATTTTCAATTTCTGTTTT
*
43469670 TTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA---TCGGG-CACATGCCAAGGTATTTTT
66 TTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTA-TTTT
*
43469731 TTAATTTTTGTTTTTCAAAAAATCA
130 TTAATTTCTGTTTTTC-AAAAATCA
* ** *
43469756 ACTCATAATGCG-GAAGTGAGTTGAGCCTCGGGTTGCACGCCGAGGTATTTTCAATTTCTATTTT
1 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCCGCACGCCGAGGTATTTTCAATTTCTGTTTT
*
43469820 TTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATGCCGAGGTATTT
66 TTC--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTT
*
43469885 TTTAACTTCTGTTTTTCAAAAATCA
129 TTTAATTTCTGTTTTTCAAAAATCA
* * *
43469910 ACTCATAATGCGAGAGGTGAGTTAAGCCTCGGGCCGCATGCCTAGGTATTTTCAATTTCTGTCTT
1 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCCGCACGCCGAGGTATTTTCAATTTCTGT-TT
* * * ** *
43469975 TTTGAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCACACGTTGAGGAATTTT
65 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTT
43470040 TTAATTTCTGTTTTTCAAAAATCA
130 TTAATTTCTGTTTTTCAAAAATCA
** ** *
43470064 ACTCATAATGCGAGAGGTGAGTTGAGCCTATGGCCGCATTCCGAGGTATTTTCAATTTTTGTTTT
1 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCCGCACGCCGAGGTATTTTCAATTTCTGTTTT
* *
43470129 TTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTAAGCCTCGGGTCACATGCCGA-GT-TCTTT
66 TTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTAT-TTT
*
43470192 TTCATTTCTGTTTTTTTCAAAAATCA
130 TTAATTTCTG--TTTTTCAAAAATCA
* * ** * *
43470218 ACTCATAATGCAAGAGGTGAGTTGAGCCCCGGG-TACACGCTGAGGTATTTTTCAATTTTTGTTT
1 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCCGCACGCCGAGGTA-TTTTCAATTTCTGTTT
* ** * *
43470282 TTTC-AAAAATCAACTCATAATGTTAGAGGTGAGTTGAGCCTCGGGTCACATACCGAAGTATTTT
65 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTT
* *
43470346 TCAATTTCTGTTTTTCAAAAGTCA
130 TTAATTTCTGTTTTTCAAAAATCA
* * * * * *
43470370 ACTCATAATGCGAGAGGTGAGTTAAGCCTCAGG-CACATGCCGATGTATCTTTCAATTTATGTTT
1 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCCGCACGCCGAGGTAT-TTTCAATTTCTGTTT
43470434 TTTCAAAAAA
65 TTTCAAAAAA
43470444 AAAAAAAGGA
Statistics
Matches: 728, Mismatches: 88, Indels: 43
0.85 0.10 0.05
Matches are distributed among these distances:
146 11 0.02
147 12 0.02
148 2 0.00
149 1 0.00
150 104 0.14
151 53 0.07
152 119 0.16
153 113 0.16
154 230 0.32
155 65 0.09
156 18 0.02
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (153 bp):
ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCCGCACGCCGAGGTATTTTCAATTTCTGTTTT
TTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTT
TAATTTCTGTTTTTCAAAAATCA
Found at i:43470635 original size:30 final size:30
Alignment explanation
Indices: 43470601--43470667 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
43470591 ATAAACACAT
*
43470601 TTGAAAATAGATATAACGTAAAAAAACCTA
1 TTGAAAATAGATATAACGTAAAAAAAACTA
*
43470631 TTGAACATAGATATAACGTAAAAAAAACTA
1 TTGAAAATAGATATAACGTAAAAAAAACTA
43470661 TTGAAAA
1 TTGAAAA
43470668 AAGAATACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.57, C:0.09, G:0.10, T:0.24
Consensus pattern (30 bp):
TTGAAAATAGATATAACGTAAAAAAAACTA
Found at i:43471803 original size:13 final size:13
Alignment explanation
Indices: 43471785--43471829 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
43471775 TTTTGATTTC
*
43471785 AATTAAAATTATA
1 AATTAAAATAATA
43471798 AATTAAAATAATA
1 AATTAAAATAATA
* * *
43471811 ATTTAAAATGATC
1 AATTAAAATAATA
43471824 AATTAA
1 AATTAA
43471830 TATATGATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (13 bp):
AATTAAAATAATA
Found at i:43475857 original size:17 final size:17
Alignment explanation
Indices: 43475832--43475870 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
43475822 AGACAACCAT
*
43475832 TATATATATATAAATAA
1 TATAAATATATAAATAA
**
43475849 TATAAATATATTGATAA
1 TATAAATATATAAATAA
43475866 TATAA
1 TATAA
43475871 TCTACAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TATAAATATATAAATAA
Found at i:43476586 original size:22 final size:22
Alignment explanation
Indices: 43476561--43476604 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
43476551 TACTATATAT
*
43476561 ATAATATACCCTTTATCTTTGC
1 ATAATATACCCTTTACCTTTGC
*
43476583 ATAATATACCTTTTACCTTTGC
1 ATAATATACCCTTTACCTTTGC
43476605 TTTCTAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.23, G:0.05, T:0.45
Consensus pattern (22 bp):
ATAATATACCCTTTACCTTTGC
Found at i:43477935 original size:11 final size:11
Alignment explanation
Indices: 43477919--43477949 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
43477909 GTCCATGGGC
43477919 CGGGCCGGGTT
1 CGGGCCGGGTT
43477930 CGGGCCGGGTT
1 CGGGCCGGGTT
*
43477941 CGCGCCGGG
1 CGGGCCGGG
43477950 CCCACAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.55, T:0.13
Consensus pattern (11 bp):
CGGGCCGGGTT
Found at i:43478155 original size:16 final size:16
Alignment explanation
Indices: 43478118--43478157 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
43478108 TTAATAAAAT
* *
43478118 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
43478134 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
43478150 TAAAATTA
1 TAAAATTA
43478158 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:43478157 original size:22 final size:22
Alignment explanation
Indices: 43478090--43478142 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
43478080 TAATTAAAAT
* * *
43478090 TAAAATTAAAATTATTTTTTAA
1 TAAAATTAAAACTAATTGTTAA
*
43478112 TAAAATTAAAACTAATTGTTAT
1 TAAAATTAAAACTAATTGTTAA
43478134 TAAAATTAA
1 TAAAATTAA
43478143 TTGTTAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAATTAAAACTAATTGTTAA
Found at i:43478236 original size:59 final size:61
Alignment explanation
Indices: 43478167--43478346 Score: 265
Period size: 68 Copynumber: 2.9 Consensus size: 61
43478157 ATCAAATTAT
*
43478167 TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC--A--A
43478232 TTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC-A
1 -TAA-T-TATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
*
43478295 -AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
43478347 ACAAACTTGA
Statistics
Matches: 110, Mismatches: 2, Indels: 11
0.89 0.02 0.09
Matches are distributed among these distances:
59 48 0.44
60 1 0.01
61 2 0.02
63 1 0.01
66 3 0.03
67 1 0.01
68 54 0.49
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (61 bp):
TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
Found at i:43478263 original size:9 final size:9
Alignment explanation
Indices: 43478230--43478257 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
43478220 TTTATCAAAT
43478230 TATTAATTG
1 TATTAATTG
43478239 TATTAATTG
1 TATTAATTG
43478248 TATTAATTG
1 TATTAATTG
43478257 T
1 T
43478258 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:43478267 original size:68 final size:68
Alignment explanation
Indices: 43478146--43478316 Score: 319
Period size: 68 Copynumber: 2.5 Consensus size: 68
43478136 AAATTAATTG
*
43478146 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
43478209 TGA
66 TGA
43478212 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
43478277 TGA
66 TGA
43478280 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
43478317 TGTAACAAAA
Statistics
Matches: 102, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
66 26 0.25
68 76 0.75
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:43478844 original size:26 final size:26
Alignment explanation
Indices: 43478789--43478847 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
43478779 TGAACTATTA
* *
43478789 TATATATAATTTATTTAAATTTCTTT
1 TATATATAATTTATTTAAATTTCATG
*
43478815 TATATATTATTTATTGTAAATTT-ATG
1 TATATATAATTTATT-TAAATTTCATG
43478841 TATATAT
1 TATATAT
43478848 CTTTCAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 22 0.76
27 7 0.24
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (26 bp):
TATATATAATTTATTTAAATTTCATG
Found at i:43483003 original size:7 final size:7
Alignment explanation
Indices: 43482991--43483032 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
43482981 CAGTGGAGGA
43482991 AAAAAAC
1 AAAAAAC
*
43482998 AAAAAAAT
1 -AAAAAAC
43483006 AAAAAAC
1 AAAAAAC
43483013 AAAAAAC
1 AAAAAAC
*
43483020 AAAAAAT
1 AAAAAAC
43483027 AAAAAA
1 AAAAAA
43483033 ACTCTACCGG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
7 25 0.81
8 6 0.19
ACGTcount: A:0.88, C:0.07, G:0.00, T:0.05
Consensus pattern (7 bp):
AAAAAAC
Found at i:43483011 original size:15 final size:15
Alignment explanation
Indices: 43482991--43483034 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
43482981 CAGTGGAGGA
*
43482991 AAAAAACAAAAAAAT
1 AAAAAACAAAAAAAC
43483006 AAAAAAC-AAAAAAC
1 AAAAAACAAAAAAAC
*
43483020 AAAAAATAAAAAAAC
1 AAAAAACAAAAAAAC
43483035 TCTACCGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.86, C:0.09, G:0.00, T:0.05
Consensus pattern (15 bp):
AAAAAACAAAAAAAC
Found at i:43483034 original size:22 final size:22
Alignment explanation
Indices: 43482991--43483032 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
43482981 CAGTGGAGGA
43482991 AAAAAACAAAAAAATAAAAAAC
1 AAAAAACAAAAAAATAAAAAAC
43483013 AAAAAAC-AAAAAATAAAAAA
1 AAAAAACAAAAAAATAAAAAA
43483033 ACTCTACCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.88, C:0.07, G:0.00, T:0.05
Consensus pattern (22 bp):
AAAAAACAAAAAAATAAAAAAC
Found at i:43483485 original size:15 final size:15
Alignment explanation
Indices: 43483465--43483494 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43483455 TACTTCACTT
*
43483465 GAAAAAAAATGAAAA
1 GAAAAAAAAAGAAAA
43483480 GAAAAAAAAAGAAAA
1 GAAAAAAAAAGAAAA
43483495 AAAGAACGAA
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:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (15 bp):
GAAAAAAAAAGAAAA
Found at i:43483497 original size:18 final size:18
Alignment explanation
Indices: 43483476--43483513 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
43483466 AAAAAAAATG
43483476 AAAAGAAAAAAAAAGAAA
1 AAAAGAAAAAAAAAGAAA
**
43483494 AAAAGAACGAAAAAGAAA
1 AAAAGAAAAAAAAAGAAA
43483512 AA
1 AA
43483514 GGAGAGGCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAAAAAGAAA
Found at i:43484662 original size:50 final size:49
Alignment explanation
Indices: 43484608--43484939 Score: 236
Period size: 50 Copynumber: 6.7 Consensus size: 49
43484598 GGCATTACGG
* * * * * *
43484608 TGGAAAAGATTGAAGCCACAATGGCGAATCTGACTTCTCTGGCGGTACAG
1 TGGAAAAGATTGAAGCTACAACGGCGAATCTTACTT-TCTGACAGTACAA
* * * * * *
43484658 TGGAACAGATTGAAGCTACAACAGCGAATCTT-GTTTCCCCGACATTGCAA
1 TGGAAAAGATTGAAGCTACAACGGCGAATCTTACTTT--CTGACAGTACAA
** * * * * *
43484708 TTAAAAATATTGAAGCCACAACGGCGAATCTTACTTCCCTGGC-GATGCAA
1 TGGAAAAGATTGAAGCTACAACGGCGAATCTTACTT-TCTGACAG-TACAA
** ** *
43484758 TGGAGCAGATTGAAGCTACAACGATGAATCTTACTTTCTCGACATTACAA
1 TGGAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCT-GACAGTACAA
** **
43484808 TTAAAAAGATTGAAGCTACAACGATGAATCTTACTTTCTCGACAGTACAA
1 TGGAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCT-GACAGTACAA
** * * * * * *
43484858 TTAAAAAGATTGAAGCCACAACGACGAATCTTACTTTCCTGGCGGTGCAG
1 TGGAAAAGATTGAAGCTACAACGGCGAATCTTACTTT-CTGACAGTACAA
* *
43484908 TGGAACAGATTGAAGCTACAACGGTGAATCTT
1 TGGAAAAGATTGAAGCTACAACGGCGAATCTT
43484940 GCTTCCCCAA
Statistics
Matches: 222, Mismatches: 52, Indels: 16
0.77 0.18 0.06
Matches are distributed among these distances:
48 1 0.00
49 4 0.02
50 213 0.96
51 4 0.02
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (49 bp):
TGGAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCTGACAGTACAA
Found at i:43484789 original size:100 final size:100
Alignment explanation
Indices: 43484611--43484896 Score: 303
Period size: 100 Copynumber: 2.9 Consensus size: 100
43484601 ATTACGGTGG
* * * * *
43484611 AAAAGATTGAAGCCACAATGGCGAATCTGACTTCTCTGGCGGTACAGTGGAACAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGATACAATGGAACAGATTGAAGCTA
* *
43484676 CAACAGCGAATCTT-GTTTCCCCGACATTGCAATTA
66 CAACAGCGAATCTTACTTT-CCCGACATTACAATTA
* * *
43484711 AAAATATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGATGCAATGGAGCAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGATACAATGGAACAGATTGAAGCTA
* *
43484776 CAAC-GATGAATCTTACTTTCTCGACATTACAATTA
66 CAACAG-CGAATCTTACTTTCCCGACATTACAATTA
* ** * * ** *
43484811 AAAAGATTGAAGCTACAACGATGAATCTTACTT-TCTCGAC-AGTACAATTAAAAAGATTGAAGC
1 AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCT-GGCGA-TACAATGGAACAGATTGAAGC
*
43484874 CACAAC-GACGAATCTTACTTTCC
64 TACAACAG-CGAATCTTACTTTCC
43484897 TGGCGGTGCA
Statistics
Matches: 156, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
99 4 0.03
100 149 0.96
101 3 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (100 bp):
AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGATACAATGGAACAGATTGAAGCTA
CAACAGCGAATCTTACTTTCCCGACATTACAATTA
Found at i:43484970 original size:50 final size:50
Alignment explanation
Indices: 43484664--43485011 Score: 306
Period size: 50 Copynumber: 7.0 Consensus size: 50
43484654 ACAGTGGAAC
**
43484664 AGATTGAAGCTACAAC-AGCGAATCTTGTTTCCCCGACATTGCAATTAAAA
1 AGATTGAAGCTACAACGA-CGAATCTTACTTCCCCGACATTGCAATTAAAA
* * * * * ** **
43484714 ATATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGA-TGCAATGGAGC
1 AGATTGAAGCTACAACGACGAATCTTACTTCCCCGAC-ATTGCAATTAAAA
* * * *
43484764 AGATTGAAGCTACAACGATGAATCTTACTTTCTCGACATTACAATTAAAA
1 AGATTGAAGCTACAACGACGAATCTTACTTCCCCGACATTGCAATTAAAA
* * * * *
43484814 AGATTGAAGCTACAACGATGAATCTTACTTTCTCGACAGTACAATTAAAA
1 AGATTGAAGCTACAACGACGAATCTTACTTCCCCGACATTGCAATTAAAA
* * * * ** * ** *
43484864 AGATTGAAGCCACAACGACGAATCTTACTTTCCTGGCGGTGCAGTGGAAC
1 AGATTGAAGCTACAACGACGAATCTTACTTCCCCGACATTGCAATTAAAA
** * *
43484914 AGATTGAAGCTACAACGGTGAATCTTGCTTCCCCAACATTGCAATTAAAA
1 AGATTGAAGCTACAACGACGAATCTTACTTCCCCGACATTGCAATTAAAA
* * * *
43484964 AAATTGAAG-TCGCAATGACGAATCTTACTTCTCCGACATTGCAATTAA
1 AGATTGAAGCT-ACAACGACGAATCTTACTTCCCCGACATTGCAATTAA
43485012 TTAGACTGAA
Statistics
Matches: 236, Mismatches: 58, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
49 2 0.01
50 233 0.99
51 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCTACAACGACGAATCTTACTTCCCCGACATTGCAATTAAAA
Found at i:43485022 original size:150 final size:150
Alignment explanation
Indices: 43484666--43485011 Score: 455
Period size: 150 Copynumber: 2.3 Consensus size: 150
43484656 AGTGGAACAG
** * *
43484666 ATTGAAGCTACAAC-AGCGAATCTTGTTTCCCCGACATTGCAATTAAAAATATTGAAGCCACAAC
1 ATTGAAGCTACAACGA-CGAATCTTACTTCTCCGACATTGCAATTAAAAAGATTGAAGCCACAAC
* * *
43484730 GGCGAATCTTACTTCCCTGGCGATGCAATGGAGCAGATTGAAGCTACAACGATGAATCTTACTTT
65 GACGAATCTTACTTCCCTGGCGATGCAATGGAACAGATTGAAGCTACAACGATGAATCTTACTTC
* * *
43484795 CTCGACATTACAATTAAAAAG
130 CCCAACATTACAATTAAAAAA
* * *
43484816 ATTGAAGCTACAACGATGAATCTTACTT-TCTCGACAGTACAATTAAAAAGATTGAAGCCACAAC
1 ATTGAAGCTACAACGACGAATCTTACTTCTC-CGACATTGCAATTAAAAAGATTGAAGCCACAAC
* * * * *
43484880 GACGAATCTTACTTTCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGTGAATCTTGCTTC
65 GACGAATCTTACTTCCCTGGCGATGCAATGGAACAGATTGAAGCTACAACGATGAATCTTACTTC
*
43484945 CCCAACATTGCAATTAAAAAA
130 CCCAACATTACAATTAAAAAA
* *
43484966 ATTGAAG-TCGCAATGACGAATCTTACTTCTCCGACATTGCAATTAA
1 ATTGAAGCT-ACAACGACGAATCTTACTTCTCCGACATTGCAATTAA
43485012 TTAGACTGAA
Statistics
Matches: 168, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
149 2 0.01
150 163 0.97
151 3 0.02
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (150 bp):
ATTGAAGCTACAACGACGAATCTTACTTCTCCGACATTGCAATTAAAAAGATTGAAGCCACAACG
ACGAATCTTACTTCCCTGGCGATGCAATGGAACAGATTGAAGCTACAACGATGAATCTTACTTCC
CCAACATTACAATTAAAAAA
Found at i:43485092 original size:44 final size:44
Alignment explanation
Indices: 43485029--43485365 Score: 262
Period size: 44 Copynumber: 7.8 Consensus size: 44
43485019 GAAGATAGCT
* * * *
43485029 AATCTTATTTCCCTGAAGTTGCAGTGGAACAAATTGAAGAAACC
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACC
* * ** *
43485073 AATCCTATCTCCCTGAAGTTACAGTGGAGTAGACAGAAGAAACT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACC
*
43485117 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACC
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACC
*** ** *
43485161 AATCCTATCTTTTTGAAGTTGCAGTGGAGTGGATT-AA-AACCAC
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAAC-C
* * * * * *
43485204 AGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATT--A-CATCT
1 A-ATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACC
* * ** *
43485246 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CAAATG-AACT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-GAAACC
* **
43485289 AA-CCTTATCTCCCT-AATGTTGCAGTGGAGCAGGTTGAAGCCA-C
1 AATCC-TATCTCCCTGAA-GTTGCAGTGGAGCAGATTGAAGAAACC
* *
43485332 AAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGA
1 AA-TCCTATCTCCCTGAAGTTGCAGTGGAGCAGA
43485366 CTAAAACCAC
Statistics
Matches: 234, Mismatches: 46, Indels: 26
0.76 0.15 0.08
Matches are distributed among these distances:
41 29 0.12
42 8 0.03
43 38 0.16
44 156 0.67
45 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACC
Found at i:43485178 original size:88 final size:88
Alignment explanation
Indices: 43485027--43485366 Score: 331
Period size: 88 Copynumber: 3.9 Consensus size: 88
43485017 CTGAAGATAG
* * *
43485027 CTAATCTTATTTCCCTGAAGTTGCAGTGGAACAAATTGAAGAAACCAATCCTATCTCCCTGAAGT
1 CTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACCAATCCTATCTCCCTGAAGT
*
43485092 TACAGTGGAGTAGACAGAAGA-AA
66 TGCAGTGGAGTAGACA-AAGACAA
***
43485115 CTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACCAATCCTATCTTTTTGAAGT
1 CTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACCAATCCTATCTCCCTGAAGT
* * *
43485180 TGCAGTGGAGTGGATTAAA-ACCA
66 TGCAGTGGAGTAGA-CAAAGACAA
* * * * * * *
43485203 C-AGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATT--A-CATCTAGTCTTATCTCCCTGAAG
1 CTA-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACCAATCCTATCTCCCTGAAG
*
43485264 TTGCAGTGGAGCAGACAAATG--AA
65 TTGCAGTGGAGTAGACAAA-GACAA
* * ** *
43485287 CTAACCTTATCTCCCT-AATGTTGCAGTGGAGCAGGTTGAAGCCA-CAAGTCTTATCTCCCTGAA
1 CTAATCTTATCTCCCTGAA-GTTGCAGTGGAGCAGATTGAAGAAACCAA-TCCTATCTCCCTGAA
* *
43485350 GTTGTAGTGGAGCAGAC
64 GTTGCAGTGGAGTAGAC
43485367 TAAAACCACA
Statistics
Matches: 208, Mismatches: 33, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
83 2 0.01
84 32 0.15
85 29 0.14
86 3 0.01
87 34 0.16
88 107 0.51
89 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (88 bp):
CTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACCAATCCTATCTCCCTGAAGT
TGCAGTGGAGTAGACAAAGACAA
Found at i:43485343 original size:128 final size:129
Alignment explanation
Indices: 43485119--43485365 Score: 299
Period size: 128 Copynumber: 1.9 Consensus size: 129
43485109 AAGAAACTAA
** ***
43485119 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACCAATCCTATCTTTTTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAGAAACCAATCCTATCTCCCTGAAGTTGCA
* *
43485184 GTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTACATCTAG
66 GTGGAGAGGATTAAAACCACAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTACATCTAG
*
43485248 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CAAATG-AACTAA-CCTTATCTCCCT-AATGTT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAA-GAAACCAATCC-TATCTCCCTGAA-GTT
* * * *
43485309 GCAGTGGAGCAGG-TTGAAGCCACA-AGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGA
63 GCAGTGGAG-AGGATTAAAACCACAGA-TCTTATCTCCCTGAAGTTGCAGTAGAGCAGA
43485366 CTAAAACCAC
Statistics
Matches: 101, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
127 5 0.05
128 62 0.61
129 34 0.34
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (129 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAGAAACCAATCCTATCTCCCTGAAGTTGCA
GTGGAGAGGATTAAAACCACAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTACATCTAG
Found at i:43486869 original size:26 final size:26
Alignment explanation
Indices: 43486802--43486890 Score: 92
Period size: 26 Copynumber: 3.4 Consensus size: 26
43486792 TGTCTTAAGT
* *
43486802 TTTTATATTTATTATTTATTTGAA-CTA
1 TTTTATA--TATTATTTATTTAAATTTA
* *
43486829 TTTTATATATAATTTATTTAAATTTC
1 TTTTATATATTATTTATTTAAATTTA
43486855 TTTTATATATTATTTATTGTAAATTTA
1 TTTTATATATTATTTATT-TAAATTTA
*
43486882 -TGTATATAT
1 TTTTATATAT
43486891 CTTTCAAATT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
25 13 0.25
26 26 0.49
27 14 0.26
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (26 bp):
TTTTATATATTATTTATTTAAATTTA
Found at i:43491143 original size:13 final size:13
Alignment explanation
Indices: 43491125--43491169 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
43491115 ATATGATTTC
*
43491125 AATTAAAATTATA
1 AATTAAAATAATA
43491138 AATTAAAATAATA
1 AATTAAAATAATA
* * *
43491151 ATTTAAAATGATC
1 AATTAAAATAATA
43491164 AATTAA
1 AATTAA
43491170 TATATTATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (13 bp):
AATTAAAATAATA
Found at i:43492526 original size:17 final size:17
Alignment explanation
Indices: 43492504--43492536 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
43492494 TATTTAACTC
43492504 TTTTAATAT-ATTATATA
1 TTTTAA-ATCATTATATA
43492521 TTTTAAATCATTATAT
1 TTTTAAATCATTATAT
43492537 GTATAAACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTAAATCATTATATA
Found at i:43505032 original size:44 final size:44
Alignment explanation
Indices: 43504928--43505172 Score: 191
Period size: 44 Copynumber: 5.6 Consensus size: 44
43504918 TATTAGAGAT
* **
43504928 CTTATCTCCCTG-AGATTACAGTGGAGTAGATC---G-CATCAAGT
1 CTTATCTCCCTGAAG-TTACAGTGGAGCAGATCGAAGACA-CAAAC
* * *
43504969 CTTATCTCCCTG-AGATTACAGAGGAGCAGATCGGAGCCACAAAC
1 CTTATCTCCCTGAAG-TTACAGTGGAGCAGATCGAAGACACAAAC
* * * * * **
43505013 CTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAATATACAAGT
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGACACAAAC
* * * * *
43505057 CTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA-ATTTCAGAT
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGACA---CAAAC
* * *
43505103 CTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGACACTATC
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGACACAAAC
43505147 C-TATCTCCCTGAAGTTACAGTGGAGC
1 CTTATCTCCCTGAAGTTACAGTGGAGC
43505173 GGATTAAAAT
Statistics
Matches: 165, Mismatches: 30, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
41 30 0.18
43 25 0.15
44 67 0.41
45 4 0.02
46 38 0.23
47 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGACACAAAC
Found at i:43505113 original size:46 final size:45
Alignment explanation
Indices: 43504924--43505305 Score: 181
Period size: 44 Copynumber: 8.8 Consensus size: 45
43504914 TGAATATTAG
* * * *
43504924 AGATCTTATCTCCCTGAGATTACAGTGGAGTAGATC---GCA-TC
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATTC
* * * * *
43504965 A-AGTCTTATCTCCCTGAGATTACAGAGGAGCAGATCGGAGCCA--C
1 AGA-TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAG-AATTC
* * * * *** * *
43505009 AAACCTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAA-TATAC
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATTC
*
43505053 A-AGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTC
1 AGA-TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAA-TTC
*
43505099 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAG-A--C
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATTC
* * * * ** **
43505141 ACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGA-TTAA-AATAAA
1 A-GATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAAT-TC
* * ** * * * * *
43505186 AGATCTTATCTCTCTAAATTTATAGTAGAGTAGATC---GCA-TC
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATTC
* ** * *
43505227 AGGTCTTATCTCCCTGATATTACAATGGAGCAGACCGAAGGATTTC
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAA-GAATTC
*
43505273 AGATCTTATCT-CCTGAGGTTACAGTAGAGCAGA
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGA
43505306 TTGAAGCCAG
Statistics
Matches: 258, Mismatches: 59, Indels: 44
0.71 0.16 0.12
Matches are distributed among these distances:
40 1 0.00
41 58 0.22
42 6 0.02
43 31 0.12
44 86 0.33
45 25 0.10
46 50 0.19
47 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (45 bp):
AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATTC
Found at i:43505217 original size:133 final size:134
Alignment explanation
Indices: 43504968--43505219 Score: 330
Period size: 133 Copynumber: 1.9 Consensus size: 134
43504958 TCGCATCAAG
* *
43504968 TCTTATCTCCCTGAGATTACAGAGGAGCAGATCGGAGCCACAAACCTTATCTCCCTGAAGTTACA
1 TCTTATCTCCCTGAGATTACAGAGGAGCAGATCGAAGACACAAACCTTATCTCCCTGAAGTTACA
* * * * * *
43505033 GTGGGGCAGGTTGAATATACAAGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTT
66 GTGGAGCAGGTTGAAAATAAAAGTCTTATCTCCCTAAAGTTACAGTAGAGTAGACCGAAGAATTT
43505098 CAGA
131 CAGA
* * * *
43505102 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGACACTATCC-TATCTCCCTGAAGTTACA
1 TCTTATCTCCCTGAGATTACAGAGGAGCAGATCGAAGACACAAACCTTATCTCCCTGAAGTTACA
* * *
43505166 GTGGAGC-GGATT-AAAATAAAAGATCTTATCTCTCTAAATTTATAGTAGAGTAGA
66 GTGGAGCAGG-TTGAAAATAAAAG-TCTTATCTCCCTAAAGTTACAGTAGAGTAGA
43505220 TCGCATCAGG
Statistics
Matches: 101, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
132 10 0.10
133 51 0.50
134 40 0.40
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (134 bp):
TCTTATCTCCCTGAGATTACAGAGGAGCAGATCGAAGACACAAACCTTATCTCCCTGAAGTTACA
GTGGAGCAGGTTGAAAATAAAAGTCTTATCTCCCTAAAGTTACAGTAGAGTAGACCGAAGAATTT
CAGA
Found at i:43505398 original size:44 final size:44
Alignment explanation
Indices: 43505349--43505511 Score: 290
Period size: 44 Copynumber: 3.7 Consensus size: 44
43505339 AGCAGATCGC
*
43505349 ATCAAGTCTTATCTCCCTAAGTAGTAGTGGAACAGACAGAAGAA
1 ATCAAGTCTTATCTCCCTAAGCAGTAGTGGAACAGACAGAAGAA
*
43505393 ATCAAGTCTTATCTCCCTAAGTAGTAGTGGAACAGACAGAAGAA
1 ATCAAGTCTTATCTCCCTAAGCAGTAGTGGAACAGACAGAAGAA
43505437 ATCAAGTCTTATCTCCCTAAGCAGTAGTGGAACAGACAGAAGAA
1 ATCAAGTCTTATCTCCCTAAGCAGTAGTGGAACAGACAGAAGAA
* *
43505481 ATCAAGTCCTATCTTCCTAAGCAGTAGTGGA
1 ATCAAGTCTTATCTCCCTAAGCAGTAGTGGA
43505512 GTAGGTTGAA
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 116 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (44 bp):
ATCAAGTCTTATCTCCCTAAGCAGTAGTGGAACAGACAGAAGAA
Found at i:43508302 original size:27 final size:29
Alignment explanation
Indices: 43508267--43508320 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
43508257 TTTAATCCAA
*
43508267 AAAATTATT-ATTACAGTTAAT-TTATTGT
1 AAAATTATTAAATACA-TTAATATTATTGT
43508295 AAAA-TATTAAATACATTAATATTATT
1 AAAATTATTAAATACATTAATATTATT
43508321 TTAATTTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (29 bp):
AAAATTATTAAATACATTAATATTATTGT
Found at i:43510072 original size:20 final size:20
Alignment explanation
Indices: 43510017--43510073 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
43510007 TTATAAGTCA
*
43510017 CGAGTTTGAGG-TTTAAGGTT
1 CGAGTTT-AGGATTTAGGGTT
43510037 CGAGGTTATA-GATTTAGGGTT
1 CGA-GTT-TAGGATTTAGGGTT
43510058 CGAGTTTAGGATTTAG
1 CGAGTTTAGGATTTAG
43510074 AGTTTAAGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
19 2 0.06
20 14 0.44
21 15 0.47
22 1 0.03
ACGTcount: A:0.23, C:0.05, G:0.33, T:0.39
Consensus pattern (20 bp):
CGAGTTTAGGATTTAGGGTT
Found at i:43512536 original size:22 final size:23
Alignment explanation
Indices: 43512511--43512555 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
43512501 TACTATATAT
43512511 ATAATATACCC-TTTATCTTTGC
1 ATAATATACCCTTTTATCTTTGC
43512533 ATAATATACCCTTTTATCTTTGC
1 ATAATATACCCTTTTATCTTTGC
43512556 TTTCTAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.27, C:0.22, G:0.04, T:0.47
Consensus pattern (23 bp):
ATAATATACCCTTTTATCTTTGC
Found at i:43514042 original size:27 final size:27
Alignment explanation
Indices: 43513975--43514045 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
43513965 GAAACCCGGA
* **
43513975 TGCCACAGGCAGCACCAAAGGTGCCTG
1 TGCCACAGGCGGCACCAAAGGTGCCAC
* * * *
43514002 TGGCAGAGGTGGCACCAAATGTGCCAC
1 TGCCACAGGCGGCACCAAAGGTGCCAC
43514029 TGCCACAGGCGGCACCA
1 TGCCACAGGCGGCACCA
43514046 CTTGTATTAT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.25, C:0.32, G:0.31, T:0.11
Consensus pattern (27 bp):
TGCCACAGGCGGCACCAAAGGTGCCAC
Found at i:43514085 original size:3 final size:3
Alignment explanation
Indices: 43514072--43514123 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
43514062 CCATCCAGCT
* *
43514072 GAA GGA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAG
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
43514120 GAA G
1 GAA G
43514124 GAGGAGGAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:43519940 original size:8 final size:7
Alignment explanation
Indices: 43519910--43519973 Score: 55
Period size: 7 Copynumber: 9.3 Consensus size: 7
43519900 TTAATATCCA
*
43519910 AATAAGT
1 AATAAAT
43519917 AATAAAT
1 AATAAAT
43519924 AAT-AA-
1 AATAAAT
43519929 AATAAAGT
1 AATAAA-T
43519937 AATAAAT
1 AATAAAT
*
43519944 AAAGTAAAG
1 -AA-TAAAT
43519953 AA-AAAT
1 AATAAAT
43519959 AATAAAT
1 AATAAAT
43519966 AA-AAAT
1 AATAAAT
43519972 AA
1 AA
43519974 AATTTGGGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
5 3 0.06
6 15 0.31
7 16 0.33
8 10 0.21
9 4 0.08
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (7 bp):
AATAAAT
Found at i:43519941 original size:13 final size:12
Alignment explanation
Indices: 43519917--43519976 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
43519907 CCAAATAAGT
43519917 AATAAATAATAA
1 AATAAATAATAA
43519929 AATAAAGTAAT-A
1 AATAAA-TAATAA
*
43519941 AATAAAGTAA-AG
1 AATAAA-TAATAA
43519953 AA-AAATAAT-A
1 AATAAATAATAA
43519963 AATAAA-AATAA
1 AATAAATAATAA
43519974 AAT
1 AAT
43519977 TTGGGTTGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
10 8 0.20
11 10 0.24
12 19 0.46
13 4 0.10
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (12 bp):
AATAAATAATAA
Found at i:43528643 original size:148 final size:147
Alignment explanation
Indices: 43528109--43528843 Score: 764
Period size: 148 Copynumber: 4.9 Consensus size: 147
43528099 ATGTGTGTAT
* *
43528109 CCCTTATTTCGGCCATTTGTTCGTA-TTTTTTCTCGAGTTTTATTACTTTAAAAAATATACTATT
1 CCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTAAAAAA-ATA-TATT
* *
43528173 TTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAAATAAATTTAGTGTG
64 TTCT--TTGTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT--ATTAATTTAGTGTG
43528238 TTTTTTAAATAAATTTA-AAAAAA
125 -TTTTTAAATAAATTTAGAAAAAA
* * * *
43528261 CCCTTATTTCGGCCCTTTGCTC--ATTTTTTTCTCGAATTTTGTTACTTTCAATAAAAATATATT
1 CCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTT--A-AAAAA-ATA-T
* * * * *
43528324 ATTTTCGTATTTTATTGTTTTACTTTATTTTAGTACATTATGTTTGAAATATATTAA-TTAAT-T
61 ATTTTC-T-TTGTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGT
* * *
43528387 CTTTTT--TTAAATTTAGTAAAAA
124 GTTTTTAAATAAATTTAGAAAAAA
*
43528409 CCCTTATTTCGACCATTTGTTCGTA-TTTTTTCCCGAATTTTATTACTTT-AAAAAATACTATTT
1 CCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTAAAAAAATA-TATTT
* *
43528472 TCCAATTT-TATTATTTTATATTATTTTAGTACATTATGTTTAAAATTTATTAATTTAGTGTGTT
65 T-C--TTTGTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTT
43528536 TTTAAATAAATTTA-AAAAAA
127 TTTAAATAAATTTAGAAAAAA
* * * * *
43528556 CCCTTATTTCGTCCCTTTGCTAGTATTTTTTTCCCAAATTTTATTACTTTCAATAAAAATATATT
1 CCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTT-AA-AAAAATATATT
* * * *
43528621 ATT-TTTGTATTTTTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAA-TTATTTCTGTT
64 -TTCTTTGTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTA-GTGTGTT
* *
43528684 TTT--TTTAATTTAGTAAAAAA
127 TTTAAATAAATTTAG-AAAAAA
* * * *
43528704 CCCTAACTTCGGCCATTTGTTCGTATTTTTTTCTCTGCATTTTATTACTTTAAAAAATATCATAT
1 CCCTTATTTCGGCCATTTGTTCGTATTTTTTTC-CCGAATTTTATTACTTTAAAAAA-AT-ATAT
* * *
43528769 TTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATCAATTTAGCGTGT
63 TTTCT--TTGTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTG-
43528834 TTTTTAAATA
125 TTTTTAAATA
43528844 TACAATTTTT
Statistics
Matches: 490, Mismatches: 60, Indels: 64
0.80 0.10 0.10
Matches are distributed among these distances:
144 49 0.10
145 12 0.02
146 14 0.03
147 44 0.09
148 143 0.29
149 47 0.10
150 8 0.02
151 81 0.17
152 32 0.07
153 1 0.00
154 58 0.12
155 1 0.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (147 bp):
CCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTAAAAAAATATATTTT
CTTTGTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTA
AATAAATTTAGAAAAAA
Found at i:43529222 original size:24 final size:24
Alignment explanation
Indices: 43529171--43529222 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
43529161 TTGCTTCCCT
* *
43529171 CTTC-TTCTTCTCCTTTCCTTTTC
1 CTTCTTTCTTCTCCTTTCCCTCTC
*
43529194 TTTCTTTCTTCTCCTTTCCCTCTC
1 CTTCTTTCTTCTCCTTTCCCTCTC
43529218 CTTCT
1 CTTCT
43529223 CCACCCACCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (24 bp):
CTTCTTTCTTCTCCTTTCCCTCTC
Found at i:43531953 original size:23 final size:22
Alignment explanation
Indices: 43531905--43531953 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
43531895 TTAACAAAAT
* * *
43531905 TTAATTTAACAAGTTTTTTAAT
1 TTAATTTAACAAATTTATTAAA
*
43531927 TTAATTTAAATAAATTTATTAAA
1 TTAATTT-AACAAATTTATTAAA
43531950 TTAA
1 TTAA
43531954 ATTCAATGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TTAATTTAACAAATTTATTAAA
Found at i:43543521 original size:13 final size:13
Alignment explanation
Indices: 43543503--43543537 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
43543493 ATTTGACTTC
*
43543503 AATTAAAATTATA
1 AATTAAAATAATA
43543516 AATTAAAATAATA
1 AATTAAAATAATA
*
43543529 ATTTAAAAT
1 AATTAAAAT
43543538 GATCAACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATTAAAATAATA
Found at i:43544233 original size:5 final size:5
Alignment explanation
Indices: 43544223--43544251 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
43544213 TGTACTTTAT
43544223 TATTA TATTA TATTA TATTA TATTA TATT
1 TATTA TATTA TATTA TATTA TATTA TATT
43544252 CAGCTTCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATTA
Found at i:43545555 original size:13 final size:14
Alignment explanation
Indices: 43545532--43545560 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
43545522 TCTATGGTCG
43545532 GATATTTTGAAAAA
1 GATATTTTGAAAAA
43545546 GATA-TTTGAAAAA
1 GATATTTTGAAAAA
43545559 GA
1 GA
43545561 AAATTGGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.31
Consensus pattern (14 bp):
GATATTTTGAAAAA
Found at i:43548063 original size:22 final size:23
Alignment explanation
Indices: 43548038--43548082 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
43548028 TACTATATAT
43548038 ATAATATACCC-TTTATCTTTGC
1 ATAATATACCCTTTTATCTTTGC
43548060 ATAATATACCCTTTTATCTTTGC
1 ATAATATACCCTTTTATCTTTGC
43548083 TTTCTAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.27, C:0.22, G:0.04, T:0.47
Consensus pattern (23 bp):
ATAATATACCCTTTTATCTTTGC
Found at i:43552056 original size:15 final size:15
Alignment explanation
Indices: 43552031--43552076 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
43552021 TATTTATTTG
43552031 AAAAATAATTTA-AA
1 AAAAATAATTTATAA
43552045 AAAAATATATTTAT-A
1 AAAAATA-ATTTATAA
43552060 AAAAA-AA-TTATAA
1 AAAAATAATTTATAA
43552073 AAAA
1 AAAA
43552077 TCATCAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.14
13 6 0.21
14 8 0.28
15 11 0.38
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAAATAATTTATAA
Found at i:43557741 original size:86 final size:86
Alignment explanation
Indices: 43557596--43557768 Score: 346
Period size: 86 Copynumber: 2.0 Consensus size: 86
43557586 GAACCATTTA
43557596 CGTCTTATTCCCATACCGAGATTGTCTGATCATGTGCTTTACAAAAAGTAATGGTTATAAACTAT
1 CGTCTTATTCCCATACCGAGATTGTCTGATCATGTGCTTTACAAAAAGTAATGGTTATAAACTAT
43557661 TATTATATGTATCCCCTTTTG
66 TATTATATGTATCCCCTTTTG
43557682 CGTCTTATTCCCATACCGAGATTGTCTGATCATGTGCTTTACAAAAAGTAATGGTTATAAACTAT
1 CGTCTTATTCCCATACCGAGATTGTCTGATCATGTGCTTTACAAAAAGTAATGGTTATAAACTAT
43557747 TATTATATGTATCCCCTTTTG
66 TATTATATGTATCCCCTTTTG
43557768 C
1 C
43557769 AAATTACTGT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (86 bp):
CGTCTTATTCCCATACCGAGATTGTCTGATCATGTGCTTTACAAAAAGTAATGGTTATAAACTAT
TATTATATGTATCCCCTTTTG
Found at i:43560400 original size:19 final size:21
Alignment explanation
Indices: 43560370--43560414 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
43560360 TACAAAATAA
*
43560370 TTAAAATAATTT-TCAAAAAT
1 TTAAAATAATTTATAAAAAAT
43560390 TTAAAAT-ATTTATAAAAAAT
1 TTAAAATAATTTATAAAAAAT
*
43560410 CTAAA
1 TTAAA
43560415 TTTTCATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (21 bp):
TTAAAATAATTTATAAAAAAT
Found at i:43560670 original size:22 final size:23
Alignment explanation
Indices: 43560629--43560680 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
43560619 TAATTAACAA
43560629 AATTTAATTTAACAAGTTTT-TT
1 AATTTAATTTAACAAGTTTTATT
*
43560651 AATTTAATTTAA-ATGATTTTATT
1 AATTTAATTTAACAAG-TTTTATT
*
43560674 AAATTAA
1 AATTTAA
43560681 ATTCAATGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 2 0.08
22 16 0.62
23 8 0.31
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (23 bp):
AATTTAATTTAACAAGTTTTATT
Found at i:43560688 original size:23 final size:22
Alignment explanation
Indices: 43560645--43560688 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
43560635 ATTTAACAAG
* *
43560645 TTTTTTAATTTAATTTAAATGA
1 TTTTTTAAATTAAATTAAATGA
*
43560667 TTTTATTAAATTAAATTCAATG
1 TTTT-TTAAATTAAATTAAATG
43560689 CTCAACCTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (22 bp):
TTTTTTAAATTAAATTAAATGA
Found at i:43568985 original size:6 final size:6
Alignment explanation
Indices: 43568976--43569025 Score: 82
Period size: 6 Copynumber: 8.2 Consensus size: 6
43568966 CAAAATTAGA
*
43568976 TTAGGA TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTTAGGG
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG -TTAGGG
43569025 T
1 T
43569026 GTTTTTAAGT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
6 36 0.86
7 6 0.14
ACGTcount: A:0.18, C:0.00, G:0.46, T:0.36
Consensus pattern (6 bp):
TTAGGG
Found at i:43570894 original size:20 final size:20
Alignment explanation
Indices: 43570856--43570894 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
43570846 CTATTATTTT
*
43570856 TAAAATCTACATAATAATTG
1 TAAAATCTACATAAAAATTG
43570876 TAAAATCTA-ATATAAAATT
1 TAAAATCTACATA-AAAATT
43570895 TACCTCATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (20 bp):
TAAAATCTACATAAAAATTG
Found at i:43575942 original size:5 final size:5
Alignment explanation
Indices: 43575932--43575992 Score: 86
Period size: 5 Copynumber: 12.2 Consensus size: 5
43575922 ATTCATTTTC
* * * *
43575932 AATTT AATTT AATTT AATTT AGTTT AGTTT AGTTT AGTTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT
43575982 AATTT AATTT A
1 AATTT AATTT A
43575993 TGCAAGAGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 54 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (5 bp):
AATTT
Found at i:43576704 original size:21 final size:21
Alignment explanation
Indices: 43576680--43576735 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
43576670 CTTTGTTTCT
* *
43576680 AATCTCACTGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
43576701 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
43576722 AATCTCACCGCTAC
1 AATCTCACCGCTAC
43576736 CGCTATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.36, G:0.09, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:43577086 original size:2 final size:2
Alignment explanation
Indices: 43577073--43577114 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
43577063 ATTATTACTG
*
43577073 TA TA TG 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
43577115 CTCTGAGATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43577294 original size:13 final size:13
Alignment explanation
Indices: 43577258--43577297 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
43577248 AGTTCTTCAT
43577258 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
***
43577271 TGCTGCGGAAAAG
1 TGCTTTTGAAAAG
43577284 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
43577297 T
1 T
43577298 TTGGTTTAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.33
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:43589096 original size:27 final size:27
Alignment explanation
Indices: 43589058--43589112 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
43589048 CCCTTGTTAG
*
43589058 TGTTTCTAATTCTCTAGTATAACCCAA
1 TGTTTCTAATTCTCTAGCATAACCCAA
43589085 TGTTTCTAATTCTCTAGCATAACCCAA
1 TGTTTCTAATTCTCTAGCATAACCCAA
43589112 T
1 T
43589113 ACAAAGGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (27 bp):
TGTTTCTAATTCTCTAGCATAACCCAA
Found at i:43591772 original size:96 final size:95
Alignment explanation
Indices: 43591596--43591773 Score: 257
Period size: 96 Copynumber: 1.9 Consensus size: 95
43591586 AATGATTTAT
* * *
43591596 TTATGAAGTTGGTATGATTATAGAGCTAGAACGAGCTAGAATAAAAGTTTCACCTCTGTTAAATT
1 TTATGAAGTTGGTATGATTATAAAGCTAGAACGAGCTAAAATAAAAGTTTCACCTCTATTAAATT
* *
43591661 AAATAGGATTATGTTAAATTCATATTATTC
66 AAATAGAATCATGTTAAATTCATATTATTC
* * * *
43591691 TTATGAAGTTGGTATGGTTATAAAGCTATAACGATGTTAAAATAAAAGTTTCACCTCTATTAGAT
1 TTATGAAGTTGGTATGATTATAAAGCTAGAACGA-GCTAAAATAAAAGTTTCACCTCTATTAAAT
*
43591756 TAAATAGAATCGTGTTAA
65 TAAATAGAATCATGTTAA
43591774 GTTTAAATTA
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
95 31 0.43
96 41 0.57
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.37
Consensus pattern (95 bp):
TTATGAAGTTGGTATGATTATAAAGCTAGAACGAGCTAAAATAAAAGTTTCACCTCTATTAAATT
AAATAGAATCATGTTAAATTCATATTATTC
Found at i:43591890 original size:20 final size:21
Alignment explanation
Indices: 43591857--43591904 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
43591847 TCTCGTTCTT
43591857 AAAAGTTTCTTTTTTTGGTAA
1 AAAAGTTTCTTTTTTTGGTAA
43591878 AAAAGTTTCTTTTTTTGGTAA
1 AAAAGTTTCTTTTTTTGGTAA
43591899 AAAAGT
1 AAAAGT
43591905 GTTTTCTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (21 bp):
AAAAGTTTCTTTTTTTGGTAA
Found at i:43594572 original size:19 final size:19
Alignment explanation
Indices: 43594538--43594575 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
43594528 AATTATATAA
43594538 AAAAACATATAAAAATATT
1 AAAAACATATAAAAATATT
43594557 AAAAA-ATATAAGAAATATT
1 AAAAACATATAA-AAATATT
43594576 TATCTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (19 bp):
AAAAACATATAAAAATATT
Found at i:43594737 original size:20 final size:20
Alignment explanation
Indices: 43594703--43594744 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
43594693 AACTATTTAA
** *
43594703 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
43594723 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
43594743 AT
1 AT
43594745 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:43597733 original size:72 final size:72
Alignment explanation
Indices: 43597619--43597789 Score: 191
Period size: 72 Copynumber: 2.4 Consensus size: 72
43597609 AAAGCGCCGC
* * ** * *
43597619 AAAAACCAAAGCCCAACGACGCCGTTTCCGAGCTTTTGGGGATTTAGCGACGTTTTTAATCAAGC
1 AAAAACCTAAGCCAAACGGTGCCGTTTCCGAGCTTTTGGGGATTTAGCGACATTTTTAAGCAAGC
43597684 GCCACTA
66 GCCACTA
* * * * ** *
43597691 ATAATCCTAAGCCAAACGGTGCCGTTTCCGTAG-TTTTTGGGATTTAGCGGCATTTTTGGGGAAG
1 AAAAACCTAAGCCAAACGGTGCCGTTTCCG-AGCTTTTGGGGATTTAGCGACATTTTTAAGCAAG
*
43597755 CGCCGCTA
65 CGCCACTA
*
43597763 AAAAACCTAAGCCAAACGGTGTCGTTT
1 AAAAACCTAAGCCAAACGGTGCCGTTT
43597790 TCTCAGCTTT
Statistics
Matches: 81, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
72 79 0.98
73 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.26
Consensus pattern (72 bp):
AAAAACCTAAGCCAAACGGTGCCGTTTCCGAGCTTTTGGGGATTTAGCGACATTTTTAAGCAAGC
GCCACTA
Found at i:43597978 original size:75 final size:77
Alignment explanation
Indices: 43597888--43598031 Score: 195
Period size: 75 Copynumber: 1.9 Consensus size: 77
43597878 AAACATATGT
* * *
43597888 CCAATGGCACCGTTTTCAGATCTTTC-GAGGCCTTAGCGGCGTTTT-TAATG-AAGCGCCGCTAA
1 CCAACGGCACCGTTTTCAGAACTTTCAGAGGACTTAGCGGCGTTTTCTAA-GAAAGCGCCGCTAA
43597950 TGCTTGGGGGTGC
65 TGCTTGGGGGTGC
** * *
43597963 CCAACGGCACCGTTTTCTTAACTTTCAGTGGATTTAGCGGCGTTTTCTAAGAAAGCGCCGCTAAT
1 CCAACGGCACCGTTTTCAGAACTTTCAGAGGACTTAGCGGCGTTTTCTAAGAAAGCGCCGCTAAT
43598028 GCTT
66 GCTT
43598032 CCTTTAGCGG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
75 22 0.37
76 17 0.29
77 20 0.34
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (77 bp):
CCAACGGCACCGTTTTCAGAACTTTCAGAGGACTTAGCGGCGTTTTCTAAGAAAGCGCCGCTAAT
GCTTGGGGGTGC
Found at i:43598064 original size:38 final size:39
Alignment explanation
Indices: 43597995--43598068 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 39
43597985 TTTCAGTGGA
43597995 TTTAGCGGCGTTTTCTAAGAAAGCGCCGCTAATGCTTCC
1 TTTAGCGGCGTTTTCTAAGAAAGCGCCGCTAATGCTTCC
** *
43598034 TTTAGCGGCGTTTT-TCGGAAAGTGCCGCTAATGCT
1 TTTAGCGGCGTTTTCTAAGAAAGCGCCGCTAATGCT
43598069 CAGGGGTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 18 0.56
39 14 0.44
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (39 bp):
TTTAGCGGCGTTTTCTAAGAAAGCGCCGCTAATGCTTCC
Found at i:43598543 original size:20 final size:20
Alignment explanation
Indices: 43598520--43598568 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
43598510 GTGTTAGAGA
43598520 TTGAGTTTGGGGTTTAAGGT
1 TTGAGTTTGGGGTTTAAGGT
* *
43598540 TTGAGTTTAGGGTTTTAGGGT
1 TTGAGTTT-GGGGTTTAAGGT
43598561 TT-AGTTTG
1 TTGAGTTTG
43598569 AAAATTGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 1 0.04
20 13 0.50
21 12 0.46
ACGTcount: A:0.14, C:0.00, G:0.37, T:0.49
Consensus pattern (20 bp):
TTGAGTTTGGGGTTTAAGGT
Found at i:43598751 original size:14 final size:13
Alignment explanation
Indices: 43598700--43598751 Score: 68
Period size: 14 Copynumber: 3.8 Consensus size: 13
43598690 AAAAAATATG
43598700 GTTTAGGTTTACA
1 GTTTAGGTTTACA
43598713 GTTTAGGGTTTACA
1 GTTTA-GGTTTACA
*
43598727 GTTTAGAGTTTAGA
1 GTTTAG-GTTTACA
43598741 GTTTTAGGTTT
1 G-TTTAGGTTT
43598752 GGGGTTTAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
13 6 0.17
14 24 0.69
15 5 0.14
ACGTcount: A:0.21, C:0.04, G:0.27, T:0.48
Consensus pattern (13 bp):
GTTTAGGTTTACA
Found at i:43598751 original size:21 final size:20
Alignment explanation
Indices: 43598699--43598766 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 20
43598689 CAAAAAATAT
*
43598699 GGTTTAGGTTTACAGTTTAG
1 GGTTTAGGTTTAGAGTTTAG
*
43598719 GGTTTACAGTTTAGAGTTTAG
1 GGTTTA-GGTTTAGAGTTTAG
* * *
43598740 AGTTTTAGGTTTGGGGTTTAG
1 -GGTTTAGGTTTAGAGTTTAG
*
43598761 GATTTA
1 GGTTTA
43598767 TGATTTAAGG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 11 0.28
21 23 0.59
22 5 0.13
ACGTcount: A:0.21, C:0.03, G:0.31, T:0.46
Consensus pattern (20 bp):
GGTTTAGGTTTAGAGTTTAG
Found at i:43602022 original size:9 final size:9
Alignment explanation
Indices: 43602008--43602362 Score: 159
Period size: 9 Copynumber: 39.6 Consensus size: 9
43601998 TTTAATTTAA
*
43602008 TACATAATT
1 TACATAACT
43602017 TACATAACT
1 TACATAACT
*
43602026 CACATAACT
1 TACATAACT
* *
43602035 TACAAAAGT
1 TACATAACT
* *
43602044 CACAT-ACA
1 TACATAACT
43602052 TACATAACT
1 TACATAACT
*
43602061 TA-ATAAAT
1 TACATAACT
*
43602069 GGTACATAGCT
1 --TACATAACT
*
43602080 TATATAACT
1 TACATAACT
43602089 TACATAA--
1 TACATAACT
43602096 TACATAACT
1 TACATAACT
* *
43602105 TAAATAA-A
1 TACATAACT
43602113 TACATAACT
1 TACATAACT
**
43602122 TATTTAA--
1 TACATAACT
*
43602129 TACATTACT
1 TACATAACT
43602138 TACATAATAACT
1 TAC---ATAACT
*
43602150 TACATAGCT
1 TACATAACT
*
43602159 TATATAACT
1 TACATAACT
43602168 TACATAACT
1 TACATAACT
*
43602177 TATATAACT
1 TACATAACT
43602186 TACAT-AC-
1 TACATAACT
*
43602193 TCCATAACT
1 TACATAACT
*
43602202 TACATAATT
1 TACATAACT
*
43602211 TACTTAA--
1 TACATAACT
43602218 TACATAA-T
1 TACATAACT
* *
43602226 CAACATATATT
1 -TACATA-ACT
*
43602237 ATATCTTAACT
1 -TA-CATAACT
43602248 TACATAATAACT
1 TAC---ATAACT
*
43602260 TACATAGCT
1 TACATAACT
* *
43602269 TATAATAACC
1 TA-CATAACT
43602279 TACATAACT
1 TACATAACT
43602288 TACATAA--
1 TACATAACT
43602295 TACATAACT
1 TACATAACT
*
43602304 TACATATCT
1 TACATAACT
**
43602313 TTTAT-ACTAT
1 TACATAAC--T
43602323 ATACATAACT
1 -TACATAACT
* *
43602333 TACACAATT
1 TACATAACT
*
43602342 TACTTAA--
1 TACATAACT
43602349 TACATAACT
1 TACATAACT
43602358 TACAT
1 TACAT
43602363 TGAGAAAAAT
Statistics
Matches: 254, Mismatches: 61, Indels: 62
0.67 0.16 0.16
Matches are distributed among these distances:
7 34 0.13
8 21 0.08
9 154 0.61
10 13 0.05
11 11 0.04
12 21 0.08
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.36
Consensus pattern (9 bp):
TACATAACT
Found at i:43602104 original size:16 final size:16
Alignment explanation
Indices: 43602083--43602309 Score: 103
Period size: 16 Copynumber: 13.8 Consensus size: 16
43602073 CATAGCTTAT
43602083 ATAACTTACATAATAC
1 ATAACTTACATAATAC
*
43602099 ATAACTTAAATAAATAC
1 ATAACTTACAT-AATAC
**
43602116 ATAACTTATTTAATAC
1 ATAACTTACATAATAC
*
43602132 ATTACTTAC---ATA-
1 ATAACTTACATAATAC
* *
43602144 ATAACTTACATAGCTTAT
1 ATAACTTACATA--ATAC
*
43602162 ATAACTTACATAACTTAT
1 ATAACTTACATAA--TAC
* *
43602180 ATAACTTACATACTCC
1 ATAACTTACATAATAC
43602196 ATAACTTACATAAT--
1 ATAACTTACATAATAC
*
43602210 -TTACTTA-ATACATA-
1 ATAACTTACATA-ATAC
* * *
43602224 ATCAACATATATTATATC
1 AT-AACTTACATAATA-C
*
43602242 TTAACTTACATAATAACTTAC
1 ATAACTTAC---ATAA--TAC
* *
43602263 ATAGCTTATAATAACCTAC
1 ATAACTTA-CATAA--TAC
43602282 ATAACTTACATAATAC
1 ATAACTTACATAATAC
43602298 ATAACTTACATA
1 ATAACTTACATA
43602310 TCTTTTATAC
Statistics
Matches: 163, Mismatches: 26, Indels: 44
0.70 0.11 0.19
Matches are distributed among these distances:
12 11 0.07
13 11 0.07
15 1 0.01
16 58 0.36
17 23 0.14
18 32 0.20
19 15 0.09
20 3 0.02
21 7 0.04
22 2 0.01
ACGTcount: A:0.45, C:0.18, G:0.01, T:0.36
Consensus pattern (16 bp):
ATAACTTACATAATAC
Found at i:43602167 original size:18 final size:18
Alignment explanation
Indices: 43602078--43602208 Score: 105
Period size: 16 Copynumber: 7.5 Consensus size: 18
43602068 TGGTACATAG
* *
43602078 CTTATATAACTTACATAA
1 CTTACATAACTTATATAA
*
43602096 --TACATAACTTAAATAA
1 CTTACATAACTTATATAA
* *
43602112 -ATACATAACTTATTTAA
1 CTTACATAACTTATATAA
*
43602129 --TACATTACTTACATAATAA
1 CTTACATAACTT--AT-ATAA
*
43602148 CTTACATAGCTTATATAA
1 CTTACATAACTTATATAA
43602166 CTTACATAACTTATATAA
1 CTTACATAACTTATATAA
**
43602184 CTTACAT-AC-TCCATAA
1 CTTACATAACTTATATAA
43602200 CTTACATAA
1 CTTACATAA
43602209 TTTACTTAAT
Statistics
Matches: 95, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
16 35 0.37
17 17 0.18
18 30 0.32
19 5 0.05
21 8 0.08
ACGTcount: A:0.45, C:0.18, G:0.01, T:0.37
Consensus pattern (18 bp):
CTTACATAACTTATATAA
Found at i:43602275 original size:19 final size:19
Alignment explanation
Indices: 43602251--43602305 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
43602241 CTTAACTTAC
* *
43602251 ATAATAACTTACATAGCTT
1 ATAATAACCTACATAACTT
43602270 ATAATAACCTACATAACTT
1 ATAATAACCTACATAACTT
*
43602289 A-CATAA--TACATAACTT
1 ATAATAACCTACATAACTT
43602305 A
1 A
43602306 CATATCTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 11 0.33
18 4 0.12
19 18 0.55
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (19 bp):
ATAATAACCTACATAACTT
Found at i:43602309 original size:25 final size:25
Alignment explanation
Indices: 43602071--43602224 Score: 97
Period size: 25 Copynumber: 6.3 Consensus size: 25
43602061 TAATAAATGG
* *
43602071 TACATAGCTTATATAACTTACATAA
1 TACATAACTTACATAACTTACATAA
* *
43602096 TACATAACTTAAATAA-ATACAT-A
1 TACATAACTTACATAACTTACATAA
* * *
43602119 -AC-TTATTTA-AT-ACATTACTTACA
1 TACATAACTTACATAAC-TTACATA-A
* *
43602142 TA-ATAACTTACATAGCTTATATAA
1 TACATAACTTACATAACTTACATAA
* *
43602166 CTTACATAACTTATATAACTTACATAC
1 --TACATAACTTACATAACTTACATAA
* * *
43602193 TCCATAACTTACATAATTTACTTAA
1 TACATAACTTACATAACTTACATAA
43602218 TACATAA
1 TACATAA
43602225 TCAACATATA
Statistics
Matches: 96, Mismatches: 22, Indels: 22
0.69 0.16 0.16
Matches are distributed among these distances:
19 1 0.01
20 2 0.02
21 9 0.09
22 2 0.02
23 2 0.02
24 12 0.12
25 47 0.49
26 3 0.03
27 18 0.19
ACGTcount: A:0.45, C:0.17, G:0.01, T:0.37
Consensus pattern (25 bp):
TACATAACTTACATAACTTACATAA
Found at i:43607884 original size:21 final size:21
Alignment explanation
Indices: 43607860--43607900 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
43607850 CTTAAAACAG
* *
43607860 AGGCGGCAGCGAGGGAAGCAA
1 AGGCGACAGCGAGAGAAGCAA
*
43607881 AGGCTACAGCGAGAGAAGCA
1 AGGCGACAGCGAGAGAAGCA
43607901 GAGGTTGCAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.20, G:0.41, T:0.02
Consensus pattern (21 bp):
AGGCGACAGCGAGAGAAGCAA
Found at i:43607911 original size:21 final size:21
Alignment explanation
Indices: 43607865--43607951 Score: 75
Period size: 21 Copynumber: 4.0 Consensus size: 21
43607855 AACAGAGGCG
* * *
43607865 GCAGCGAGGGAAGCAAAGGCT
1 GCAGCGAGAGAAGCAGAGGTT
*
43607886 ACAGCGAGAGAAGCAGAGGTT
1 GCAGCGAGAGAAGCAGAGGTT
* **
43607907 GCAGCAAGAGAAGCAGCGAGAGAA
1 GCAGCGAGAGAAGCA--GAG-GTT
*
43607931 GCAGCGATAGAAGCAGAGGTT
1 GCAGCGAGAGAAGCAGAGGTT
43607952 CAAAAGAAAT
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
21 31 0.61
22 3 0.06
23 3 0.06
24 14 0.27
ACGTcount: A:0.38, C:0.16, G:0.39, T:0.07
Consensus pattern (21 bp):
GCAGCGAGAGAAGCAGAGGTT
Found at i:43607922 original size:12 final size:12
Alignment explanation
Indices: 43607907--43607946 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
43607897 AGCAGAGGTT
*
43607907 GCAGCAAGAGAA
1 GCAGCGAGAGAA
43607919 GCAGCGAGAGAA
1 GCAGCGAGAGAA
*
43607931 GCAGCGATAGAA
1 GCAGCGAGAGAA
43607943 GCAG
1 GCAG
43607947 AGGTTCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.42, C:0.17, G:0.38, T:0.03
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:43608482 original size:43 final size:42
Alignment explanation
Indices: 43608380--43608630 Score: 278
Period size: 42 Copynumber: 6.0 Consensus size: 42
43608370 GTTTGTGAAA
* * *
43608380 TAAGCGCCGCTAAAGAATACT-A-CTTTTAGCGGTGTTTTTGACC
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTT-TCC
* * *
43608423 -AAGCGCCGCTATAGAACATTA-CTTTTAGCAGCGTTTTCTTCC
1 TAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTT-TTCC
43608465 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGC-TTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
* * * **
43608506 TAAGCGCCGCTAAAGAACATGATATTTAGCTGCATTTTTTAA
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
* * *
43608548 TAAGCGCCGCTAAAGAAAATAATCTTTAACGGCGTTTATTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTCC
*
43608591 TTAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
43608631 TTCTGTAAGC
Statistics
Matches: 178, Mismatches: 24, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
41 36 0.20
42 77 0.43
43 64 0.36
44 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
Found at i:43612469 original size:27 final size:27
Alignment explanation
Indices: 43612431--43612485 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
43612421 CCCTTGTTAG
43612431 TGTTTCTAATTCTCTAGCATAACCCAA
1 TGTTTCTAATTCTCTAGCATAACCCAA
43612458 TGTTTCTAATTCTCTAGCATAACCCAA
1 TGTTTCTAATTCTCTAGCATAACCCAA
43612485 T
1 T
43612486 ACAAAGGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.38
Consensus pattern (27 bp):
TGTTTCTAATTCTCTAGCATAACCCAA
Found at i:43615038 original size:96 final size:96
Alignment explanation
Indices: 43614922--43615117 Score: 277
Period size: 96 Copynumber: 2.1 Consensus size: 96
43614912 AAATGATTAT
*
43614922 TTATAAAGTTGGTATGATTATAGAGCTACAACGACGCTAGAATAAAAGTTTCACCTCTATTAAAT
1 TTATAAAGTTGGTATGATTATAGAGCTACAACGACGCTAAAATAAAAGTTTCACCTCTATTAAAT
* *
43614987 TAAATAGGATTGTGTTAAATTCATATTATTC
66 TAAATAGAATCGTGTTAAATTCATATTATTC
* * * * * *
43615018 TTATGAAGTTGGTATGATTATAGAGCTATAACGATGTTAAAATAAAAGTTTCACCTTTATTAGAT
1 TTATAAAGTTGGTATGATTATAGAGCTACAACGACGCTAAAATAAAAGTTTCACCTCTATTAAAT
* * *
43615083 TAAATAGAATCGTGTTAAGTTTAGATTATT-
66 TAAATAGAATCGTGTTAAATTCATATTATTC
43615113 TTATA
1 TTATA
43615118 TCTTAATTAA
Statistics
Matches: 87, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
95 4 0.05
96 83 0.95
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (96 bp):
TTATAAAGTTGGTATGATTATAGAGCTACAACGACGCTAAAATAAAAGTTTCACCTCTATTAAAT
TAAATAGAATCGTGTTAAATTCATATTATTC
Found at i:43617870 original size:54 final size:53
Alignment explanation
Indices: 43617784--43617914 Score: 174
Period size: 54 Copynumber: 2.5 Consensus size: 53
43617774 ATCGACAATT
43617784 GATTCAAAAGAAACAATATTCCAACATAACAATCGAATTAAACATATAAAAAATC
1 GATTCAAAAGAAACAATATTCCAACATAACAATCG-ATTAAA-ATATAAAAAATC
* * * * *
43617839 GATTCAAAA-AAGCAGTATTCCAACATGACAATCGATTTAAATGTAAAAAATC
1 GATTCAAAAGAAACAATATTCCAACATAACAATCGATTAAAATATAAAAAATC
* *
43617891 AATTCAAAAGAATCAATATTCCAA
1 GATTCAAAAGAAACAATATTCCAA
43617915 AAATTAAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
52 19 0.28
53 17 0.25
54 22 0.33
55 9 0.13
ACGTcount: A:0.53, C:0.16, G:0.08, T:0.24
Consensus pattern (53 bp):
GATTCAAAAGAAACAATATTCCAACATAACAATCGATTAAAATATAAAAAATC
Found at i:43619583 original size:47 final size:47
Alignment explanation
Indices: 43619526--43619619 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
43619516 TGTCACAGTA
* *
43619526 ATGCAGATAAACTGCCACTTAATAATATTGTGTACAAGCCACCACTT
1 ATGCAAATAAACTGCCACTTAATAATATTGTGGACAAGCCACCACTT
*
43619573 ATGCAAATAAACTGCCACTTTATAATATTGTGGACAAGCCACCACTT
1 ATGCAAATAAACTGCCACTTAATAATATTGTGGACAAGCCACCACTT
43619620 TTTAGATAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (47 bp):
ATGCAAATAAACTGCCACTTAATAATATTGTGGACAAGCCACCACTT
Found at i:43623836 original size:31 final size:29
Alignment explanation
Indices: 43623763--43623836 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
43623753 GGCTCAGGTT
* *
43623763 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* * **
43623792 ACGTTTTAATCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
43623823 ACATTTTAGTCACT
1 ACATTTTAGTCACT
43623837 GAGCCGTTAG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 18 0.51
30 2 0.06
31 15 0.43
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:43637039 original size:13 final size:13
Alignment explanation
Indices: 43636989--43637039 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
43636979 ACACTTAAAT
*
43636989 TTTTCAAAAACA-
1 TTTTCAAAAGCAC
43637001 TTTCTCAAAAGCAC
1 TTT-TCAAAAGCAC
* *
43637015 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
43637028 TTTTCAAAAGCA
1 TTTTCAAAAGCA
43637040 TGGCCAAACT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
12 3 0.09
13 26 0.81
14 3 0.09
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:43645495 original size:20 final size:20
Alignment explanation
Indices: 43645448--43645485 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
43645438 TGTATCTAGG
*
43645448 ATAAT-AAAATTTTATTCCT
1 ATAATAAAAAATTTATTCCT
43645467 ATAATAAAAAATTTATTCC
1 ATAATAAAAAATTTATTCC
43645486 ATTACTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAATAAAAAATTTATTCCT
Found at i:43646429 original size:29 final size:29
Alignment explanation
Indices: 43646382--43646437 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
43646372 AGAGGACATG
**
43646382 CGTTCGAGTGTACTGAAGCACATTATCAA
1 CGTTCGAGTGTACAAAAGCACATTATCAA
*
43646411 CGTTTGAGTGTACAAAAGCACATTATC
1 CGTTCGAGTGTACAAAAGCACATTATC
43646438 GATAGTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (29 bp):
CGTTCGAGTGTACAAAAGCACATTATCAA
Found at i:43653188 original size:2 final size:2
Alignment explanation
Indices: 43653181--43653208 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43653171 CATAATTTTC
43653181 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
43653209 GAAATCTCTA
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:43653574 original size:22 final size:22
Alignment explanation
Indices: 43653547--43653595 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
43653537 TTTTATAATT
43653547 TATAACATATAAAAATAAAATC
1 TATAACATATAAAAATAAAATC
* * * *
43653569 TATAACTTTTAAAAATAATATT
1 TATAACATATAAAAATAAAATC
43653591 TATAA
1 TATAA
43653596 TGTATGACAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (22 bp):
TATAACATATAAAAATAAAATC
Found at i:43659356 original size:20 final size:20
Alignment explanation
Indices: 43659311--43659365 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
43659301 GCAAAAATCA
**
43659311 AAAGTATCGATACCCTTGTC
1 AAAGTATCGATACCCTCCTC
*
43659331 ATAGTATCGATA-CCTCCCTC
1 AAAGTATCGATACCCT-CCTC
*
43659351 AAAGTATTGATACCC
1 AAAGTATCGATACCC
43659366 CTGACAGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 3 0.11
20 23 0.82
21 2 0.07
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (20 bp):
AAAGTATCGATACCCTCCTC
Found at i:43664813 original size:24 final size:24
Alignment explanation
Indices: 43664767--43664815 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
43664757 TAATATACAT
* * *
43664767 ACCAACTGTGCTGAGACTCAATCG
1 ACCAACTGAGCTAAAACTCAATCG
*
43664791 ACCAACTGAGCTAAAACTTAATCG
1 ACCAACTGAGCTAAAACTCAATCG
43664815 A
1 A
43664816 TTTTTTTTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.27, G:0.16, T:0.20
Consensus pattern (24 bp):
ACCAACTGAGCTAAAACTCAATCG
Found at i:43667380 original size:83 final size:83
Alignment explanation
Indices: 43667272--43667476 Score: 243
Period size: 83 Copynumber: 2.5 Consensus size: 83
43667262 TGTCCCGTAC
* * * ** *
43667272 ACATGATCTT-GAATTTGTATTGTAAAAGTAGTGTCTTTTTATGCATAGTGTTTAAGTTTTAGGG
1 ACATGAT-TTCGAATTTGTATAGTAAAAGTAATGTCTTTTTATACATACAGTTTAAGGTTTAGGG
43667336 TTTATTTT-GGTACCCTCAA
65 TTT-TTTTGGGTACCCTCAA
* * * *
43667355 ACATGATTTCGAATTTGTATAGTAAAAGAAATGCCTTTTTATATATACAGTTTGAGGTTTAGGGT
1 ACATGATTTCGAATTTGTATAGTAAAAGTAATGTCTTTTTATACATACAGTTTAAGGTTTAGGGT
*
43667420 TTTTTTGGGTACCCTTAA
66 TTTTTTGGGTACCCTCAA
* ** *
43667438 ACATGATCTCGAATTTGTATAACAAAAGTAATGTATTTT
1 ACATGATTTCGAATTTGTATAGTAAAAGTAATGTCTTTT
43667477 ATGTACAGGA
Statistics
Matches: 103, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
82 6 0.06
83 97 0.94
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.43
Consensus pattern (83 bp):
ACATGATTTCGAATTTGTATAGTAAAAGTAATGTCTTTTTATACATACAGTTTAAGGTTTAGGGT
TTTTTTGGGTACCCTCAA
Found at i:43667957 original size:5 final size:5
Alignment explanation
Indices: 43667940--43667978 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
43667930 AATCATTATA
* *
43667940 TTTTC TTTCC TTTTC TTTTC TTCTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
43667979 TAACCAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:43668796 original size:2 final size:2
Alignment explanation
Indices: 43668789--43668842 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
43668779 AATATCTACA
43668789 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
43668831 AT AT AT AT AT AT
1 AT AT AT AT AT AT
43668843 CTGCTCTGCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43680745 original size:17 final size:18
Alignment explanation
Indices: 43680720--43680753 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
43680710 TTTTTTAATT
43680720 AAATATTTATAA-TTTTA
1 AAATATTTATAACTTTTA
*
43680737 AAATGTTTATAACTTTT
1 AAATATTTATAACTTTT
43680754 TTTAATAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
AAATATTTATAACTTTTA
Found at i:43693744 original size:2 final size:2
Alignment explanation
Indices: 43693737--43693767 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
43693727 TAAGCTCACT
43693737 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43693768 AAAGGTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43695530 original size:11 final size:12
Alignment explanation
Indices: 43695507--43695536 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
43695497 TCTAACAACT
43695507 ATAAAATATAAA
1 ATAAAATATAAA
43695519 ATAAAA-ATAAA
1 ATAAAATATAAA
43695530 ATAAAAT
1 ATAAAAT
43695537 GGTGATTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
ATAAAATATAAA
Found at i:43695701 original size:11 final size:11
Alignment explanation
Indices: 43695681--43695747 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
43695671 ACAAATTAAA
43695681 AAAAATTATTTT
1 AAAAA-TATTTT
43695693 AAAAATATTTT
1 AAAAATATTTT
*
43695704 --TAA-A--TT
1 AAAAATATTTT
*
43695710 AAAAAAATTTT
1 AAAAATATTTT
*
43695721 ACAAAGTATTTT
1 A-AAAATATTTT
43695733 AAAAATATTTT
1 AAAAATATTTT
43695744 AAAA
1 AAAA
43695748 TTAAAAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
6 2 0.05
8 3 0.07
9 3 0.07
11 22 0.50
12 14 0.32
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:43695778 original size:40 final size:41
Alignment explanation
Indices: 43695673--43695777 Score: 158
Period size: 40 Copynumber: 2.6 Consensus size: 41
43695663 ATTATTTTAC
* * *
43695673 AAATTAAAAAAAATTATTTTAAAAATATTTTTAAATTAAAA
1 AAATTTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
* *
43695714 AAATTT-TACAAAGTATTTTAAAAATATTTTAAAATTAAAA
1 AAATTTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
43695754 AAATTTAAAAAAAGTATTTTAAAA
1 AAATTTAAAAAAAGTATTTTAAAA
43695778 TTAAAAAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 36 0.64
41 20 0.36
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (41 bp):
AAATTTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
Found at i:43695805 original size:29 final size:29
Alignment explanation
Indices: 43695733--43695791 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
43695723 AAAGTATTTT
43695733 AAAAA-TATTTTAAAATTAAAAAAATTTAA
1 AAAAAGTATTTTAAAATTAAAAAAA-TTAA
43695762 AAAAAGTATTTTAAAATTAAAAAAA-TAA
1 AAAAAGTATTTTAAAATTAAAAAAATTAA
43695790 AA
1 AA
43695792 TATTTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 5 0.17
29 5 0.17
30 19 0.66
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (29 bp):
AAAAAGTATTTTAAAATTAAAAAAATTAA
Found at i:43709049 original size:12 final size:12
Alignment explanation
Indices: 43709032--43709056 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43709022 GAGAGAAGCT
43709032 TTAATTAAATGA
1 TTAATTAAATGA
43709044 TTAATTAAATGA
1 TTAATTAAATGA
43709056 T
1 T
43709057 GGGGGATTTC
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (12 bp):
TTAATTAAATGA
Found at i:43712271 original size:9 final size:10
Alignment explanation
Indices: 43712257--43712295 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
43712247 CCATTTTTTC
43712257 TCTTC-TCAT
1 TCTTCTTCAT
43712266 TCTTCTTC-T
1 TCTTCTTCAT
43712275 TCTTCTTCA-
1 TCTTCTTCAT
43712284 TCTTCTT-AT
1 TCTTCTTCAT
43712293 TCT
1 TCT
43712296 CTTATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 1 0.04
9 24 0.89
10 2 0.07
ACGTcount: A:0.08, C:0.31, G:0.00, T:0.62
Consensus pattern (10 bp):
TCTTCTTCAT
Found at i:43738557 original size:144 final size:141
Alignment explanation
Indices: 43738231--43738563 Score: 418
Period size: 144 Copynumber: 2.3 Consensus size: 141
43738221 AAGGTTTGGT
* * *
43738231 GGAATAGAAGTCTTGCCAGACTGGTTGGGAAATCTCTCTTCTCTAAGGCGTCTATATTTGAGTGG
1 GGAATAGAAGCCTTGCCAGAATGGTTGGGAAATCTCTCTTCTCTAAGGCATCTATATTTGAGTGG
* * * *
43738296 TTTTGGAAAGCTAAAGATTCCTCACCAACTTCAACTCCTCACTGCCCTTGAAGATTTGACTATGC
66 TTTTGGAAAGCTAAAGATTACTCACCAACTTCAACTCCTCACTACCCTTGAAGATTTAACGATGC
* * *
43738361 AGGGGTTTCAT
131 AAGAGTTTCAA
* *
43738372 GAAATATAAGCCTTGCCAGAATGGTTGGGAAATCTCTCTTCTCTAAGGCATCTATATTTGAGTGG
1 GGAATAGAAGCCTTGCCAGAATGGTTGGGAAATCTCTCTTCTCTAAGGCATCTATATTTGAGTGG
** * *
43738437 TTTTCGG-AAGCTAAAGAGTTTTACTCACCAACTTCAACTCCTTTCTACCCTTTAATATTTAACG
66 TTTT-GGAAAGCTAAAGA---TTACTCACCAACTTCAACTCCTCACTACCCTTGAAGATTTAACG
43738501 ATAG-AAGAGTTTCAA
127 AT-GCAAGAGTTTCAA
* ** **
43738516 GGAATAGAAGCCTTGCCAGAGTCATTCAGAAATCTCTCTTCTCTAAGG
1 GGAATAGAAGCCTTGCCAGAATGGTTGGGAAATCTCTCTTCTCTAAGG
43738564 AGGCTGAGAA
Statistics
Matches: 164, Mismatches: 23, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
141 74 0.45
142 2 0.01
144 87 0.53
145 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (141 bp):
GGAATAGAAGCCTTGCCAGAATGGTTGGGAAATCTCTCTTCTCTAAGGCATCTATATTTGAGTGG
TTTTGGAAAGCTAAAGATTACTCACCAACTTCAACTCCTCACTACCCTTGAAGATTTAACGATGC
AAGAGTTTCAA
Found at i:43741866 original size:3 final size:3
Alignment explanation
Indices: 43741858--43741939 Score: 128
Period size: 3 Copynumber: 26.7 Consensus size: 3
43741848 CCTTTTTAGC
*
43741858 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT CTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT
*
43741904 CTT CATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
43741940 ACTAGTTCAT
Statistics
Matches: 75, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
3 71 0.95
4 4 0.05
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:43742316 original size:22 final size:20
Alignment explanation
Indices: 43742279--43742320 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
43742269 TTTATATTTT
43742279 TATATCTTATAATTTATGTA
1 TATATCTTATAATTTATGTA
*
43742299 TATATTTTAATAATTTTATGTA
1 TATATCTT-ATAA-TTTATGTA
43742321 CATACATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (20 bp):
TATATCTTATAATTTATGTA
Found at i:43746121 original size:37 final size:37
Alignment explanation
Indices: 43746060--43746243 Score: 300
Period size: 37 Copynumber: 5.0 Consensus size: 37
43746050 TACGTATGAT
*
43746060 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
* *
43746095 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
43746132 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
*
43746169 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
* *
43746206 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
43746243 C
1 C
43746244 GAAGCTATCA
Statistics
Matches: 138, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
35 9 0.07
36 4 0.03
37 125 0.91
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:43746257 original size:46 final size:46
Alignment explanation
Indices: 43746206--43746376 Score: 243
Period size: 46 Copynumber: 3.6 Consensus size: 46
43746196 TAAGTGTAGC
43746206 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
43746252 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* * ** *
43746298 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
43746350 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
43746377 AGTACTCAAA
Statistics
Matches: 113, Mismatches: 6, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
46 71 0.63
48 1 0.01
50 1 0.01
52 40 0.35
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:43746328 original size:52 final size:52
Alignment explanation
Indices: 43746249--43746362 Score: 158
Period size: 52 Copynumber: 2.2 Consensus size: 52
43746239 TAGCCGAAGC
* **
43746249 TATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTT-TCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT
* *
43746302 TATCACTTTCCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTT-CACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT
43746354 TATCACTTT
1 TATCACTTT
43746363 GTCACTTGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
52 44 0.80
53 11 0.20
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (52 bp):
TATCACTTTCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT
Found at i:43748883 original size:9 final size:9
Alignment explanation
Indices: 43748869--43748897 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
43748859 ATGAGTTCAA
43748869 AAAAAAATC
1 AAAAAAATC
43748878 AAAAAAAT-
1 AAAAAAATC
43748886 AAAAAAATC
1 AAAAAAATC
43748895 AAA
1 AAA
43748898 GTCAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATC
Found at i:43748917 original size:7 final size:7
Alignment explanation
Indices: 43748901--43748951 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 7
43748891 AATCAAAGTC
43748901 AAAAAGAG
1 AAAAA-AG
43748909 AAAAAAG
1 AAAAAAG
43748916 -AAAAAG
1 AAAAAAG
43748922 AAAAAAG
1 AAAAAAG
43748929 -AAAAAG
1 AAAAAAG
43748935 -AAAAA-
1 AAAAAAG
*
43748940 TAAAAAG
1 AAAAAAG
43748947 AAAAA
1 AAAAA
43748952 GAAGAGGTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
6 22 0.56
7 12 0.31
8 5 0.13
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:43748919 original size:6 final size:6
Alignment explanation
Indices: 43748910--43748954 Score: 72
Period size: 6 Copynumber: 7.3 Consensus size: 6
43748900 CAAAAAGAGA
*
43748910 AAAAAG AAAAAG AAAAAAG AAAAAG AAAAAT AAAAAG AAAAAG AA
1 AAAAAG AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AA
43748955 GAGGTCAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 30 0.83
7 6 0.17
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:43748923 original size:13 final size:13
Alignment explanation
Indices: 43748902--43748951 Score: 75
Period size: 13 Copynumber: 3.8 Consensus size: 13
43748892 ATCAAAGTCA
43748902 AAAAGAGAAAAAAG
1 AAAA-AGAAAAAAG
43748916 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
*
43748929 AAAAAG-AAAAAT
1 AAAAAGAAAAAAG
43748941 AAAAAGAAAAA
1 AAAAAGAAAAA
43748952 GAAGAGGTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 11 0.32
13 19 0.56
14 4 0.12
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:43749320 original size:20 final size:20
Alignment explanation
Indices: 43749281--43749321 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
43749271 AAAGAAAAAG
* **
43749281 ATGAAGAATGAAAATGGAAA
1 ATGAAAAATGAAAAAAGAAA
43749301 ATGAAAAATGAAAAAAGAAA
1 ATGAAAAATGAAAAAAGAAA
43749321 A
1 A
43749322 GAGTAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.12
Consensus pattern (20 bp):
ATGAAAAATGAAAAAAGAAA
Done.