Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008182.1 Hibiscus syriacus cultivar Beakdansim tig00110782_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1042344
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:161589 original size:30 final size:30
Alignment explanation
Indices: 161500--161599 Score: 119
Period size: 30 Copynumber: 3.3 Consensus size: 30
161490 TCCGAAGGAC
* *
161500 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCACAAAGATCCTCGGTAA
* *
161530 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCACAAAGATCCTCGGTAA
* * * *
161560 CTATCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCATAGGTCACAAAGATCCTCGGT-AA
161591 CTATCCATA
1 CTATCCATA
161600 TGTTCCTTAG
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
30 52 0.83
31 11 0.17
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (30 bp):
CTATCCATAGGTCACAAAGATCCTCGGTAA
Found at i:161612 original size:31 final size:31
Alignment explanation
Indices: 161558--161650 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
161548 GATCCTCGGT
* *
161558 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
161589 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * *
161620 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
161651 GTTCTTTGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
30 1 0.02
31 49 0.98
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:161832 original size:4 final size:4
Alignment explanation
Indices: 161823--161847 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
161813 ATATAACCAT
161823 TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA T
161848 GTCATCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:162643 original size:19 final size:20
Alignment explanation
Indices: 162606--162643 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
162596 TTTTTCATTA
*
162606 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
162626 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
162644 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:163175 original size:3 final size:3
Alignment explanation
Indices: 163167--163200 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
163157 CTTCACACGT
*
163167 GAA GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
163201 GGAACTCTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:163757 original size:2 final size:2
Alignment explanation
Indices: 163750--163809 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
163740 TTAAGCCAAT
163750 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
163792 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
163810 AAGCGTAAGC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:165398 original size:13 final size:13
Alignment explanation
Indices: 165380--165414 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
165370 AATGAGCAAT
165380 TTTGAAAACTAA-G
1 TTTGAAAA-TAATG
165393 TTTGAAAATAATG
1 TTTGAAAATAATG
165406 TTTGAAAAT
1 TTTGAAAAT
165415 CAATATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 3 0.14
13 18 0.86
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.37
Consensus pattern (13 bp):
TTTGAAAATAATG
Found at i:165930 original size:23 final size:23
Alignment explanation
Indices: 165886--165935 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
165876 TAAATACGAA
*
165886 AATCGGTTCCCATTCAAAGGGGG
1 AATCGGTTCCCATGCAAAGGGGG
*
165909 AATCGGTTCCCCTGC-AAGGGGG
1 AATCGGTTCCCATGCAAAGGGGG
*
165931 TATCG
1 AATCG
165936 ATTCATCCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.22, C:0.24, G:0.32, T:0.22
Consensus pattern (23 bp):
AATCGGTTCCCATGCAAAGGGGG
Found at i:180691 original size:31 final size:31
Alignment explanation
Indices: 180593--180683 Score: 150
Period size: 31 Copynumber: 3.0 Consensus size: 31
180583 CAATTTAAGG
180593 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
*
180624 AAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
*
180655 CAAAAT-GTTTTTAGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
180684 TTCAAAATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 11 0.19
30 11 0.19
31 35 0.61
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:182858 original size:14 final size:15
Alignment explanation
Indices: 182839--182867 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
182829 AAGTGTGAAA
182839 TGATAT-AAGTTATG
1 TGATATGAAGTTATG
182853 TGATATGAAGTTATG
1 TGATATGAAGTTATG
182868 GGTATATGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.41
Consensus pattern (15 bp):
TGATATGAAGTTATG
Found at i:183345 original size:32 final size:32
Alignment explanation
Indices: 183304--183366 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
183294 AGAGTCGAGG
* *
183304 GTTACCTATGTCTTTCGAGACATATGGACAGT
1 GTTACCTATGTCCTTCGAGACATATAGACAGT
* *
183336 GTTACCTATGTCCTTCGGGATATATAGACAG
1 GTTACCTATGTCCTTCGAGACATATAGACAG
183367 GATTACATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (32 bp):
GTTACCTATGTCCTTCGAGACATATAGACAGT
Found at i:183774 original size:4 final size:4
Alignment explanation
Indices: 183765--184207 Score: 872
Period size: 4 Copynumber: 111.2 Consensus size: 4
183755 AAATGATGAC
183765 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
183813 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
183861 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
183909 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
183957 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
184005 ATGT ATGT ATGT ATGT A--T ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
184051 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
184099 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
184147 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
184195 ATGT ATGT ATGT A
1 ATGT ATGT ATGT A
184208 CTTACTGGAT
Statistics
Matches: 437, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
2 2 0.00
4 435 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:187602 original size:43 final size:43
Alignment explanation
Indices: 187470--187737 Score: 226
Period size: 42 Copynumber: 6.2 Consensus size: 43
187460 TGTGATATAA
* * *
187470 AAACGCCGCAAAAAGTCAAGATCTATAGCGGCGTTTTTGGA-AC
1 AAACGCCGCAAAAGGTC-AGATATATAGCGGTGTTTTTGGATAC
** *
187513 AAACG-CGCAAAAGGTCGAGATATATAGCGACGTTTTTAGCA-A-
1 AAACGCCGCAAAAGGTC-AGATATATAGCGGTGTTTTT-GGATAC
* *
187555 AAACGCCGCAAAAGGGT-AGATATATAGTGGTGTTGTTGGATAC
1 AAACGCCGCAAAA-GGTCAGATATATAGCGGTGTTTTTGGATAC
* * * *
187598 AAACGCCACAAAAGGTCAAGATCTATAGCGG-GTTTTTGGAGAGAAA
1 AAACGCCGCAAAAGGTC-AGATATATAGCGGTGTTTTT-G-GA-TAC
* * * *
187644 AAACACCGCAAAAGGTTAGATATATAGC-GCGTTTTTGGACAC
1 AAACGCCGCAAAAGGTCAGATATATAGCGGTGTTTTTGGATAC
* * * * *
187686 AAACGCTGCAAAAGGTCAGATCTATAGCAGCGTTTTTGGATAT
1 AAACGCCGCAAAAGGTCAGATATATAGCGGTGTTTTTGGATAC
187729 AAACGCCGC
1 AAACGCCGC
187738 TAATTACCAT
Statistics
Matches: 184, Mismatches: 29, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
41 2 0.01
42 78 0.42
43 54 0.29
44 17 0.09
45 18 0.10
46 15 0.08
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAGATATATAGCGGTGTTTTTGGATAC
Found at i:187658 original size:89 final size:88
Alignment explanation
Indices: 187488--187725 Score: 260
Period size: 88 Copynumber: 2.7 Consensus size: 88
187478 CAAAAAGTCA
* * *
187488 AGATCTATAGCGGCGTTTTTGGA-ACAAACG-CGCAAAAGGTCGAGATATATAGC-GACGTTTTT
1 AGATATATAGC-GCGTTTTTGGACACAAACGCCACAAAAGGTC-AGATCTATAGCAG-CGTTTTT
* *
187550 ----AGCAAAAACGCCGCAAAAGGGT
63 GGAGAGAAAAAACACCGCAAAAGGGT
* * *
187572 AGATATATAGTG-GTGTTGTTGGATACAAACGCCACAAAAGGTCAAGATCTATAGC-GGGTTTTT
1 AGATATATAGCGCGT-TT-TTGGACACAAACGCCACAAAAGGTC-AGATCTATAGCAGCGTTTTT
*
187635 GGAGAGAAAAAACACCGCAAAAGGTT
63 GGAGAGAAAAAACACCGCAAAAGGGT
**
187661 AGATATATAGCGCGTTTTTGGACACAAACGCTGCAAAAGGTCAGATCTATAGCAGCGTTTTTGGA
1 AGATATATAGCGCGTTTTTGGACACAAACGCCACAAAAGGTCAGATCTATAGCAGCGTTTTTGGA
187726 TATAAACGCC
Statistics
Matches: 130, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
82 2 0.02
83 3 0.02
84 14 0.11
85 13 0.10
86 21 0.16
87 11 0.08
88 32 0.25
89 32 0.25
90 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (88 bp):
AGATATATAGCGCGTTTTTGGACACAAACGCCACAAAAGGTCAGATCTATAGCAGCGTTTTTGGA
GAGAAAAAACACCGCAAAAGGGT
Found at i:187712 original size:131 final size:128
Alignment explanation
Indices: 187470--187735 Score: 315
Period size: 131 Copynumber: 2.1 Consensus size: 128
187460 TGTGATATAA
* * *
187470 AAACGCCGCAAAAAGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCGCAAAAGGTCGAGATA
1 AAACGCCACAAAAAGTCAAGATCTATAGCGGCGTTTTTGGAAAAAACCCGCAAAAGGTCGAGATA
** *
187535 TATAGCGACGTTTTTAGCAAAAACGCCGCAAAAGGGTAGATATATAGTGGTGTTGTTGGATAC
66 TATAGCGACGTTTTTAGCAAAAACGCCGCAAAAGGGTAGATATATAGCAGCGTTGTTGGATAC
* *
187598 AAACGCCACAAAAGGTCAAGATCTATAGCGG-GTTTTTGGAGAGAAAAAACACCGCAAAAGGT-T
1 AAACGCCACAAAAAGTCAAGATCTATAGCGGCGTTTTT---G-GAAAAAAC-CCGCAAAAGGTCG
* * * * *
187661 AGATATATAGCG-CGTTTTTGGACACAAACGCTGCAAAA-GGTCAGATCTATAGCAGCGTTTTTG
61 AGATATATAGCGACGTTTTTAG-CAAAAACGCCGCAAAAGGGT-AGATATATAGCAGCGTTGTTG
*
187724 GATAT
124 GATAC
187729 AAACGCC
1 AAACGCC
187736 GCTAATTACC
Statistics
Matches: 117, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
127 6 0.05
128 29 0.25
130 12 0.10
131 60 0.51
132 10 0.09
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (128 bp):
AAACGCCACAAAAAGTCAAGATCTATAGCGGCGTTTTTGGAAAAAACCCGCAAAAGGTCGAGATA
TATAGCGACGTTTTTAGCAAAAACGCCGCAAAAGGGTAGATATATAGCAGCGTTGTTGGATAC
Found at i:193030 original size:83 final size:81
Alignment explanation
Indices: 192898--193076 Score: 243
Period size: 83 Copynumber: 2.2 Consensus size: 81
192888 TTATAGTTAC
* * ** * *
192898 AAACGCCACTAAAGTACTATTATGTTGCGGCGTTTGTTGAAAAATGCCACTATGGATGAACCTAT
1 AAACGCCGCTAAAGTACTATCACATTGCGGCGTTTGTTGAAAAACGCCACTATAGATGAACCTAT
* *
192963 TGCGGCGTTTGTACT-G
66 TGCGGAGTTTGTA-TAA
*
192979 AAACGCCGCTAAAGTACTACTCACATTGCGTCGTTTGTTGGAAAAACGCCACTATAGATGAACCT
1 AAACGCCGCTAAAGTACTA-TCACATTGCGGCGTTTGTT-GAAAAACGCCACTATAGATGAACCT
193044 ATTGCGGAGTTTGTATAA
64 ATTGCGGAGTTTGTATAA
193062 AAACGCCGCTAAAGT
1 AAACGCCGCTAAAGT
193077 GATACCCTAT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
81 18 0.21
82 16 0.19
83 52 0.60
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (81 bp):
AAACGCCGCTAAAGTACTATCACATTGCGGCGTTTGTTGAAAAACGCCACTATAGATGAACCTAT
TGCGGAGTTTGTATAA
Found at i:193086 original size:41 final size:41
Alignment explanation
Indices: 192857--193115 Score: 139
Period size: 41 Copynumber: 6.3 Consensus size: 41
192847 TTTCAATTTC
* * *
192857 AAACGCCACTAAAGT-ACTA--CTATTACGGCGTTTATAGTTAC
1 AAACGCCACTAAAGTGA-TACCCTATTGCGGCGTTTGTA--TAA
*** *
192898 AAACGCCACTAAAGT-ACTATTATGTTGCGGCGTTTGT-TGAA
1 AAACGCCACTAAAGTGA-TACCCTATTGCGGCGTTTGTAT-AA
* * * *
192939 AAATGCCACT-ATG-GATGAACCTATTGCGGCGTTTGTACT-G
1 AAACGCCACTAAAGTGAT-ACCCTATTGCGGCGTTTGTA-TAA
* *
192979 AAACGCCGCTAAAGT-ACTACTCAC-ATTGCGTCGTTTGT-TGGAA
1 AAACGCCACTAAAGTGA-TAC-C-CTATTGCGGCGTTTGTAT--AA
* *
193022 AAACGCCACTATAGATGA-A-CCTATTGCGGAGTTTGTATAA
1 AAACGCCACTAAAG-TGATACCCTATTGCGGCGTTTGTATAA
* * *
193062 AAACGCCGCTAAAGTGATACCCTATCGCGGCGTTTTTATAA
1 AAACGCCACTAAAGTGATACCCTATTGCGGCGTTTGTATAA
*
193103 AAACACCACTAAA
1 AAACGCCACTAAA
193116 ACTACCATTT
Statistics
Matches: 168, Mismatches: 29, Indels: 42
0.70 0.12 0.18
Matches are distributed among these distances:
39 4 0.02
40 44 0.26
41 75 0.45
42 17 0.10
43 26 0.15
44 1 0.01
45 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (41 bp):
AAACGCCACTAAAGTGATACCCTATTGCGGCGTTTGTATAA
Found at i:194439 original size:66 final size:66
Alignment explanation
Indices: 194333--194464 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
194323 AAAGAATAAA
194333 TCATTACGTGATTTTTCGTTTAAATTAAAAAGAACGAATTATCAATTAAAGAAATGATATAAAAA
1 TCATTACGTGATTTTTCGTTTAAATTAAAAAGAACGAATTATCAATTAAAGAAATGATATAAAAA
194398 T
66 T
194399 TCATTACGTGATTTTTCGTTTAAATTAAAAAGAACGAATTATCAATTAAAGAAATGATATAAAAA
1 TCATTACGTGATTTTTCGTTTAAATTAAAAAGAACGAATTATCAATTAAAGAAATGATATAAAAA
194464 T
66 T
194465 ATTAAATAAG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.35
Consensus pattern (66 bp):
TCATTACGTGATTTTTCGTTTAAATTAAAAAGAACGAATTATCAATTAAAGAAATGATATAAAAA
T
Found at i:196988 original size:4 final size:4
Alignment explanation
Indices: 196954--197012 Score: 68
Period size: 4 Copynumber: 14.5 Consensus size: 4
196944 AATAAAATGG
*
196954 ATAA ATAGA GATAA A-AA ATAA AT-A TTAAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATA-A -ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA ATAA
197003 ATAA ATAA AT
1 ATAA ATAA AT
197013 GAAGAAACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
3 5 0.10
4 36 0.75
5 4 0.08
6 3 0.06
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:197074 original size:17 final size:16
Alignment explanation
Indices: 197054--197099 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
197044 AGGAAAATGC
*
197054 AAAAATAAAAATATTAA
1 AAAAATAAAAA-AATAA
197071 AAAAATAGAAAAAATAA
1 AAAAATA-AAAAAATAA
*
197088 ATAAATAAAAAA
1 AAAAATAAAAAA
197100 TGATCAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 5 0.19
17 17 0.65
18 4 0.15
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (16 bp):
AAAAATAAAAAAATAA
Found at i:198931 original size:34 final size:33
Alignment explanation
Indices: 198851--198938 Score: 133
Period size: 33 Copynumber: 2.7 Consensus size: 33
198841 GTAGTCGAAC
* *
198851 TCAAAGG-TCTTTGTGTTTCAAGAGAAACATTT
1 TCAAAGGTTTTTTGTGTTTCAAGAGAAACAATT
*
198883 TTAAAGGTTTTTTGTGTTTCAAGAGAAACAATT
1 TCAAAGGTTTTTTGTGTTTCAAGAGAAACAATT
198916 TCAAAGGGTTTTTTGTGTTTCAA
1 TCAAA-GGTTTTTTGTGTTTCAA
198939 TAAAAAATGT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 6 0.12
33 27 0.54
34 17 0.34
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (33 bp):
TCAAAGGTTTTTTGTGTTTCAAGAGAAACAATT
Found at i:199032 original size:67 final size:69
Alignment explanation
Indices: 198897--199049 Score: 186
Period size: 67 Copynumber: 2.2 Consensus size: 69
198887 AGGTTTTTTG
* * * **
198897 TGTTTCAAGAGAAACAATTTCAAAGGGTTTTTTGTGTTTCAATAAAAAATGTCTCCAGAGAGGTA
1 TGTTTCAAGAGAAACAATTTCAAAGGG--TTTGGTGTTTCAAGAAAAAATGTCTCAAGAGAGACA
198962 AAATTT
64 AAATTT
* *
198968 TGTTTCAAGAGAAAC-ATATTCAAA-GG-TTGGTGTTTCAAGAGAAATTGTCTCAAGAGAGACAA
1 TGTTTCAAGAGAAACAAT-TTCAAAGGGTTTGGTGTTTCAAGAAAAAATGTCTCAAGAGAGACAA
199030 AATTT
65 AATTT
*
199035 TGTTTCAAGGGAAAC
1 TGTTTCAAGAGAAAC
199050 TGTCTCAAGA
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
67 48 0.66
70 4 0.05
71 21 0.29
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.32
Consensus pattern (69 bp):
TGTTTCAAGAGAAACAATTTCAAAGGGTTTGGTGTTTCAAGAAAAAATGTCTCAAGAGAGACAAA
ATTT
Found at i:199054 original size:37 final size:36
Alignment explanation
Indices: 198998--199082 Score: 143
Period size: 37 Copynumber: 2.3 Consensus size: 36
198988 CAAAGGTTGG
*
198998 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
*
199035 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
199071 TGTTTCAAGAGA
1 TGTTTCAAGAGA
199083 GACAAAACTT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
36 13 0.29
37 32 0.71
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:199080 original size:21 final size:21
Alignment explanation
Indices: 199012--199089 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
199002 TCAAGAGAAA
199012 TTGTCTCAAGAGAGACAAAATT
1 TTGTCTCAAGAGAGACAAAA-T
*
199034 TTGTTTCAAG-G-G---AAA-
1 TTGTCTCAAGAGAGACAAAAT
*
199049 CTGTCTCAAGAGAGACAAAAT
1 TTGTCTCAAGAGAGACAAAAT
*
199070 TTGTTTCAAGAGAGACAAAA
1 TTGTCTCAAGAGAGACAAAA
199090 CTTAGTTCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
15 8 0.18
16 1 0.02
17 4 0.09
20 4 0.09
21 19 0.42
22 9 0.20
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.26
Consensus pattern (21 bp):
TTGTCTCAAGAGAGACAAAAT
Found at i:199107 original size:58 final size:58
Alignment explanation
Indices: 199012--199137 Score: 171
Period size: 58 Copynumber: 2.2 Consensus size: 58
199002 TCAAGAGAAA
* * * * **
199012 TTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
1 TTGTTTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACAAAAT
* * *
199070 TTGTTTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGATACGAAAT
1 TTGTTTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACAAAAT
199128 TTGTTTCAAG
1 TTGTTTCAAG
199138 GAAAACATAT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (58 bp):
TTGTTTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACAAAAT
Found at i:199173 original size:103 final size:101
Alignment explanation
Indices: 199070--199454 Score: 423
Period size: 101 Copynumber: 3.7 Consensus size: 101
199060 GAGACAAAAT
* * * ** *
199070 TTGTTTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGATACGAAATTTGTTTC
1 TTGTATCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTGTTTC
*
199135 AAGGAAAACATATTCAAAGATTTTGTTTCAAGGGAAA
65 AAGGAAAACATATTCAAAGACTTTGTTTCAAGGGAAA
*
199172 TTGTATCATGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTGTTTCA
1 TTGTATCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTGTTTCA
* *
199237 AGGAAAACATATTCAAATACTTTGTTTCGAGGGAAA
66 AGGAAAACATATTCAAAGACTTTGTTTCAAGGGAAA
** * * *
199273 CCGTCTCAAGAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTT
1 TTGTATC-A-AGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTGTTT
* * *
199338 -AAAGAGAAAC-TGACTCAAGAGAGACAAAATTTATTTCAAGGGAAA
64 CAAGGA-AAACAT-ATTC-A-A-AGAC----TTTGTTTCAAGGGAAA
* * * * * *
199383 TTGTCTCAATAGAGATAAAATTTGTTTCAAGTGAAACTGTCTCAAGAGAGACAAAATTTGTTTCA
1 TTGTATCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTGTTTCA
199448 AGAGAAA
66 AG-GAAA
199455 CTGTCTCAAG
Statistics
Matches: 243, Mismatches: 27, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
101 77 0.32
102 24 0.10
103 59 0.24
104 1 0.00
105 1 0.00
106 3 0.01
108 52 0.21
109 5 0.02
110 21 0.09
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (101 bp):
TTGTATCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTGTTTCA
AGGAAAACATATTCAAAGACTTTGTTTCAAGGGAAA
Found at i:199203 original size:36 final size:36
Alignment explanation
Indices: 199156--199482 Score: 391
Period size: 36 Copynumber: 9.2 Consensus size: 36
199146 ATTCAAAGAT
* * *
199156 TTTGTTTCAAGGGAAATTGTATCATGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
199192 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
199228 TTTGTTTCAAGGAAAACATAT-TC-A-A-ATAC----
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
* *
199257 TTTGTTTCGAGGGAAACCGTCTCAAGAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTC-A-AGAGAGACAAAA
199295 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
199331 TTTGTTTAAAGAGAAACTGACTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * *
199367 TTTATTTCAAGGGAAATTGTCTCAATAGAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
199403 TTTGTTTCAAGTGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
199439 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
199475 CTTTGTTT
1 -TTTGTTT
199483 TGAGTAAATT
Statistics
Matches: 247, Mismatches: 32, Indels: 23
0.82 0.11 0.08
Matches are distributed among these distances:
28 1 0.00
29 17 0.07
32 1 0.00
33 4 0.02
34 3 0.01
35 1 0.00
36 189 0.77
37 10 0.04
38 21 0.09
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:201170 original size:14 final size:13
Alignment explanation
Indices: 201143--201213 Score: 58
Period size: 14 Copynumber: 5.4 Consensus size: 13
201133 TTTTCTTCAC
201143 TTTTTCT-TTGTTT
1 TTTTTCTCTT-TTT
201156 TTGTTTCTCTTTTT
1 TT-TTTCTCTTTTT
**
201170 TATTTTCTCTTTGC
1 T-TTTTCTCTTTTT
*
201184 TTTTT-TC-TTCT
1 TTTTTCTCTTTTT
201195 TTTTTCTCTTTTT
1 TTTTTCTCTTTTT
201208 TCTTTT
1 T-TTTT
201214 TGTTCTGATT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
11 7 0.15
12 4 0.09
13 10 0.21
14 23 0.49
15 3 0.06
ACGTcount: A:0.01, C:0.15, G:0.04, T:0.79
Consensus pattern (13 bp):
TTTTTCTCTTTTT
Found at i:205040 original size:36 final size:35
Alignment explanation
Indices: 204995--205105 Score: 107
Period size: 36 Copynumber: 3.4 Consensus size: 35
204985 ATTTTATTTT
204995 TATTTTAATATTACTTTTTAAATAATTAAATATTAA
1 TATTTTAATATTA-TTTTTAAATAATTAAATATTAA
* * *
205031 TATTTTAATATTA-TTATAGAT-ATT-AATTTTAA
1 TATTTTAATATTATTTTTAAATAATTAAATATTAA
205063 TA--TT-A-A-T-TTTTTAAATAAATTAAATATTAA
1 TATTTTAATATTATTTTTAAAT-AATTAAATATTAA
205093 T-TTTTAATATTAT
1 TATTTTAATATTAT
205106 ATTATAGATA
Statistics
Matches: 59, Mismatches: 6, Indels: 21
0.69 0.07 0.24
Matches are distributed among these distances:
27 7 0.12
28 1 0.02
29 4 0.07
30 10 0.17
31 2 0.03
32 10 0.17
33 4 0.07
34 7 0.12
35 1 0.02
36 13 0.22
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (35 bp):
TATTTTAATATTATTTTTAAATAATTAAATATTAA
Found at i:205046 original size:24 final size:23
Alignment explanation
Indices: 204979--205067 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 23
204969 TATTTAATTT
* * *
204979 TATTATATTTTATTTTTATTTTAA
1 TATTATATTTTAATATTA-TTAAA
*
205003 TATTACT-TTTTAA-ATAATTAAA
1 TATTA-TATTTTAATATTATTAAA
205025 TATTAATATTTTAATATTATTATAGA
1 TATT-ATATTTTAATATTATTA-A-A
205051 TATTA-ATTTTAATATTA
1 TATTATATTTTAATATTA
205068 ATTTTTTAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
22 9 0.17
23 9 0.17
24 28 0.52
25 3 0.06
26 5 0.09
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (23 bp):
TATTATATTTTAATATTATTAAA
Found at i:205075 original size:38 final size:37
Alignment explanation
Indices: 205023--205108 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 37
205013 TAAATAATTA
*
205023 AATATTAATATTTT-AATATTATTATAGATATTAA-TTTT
1 AATATTAATATTTTAAATA-AATTA-A-ATATTAATTTTT
*
205061 AATATTAATTTTTTAAATAAATTAAATATTAATTTTT
1 AATATTAATATTTTAAATAAATTAAATATTAATTTTT
205098 AATATT-ATATT
1 AATATTAATATT
205109 ATAGATATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
36 11 0.26
37 11 0.26
38 17 0.40
39 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (37 bp):
AATATTAATATTTTAAATAAATTAAATATTAATTTTT
Found at i:205104 original size:61 final size:63
Alignment explanation
Indices: 204996--205125 Score: 205
Period size: 61 Copynumber: 2.1 Consensus size: 63
204986 TTTTATTTTT
204996 ATTTTAATATTACTTTTTAAATAATTAAATATTAATATTTTAATA-T-TATTATAGATA-TTA
1 ATTTTAATATTACTTTTTAAATAATTAAATATTAATATTTTAATATTATATTATAGATATTTA
*
205056 ATTTTAATATTAATTTTTTAAATAAATTAAATATTAAT-TTTTAATATTATATTATAGATATTTA
1 ATTTTAATATT-ACTTTTTAAAT-AATTAAATATTAATATTTTAATATTATATTATAGATATTTA
205120 ATTTTA
1 ATTTTA
205126 TCATATAAAC
Statistics
Matches: 64, Mismatches: 1, Indels: 6
0.90 0.01 0.08
Matches are distributed among these distances:
60 11 0.17
61 18 0.28
62 15 0.23
63 11 0.17
64 9 0.14
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.55
Consensus pattern (63 bp):
ATTTTAATATTACTTTTTAAATAATTAAATATTAATATTTTAATATTATATTATAGATATTTA
Found at i:205328 original size:27 final size:27
Alignment explanation
Indices: 205298--205350 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
205288 TTTGTTTGAT
205298 AATTAAGATTTTAAAATATAAAAATAA
1 AATTAAGATTTTAAAATATAAAAATAA
* * * *
205325 AATTATGTTTTTAAAATTTTAAAATA
1 AATTAAGATTTTAAAATATAAAAATA
205351 TAATCACAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (27 bp):
AATTAAGATTTTAAAATATAAAAATAA
Found at i:205442 original size:13 final size:14
Alignment explanation
Indices: 205420--205462 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
205410 TAAAAATATC
205420 ATATAATTATAAAA
1 ATATAATTATAAAA
* *
205434 ATA-AATTATGAAT
1 ATATAATTATAAAA
*
205447 ATATAATTAAAAAA
1 ATATAATTATAAAA
205461 AT
1 AT
205463 TAAAAGTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
ATATAATTATAAAA
Found at i:205671 original size:31 final size:31
Alignment explanation
Indices: 205634--205693 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
205624 TAGTTGTATG
* *
205634 AATTATTTAAATTTAAGTATTGTAAAACTAA
1 AATTATTTAAATCTAAGTATTGCAAAACTAA
*
205665 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTAAGTATTGCAAAACT
205694 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTAAGTATTGCAAAACTAA
Found at i:205845 original size:27 final size:27
Alignment explanation
Indices: 205784--205837 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
205774 CTTCTTGTAG
205784 ACTGCAGACTTTTGGTCCACCTCTTCT
1 ACTGCAGACTTTTGGTCCACCTCTTCT
205811 ACTGCAGACTTTTGGTCCACCTCTTCT
1 ACTGCAGACTTTTGGTCCACCTCTTCT
205838 GTTGCAGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.33, G:0.15, T:0.37
Consensus pattern (27 bp):
ACTGCAGACTTTTGGTCCACCTCTTCT
Found at i:206675 original size:3 final size:3
Alignment explanation
Indices: 206656--206699 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
206646 ATAAAAAAGA
206656 AAT AA- AAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
206700 ACAAAAATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:215222 original size:92 final size:93
Alignment explanation
Indices: 215053--215230 Score: 259
Period size: 92 Copynumber: 1.9 Consensus size: 93
215043 GGGGGTAGAG
215053 TCCAAAATTCAGATATTTTAAGTAAGTGTAAATCATCAGTGCTTGAACATACATTGCAATTTTCT
1 TCCAAAATTCAGATATTTTAAGTAAGTGTAAATCATCAGTGCTTGAACATACATTGCAATTTTCT
*
215118 ATACCGGCTATAGTCAGCCATGGGAATA
66 ATACCGGCTATAGTCAACCATGGGAATA
* * * * * * *
215146 TCCACAATTCAGATA-TTTATGTAAGTTTCAATCATCAGTGCTTGAACATGCATTGCAGTTTTTT
1 TCCAAAATTCAGATATTTTAAGTAAGTGTAAATCATCAGTGCTTGAACATACATTGCAATTTTCT
* *
215210 ATACTGGTTATAGTCAACCAT
66 ATACCGGCTATAGTCAACCAT
215231 CTAAAGAAAG
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
92 61 0.81
93 14 0.19
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (93 bp):
TCCAAAATTCAGATATTTTAAGTAAGTGTAAATCATCAGTGCTTGAACATACATTGCAATTTTCT
ATACCGGCTATAGTCAACCATGGGAATA
Found at i:219608 original size:21 final size:20
Alignment explanation
Indices: 219591--219644 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 20
219581 TTATAAAATC
219591 TAGGGTTTAGGATTTAAAGTT
1 TAGGGTTTAGG-TTTAAAGTT
219612 TAGGGTTTAAGGTTTAAATGTT
1 TAGGGTTT-AGGTTTAAA-GTT
219634 TAGGGTTTAGG
1 TAGGGTTTAGG
219645 GTTTGTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (20 bp):
TAGGGTTTAGGTTTAAAGTT
Found at i:219637 original size:22 final size:21
Alignment explanation
Indices: 219591--219648 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 21
219581 TTATAAAATC
219591 TAGGGTTT-AGGATTTAAAGTT
1 TAGGGTTTAAGG-TTTAAAGTT
219612 TAGGGTTTAAGGTTTAAATGTT
1 TAGGGTTTAAGGTTTAAA-GTT
*
219634 TAGGGTTTAGGGTTT
1 TAGGGTTTAAGGTTT
219649 GTATTATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 14 0.41
22 20 0.59
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (21 bp):
TAGGGTTTAAGGTTTAAAGTT
Found at i:219641 original size:7 final size:7
Alignment explanation
Indices: 219591--219648 Score: 53
Period size: 7 Copynumber: 8.1 Consensus size: 7
219581 TTATAAAATC
219591 TAGGGTT
1 TAGGGTT
*
219598 TAGGATT
1 TAGGGTT
**
219605 TAAAGTT
1 TAGGGTT
219612 TAGGGTT
1 TAGGGTT
*
219619 TAAGGTT
1 TAGGGTT
**
219626 TAAATGTT
1 T-AGGGTT
219634 TAGGGTT
1 TAGGGTT
219641 TAGGGTT
1 TAGGGTT
219648 T
1 T
219649 GTATTATATA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
7 34 0.85
8 6 0.15
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (7 bp):
TAGGGTT
Found at i:219676 original size:2 final size:2
Alignment explanation
Indices: 219671--219797 Score: 106
Period size: 2 Copynumber: 71.5 Consensus size: 2
219661 TAATAAAATA
* *
219671 AT AT AT AT AT AT AT A- AT -T A- AT AT A- AA AT AT AT A- AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
219708 AT -T AT AT AT A- AT -T A- AT AT A- AA AT AT AT A- AA AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
219743 AT AT AT AT A- AT -T A- AT AT A- 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
219781 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
219798 ATCGGGGCGG
Statistics
Matches: 105, Mismatches: 4, Indels: 32
0.74 0.03 0.23
Matches are distributed among these distances:
1 16 0.15
2 89 0.85
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:219695 original size:9 final size:9
Alignment explanation
Indices: 219654--219762 Score: 60
Period size: 9 Copynumber: 12.8 Consensus size: 9
219644 GGTTTGTATT
219654 ATATAATTA
1 ATATAATTA
*
219663 ATA-AAATA
1 ATATAATTA
219671 ATAT-ATATA
1 ATATAAT-TA
219680 TATATAATTA
1 -ATATAATTA
219690 ATATAA--A
1 ATATAATTA
219697 ATAT-A-TA
1 ATATAATTA
*
219704 AAAT-ATTA
1 ATATAATTA
219712 TATATAATTA
1 -ATATAATTA
219722 ATATAA--A
1 ATATAATTA
219729 ATAT-A-TA
1 ATATAATTA
* *
219736 AAATATTATA
1 ATATAAT-TA
219746 TATATAATTA
1 -ATATAATTA
219756 ATATAAT
1 ATATAAT
219763 ATATATATAT
Statistics
Matches: 79, Mismatches: 8, Indels: 26
0.70 0.07 0.23
Matches are distributed among these distances:
6 2 0.03
7 19 0.24
8 10 0.13
9 27 0.34
10 14 0.18
11 7 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
ATATAATTA
Found at i:219735 original size:34 final size:33
Alignment explanation
Indices: 219668--219785 Score: 184
Period size: 34 Copynumber: 3.5 Consensus size: 33
219658 AATTAATAAA
*
219668 ATAATATATATATATATAATTAATATAAAATAT
1 ATAAAATATATATATATAATTAATATAAAATAT
219701 ATAAAATAT-TATATATAATTAATATAAAATAT
1 ATAAAATATATATATATAATTAATATAAAATAT
*
219733 ATAAAATATTATATATATAATTAATATAATATAT
1 ATAAAATA-TATATATATAATTAATATAAAATAT
*
219767 ATATATATATATATATATA
1 ATA-AAATATATATATATA
219786 TATATATATA
Statistics
Matches: 79, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
32 31 0.39
33 9 0.11
34 35 0.44
35 4 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (33 bp):
ATAAAATATATATATATAATTAATATAAAATAT
Found at i:219797 original size:32 final size:29
Alignment explanation
Indices: 219653--219797 Score: 140
Period size: 34 Copynumber: 4.9 Consensus size: 29
219643 GGGTTTGTAT
*
219653 TATATA-ATTAATAAAATA-ATATATATA
1 TATATATATTAATATAATATATATATATA
* *
219680 TATATA-ATTAATATAAAATATATAAAATA
1 TATATATATTAATATAATATATAT-ATATA
*
219709 TTATATATAATTAATATAAAATATATAAAATATTA
1 -TATATAT-ATTAATAT--AATATAT-ATATA-TA
219744 TATATATAATTAATATAATATATATATATA
1 TATATAT-ATTAATATAATATATATATATA
219774 TATATATA-T-ATAT-ATATATATATA
1 TATATATATTAATATAATATATATATA
219798 ATCGGGGCGG
Statistics
Matches: 102, Mismatches: 7, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
26 11 0.11
27 20 0.20
28 5 0.05
29 5 0.05
30 15 0.15
31 4 0.04
32 15 0.15
34 24 0.24
35 3 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
TATATATATTAATATAATATATATATATA
Found at i:220824 original size:30 final size:30
Alignment explanation
Indices: 220788--220851 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
220778 ATTACTGATA
220788 AGGGAAACAGGGGAACATAGTTTACCTATC
1 AGGGAAACAGGGGAACATAGTTTACCTATC
220818 AGGGAAACAGGGGAACATAGTTTACCTATC
1 AGGGAAACAGGGGAACATAGTTTACCTATC
220848 AGGG
1 AGGG
220852 GAACTAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.30, T:0.19
Consensus pattern (30 bp):
AGGGAAACAGGGGAACATAGTTTACCTATC
Found at i:225391 original size:23 final size:23
Alignment explanation
Indices: 225365--225442 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
225355 CACCACAGTT
225365 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
225388 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * * *
225411 CGTAGAATTGAACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
225434 TATAATAAT
1 CAT-ATAAT
225443 GTCCATAAGG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 40 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:225620 original size:103 final size:103
Alignment explanation
Indices: 225449--225666 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
225439 TAATGTCCAT
* * *
225449 AAGGACCACATATCATTCTTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAAGGATCAAGTATGTGTCTCACCA
*
225514 GACTTTACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
225552 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCAAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAAGGATCAAGTATGTGTCTCACCA
225617 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
225655 AAGGACCACATA
1 AAGGACCACATA
225667 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:226605 original size:64 final size:63
Alignment explanation
Indices: 226451--226613 Score: 152
Period size: 64 Copynumber: 2.6 Consensus size: 63
226441 ATTCCCTATC
* * ** * * **
226451 GGTGCATCGATGCACTACCTGAGCATCGGTGCATAAAATACATTCGATGTTTGTTTATTACTA
1 GGTGCATCGATGCACTACCTGTGCATCGATGCACCAAATACAGTCGATGTTTGTTGATTAAAA
** *
226514 GGATGCATCGATGCA-TGTCT-TACGCATCGATGCACCAATTACAGTCGATGTTT-TTAGATTAA
1 GG-TGCATCGATGCACTACCTGT--GCATCGATGCACCAAATACAGTCGATGTTTGTT-GATTAA
226576 AA
62 AA
*
226578 GAGTGCATCGATGCACTACCTGTGCATCGATACACC
1 G-GTGCATCGATGCACTACCTGTGCATCGATGCACC
226614 TTCAAACAAT
Statistics
Matches: 79, Mismatches: 14, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
63 7 0.09
64 67 0.85
65 4 0.05
66 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (63 bp):
GGTGCATCGATGCACTACCTGTGCATCGATGCACCAAATACAGTCGATGTTTGTTGATTAAAA
Found at i:231401 original size:103 final size:103
Alignment explanation
Indices: 231230--231447 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
231220 TAATGTCCAT
* * *
231230 AAGGACCACATATCATTCTTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
231295 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
231333 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
231398 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
231436 AAGGACCACATA
1 AAGGACCACATA
231448 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:237506 original size:30 final size:31
Alignment explanation
Indices: 237479--237604 Score: 76
Period size: 31 Copynumber: 4.1 Consensus size: 31
237469 CAGAGGTCAT
* *
237479 AAAGAACCTCGG-CAACTGTCCATAGGTCTC
1 AAAGAACCTAGGTAAACTGTCCATAGGTCTC
* *
237509 GAAGAACCTAGGTAAACTGTCCATATGT-TCC
1 AAAGAACCTAGGTAAACTGTCCATAGGTCT-C
** * * * * *
237540 TTAGAACATAGGTATATTGTCCATATGTTTC
1 AAAGAACCTAGGTAAACTGTCCATAGGTCTC
** * * * *
237571 TGAGAACATAGGTATATTGTCCATATGTCTC
1 AAAGAACCTAGGTAAACTGTCCATAGGTCTC
237602 AAA
1 AAA
237605 AGACATAGAT
Statistics
Matches: 80, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
30 11 0.14
31 68 0.85
32 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (31 bp):
AAAGAACCTAGGTAAACTGTCCATAGGTCTC
Found at i:237546 original size:31 final size:31
Alignment explanation
Indices: 237511--237598 Score: 131
Period size: 31 Copynumber: 2.8 Consensus size: 31
237501 TAGGTCTCGA
* * * *
237511 AGAACCTAGGTAAACTGTCCATATGTTCCTT
1 AGAACATAGGTATATTGTCCATATGTTCCTG
*
237542 AGAACATAGGTATATTGTCCATATGTTTCTG
1 AGAACATAGGTATATTGTCCATATGTTCCTG
237573 AGAACATAGGTATATTGTCCATATGT
1 AGAACATAGGTATATTGTCCATATGT
237599 CTCAAAAGAC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (31 bp):
AGAACATAGGTATATTGTCCATATGTTCCTG
Found at i:237637 original size:32 final size:32
Alignment explanation
Indices: 237576--237694 Score: 154
Period size: 32 Copynumber: 3.8 Consensus size: 32
237566 GTTTCTGAGA
*
237576 ACATAGGT-ATAT-TGTCCATATGTCTCAAAAG
1 ACATAGGTAAT-TCTGTCCATATGTCCCAAAAG
* *
237607 ACATAGATAA-TCATGTCCATATATCCCAAAAG
1 ACATAGGTAATTC-TGTCCATATGTCCCAAAAG
* *
237639 ACATAGGTAATTCTGTCCATTTGTCCCGAAAG
1 ACATAGGTAATTCTGTCCATATGTCCCAAAAG
237671 ACATAGGTAATTCTGTCCATATGT
1 ACATAGGTAATTCTGTCCATATGT
237695 TCCTTAGAAC
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
30 1 0.01
31 7 0.09
32 66 0.87
33 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.31
Consensus pattern (32 bp):
ACATAGGTAATTCTGTCCATATGTCCCAAAAG
Found at i:237707 original size:32 final size:32
Alignment explanation
Indices: 237510--237711 Score: 152
Period size: 32 Copynumber: 6.4 Consensus size: 32
237500 ATAGGTCTCG
* *
237510 AAGAACCTAGGTAA-ACTGTCCATATGTTCCT
1 AAGAACATAGGTAATTCTGTCCATATGTTCCT
* *
237541 TAGAACATAGGT-ATAT-TGTCCATATGTTTCT
1 AAGAACATAGGTAAT-TCTGTCCATATGTTCCT
* **
237572 GAGAACATAGGT-ATAT-TGTCCATATGTCTCAA
1 AAGAACATAGGTAAT-TCTGTCCATATGT-TCCT
* * *
237604 AAG-ACATAGATAA-TCATGTCCATAT-ATCCC
1 AAGAACATAGGTAATTC-TGTCCATATGTTCCT
* * * *
237634 AAAAGACATAGGTAATTCTGTCCATTTGTCCCG
1 AAGA-ACATAGGTAATTCTGTCCATATGTTCCT
237667 AA-AGACATAGGTAATTCTGTCCATATGTTCCT
1 AAGA-ACATAGGTAATTCTGTCCATATGTTCCT
*
237699 TAGAACATAGGTA
1 AAGAACATAGGTA
237712 TACCCTCGAA
Statistics
Matches: 137, Mismatches: 23, Indels: 21
0.76 0.13 0.12
Matches are distributed among these distances:
30 6 0.04
31 57 0.42
32 67 0.49
33 7 0.05
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (32 bp):
AAGAACATAGGTAATTCTGTCCATATGTTCCT
Found at i:237707 original size:64 final size:64
Alignment explanation
Indices: 237510--237711 Score: 168
Period size: 64 Copynumber: 3.2 Consensus size: 64
237500 ATAGGTCTCG
* * * ** *
237510 AAGAACCTAGGTAA-ACTGTCCATATGTTCC-TTAGAACATAGGT-ATAT-TGTCCATATGTTTC
1 AAGAACATAGGTAATATTGTCCATATGTCCCAAAAG-ACATAGGTAAT-TCTGTCCATATGTTCC
237571 T
64 T
* * * * *
237572 GAGAACATAGGT-ATATTGTCCATATGTCTCAAAAGACATAGATAA-TCATGTCCATAT-ATCCC
1 AAGAACATAGGTAATATTGTCCATATGTCCCAAAAGACATAGGTAATTC-TGTCCATATGTTCCT
* * *
237634 AAAAGACATAGGTAAT-TCTGTCCATTTGTCCCGAAAGACATAGGTAATTCTGTCCATATGTTCC
1 AAGA-ACATAGGTAATAT-TGTCCATATGTCCCAAAAGACATAGGTAATTCTGTCCATATGTTCC
237698 T
64 T
*
237699 TAGAACATAGGTA
1 AAGAACATAGGTA
237712 TACCCTCGAA
Statistics
Matches: 109, Mismatches: 21, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
61 2 0.02
62 34 0.31
63 21 0.19
64 45 0.41
65 7 0.06
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (64 bp):
AAGAACATAGGTAATATTGTCCATATGTCCCAAAAGACATAGGTAATTCTGTCCATATGTTCCT
Found at i:238105 original size:9 final size:10
Alignment explanation
Indices: 238096--238172 Score: 80
Period size: 9 Copynumber: 8.5 Consensus size: 10
238086 TTTACCCATT
238096 TTATTTA-T-
1 TTATTTATTA
238104 TTATTTATTA
1 TTATTTATTA
238114 TTA-TTATTA
1 TTATTTATTA
*
238123 TTA-TTATAA
1 TTATTTATTA
238132 TTA-TTATTA
1 TTATTTATTA
238141 TTA-TTATTA
1 TTATTTATTA
*
238150 TTATATA-TA
1 TTATTTATTA
238159 TTA-TTATTA
1 TTATTTATTA
238168 TTATT
1 TTATT
238173 AAAAAAATAA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
8 9 0.15
9 45 0.75
10 6 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATTTATTA
Found at i:238116 original size:3 final size:3
Alignment explanation
Indices: 238108--238173 Score: 107
Period size: 3 Copynumber: 22.0 Consensus size: 3
238098 ATTTATTTAT
*
238108 TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
238155 TATA TTA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA TTA
238174 AAAAAATAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.03
3 54 0.92
4 3 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:238185 original size:21 final size:21
Alignment explanation
Indices: 238140--238185 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
238130 AATTATTATT
* * * *
238140 ATTATTATTATTATATATATT
1 ATTATTATTATTAAAAAAATA
238161 ATTATTATTATTAAAAAAATA
1 ATTATTATTATTAAAAAAATA
238182 ATTA
1 ATTA
238186 CAATCCCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTATTATTATTAAAAAAATA
Found at i:239381 original size:3 final size:3
Alignment explanation
Indices: 239373--239465 Score: 79
Period size: 3 Copynumber: 32.0 Consensus size: 3
239363 TTTATTTTTG
* *
239373 ATT ATT ATT ATT ATT -TT A-T ATT -TT AAT ATT A-T ATT TTT AATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
* * * *
239415 AGT ATT -TGC AAT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT CTT
1 ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
239460 ATT ATT
1 ATT ATT
239466 TATATAAATA
Statistics
Matches: 71, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
2 9 0.13
3 60 0.85
4 2 0.03
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:239410 original size:21 final size:21
Alignment explanation
Indices: 239334--239411 Score: 70
Period size: 21 Copynumber: 3.5 Consensus size: 21
239324 TACTCTAGTT
239334 TTATAATTTTATATTTTAATCA
1 TTATAATTTTATATTTTAAT-A
239356 TTCA-AATTTTAT-TTTTGATTATTA
1 TT-ATAATTTTATATTTT-A--A-TA
*
239380 TTATTATTTTATATTTTAATA
1 TTATAATTTTATATTTTAATA
*
239401 TTATATTTTTA
1 TTATAATTTTA
239412 ATTAGTATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
21 15 0.33
22 12 0.26
23 2 0.04
24 12 0.26
25 5 0.11
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (21 bp):
TTATAATTTTATATTTTAATA
Found at i:239681 original size:20 final size:19
Alignment explanation
Indices: 239656--239697 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
239646 TTATTTTATA
239656 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
239676 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
239695 AAT
1 AAT
239698 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:239689 original size:119 final size:120
Alignment explanation
Indices: 239560--239789 Score: 286
Period size: 120 Copynumber: 1.9 Consensus size: 120
239550 TTTTAATATA
* * * * *
239560 TATTTATTTATTTTTCAATAT-TAAG-AAAGGGCGGTCTTAAAATAACTGGATGTCCATTTTCTG
1 TATTTATTTATTTTTCAATATCAAAGAAAAGAGCGGTCTTAAAACAACTAGAAGT-CATTTTCTG
* *
239623 ATATTTTTAAATAAATAAATATCTTATTTTATAAAT-TATATATTAATTGTTTTAAT
65 ATATTTCTAAATAAATAAATATCTTA-TTTATAAATATATAAATTAATTGTTTTAAT
* * ** * *
239679 TATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCATTTTCTTA
1 TATTTATTTATTTTTCAATATCAAAGAAAAGAGCGGTCTTAAAACAACTAGAAGTCATTTTCTGA
* *
239744 TATTTCTAAATAAATAAATATTTTATTTATAAGTATATAAATTAAT
66 TATTTCTAAATAAATAAATATCTTATTTATAAATATATAAATTAAT
239790 ATATATATAT
Statistics
Matches: 93, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
119 28 0.30
120 45 0.48
121 20 0.22
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (120 bp):
TATTTATTTATTTTTCAATATCAAAGAAAAGAGCGGTCTTAAAACAACTAGAAGTCATTTTCTGA
TATTTCTAAATAAATAAATATCTTATTTATAAATATATAAATTAATTGTTTTAAT
Found at i:241935 original size:15 final size:15
Alignment explanation
Indices: 241898--241937 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
241888 AATAATTTAC
241898 ATTTACATTT-GCAT
1 ATTTACATTTGGCAT
241912 ATTTACATTTGGCAT
1 ATTTACATTTGGCAT
* *
241927 CTTTGCATTTG
1 ATTTACATTTG
241938 TATTTTTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (15 bp):
ATTTACATTTGGCAT
Found at i:245482 original size:12 final size:12
Alignment explanation
Indices: 245465--245524 Score: 79
Period size: 12 Copynumber: 5.1 Consensus size: 12
245455 CTCATCCAGC
245465 AAAGAAAGAAAA
1 AAAGAAAGAAAA
245477 AAAGAAAGAAAA
1 AAAGAAAGAAAA
*
245489 AAA-AGA-AAAA
1 AAAGAAAGAAAA
245499 AAAGAAAGAAAAA
1 AAAGAAAG-AAAA
*
245512 AAAGAAGGAAAA
1 AAAGAAAGAAAA
245524 A
1 A
245525 GAAAAAGGGG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
10 7 0.17
11 4 0.10
12 20 0.48
13 11 0.26
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAAAA
Found at i:245493 original size:9 final size:9
Alignment explanation
Indices: 245469--245530 Score: 58
Period size: 9 Copynumber: 7.0 Consensus size: 9
245459 TCCAGCAAAG
245469 AAAG-AAAA
1 AAAGAAAAA
245477 AAAGAAAGAA
1 AAAGAAA-AA
*
245487 AAA-AAAGA
1 AAAGAAAAA
*
245495 AAA-AAAAG
1 AAAGAAAAA
245503 AAAGAAAAA
1 AAAGAAAAA
*
245512 AAAGAAGGAA
1 AAAGAA-AAA
245522 AAAGAAAAA
1 AAAGAAAAA
245531 GGGGAGAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
8 14 0.32
9 17 0.39
10 13 0.30
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:245501 original size:22 final size:22
Alignment explanation
Indices: 245469--245528 Score: 95
Period size: 22 Copynumber: 2.7 Consensus size: 22
245459 TCCAGCAAAG
245469 AAAG-AAAAAAAGAAAGAAAAA
1 AAAGAAAAAAAAGAAAGAAAAA
245490 AAAGAAAAAAAAGAAAGAAAAA
1 AAAGAAAAAAAAGAAAGAAAAA
*
245512 AAAGAAGGAAAAAGAAA
1 AAAGAA-AAAAAAGAAA
245529 AAGGGGAGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 4 0.11
22 23 0.64
23 9 0.25
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAGAAAAAAAAGAAAGAAAAA
Found at i:245532 original size:13 final size:12
Alignment explanation
Indices: 245465--245531 Score: 80
Period size: 13 Copynumber: 5.3 Consensus size: 12
245455 CTCATCCAGC
*
245465 AAAGAAAGAAAA
1 AAAGAAAAAAAA
245477 AAAGAAAGAAAAA
1 AAAGAAA-AAAAA
245490 AAAGAAAAAAAA
1 AAAGAAAAAAAA
245502 GAAAGAAAAAAAA
1 -AAAGAAAAAAAA
* *
245515 GAAGGAAAAAGAA
1 -AAAGAAAAAAAA
245528 AAAG
1 AAAG
245532 GGGAGAAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
12 15 0.31
13 34 0.69
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:248991 original size:76 final size:76
Alignment explanation
Indices: 248911--249105 Score: 338
Period size: 76 Copynumber: 2.6 Consensus size: 76
248901 ACAAGAAGTG
*
248911 AATGTT-GTGGCATTCTGAAAACCCCTTTCAATCAGAATCAGGAATATTAAAGTATTCTGAATAT
1 AATGTTAG-GGCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATATTAAAGTATTCTGAATAT
248975 TTATATCAGCAA
65 TTATATCAGCAA
*
248987 AATGTTAGGGCATGCTGAAAACCCCTTGCAATCAGAATCAGGAATATTAAAGTATTCTGAATATT
1 AATGTTAGGGCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATATTAAAGTATTCTGAATATT
249052 TATATCAGCAA
66 TATATCAGCAA
* *
249063 AATGTTAGGGCATGCTGAAAGCCCCCTTCAATCAGAATCAGGA
1 AATGTTAGGGCATGCTGAAAACCCCTTTCAATCAGAATCAGGA
249106 CTGCTGATGC
Statistics
Matches: 113, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
76 112 0.99
77 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (76 bp):
AATGTTAGGGCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATATTAAAGTATTCTGAATATT
TATATCAGCAA
Found at i:250529 original size:22 final size:22
Alignment explanation
Indices: 250498--250552 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
250488 ATCTACACTC
*
250498 TTCAAAGATGATAGATTC-CTTT
1 TTCAAAGATGACAGATTCTC-TT
*
250520 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
250542 TTCAAAGATGA
1 TTCAAAGATGA
250553 AAGCTTTATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:251136 original size:113 final size:113
Alignment explanation
Indices: 250938--251604 Score: 861
Period size: 113 Copynumber: 5.8 Consensus size: 113
250928 TAGCAAAGAT
* *
250938 TCAAATCCATCACTTGATGGATCAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCATTGCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
251003 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
251051 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCATTGCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
251116 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *** * * * *
251164 TCAAATCCATCA-TTCGATGGATCATCATTTTAAAAGAAAGTTCATAATGAGAAGAACTTATTTG
1 TCAAATCCATCACTT-GATGGATCAGCATTGCCAGATAAAGTTCATAATGAGAAGAACTCATCTG
* * ** *
251228 AAAAAGAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGT
65 AAGAAG--GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * ** * * *
251279 TTAAATTCATCACTTGATATATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATC
1 TCAAATCCATCACTTGATGGATCAGCATTGCCAGATAAAGTTCATAATGAGAAGAA--C-TCATC
* *
251344 TGAAGAATGAAGAAGAAATTCATAATAAGAAGAATTTGTTCAACCTTTTTGC
63 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACC-TTTTGC
* * * *
251396 TCAAATCCATCACTTGATGAATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCATTGCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
* *
251461 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * * *
251509 TTGAATTCATCATTTGATGGATCAACATTGCCATG-TAGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCATTGCCA-GATAAAGTTCATAATGAGAAGAACTCATCTG
* * *
251573 AAGAAAGAAGAAGAAGTTCACAATGAGAAGAA
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAA
251605 CTTATCTGAA
Statistics
Matches: 479, Mismatches: 66, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
112 2 0.00
113 252 0.53
114 48 0.10
115 81 0.17
116 35 0.07
117 52 0.11
118 9 0.02
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAGCATTGCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:251602 original size:40 final size:42
Alignment explanation
Indices: 251547--251645 Score: 157
Period size: 42 Copynumber: 2.4 Consensus size: 42
251537 TGCCATGTAG
*
251547 AGTTCATAATGAGAAGAACTCATCTG-AAGA-AAGAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCTGAAAAAGAAGAAGAAGA
* *
251587 AGTTCACAATGAGAAGAACTTATCTGAAAAAGAAGAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCTGAAAAAGAAGAAGAAGA
251629 AGTTCATAATGAGAAGA
1 AGTTCATAATGAGAAGA
251646 GCTTGTTCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 24 0.45
41 3 0.06
42 26 0.49
ACGTcount: A:0.51, C:0.09, G:0.22, T:0.18
Consensus pattern (42 bp):
AGTTCATAATGAGAAGAACTCATCTGAAAAAGAAGAAGAAGA
Found at i:251652 original size:155 final size:154
Alignment explanation
Indices: 251433--251809 Score: 615
Period size: 155 Copynumber: 2.5 Consensus size: 154
251423 TTTCCAGAGA
* * *
251433 AAGTTCATAATGAGAAGAACTCATCTG--AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
1 AAGTTCACAATGAGAAGAACTTATCTGAAAAGAA-GAAGAAGAAGTTCATAATGAGAAGAGTTTG
* *
251496 TTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCATGTAGAGTTCATAATGAGA
65 TTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGA
251561 AGAACTCATCTGAAGAAAGAAGAAG
130 AGAACTCATCTGAAGAAAGAAGAAG
*
251586 AAGTTCACAATGAGAAGAACTTATCTGAAAAAGAAGAAGAAGAAGTTCATAATGAGAAGAGCTTG
1 AAGTTCACAATGAGAAGAACTTATCTG-AAAAGAAGAAGAAGAAGTTCATAATGAGAAGAGTTTG
*
251651 TTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAGCATTGCCAGGTAGAGTTCATAATGAGA
65 TTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGA
251716 AGAACTCATCTGAAGAAAGAAGAAG
130 AGAACTCATCTGAAGAAAGAAGAAG
*
251741 AAGTTCACAATGAGAAGAACTTATCT-----GAAGAAGAAGAAGTTCACAATGAGAAGAGTTTGT
1 AAGTTCACAATGAGAAGAACTTATCTGAAAAGAAGAAGAAGAAGTTCATAATGAGAAGAGTTTGT
251801 TCAACCTTT
66 TCAACCTTT
251810 GCTAGATTAC
Statistics
Matches: 212, Mismatches: 9, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
149 41 0.19
153 25 0.12
155 141 0.67
156 5 0.02
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (154 bp):
AAGTTCACAATGAGAAGAACTTATCTGAAAAGAAGAAGAAGAAGTTCATAATGAGAAGAGTTTGT
TCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAA
GAACTCATCTGAAGAAAGAAGAAG
Found at i:251758 original size:17 final size:17
Alignment explanation
Indices: 251736--251794 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
251726 TGAAGAAAGA
251736 AGAAGAAGTTCACAATG
1 AGAAGAAGTTCACAATG
*
251753 AGAAGAACTT-ATCTGAA-G
1 AGAAGAAGTTCA-C--AATG
251771 AAGAAGAAGTTCACAATG
1 -AGAAGAAGTTCACAATG
251789 AGAAGA
1 AGAAGA
251795 GTTTGTTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
16 1 0.03
17 18 0.53
18 2 0.06
19 12 0.35
20 1 0.03
ACGTcount: A:0.49, C:0.10, G:0.24, T:0.17
Consensus pattern (17 bp):
AGAAGAAGTTCACAATG
Found at i:251779 original size:36 final size:38
Alignment explanation
Indices: 251702--251794 Score: 136
Period size: 36 Copynumber: 2.4 Consensus size: 38
251692 TGCCAGGTAG
*
251702 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGA
1 AGTTCACAATGAGAAGAACTCATCT--AGAAAGAAGAAGA
*
251742 AGTTCACAATGAGAAGAACTTATCT-G-AAGAAGAAGA
1 AGTTCACAATGAGAAGAACTCATCTAGAAAGAAGAAGA
251778 AGTTCACAATGAGAAGA
1 AGTTCACAATGAGAAGA
251795 GTTTGTTCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
36 27 0.53
37 1 0.02
40 23 0.45
ACGTcount: A:0.48, C:0.11, G:0.23, T:0.18
Consensus pattern (38 bp):
AGTTCACAATGAGAAGAACTCATCTAGAAAGAAGAAGA
Found at i:251891 original size:155 final size:150
Alignment explanation
Indices: 251433--251881 Score: 440
Period size: 155 Copynumber: 2.9 Consensus size: 150
251423 TTTCCAGAGA
* * * **
251433 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 AAGTTCACAATGAGAAGAACTTATCT--AGAA-GAAGAAGAAGTTCACAATGAGAAGAGCTTGTT
* * ** * ** * * *
251498 CAACCTTTTGTTTGAATTCATCATTTGATGGATCAA-CATTGCCATGTAGAGTTCATAATGAGAA
63 CAACCTTTTGTCTAAATTCATCATCAGAGGGAT-AAGCATCCCCAGGAAAAGTTCATAATGAGAA
251562 GAACTCATCTGAAGAAAGAAGAAG
127 GAACTCATCTGAAGAAAGAAGAAG
*
251586 AAGTTCACAATGAGAAGAACTTATCTGAAAAAGAAGAAGAAGAAGTTCATAATGAGAAGAGCTTG
1 AAGTTCACAATGAGAAGAACTTATCT-----AGAAGAAGAAGAAGTTCACAATGAGAAGAGCTTG
* ** * * ** * *
251651 TTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAGCATTGCCAGGTAGAGTTCATAATGAGA
61 TTCAACCTTTTGTCTAAATTCATCATCAGAGGGATAAGCATCCCCAGGAAAAGTTCATAATGAGA
251716 AGAACTCATCTGAAGAAAGAAGAAG
126 AGAACTCATCTGAAGAAAGAAGAAG
*
251741 AAGTTCACAATGAGAAGAACTTATCT-GAAGAAGAAGAAGTTCACAATGAGAAGAGTTTGTTCAA
1 AAGTTCACAATGAGAAGAACTTATCTAGAAGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAA
*
251805 CC-TTTG-CTAGATTACATCA-CAGAAGGAGATAAATTGTCATCCCCAGTGGAAAAGTTCATAAT
66 CCTTTTGTCTAAATT-CATCATCAG-AGG-GAT-AA--G-CATCCCCA--GGAAAAGTTCATAAT
* *
251867 TAGAAGAACTAATCT
122 GAGAAGAACTCATCT
251882 CAAAGAAGAA
Statistics
Matches: 261, Mismatches: 22, Indels: 24
0.85 0.07 0.08
Matches are distributed among these distances:
147 6 0.02
148 11 0.04
149 41 0.16
150 1 0.00
152 1 0.00
153 30 0.11
154 1 0.00
155 165 0.63
156 5 0.02
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.26
Consensus pattern (150 bp):
AAGTTCACAATGAGAAGAACTTATCTAGAAGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAA
CCTTTTGTCTAAATTCATCATCAGAGGGATAAGCATCCCCAGGAAAAGTTCATAATGAGAAGAAC
TCATCTGAAGAAAGAAGAAG
Found at i:252048 original size:3 final size:3
Alignment explanation
Indices: 252040--252123 Score: 118
Period size: 3 Copynumber: 28.0 Consensus size: 3
252030 TTTTATTTAT
* *
252040 TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
252088 -TA TATA TTA TTA -TA TATA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
252124 AAAAAATAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.05
3 63 0.86
4 6 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:253354 original size:20 final size:20
Alignment explanation
Indices: 253283--253355 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
253273 TACTCTAGTT
253283 TTATAATTTTATATTTTAATCA
1 TTATAATTTTATA-TTTAAT-A
*
253305 TTCA-AATTTTAT-TTTGATTA
1 TT-ATAATTTTATATTT-AATA
*
253325 TTATTATTTTATATTTAATA
1 TTATAATTTTATATTTAATA
*
253345 TTATATTTTTA
1 TTATAATTTTA
253356 ATTAGTATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
19 1 0.02
20 25 0.60
21 5 0.12
22 10 0.24
23 1 0.02
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (20 bp):
TTATAATTTTATATTTAATA
Found at i:253384 original size:3 final size:3
Alignment explanation
Indices: 253370--253413 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
253360 GTATTTGCAA
* * *
253370 TAT TAT TTT TAT TAT TAT TACT TTT TAT TAT TAT TCT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
253414 TATATAAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 32 0.94
4 2 0.06
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:253385 original size:12 final size:12
Alignment explanation
Indices: 253313--253414 Score: 59
Period size: 12 Copynumber: 8.5 Consensus size: 12
253303 CATTCAAATT
*
253313 TTATTTTGATTA
1 TTATTTTTATTA
*
253325 TTATTATT-TTA
1 TTATTTTTATTA
*
253336 -TATTTAATATTA
1 TTATTT-TTATTA
253348 -TATTTTTAATTA
1 TTATTTTT-ATTA
* ** *
253360 GTATTTGCAATA
1 TTATTTTTATTA
253372 TTATTTTTATTA
1 TTATTTTTATTA
253384 TTATTACTTT-TTA
1 TTATT--TTTATTA
* *
253397 TTATTATTCTTA
1 TTATTTTTATTA
253409 TTATTT
1 TTATTT
253415 ATATAAATAA
Statistics
Matches: 69, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
10 4 0.06
11 7 0.10
12 42 0.61
13 13 0.19
14 3 0.04
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (12 bp):
TTATTTTTATTA
Found at i:253642 original size:20 final size:19
Alignment explanation
Indices: 253617--253658 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
253607 TTATTTTATA
253617 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
253637 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
253656 AAT
1 AAT
253659 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:254509 original size:74 final size:74
Alignment explanation
Indices: 254417--254560 Score: 270
Period size: 74 Copynumber: 1.9 Consensus size: 74
254407 GTATGAACTC
254417 ATCATGTTTCATAATATGAAATAAATCATATATCAAAGTATTAAATCTAGACTTATCACAAGTCT
1 ATCATGTTTCATAATATGAAATAAATCATATATCAAAGTATTAAATCTAGACTTATCACAAGTCT
254482 AGAACGCAT
66 AGAACGCAT
* *
254491 ATCATGTTTCATAATATGAAATGAATCATATATTAAAGTATTAAATCTAGACTTATCACAAGTCT
1 ATCATGTTTCATAATATGAAATAAATCATATATCAAAGTATTAAATCTAGACTTATCACAAGTCT
254556 AGAAC
66 AGAAC
254561 TAAATATACT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (74 bp):
ATCATGTTTCATAATATGAAATAAATCATATATCAAAGTATTAAATCTAGACTTATCACAAGTCT
AGAACGCAT
Found at i:254850 original size:19 final size:19
Alignment explanation
Indices: 254826--254937 Score: 170
Period size: 19 Copynumber: 5.8 Consensus size: 19
254816 CGAAATATAC
254826 ATGCATCGATGCACCCCTA
1 ATGCATCGATGCACCCCTA
254845 ATGCATCGATGCACCCCTA
1 ATGCATCGATGCACCCCTA
**
254864 ATGCATCGATGCATCCTTTA
1 ATGCATCGATGCA-CCCCTA
254884 ATGCATCGATGCACCCCTA
1 ATGCATCGATGCACCCCTA
**
254903 ATGCATCGATGCATCCTTTA
1 ATGCATCGATGCA-CCCCTA
254923 ATGCATCGATGCACC
1 ATGCATCGATGCACC
254938 TACCCAGAAA
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
19 51 0.60
20 34 0.40
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (19 bp):
ATGCATCGATGCACCCCTA
Found at i:254894 original size:39 final size:39
Alignment explanation
Indices: 254826--254937 Score: 199
Period size: 39 Copynumber: 2.9 Consensus size: 39
254816 CGAAATATAC
**
254826 ATGCATCGATGCA-CCCCTAATGCATCGATGCACCCCTA
1 ATGCATCGATGCATCCTTTAATGCATCGATGCACCCCTA
254864 ATGCATCGATGCATCCTTTAATGCATCGATGCACCCCTA
1 ATGCATCGATGCATCCTTTAATGCATCGATGCACCCCTA
254903 ATGCATCGATGCATCCTTTAATGCATCGATGCACC
1 ATGCATCGATGCATCCTTTAATGCATCGATGCACC
254938 TACCCAGAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
38 13 0.18
39 58 0.82
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (39 bp):
ATGCATCGATGCATCCTTTAATGCATCGATGCACCCCTA
Found at i:261653 original size:16 final size:16
Alignment explanation
Indices: 261616--261657 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
261606 CAGATCAAGA
* *
261616 AAACATACATCAATAT
1 AAACATACATCAACAC
261632 AAACATACATCAACAC
1 AAACATACATCAACAC
*
261648 ATACATACAT
1 AAACATACAT
261658 AATACATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (16 bp):
AAACATACATCAACAC
Found at i:262907 original size:195 final size:194
Alignment explanation
Indices: 262575--263147 Score: 713
Period size: 195 Copynumber: 2.9 Consensus size: 194
262565 ACCATTAGAT
* * * * * *
262575 GACCAGATATCTTTAACACAGA-CAAGCAGTGTCGTCTTAAACATCAAATTGACATGATCTCTTC
1 GACCAGATCTCTTCAACACGGATCAA-CAGTGTCGTCTTCAACATCAAATTGACCTGATCTCCTC
* * * * * *
262639 ATCGCGTATGAGCAGTGTCATCTTCAGATAATCAGACTTTCTCATCACAAAGGAACTGTATTGTC
65 AACACGAAGGAGCAGTGTCATCTTCAGAAAATCAGAC-TTCTCATCACAAAGGAACCGTATTGTC
* *
262704 CTCAAATTATCTCCTGATTGACCCGATTTCCTCAACGCGAATGAACAACTTCATTTACCCAAAAA
129 CTCAAATTATCTCCTGATTGACCCGATTTCCTCAACGCGAAGGAACAACATCATTTACCCAAAAA
262769 C
194 C
*
262770 GACCAGATCTCTTCAACACGGATCAACAGTGTCGTCTTCATA-ATCAAATTGACCTAATCTCCTC
1 GACCAGATCTCTTCAACACGGATCAACAGTGTCGTCTTCA-ACATCAAATTGACCTGATCTCCTC
* * *
262834 ACCACGAAGGAGCAGTGTCATTTTCAGAAAATCAGACTTCATCATCACGAAA-GAACCGTATTAT
65 AACACGAAGGAGCAGTGTCATCTTCAGAAAATCAGACTTC-TCATCAC-AAAGGAACCGTATTGT
* * * *
262898 CCTCAAATTATCTCCTGATTAACCCGATTTCCTCAATGCGAAGGAACAACGTCATTTACTCAAAA
128 CCTCAAATTATCTCCTGATTGACCCGATTTCCTCAACGCGAAGGAACAACATCATTTACCCAAAA
*
262963 AT
193 AC
* * * ** * *
262965 GACTATATCTCTTCAACACGGATGAGTAGTGTCATCTTCAACATCAAATTGACCCGATCTCCTCA
1 GACCAGATCTCTTCAACACGGATCAACAGTGTCGTCTTCAACATCAAATTGACCTGATCTCCTCA
* * * * *
263030 ACATGAAGGATCAATGTCATCTTCAGACAATCAGACTTCCTCATCACAAAGGGACCGTATTGT-C
66 ACACGAAGGAGCAGTGTCATCTTCAGAAAATCAGACTT-CTCATCACAAAGGAACCGTATTGTCC
* * *
263094 TCCAAATTATCTCTTGATTGACCCGATTTCCTCAACTCAAAGGAACAACATCAT
130 T-CAAATTATCTCCTGATTGACCCGATTTCCTCAACGCGAAGGAACAACATCAT
263148 CTTCAACAAA
Statistics
Matches: 327, Mismatches: 43, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
194 9 0.03
195 310 0.95
196 8 0.02
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.28
Consensus pattern (194 bp):
GACCAGATCTCTTCAACACGGATCAACAGTGTCGTCTTCAACATCAAATTGACCTGATCTCCTCA
ACACGAAGGAGCAGTGTCATCTTCAGAAAATCAGACTTCTCATCACAAAGGAACCGTATTGTCCT
CAAATTATCTCCTGATTGACCCGATTTCCTCAACGCGAAGGAACAACATCATTTACCCAAAAAC
Found at i:263436 original size:20 final size:20
Alignment explanation
Indices: 263411--263453 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
263401 ACACCAATTC
263411 CACCAACTCCACTAATGTCG
1 CACCAACTCCACTAATGTCG
* *
263431 CACCAACTCCATTAATGTTG
1 CACCAACTCCACTAATGTCG
263451 CAC
1 CAC
263454 ACCACCCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.37, G:0.09, T:0.23
Consensus pattern (20 bp):
CACCAACTCCACTAATGTCG
Found at i:264679 original size:17 final size:17
Alignment explanation
Indices: 264657--264692 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
264647 GTAAATAAGA
*
264657 AAATTTTATTGTGAAGG
1 AAATTTGATTGTGAAGG
*
264674 AAATTTGATTGTGAGGG
1 AAATTTGATTGTGAAGG
264691 AA
1 AA
264693 GTCTACGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.28, T:0.36
Consensus pattern (17 bp):
AAATTTGATTGTGAAGG
Found at i:280557 original size:66 final size:66
Alignment explanation
Indices: 280434--280559 Score: 182
Period size: 66 Copynumber: 1.9 Consensus size: 66
280424 CATTAAAAAG
** * *
280434 CAATTAAGGGTTGAAATACTCAGGCCAATGTAAAACTTTGACCTTACTTCGTTTATATATATTAA
1 CAATTAAGGGTTGAAATACTCAGGAAAATGTAAAACTTTGACCTTACTTCATATATATATATTAA
280499 A
66 A
* *
280500 CAATTAAGGG-TGAAATATTCAGGGAAAATGTAAAACTTTGACCTTACTTTATATATATAT
1 CAATTAAGGGTTGAAATACTCA-GGAAAATGTAAAACTTTGACCTTACTTCATATATATAT
280560 GTGTGTGTGT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 10 0.19
66 43 0.81
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (66 bp):
CAATTAAGGGTTGAAATACTCAGGAAAATGTAAAACTTTGACCTTACTTCATATATATATATTAA
A
Found at i:285728 original size:31 final size:31
Alignment explanation
Indices: 285692--285754 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
285682 GATCATTATT
* *
285692 TAAATTCA-AATATTTAATTCAAT-TATACTCA
1 TAAATT-ATAATAATTAATTAAATATATA-TCA
285723 TAAATTATAATAATTAATTAAATATATATCA
1 TAAATTATAATAATTAATTAAATATATATCA
285754 T
1 T
285755 CCATTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 1 0.04
31 23 0.82
32 4 0.14
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (31 bp):
TAAATTATAATAATTAATTAAATATATATCA
Found at i:288421 original size:36 final size:36
Alignment explanation
Indices: 288374--288442 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
288364 AATACTTTGT
288374 CAAAGTCAACCACTAAGAAATATCATCATCCGCTGA
1 CAAAGTCAACCACTAAGAAATATCATCATCCGCTGA
288410 CAAAGTCAACCACTAAGAAATATCATCATCCGC
1 CAAAGTCAACCACTAAGAAATATCATCATCCGC
288443 CTCAACAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (36 bp):
CAAAGTCAACCACTAAGAAATATCATCATCCGCTGA
Found at i:292219 original size:21 final size:20
Alignment explanation
Indices: 292192--292290 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
292182 AATCAGTTTC
292192 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
292213 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
292234 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
292254 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
292275 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
292291 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:292306 original size:40 final size:40
Alignment explanation
Indices: 292257--292411 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
292247 CGATTTTCCA
* ** *
292257 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
292297 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
292337 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
292377 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
292412 TATTTAAAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 62 0.65
41 33 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:292319 original size:20 final size:20
Alignment explanation
Indices: 292257--292410 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
292247 CGATTTTCCA
* ** *
292257 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
292277 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
292297 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
292317 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
292337 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
292357 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
292377 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
292398 AAATCGCAACGCG
1 AAATCGCAACGCG
292411 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.82
21 17 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:292832 original size:33 final size:33
Alignment explanation
Indices: 292793--292863 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
292783 TTCACTTAGA
*
292793 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
292826 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
292859 TTTCA
1 TTTCA
292864 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:292969 original size:21 final size:20
Alignment explanation
Indices: 292943--293032 Score: 110
Period size: 21 Copynumber: 4.5 Consensus size: 20
292933 TGCAGAAGAG
292943 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
292964 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
292984 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
293005 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
293024 TCGCAACGA
1 TCGCAACGA
293033 AAGAATCGCA
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
19 17 0.29
20 16 0.28
21 25 0.43
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:293000 original size:41 final size:40
Alignment explanation
Indices: 292942--293020 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 40
292932 TTGCAGAAGA
*
292942 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGA-AATGACT
*
292983 GTCGCAACGAGAGAAATGAAAATCGCAACGCGAAATGA
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAAATGA
293021 AAATCGCAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 5 0.14
41 31 0.86
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (40 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAAATGACT
Found at i:293079 original size:19 final size:19
Alignment explanation
Indices: 293057--293121 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
293047 GAAACCAAAA
*
293057 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
293076 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
293090 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
293109 TCGCGTTGCGATT
1 TCGCGTTGCGATT
293122 CTCTCGTTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
16 3 0.08
17 3 0.08
19 22 0.58
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:293098 original size:14 final size:14
Alignment explanation
Indices: 293079--293135 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
293069 TTTCATTTCG
293079 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
293093 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
293112 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
293126 CGTTGCGATT
1 CGTTGCGATT
293136 TTCATTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:293104 original size:33 final size:33
Alignment explanation
Indices: 293062--293143 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
293052 CAAAATCGCA
293062 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
293095 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
293128 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
293144 AACCAAAAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:295001 original size:93 final size:93
Alignment explanation
Indices: 294842--295682 Score: 1666
Period size: 93 Copynumber: 9.1 Consensus size: 93
294832 TAGATTGCTT
*
294842 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
294907 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
294935 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
295000 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
295028 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
295093 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
295121 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
295186 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
295214 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
295279 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
295307 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
295372 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
295400 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
295465 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
295493 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
295558 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
295586 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
295651 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
295678 AGTAA
1 AGTAA
295683 TGCAATCCAT
Statistics
Matches: 747, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
92 6 0.01
93 741 0.99
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:295770 original size:19 final size:19
Alignment explanation
Indices: 295730--295858 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
295720 TAGTTTACTT
* *
295730 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
295750 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
295769 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
295788 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
295802 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
295821 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
295835 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
295854 TCGCA
1 TCGCA
295859 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:295809 original size:33 final size:32
Alignment explanation
Indices: 295766--295858 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
295756 CGCGAAACCA
**
295766 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
295798 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
295831 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
295859 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:295856 original size:52 final size:52
Alignment explanation
Indices: 295730--295858 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
295720 TAGTTTACTT
**
295730 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
295782 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
295835 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
295859 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:295876 original size:19 final size:19
Alignment explanation
Indices: 295854--295988 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
295844 GAAACCAAAA
*
295854 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
295873 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
295889 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
295906 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
295922 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
295939 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
295958 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
295978 TCGTGTTGCGA
1 TCGCGTTGCGA
295989 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:295895 original size:14 final size:14
Alignment explanation
Indices: 295876--295932 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
295866 TTTCATTTCG
295876 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
295890 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
295907 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
295923 CGTTGCGATT
1 CGTTGCGATT
295933 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:295901 original size:33 final size:33
Alignment explanation
Indices: 295859--295951 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
295849 CAAAATCGCA
*
295859 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
295892 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
295925 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
295952 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:297953 original size:14 final size:14
Alignment explanation
Indices: 297911--297947 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
297901 GATTGTTTAA
*
297911 TTGATTTGTAAAAG
1 TTGATTTGTAAAAT
*
297925 ATGATTTGTAAAAT
1 TTGATTTGTAAAAT
297939 TTGATTTGT
1 TTGATTTGT
297948 GTAATTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAT
Found at i:298078 original size:19 final size:19
Alignment explanation
Indices: 298054--298150 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
298044 AAAATTGACT
298054 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
298073 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
298091 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
298105 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
298124 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
298144 ATCGCAA
1 ATCGCAA
298151 CGGGAGAATC
Statistics
Matches: 69, Mismatches: 2, Indels: 13
0.82 0.02 0.15
Matches are distributed among these distances:
13 1 0.01
14 9 0.13
16 4 0.06
18 10 0.14
19 29 0.42
20 16 0.23
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:298130 original size:51 final size:53
Alignment explanation
Indices: 298054--298169 Score: 209
Period size: 51 Copynumber: 2.2 Consensus size: 53
298044 AAAATTGACT
298054 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATG-AAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
298105 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
298158 ATCGCAATGCGA
1 ATCGCAATGCGA
298170 TTTTAATTTC
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
51 29 0.47
52 6 0.10
53 27 0.44
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:298187 original size:19 final size:19
Alignment explanation
Indices: 298159--298361 Score: 203
Period size: 19 Copynumber: 11.7 Consensus size: 19
298149 AACGGGAGAA
* *
298159 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
298178 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
298194 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
298211 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
298230 TCGCATTGCGA--TT-ATC
1 TCGCATTGCGATTTTCATT
298246 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
298263 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
298282 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
298298 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
298315 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
298333 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
298349 TCGCATTGCGATT
1 TCGCATTGCGATT
298362 CTCTCGTTGC
Statistics
Matches: 153, Mismatches: 10, Indels: 42
0.75 0.05 0.20
Matches are distributed among these distances:
14 29 0.19
16 23 0.15
17 19 0.12
18 3 0.02
19 67 0.44
20 12 0.08
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:298222 original size:52 final size:52
Alignment explanation
Indices: 298159--298333 Score: 314
Period size: 52 Copynumber: 3.3 Consensus size: 52
298149 AACGGGAGAA
* *
298159 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
298211 TCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
298263 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
298315 TCCGCATTGCGATTTTCAT
1 T-CGCATTGCGATTTTCAT
298334 GTTGGGATTT
Statistics
Matches: 118, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 101 0.86
53 17 0.14
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:298383 original size:33 final size:33
Alignment explanation
Indices: 298165--298375 Score: 223
Period size: 33 Copynumber: 6.2 Consensus size: 33
298155 AGAATCGCAA
*
298165 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
298198 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
298236 TGCGATTATCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
298269 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
298302 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
*
298336 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
298369 TGCGATT
1 TGCGATT
298376 GTAATTTCCG
Statistics
Matches: 147, Mismatches: 17, Indels: 28
0.77 0.09 0.15
Matches are distributed among these distances:
31 9 0.06
32 6 0.04
33 71 0.48
34 29 0.20
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.06
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:300890 original size:24 final size:24
Alignment explanation
Indices: 300856--300902 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
300846 CTGAAACATC
300856 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
300880 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
300903 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:301613 original size:20 final size:20
Alignment explanation
Indices: 301585--301854 Score: 290
Period size: 20 Copynumber: 13.5 Consensus size: 20
301575 AAATTTCAGT
* * *
301585 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
301605 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
301625 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
301645 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
301665 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
301685 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
301705 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
301725 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
301745 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
301765 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
301785 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
301805 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
301825 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
301845 GTTGCGATTT
1 GTTGCGATTT
301855 TGGAAAATCG
Statistics
Matches: 220, Mismatches: 28, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 219 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:301871 original size:21 final size:21
Alignment explanation
Indices: 301841--301923 Score: 85
Period size: 21 Copynumber: 4.0 Consensus size: 21
301831 ATTTTCATAT
*
301841 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
301862 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
**
301883 TCGCATTGCGATTTTCAAAAA
1 TCGCATTGCGATTTTGGAAAA
*
301904 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
301924 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:301914 original size:42 final size:43
Alignment explanation
Indices: 301821--301919 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
301811 ATTTATGTGT
* **
301821 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTCAAAAA
**
301862 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTTCAAAAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTCAAAAA
*
301904 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
301920 GAAACTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
41 8 0.17
42 36 0.77
43 3 0.06
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTCAAAAA
Found at i:305093 original size:45 final size:46
Alignment explanation
Indices: 305028--305127 Score: 193
Period size: 45 Copynumber: 2.2 Consensus size: 46
305018 TTTTGTTAAG
305028 AAAAATATTTTTAAACCAAAAGAATATTTCAATAAATATATTTTTT
1 AAAAATATTTTTAAACCAAAAGAATATTTCAATAAATATATTTTTT
305074 -AAAATATTTTTAAACCAAAAGAATATTTCAATAAATATATTTTTT
1 AAAAATATTTTTAAACCAAAAGAATATTTCAATAAATATATTTTTT
305119 AAAAATATT
1 AAAAATATT
305128 CAACTAACGG
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 45 0.85
46 8 0.15
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (46 bp):
AAAAATATTTTTAAACCAAAAGAATATTTCAATAAATATATTTTTT
Found at i:306098 original size:174 final size:174
Alignment explanation
Indices: 305800--306157 Score: 565
Period size: 174 Copynumber: 2.1 Consensus size: 174
305790 CCCATCAGCC
*
305800 CCAGAATAAGAACTTGCTGGGATGACACCGATATCGCTGCTTTCAACACCAGTGGTTACTTCCAT
1 CCAGAAT-AGAACTTGCTGGGATGACACCGATATCGCTGCTTTCAACACCAGTGGTTACTCCCAT
* * * * *
305865 CTGGCCCGTCTCATTTCCTCGAAGAGAACAAGTTGATCCATGTGGAGTAGAAGAGGCAAC-GAGA
65 CTGGACCGTCTCATTTCCACGAAAAGAACAAGTTGATCCATGTAGAGCAGAAGAGGCAACAG-GA
*
305929 TCATTGTTGGCATTACAAGAATTAGGGACCAAATCATCGCCTTCGG
129 TCATTGTTGGCATTACAAGAATTAGGGACCAAACCATCGCCTTCGG
* *
305975 TCAGAATAGAACTTGCTGGGATGACACCGATATCGCTGCTTTCAACACCAGTGGTTCCTCCCATC
1 CCAGAATAGAACTTGCTGGGATGACACCGATATCGCTGCTTTCAACACCAGTGGTTACTCCCATC
* * * *
306040 TGGACTGTCTCATTTCCAGGAAAAGAACATGTTGATCCATGTAGTGCAGAAGAGGCAACAGGATC
66 TGGACCGTCTCATTTCCACGAAAAGAACAAGTTGATCCATGTAGAGCAGAAGAGGCAACAGGATC
*
306105 ATTGTTGGCATTACAAGAATTAGGGACCAAACCATTGCCTTCGG
131 ATTGTTGGCATTACAAGAATTAGGGACCAAACCATCGCCTTCGG
306149 CCAGAATAG
1 CCAGAATAG
306158 CAGTCGGTTG
Statistics
Matches: 167, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
174 160 0.96
175 7 0.04
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (174 bp):
CCAGAATAGAACTTGCTGGGATGACACCGATATCGCTGCTTTCAACACCAGTGGTTACTCCCATC
TGGACCGTCTCATTTCCACGAAAAGAACAAGTTGATCCATGTAGAGCAGAAGAGGCAACAGGATC
ATTGTTGGCATTACAAGAATTAGGGACCAAACCATCGCCTTCGG
Found at i:313725 original size:22 final size:22
Alignment explanation
Indices: 313698--313739 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
313688 AAACCATTCA
313698 GGGGGGAATCGGTACCCTCTTG
1 GGGGGGAATCGGTACCCTCTTG
*
313720 GGGGGGAATCGGTTCCCTCT
1 GGGGGGAATCGGTACCCTCT
313740 GAGTAATCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.24, G:0.40, T:0.24
Consensus pattern (22 bp):
GGGGGGAATCGGTACCCTCTTG
Found at i:316433 original size:23 final size:23
Alignment explanation
Indices: 316404--316447 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
316394 TTCCCCTAGT
316404 GGGGAATCGGTTCCCCTTCAAAA
1 GGGGAATCGGTTCCCCTTCAAAA
316427 GGGGAATCGGTTCCCCTTCAA
1 GGGGAATCGGTTCCCCTTCAA
316448 GGGGGTATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.23
Consensus pattern (23 bp):
GGGGAATCGGTTCCCCTTCAAAA
Done.