Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_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: 8249038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 29 of 38
Found at i:5826760 original size:21 final size:21
Alignment explanation
Indices: 5826729--5826804 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
5826719 ATAGTCAGTA
*
5826729 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
** * **
5826750 TCATGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
*
5826770 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
5826791 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
5826805 ACTTATTCGC
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
20 14 0.34
21 27 0.66
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.42
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:5826778 original size:20 final size:20
Alignment explanation
Indices: 5826755--5826821 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
5826745 CCAATTCATG
5826755 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
* ** *
5826775 TTGCGATTTTCCCAATTCGCG
1 TTGCGA-TTTACTTATTCGCA
5826796 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
5826816 TTGCGA
1 TTGCGA
5826822 ATTGGGAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (20 bp):
TTGCGATTTACTTATTCGCA
Found at i:5827273 original size:23 final size:23
Alignment explanation
Indices: 5827201--5827265 Score: 130
Period size: 23 Copynumber: 2.8 Consensus size: 23
5827191 AATAACATAT
5827201 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
5827224 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
5827247 TAGGTAGCGCTTATATAAT
1 TAGGTAGCGCTTATATAAT
5827266 AAAATAGGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATGTAA
Found at i:5827777 original size:200 final size:196
Alignment explanation
Indices: 5827350--5827875 Score: 680
Period size: 200 Copynumber: 2.6 Consensus size: 196
5827340 GCGCTTATAT
* *
5827350 TGACCTATTTTCTAAGT-AAACCGGTATATTTATACCGGTAACATTGCAAATTTACCTATTACAT
1 TGACCTATTTTCTAA-TAAAACCGGTATATTTATACAGGT-ACATTGTAAATTTACCTATTACAT
* **
5827414 TATAATTATCGGTTTCGATGTTTTTTGGATCGATACAATTT--TAAATGTATCGACACTTTATGC
64 TATAATTATCGGTTTCGATG-TTTTTGGATCGATAC-TTTTAATAAATGTATCGACACTTTATAT
* * **
5827477 ATGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAAAGTGTTGATACA
127 ATGCACCCCGTTGGGCATTCATTATGGAAAAAAGTATCGACACAAACTTAAAAAGTGTCAATACA
*
5827542 TTATT
192 TTATC
* * * * *
5827547 TAGACCTATTTTCTCATAAAACCGGTATATTTCTATCGGGTACATTGTAAATTTACTTATCACAT
1 T-GACCTATTTTCTAATAAAACCGGTATATTTATA-CAGGTACATTGTAAATTTACCTATTACAT
* * *
5827612 TGTAATTATCGGTTTCGATGTTTGTAGGATCGATACTTTTAATAAATGTATCGACACTTTATATG
64 TATAATTATCGGTTTCGATGTTT-TTGGATCGATACTTTTAATAAATGTATCGACACTTTATATA
* * ** *
5827677 TGCACCCCGTTTGGCATTCATTATGGACAAAAAGTATCGACACAAATTTAAATGGTGTCAATACT
128 TGCACCCCGTTGGGCATTCATTATGGA-AAAAAGTATCGACACAAACTTAAAAAGTGTCAATACA
5827742 TTATGC
192 TTAT-C
* * *
5827748 TGACCTATTTTCTTATAAAATCGGTATATTTATACTAGTTACATTGTAAATTTACCTATTACATT
1 TGACCTATTTTCTAATAAAACCGGTATATTTATAC-AGGTACATTGTAAATTTACCTATTACATT
* *
5827813 ATAATTATCGGTTTTGATGTTATTTGGATCGATACTTTTAATAAATGTATCGACAGTTTATAT
65 ATAATTATCGGTTTCGATGTT-TTTGGATCGATACTTTTAATAAATGTATCGACACTTTATAT
5827876 TCTGGACAAT
Statistics
Matches: 286, Mismatches: 33, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
197 8 0.03
198 80 0.28
199 49 0.17
200 147 0.51
201 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (196 bp):
TGACCTATTTTCTAATAAAACCGGTATATTTATACAGGTACATTGTAAATTTACCTATTACATTA
TAATTATCGGTTTCGATGTTTTTGGATCGATACTTTTAATAAATGTATCGACACTTTATATATGC
ACCCCGTTGGGCATTCATTATGGAAAAAAGTATCGACACAAACTTAAAAAGTGTCAATACATTAT
C
Found at i:5828513 original size:19 final size:19
Alignment explanation
Indices: 5828472--5828516 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
5828462 ATTCACATAA
* **
5828472 AAAATTTTAAATCGTATGT
1 AAAATTATAAATCGTATAC
*
5828491 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
5828510 AAAATTA
1 AAAATTA
5828517 ACCCTACATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:5830715 original size:199 final size:198
Alignment explanation
Indices: 5830115--5831279 Score: 1407
Period size: 199 Copynumber: 5.9 Consensus size: 198
5830105 CAAATTATTT
*
5830115 AAAAAGTATCGACACAAATTTAAAAGTGTCGATACATTATGTTGACCTATTCTCTCATAAAACCG
1 AAAAAGTATCGACACAAATCTAAAAGTGTCGATACATTATGTTGACCTATTCTCTCATAAAACCG
** *
5830180 GTATATTTATACC-GATTACATTGTAAATTTACCTATTACGGTATAATTATCGGTTTCGATATTT
66 GTATATTTATACCAG-TTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * * *
5830244 TTGGGATCGATA-GTTTTAATAAATGTATTGACACATTT-TGCCTGCACCCCATTTGGCATTCAT
130 TTGGGATCGATACTTTTTAA-AAATGTATCGACAC-TTTATGCGTGCA-CCCGTTTGGCATTCAT
5830307 TCTGGAC
192 TCTGGAC
* * * *
5830314 AAAATGTATCGACATAAATCTAAAACGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACC
1 AAAAAGTATCGACACAAATCTAAAA-GTGTCGATACATTATGTTGACCTATTCTCTCATAAAACC
* * ** * *
5830379 GGTAAATTTATACCAGTTAAATTGTAAATTTATGTATTACATTATAATAATAGGTTTCGATGTTT
65 GGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
** * * * * * *
5830444 TTGGGATCGATACAATTT-CAAATGTATCGACACTTTTTACCTACACCTCGGTTGGCATTCATTC
130 TTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACC-CGTTTGGCATTCATTC
5830508 TGGAC
194 TGGAC
* *
5830513 -AAAATTATCGACACAAATCTAAAACGTGTCGATACATTATGTTCACCTATT-TGCTCATAAAAC
1 AAAAAGTATCGACACAAATCTAAAA-GTGTCGATACATTATGTTGACCTATTCT-CTCATAAAAC
* * **
5830576 CGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAATTTCGATGTT
64 CGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
*
5830641 TTTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCAACCCTTTTGGCATTCATT
129 TTTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGC-ACCCGTTTGGCATTCATT
* *
5830706 TTAGAC
193 CTGGAC
* *
5830712 AAAAAGTATTGACACAAAT-TACATAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAAC
1 AAAAAGTATCGACACAAATCTA-A-AAGTGTCGATACATTATGTTGACCTATTCTCTCATAAAAC
* * * *
5830776 CGATATAGTTATACTAGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTT
64 CGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
* * * * ** *
5830841 TCTGGGATCGATACTTTTTATAAATGTATCGACACTTAATGCGTTCACCATTTTGGGATTCATTC
129 TTTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCCGTTTGGCATTCATTC
5830906 TGGAC
194 TGGAC
* * *
5830911 AAAAAGTATCGACACAGAAT-TCAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAAC
1 AAAAAGTATCGACACA-AATCT-AAAAGTGTCGATACATTATGTTGACCTATTCTCTCATAAAAC
* * ** * * * *
5830975 CGATATATTTATACC-GATTATATTACAAAATTACCTATTACATTATAATTATGGGTTTTGATGG
64 CGGTATATTTATACCAG-TTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGT
* * * * *
5831039 TTTTGGGATCGATACTTTTTATAAATGTATCGACAATGTATGGGCGCACCACGTTTGGCATTCAT
128 TTTTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACC-CGTTTGGCATTCAT
*
5831104 TTTGGAC
192 TCTGGAC
* * * * * * *
5831111 AAAAAATATCAACGCAAATTCTACAAGTGTCGATACATTATGTAT-ATCTATT-TCTCAAAAAAT
1 AAAAAGTATCGACACAAA-TCTAAAAGTGTCGATACATTATGT-TGACCTATTCTCTCATAAAAC
* * * *
5831174 CGGTATATGTATACCAGTTACATTGTAAATTTACCTATTATATTATAATTTTCGATTTCGATGTT
64 CGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
*
5831239 TTTGGGATCGATACTTTTTAAACATGTATCGACACTTTATG
129 TTTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATG
5831280 GGAAACTTTA
Statistics
Matches: 834, Mismatches: 112, Indels: 40
0.85 0.11 0.04
Matches are distributed among these distances:
197 1 0.00
198 138 0.17
199 368 0.44
200 318 0.38
201 9 0.01
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (198 bp):
AAAAAGTATCGACACAAATCTAAAAGTGTCGATACATTATGTTGACCTATTCTCTCATAAAACCG
GTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
TGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCCGTTTGGCATTCATTCTG
GAC
Found at i:5831300 original size:15 final size:15
Alignment explanation
Indices: 5831280--5831319 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
5831270 ACACTTTATG
5831280 GGAAACTTTAAGTTT
1 GGAAACTTTAAGTTT
5831295 GGAAACTTTAAGTTT
1 GGAAACTTTAAGTTT
5831310 GGAAACTTTA
1 GGAAACTTTA
5831320 TGTGTCAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (15 bp):
GGAAACTTTAAGTTT
Found at i:5831659 original size:30 final size:30
Alignment explanation
Indices: 5831625--5831690 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
5831615 AAACTCAAAT
5831625 TGAAATTGAAATTCAAACTCCAATTACATA
1 TGAAATTGAAATTCAAACTCCAATTACATA
5831655 TGAAATTGAAATTCAAACTCCAATTACATA
1 TGAAATTGAAATTCAAACTCCAATTACATA
5831685 TGAAAT
1 TGAAAT
5831691 GAATTTGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (30 bp):
TGAAATTGAAATTCAAACTCCAATTACATA
Found at i:5834851 original size:181 final size:182
Alignment explanation
Indices: 5834547--5835158 Score: 892
Period size: 182 Copynumber: 3.4 Consensus size: 182
5834537 GTAGTGCTTT
* *
5834547 ACCGGTTTTGTCATATTTTTACATGTTATATCGTTGTGGACCGATACATTGTTATAAAGTATCGA
1 ACCGGTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGA
* * *
5834612 TACTTTATAGGCGCTAAAATTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGT
66 CACTTTATGGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGT
* * * *
5834677 ATCGACACTTTAAATATATCTGATCCCTCTATATCGG-TTTGTCCTTTATAG
131 ATCGACACTTTCAATATATCCGATACCTCTATATCGGTTTTGTCATTTATAG
* * *
5834728 ACCGGTTTTGTCATATTTTTACCTGTTATATCGTTTTGGATCGATATATTTTTATAAAGTATCGA
1 ACCGGTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGA
*
5834793 CACTTTATGGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCTATACTTATATTAAAGT
66 CACTTTATGGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGT
* * * *
5834858 ATCGACACTTTCAATATATCCGGTTA-CTCTATATCGGTTTTATCTTTTAGAG
131 ATCGACACTTTCAATATATCC-GATACCTCTATATCGGTTTTGTCATTTATAG
* * *
5834910 ACCGATTTTGTCATATTTTTACTTGTTATATCGTTGTGGATCGATACATTATTATAAAGTATC-A
1 ACCGGTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGA
*
5834974 GCACTTTATGGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTTTCGATACTTATATTAAAG
66 -CACTTTATGGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAG
* * *
5835039 TATCGACACTTTCAATATATCCGATACCGCTTTA-CTGGTTTTGTCATTTCGT-G
130 TATCGACACTTTCAATATATCCGATACCTCTATATC-GGTTTTGTCATTT-ATAG
* * * * *
5835092 ATCGGTTTTGTCATATTTTTACATGTTATATTGATGTGAATCGATACAGTTTTATAAAGTATCGA
1 ACCGGTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGA
5835157 CA
66 CA
5835159 TATACCGCCA
Statistics
Matches: 386, Mismatches: 38, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
181 156 0.40
182 229 0.59
183 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (182 bp):
ACCGGTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGA
CACTTTATGGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGT
ATCGACACTTTCAATATATCCGATACCTCTATATCGGTTTTGTCATTTATAG
Found at i:5844447 original size:19 final size:19
Alignment explanation
Indices: 5844382--5844525 Score: 199
Period size: 19 Copynumber: 7.7 Consensus size: 19
5844372 AATAAATTAG
*
5844382 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
5844401 TTTTCGCATTGCGA--TT-A
1 -TTTCGCATTGCGATTTTCA
**
5844418 ACTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
5844435 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
5844454 TTTCGCATTACGATTTTCA
1 TTTCGCATTGCGATTTTCA
5844473 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
5844492 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
5844511 TTTCCGCATTGCGAT
1 TTT-CGCATTGCGAT
5844526 AGTCTGTTTT
Statistics
Matches: 111, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
14 6 0.05
16 5 0.05
17 5 0.05
18 2 0.02
19 70 0.63
20 23 0.21
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:5844646 original size:14 final size:14
Alignment explanation
Indices: 5844627--5844663 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5844617 CATCAATTAA
5844627 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
5844641 ACAAATCATCTTTT
1 ACAAATCAACATTT
5844655 ACAAATCAA
1 ACAAATCAA
5844664 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:5846081 original size:42 final size:42
Alignment explanation
Indices: 5846005--5846127 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
5845995 GTGAATCGGG
* ** *
5846005 CTCTTGAATGGTGGGA-GGGACCTCTTC-AACAATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGAATGACAGGGGC
*
5846047 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGACAGGGGC
* * * * * *
5846089 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGACAGG
5846128 TGAGTCGGGC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 2 0.03
42 61 0.91
43 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGACAGGGGC
Found at i:5848129 original size:20 final size:20
Alignment explanation
Indices: 5848106--5848157 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
5848096 ATGAAAATCG
5848106 CAACGAGAGAATGACTATCA
1 CAACGAGAGAATGACTATCA
* *
5848126 CAACGCGAAAATGACTATCA
1 CAACGAGAGAATGACTATCA
5848146 CAACGAGAGAAT
1 CAACGAGAGAAT
5848158 CGCAACGCGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.13
Consensus pattern (20 bp):
CAACGAGAGAATGACTATCA
Found at i:5848179 original size:19 final size:19
Alignment explanation
Indices: 5848155--5848246 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 19
5848145 ACAACGAGAG
5848155 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
5848174 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
* *
5848188 AATCGCAACGCAAAATTAA
1 AATCGCAACGCGAAATGAA
*
5848207 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
5848221 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
5848240 AATCGCA
1 AATCGCA
5848247 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
14 19 0.35
15 2 0.04
16 3 0.05
17 3 0.05
18 2 0.04
19 26 0.47
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:5848183 original size:33 final size:33
Alignment explanation
Indices: 5848093--5848246 Score: 191
Period size: 33 Copynumber: 4.5 Consensus size: 33
5848083 TCTTTTGGTT
*
5848093 GAAATGAAAATCGCAACGAGAGAATGACTATCACAACGC
1 GAAATGAAAATCGCAAC--GAG-A-GA--ATCGCAACGC
** *
5848132 GAAAATGACTATCACAACGAGAGAATCGCAACGC
1 G-AAATGAAAATCGCAACGAGAGAATCGCAACGC
5848166 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
5848199 AAAATTAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
5848232 GAAATGAAAATCGCA
1 GAAATGAAAATCGCA
5848247 TTGCGATTTT
Statistics
Matches: 103, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
33 73 0.71
34 10 0.10
36 2 0.02
37 1 0.01
38 3 0.03
39 1 0.01
40 13 0.13
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:5848193 original size:14 final size:14
Alignment explanation
Indices: 5848146--5848230 Score: 53
Period size: 14 Copynumber: 5.4 Consensus size: 14
5848136 ATGACTATCA
5848146 CAACGAGAGAATCG
1 CAACGAGAGAATCG
*
5848160 CAACGCGAAATGAAAATCG
1 CAA--CG--A-GAGAATCG
5848179 CAACGAGAGAATCG
1 CAACGAGAGAATCG
* *
5848193 CAACGCAAAATTAAAATCG
1 CAACG----A-GAGAATCG
5848212 CAACGAGAGAATCG
1 CAACGAGAGAATCG
5848226 CAACG
1 CAACG
5848231 CGAAATGAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 20
0.68 0.07 0.25
Matches are distributed among these distances:
14 26 0.47
15 2 0.04
16 2 0.04
17 2 0.04
18 2 0.04
19 21 0.38
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.09
Consensus pattern (14 bp):
CAACGAGAGAATCG
Found at i:5848281 original size:19 final size:19
Alignment explanation
Indices: 5848242--5848321 Score: 61
Period size: 19 Copynumber: 4.1 Consensus size: 19
5848232 GAAATGAAAA
* **
5848242 TCGCATTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
5848261 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
5848280 TCTCTTGTTGCGATAGTCATTT
1 TCGC--GTTGCGATTTTCA-TT
* *
5848302 TTGTGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5848321 T
1 T
5848322 TCATGTTGCA
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
19 22 0.47
20 11 0.23
21 11 0.23
22 3 0.06
ACGTcount: A:0.11, C:0.16, G:0.21, T:0.51
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5848291 original size:21 final size:20
Alignment explanation
Indices: 5848265--5848336 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
5848255 TTGGTTTCGC
5848265 GTTGCGATTTTCATTTCTCTT
1 GTTGCGATTTTCATTT-TCTT
**
5848286 GTTGCGATAGTCATTTT-TGT
1 GTTGCGATTTTCATTTTCT-T
*
5848306 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCTT
*
5848326 GTTGCAATTTT
1 GTTGCGATTTT
5848337 AAGTTTAGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.02
20 28 0.65
21 14 0.33
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.54
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCTT
Found at i:5848923 original size:20 final size:20
Alignment explanation
Indices: 5848898--5849111 Score: 205
Period size: 20 Copynumber: 10.6 Consensus size: 20
5848888 CTTTAAAAAT
5848898 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5848918 CGCGTTGCGATTTTACGTATT
1 CGCGTTGCGA-TTTACGGATA
** *
5848939 TTCGTTGCGGTTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * * *
5848959 CGCATTTCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* * **
5848979 CTCGTTGTGATTTACATATA
1 CGCGTTGCGATTTACGGATA
* *
5848999 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
5849019 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5849039 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
5849059 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
5849080 CGCATTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
5849101 CTCGTTGCGAT
1 CGCGTTGCGAT
5849112 AGTCAGAATC
Statistics
Matches: 154, Mismatches: 35, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
20 104 0.68
21 50 0.32
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:5849133 original size:41 final size:41
Alignment explanation
Indices: 5848900--5849111 Score: 311
Period size: 41 Copynumber: 5.2 Consensus size: 41
5848890 TTAAAAATCG
*
5848900 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
5848941 CGTTGCGGTTTACGGATACGCATTTCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* **
5848981 CGTTGTGATTTACATATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
5849021 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
5849062 CGTTGCGATTTACGGATACGCATTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
5849103 CGTTGCGAT
1 CGTTGCGAT
5849112 AGTCAGAATC
Statistics
Matches: 152, Mismatches: 18, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
40 70 0.46
41 82 0.54
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:5849145 original size:20 final size:20
Alignment explanation
Indices: 5849120--5849172 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
5849110 ATAGTCAGAA
*
5849120 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
*
5849140 TTGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
5849160 TCGCGTTGCGATT
1 TCGCGTTGCGATT
5849173 ATGGAAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:5849164 original size:40 final size:39
Alignment explanation
Indices: 5848900--5849172 Score: 187
Period size: 40 Copynumber: 6.8 Consensus size: 39
5848890 TTAAAAATCG
* * *
5848900 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTTT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTATGTA--CT
* * * * *
5848941 CGTTGCGGTTTACGGATACGCATTTCGA-TTTACGTATTCT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTATGTA--CT
* * *
5848981 CGTTGTGATTTACATATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTATGTA--CT
* * *
5849021 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTATGTA--CT
* * *
5849062 CGTTGCGATTTACGGATACGCATTGCGATTTTACGGATACT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTA-TG-TACT
* *
5849103 CGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATGT-TT
1 CGTTGCGAT-TTACAGATA-CGCGTTGCGATTT-TATGTACT
* * *
5849142 GCGTTGCGATTTTCATATTCGCGTTGCGATT
1 -CGTTGCGATTTACAGATACGCGTTGCGATT
5849173 ATGGAAAATC
Statistics
Matches: 198, Mismatches: 25, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
39 2 0.01
40 96 0.48
41 94 0.47
42 4 0.02
43 2 0.01
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (39 bp):
CGTTGCGATTTACAGATACGCGTTGCGATTTTATGTACT
Found at i:5849271 original size:20 final size:20
Alignment explanation
Indices: 5849224--5849275 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
5849214 TCTTCATAAT
5849224 TGCGTTGCGATTCTGGGAAC
1 TGCGTTGCGATTCTGGGAAC
** *
5849244 TGATTTGCGATTCTGGAGATC
1 TGCGTTGCGATTCTGG-GAAC
5849265 -GCGTTGCGATT
1 TGCGTTGCGATT
5849276 TTTATTTCGC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.15, C:0.17, G:0.33, T:0.35
Consensus pattern (20 bp):
TGCGTTGCGATTCTGGGAAC
Found at i:5851084 original size:21 final size:21
Alignment explanation
Indices: 5851058--5851097 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5851048 ATATCTCTAA
*
5851058 CTTAAACCCTAAATTATAAAT
1 CTTAAACCCTAAATCATAAAT
*
5851079 CTTAAATCCTAAATCATAA
1 CTTAAACCCTAAATCATAA
5851098 CCCAATAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (21 bp):
CTTAAACCCTAAATCATAAAT
Found at i:5853366 original size:20 final size:20
Alignment explanation
Indices: 5853341--5853392 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
5853331 GTTCATATTT
*
5853341 ATATTATGTTTTTTAATTGA
1 ATATTATGTTTTTGAATTGA
* *
5853361 ATATTATATTTTTGAATTTA
1 ATATTATGTTTTTGAATTGA
*
5853381 ATTTTTATGTTT
1 A-TATTATGTTT
5853393 AATATTATGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (20 bp):
ATATTATGTTTTTGAATTGA
Found at i:5853453 original size:23 final size:22
Alignment explanation
Indices: 5853423--5853482 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 22
5853413 TTATTTTTAC
*
5853423 TATATTTACTTTTGATATTATGT
1 TATATTTATTTTTG-TATTATGT
5853446 TATATTTAATTTTTTGTATTATGT
1 TATATTT-A-TTTTTGTATTATGT
5853470 TATATTTATTTTT
1 TATATTTATTTTT
5853483 TTTAATATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
22 5 0.15
23 8 0.24
24 16 0.47
25 5 0.15
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.67
Consensus pattern (22 bp):
TATATTTATTTTTGTATTATGT
Found at i:5853484 original size:24 final size:25
Alignment explanation
Indices: 5853432--5853484 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 25
5853422 CTATATTTAC
5853432 TTTTGATATTATGTTATATTTAATT
1 TTTTGATATTATGTTATATTTAATT
*
5853457 TTTTG-TATTATGTTATATTTATTT
1 TTTTGATATTATGTTATATTTAATT
5853481 TTTT
1 TTTT
5853485 TAATATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.70
Consensus pattern (25 bp):
TTTTGATATTATGTTATATTTAATT
Found at i:5853492 original size:16 final size:17
Alignment explanation
Indices: 5853471--5853504 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5853461 GTATTATGTT
5853471 ATATTTAT-TTTTTTTA
1 ATATTTATATTTTTTTA
*
5853487 ATATTTTTATTTTTTTA
1 ATATTTATATTTTTTTA
5853504 A
1 A
5853505 ATATAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
ATATTTATATTTTTTTA
Found at i:5853496 original size:24 final size:24
Alignment explanation
Indices: 5853432--5853498 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
5853422 CTATATTTAC
*
5853432 TTTTGATATTATGTTATATTTAATT
1 TTTTG-TAATATGTTATATTTAATT
*
5853457 TTTTGTATTATGTTATATTT-ATT
1 TTTTGTAATATGTTATATTTAATT
* *
5853480 TTTTTTAATAT-TTTTATTT
1 TTTTGTAATATGTTATATTT
5853499 TTTTAAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
22 7 0.18
23 12 0.31
24 15 0.38
25 5 0.13
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (24 bp):
TTTTGTAATATGTTATATTTAATT
Found at i:5853497 original size:18 final size:18
Alignment explanation
Indices: 5853474--5853508 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5853464 TTATGTTATA
*
5853474 TTTATTTTTTTTAATATT
1 TTTATTTTTTTAAATATT
5853492 TTTATTTTTTTAAATAT
1 TTTATTTTTTTAAATAT
5853509 AAAAGAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTTTTTAAATATT
Found at i:5853725 original size:20 final size:19
Alignment explanation
Indices: 5853682--5853726 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
5853672 TTATTTTCTT
**
5853682 TTTGTTTTTTAAAATTTTTG
1 TTTG-TTTTTAAAATCATTG
5853702 TTTGTTTTTAAAATCATTG
1 TTTGTTTTTAAAATCATTG
5853721 ATTTGT
1 -TTTGT
5853727 CACAAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.22, C:0.02, G:0.11, T:0.64
Consensus pattern (19 bp):
TTTGTTTTTAAAATCATTG
Found at i:5856207 original size:62 final size:62
Alignment explanation
Indices: 5856104--5856285 Score: 251
Period size: 61 Copynumber: 3.0 Consensus size: 62
5856094 TCTTCAAAAC
* * *
5856104 TATTTTTATCTTTTTTGAGATTATTATAAGGATAAACTATGCAAATAGTTCCCTTTGTTAAA
1 TATTTTTATCTTTTTTGAGATTATTTTAAGGGTAAACTATGCAAATAGTTCCCTTTATTAAA
* *
5856166 TATTTTTATCTTTTTTGAGATTATTTTAAGGGTAAAATATGC-AATAG-TCATCTTTATTAAA
1 TATTTTTATCTTTTTTGAGATTATTTTAAGGGTAAACTATGCAAATAGTTC-CCTTTATTAAA
* * * * *
5856227 TACTTTTATCTTTTCTGATATTATTTTAAGGGTAAACTATGTAAATAGTCCCCTTTATT
1 TATTTTTATCTTTTTTGAGATTATTTTAAGGGTAAACTATGCAAATAGTTCCCTTTATT
5856286 TTCGGTCTGA
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
60 2 0.02
61 51 0.49
62 51 0.49
63 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.11, T:0.48
Consensus pattern (62 bp):
TATTTTTATCTTTTTTGAGATTATTTTAAGGGTAAACTATGCAAATAGTTCCCTTTATTAAA
Found at i:5857424 original size:37 final size:35
Alignment explanation
Indices: 5857339--5857474 Score: 150
Period size: 37 Copynumber: 3.8 Consensus size: 35
5857329 TTTCGTCCTA
* *
5857339 CTAGGATTTAAACTCTTAAAAATAGGATAGAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
5857374 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
*
5857409 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCT
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGAATT-T
* * * *
5857446 ACTAAGATTTAAATTCCTAAAGATAGGAT
1 -CTAGGATTCAAACTCCTAAAAATAGGAT
5857475 CCACAAGCAC
Statistics
Matches: 87, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
33 1 0.01
34 27 0.31
35 3 0.03
36 2 0.02
37 53 0.61
38 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:5857872 original size:18 final size:17
Alignment explanation
Indices: 5857833--5857875 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
5857823 ATTATATGAA
5857833 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
5857849 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
5857867 TATTATTAT
1 TATTATTAT
5857876 GTATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:5857924 original size:57 final size:56
Alignment explanation
Indices: 5857840--5857946 Score: 164
Period size: 57 Copynumber: 1.9 Consensus size: 56
5857830 GAATATTTTA
5857840 TTCATTTATTTTTATTATTCATGTTATTATTATTATGTATATATATATATAATTATT
1 TTCATTTATTTTTATTATTCATGTTATTATTATTAT-TATATATATATATAATTATT
*
5857897 TTCATTTATTTTT-TTACTAT-ATTTTATTATTATTATTATATATATATATA
1 TTCATTTATTTTTATTA-T-TCATGTTATTATTATTATTATATATATATATA
5857947 TATATTTAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
56 17 0.36
57 29 0.62
58 1 0.02
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (56 bp):
TTCATTTATTTTTATTATTCATGTTATTATTATTATTATATATATATATAATTATT
Found at i:5857979 original size:60 final size:59
Alignment explanation
Indices: 5857863--5857979 Score: 128
Period size: 60 Copynumber: 1.9 Consensus size: 59
5857853 ATTATTCATG
* * *** *
5857863 TTATTATTATTATGTATATATATATATAATTATTTTCATTTATTTTTTTACTATATTTTA
1 TTATTATTATTATATATATATATATATAATTATTTTCACTTATAAGTCTAC-ATATTTTA
* *
5857923 TTATTATTATTATATATATATATATATATTTAATATTTTACTTATAAGTCTA-ATATT
1 TTATTATTATTATATATATATATATATAATT-AT-TTTCACTTATAAGTCTACATATT
5857980 ACTATATATA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
60 34 0.72
61 2 0.04
62 11 0.23
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (59 bp):
TTATTATTATTATATATATATATATATAATTATTTTCACTTATAAGTCTACATATTTTA
Found at i:5858188 original size:21 final size:21
Alignment explanation
Indices: 5858135--5858189 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
5858125 CTTTATAACT
* * *
5858135 TTATATTATTTTTTATTATTT
1 TTATATTATTATTCATTATTA
* * *
5858156 TTGTTTTTTTATTCATTATTA
1 TTATATTATTATTCATTATTA
5858177 TTATATTATTATT
1 TTATATTATTATT
5858190 TTCTTTAAAA
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (21 bp):
TTATATTATTATTCATTATTA
Found at i:5861535 original size:7 final size:7
Alignment explanation
Indices: 5861523--5861604 Score: 60
Period size: 7 Copynumber: 11.3 Consensus size: 7
5861513 TCCAATCAAG
5861523 AAGAAAA
1 AAGAAAA
5861530 AAGAAAA
1 AAGAAAA
5861537 GAAGCAAAA
1 -AAG-AAAA
*
5861546 AA-AACA
1 AAGAAAA
5861552 AAGAAAA
1 AAGAAAA
* *
5861559 AACAAAG
1 AAGAAAA
5861566 AA-AAAA
1 AAGAAAA
* *
5861572 GAGAAAC
1 AAGAAAA
5861579 AAGAACAA
1 AAGAA-AA
5861587 AAGGAAAA
1 AA-GAAAA
5861595 AAGGAAAA
1 AA-GAAAA
5861603 AA
1 AA
5861605 CAAGAATAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
6 9 0.15
7 24 0.40
8 20 0.33
9 7 0.12
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:5861555 original size:22 final size:21
Alignment explanation
Indices: 5861520--5861621 Score: 63
Period size: 20 Copynumber: 4.8 Consensus size: 21
5861510 AGATCCAATC
5861520 AAGAAGAAA-AAAGAAAAGAAGCA
1 AAGAA-AAACAAAGAAAA-AA-CA
5861543 AA-AAAAACAAAGAAAAAACA
1 AAGAAAAACAAAGAAAAAACA
*
5861563 AAGAAAAA-AGAGAAACAAGAACAA
1 AAGAAAAACAAAG-AA-AA-AAC-A
* *
5861587 AAGGAAAA-AAGGAAAAAAC-
1 AAGAAAAACAAAGAAAAAACA
5861606 AAGAATAAA-AAAGAAA
1 AAGAA-AAACAAAGAAA
5861622 GATGAACAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
19 4 0.06
20 16 0.24
21 15 0.23
22 14 0.21
23 7 0.11
24 10 0.15
ACGTcount: A:0.77, C:0.06, G:0.16, T:0.01
Consensus pattern (21 bp):
AAGAAAAACAAAGAAAAAACA
Found at i:5861558 original size:11 final size:11
Alignment explanation
Indices: 5861544--5861571 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5861534 AAAGAAGCAA
5861544 AAAAAACAAAG
1 AAAAAACAAAG
5861555 AAAAAACAAAG
1 AAAAAACAAAG
5861566 AAAAAA
1 AAAAAA
5861572 GAGAAACAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAG
Found at i:5861582 original size:27 final size:28
Alignment explanation
Indices: 5861519--5861621 Score: 86
Period size: 28 Copynumber: 3.6 Consensus size: 28
5861509 AAGATCCAAT
* *
5861519 CAAGAAGAAAAAAGAAAAGAAGCAAAAAAAA
1 CAAGAAAAAAAAAGAAAA-AAG--GAAAAAA
*
5861550 CAAAGAAAAAACAAAGAAAAAA-G-AGAAA
1 C-AAGAAAAAA-AAAGAAAAAAGGAAAAAA
* *
5861578 CAAG-AACAAAAGGAAAAAAGGAAAAAA
1 CAAGAAAAAAAAAGAAAAAAGGAAAAAA
*
5861605 CAAGAATAAAAAAGAAA
1 CAAGAAAAAAAAAGAAA
5861622 GATGAACAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
25 9 0.16
26 5 0.09
27 11 0.19
28 14 0.24
31 1 0.02
32 10 0.17
33 8 0.14
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.01
Consensus pattern (28 bp):
CAAGAAAAAAAAAGAAAAAAGGAAAAAA
Found at i:5861593 original size:16 final size:17
Alignment explanation
Indices: 5861558--5861604 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
5861548 AACAAAGAAA
5861558 AAACAAAGAAAAAAGAG
1 AAACAAAGAAAAAAGAG
5861575 AAAC-AAGAACAAAAG-G
1 AAACAAAGAA-AAAAGAG
5861591 AAA-AAAGGAAAAAA
1 AAACAAA-GAAAAAA
5861605 CAAGAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (17 bp):
AAACAAAGAAAAAAGAG
Found at i:5861604 original size:44 final size:42
Alignment explanation
Indices: 5861523--5861633 Score: 122
Period size: 44 Copynumber: 2.6 Consensus size: 42
5861513 TCCAATCAAG
5861523 AAGAAAAAAGA-AAAGAAG--CAAAAAAAACAAAGAAAAAAC
1 AAGAAAAAAGAGAAAGAAGAACAAAAAAAACAAAGAAAAAAC
* *
5861562 AAAGAAAAAAGAGAAACAAGAACAAAAGGAAAA-AAGGAAAAAAC
1 -AAGAAAAAAGAGAAAGAAGAACAAAA--AAAACAAAGAAAAAAC
* *
5861606 AAGAATAAAAAAGAAAGATGAACAAAAA
1 AAGAA-AAAAGAGAAAGAAGAACAAAAA
5861634 GCACATGCAA
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
40 11 0.18
41 6 0.10
42 1 0.02
43 10 0.17
44 28 0.47
45 4 0.07
ACGTcount: A:0.77, C:0.06, G:0.15, T:0.02
Consensus pattern (42 bp):
AAGAAAAAAGAGAAAGAAGAACAAAAAAAACAAAGAAAAAAC
Found at i:5861619 original size:10 final size:9
Alignment explanation
Indices: 5861520--5861621 Score: 55
Period size: 9 Copynumber: 10.7 Consensus size: 9
5861510 AGATCCAATC
5861520 AAGAAGAAAA
1 AAGAA-AAAA
5861530 AAGAAAAGAA
1 AAGAAAA-AA
*
5861540 GCAAAAAAAACA
1 --AAGAAAAA-A
5861552 AAGAAAAAA
1 AAGAAAAAA
*
5861561 CAA-AGAAAA
1 -AAGAAAAAA
* *
5861570 AAGAGAAAC
1 AAGAAAAAA
*
5861579 AAG-AACAA
1 AAGAAAAAA
*
5861587 AAGGAAAAA
1 AAGAAAAAA
*
5861596 AGGAAAAAA
1 AAGAAAAAA
5861605 CAAGAATAAAA
1 -AAGAA-AAAA
5861616 AAGAAA
1 AAGAAA
5861622 GATGAACAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 19
0.71 0.11 0.19
Matches are distributed among these distances:
8 7 0.10
9 28 0.39
10 25 0.35
11 5 0.07
12 7 0.10
ACGTcount: A:0.77, C:0.06, G:0.16, T:0.01
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:5862285 original size:22 final size:22
Alignment explanation
Indices: 5862254--5862308 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
5862244 GCTATCCCAT
*
5862254 CAAACATTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
5862276 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
5862298 CAAACCTTTGA
1 CAAACCTTTGA
5862309 CCAAACACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:5862735 original size:18 final size:18
Alignment explanation
Indices: 5862712--5862747 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5862702 TCAACATCAA
* *
5862712 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
5862730 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
5862748 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:5863216 original size:36 final size:36
Alignment explanation
Indices: 5863169--5863431 Score: 245
Period size: 36 Copynumber: 7.4 Consensus size: 36
5863159 ATTGAAAACA
* *
5863169 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
5863205 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* * * *
5863242 TTTCCCTTGAAATAAATTTTGTCTCTCTTGATACAA
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * *
5863278 TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
* * *
5863307 TTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* ** * * *
5863343 TTGCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* * *
5863380 TTTCTCTTAAAACAAATTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
5863416 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
5863432 ATCTTTGAAT
Statistics
Matches: 183, Mismatches: 33, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
28 2 0.01
29 18 0.10
30 2 0.01
35 1 0.01
36 96 0.52
37 64 0.35
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:5863291 original size:138 final size:138
Alignment explanation
Indices: 5863110--5863494 Score: 441
Period size: 138 Copynumber: 2.8 Consensus size: 138
5863100 GATTGCTTTT
* *
5863110 TTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA-TTGAAAACATTTCC
1 TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAACATTTGAAAACATTTCC
* * * *
5863174 CTTGAAATAAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGA
65 CTTGAAACAAATTTCGTCTCCCTTGAGACAGTTGCCCTTGAAACAAAATTTTGTCTCTCTTGAGA
5863239 CAGTTTCCC
130 CAGTTTCCC
* * * * * * ** * *
5863248 TTGAAATAAATTTTGTCTCTCTTGATACAATTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
1 TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACATTTGAAAACATTTCCC
** * * *
5863313 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTGCTTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
66 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTGCCCTTGAAACAAAATTTTGTCTCTCTTGAGAC
*
5863378 AGTTTCTC
131 AGTTTCCC
* * ***
5863386 TTAAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATC-TTTGAATTTATTTCC
1 TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA-CATTTGAAAACATTTCC
* * * * * *
5863450 CCTAAAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACA
65 CTTGAAACAAATTTCGTCTCCCTTGAGACAGTTGCCCTTGAAACA
5863495 CAAAATCTTC
Statistics
Matches: 204, Mismatches: 41, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
137 4 0.02
138 200 0.98
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (138 bp):
TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACATTTGAAAACATTTCCC
TTGAAACAAATTTCGTCTCCCTTGAGACAGTTGCCCTTGAAACAAAATTTTGTCTCTCTTGAGAC
AGTTTCCC
Found at i:5863317 original size:102 final size:102
Alignment explanation
Indices: 5863211--5863395 Score: 255
Period size: 102 Copynumber: 1.8 Consensus size: 102
5863201 ATAGTTTCCC
* * * *
5863211 TTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCTTGATA
1 TTGAAAC-AAATTTCGTCTCCCTTGAGACAGTTGCCCTTGGAAATAAATTTTGTCTCTCTTGAGA
*
5863275 CAATTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
65 CAATTTCCCTTAAAACAAAATATTTGAATATGTTTTCT
** * *
5863313 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTGCTTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
1 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTGCCCTTGGAAATAAATTTTGTCTCTCTTGAGAC
* *
5863378 AGTTTCTCTTAAAACAAA
66 AATTTCCCTTAAAACAAA
5863396 TTTCGTCTAT
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
101 26 0.37
102 45 0.63
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (102 bp):
TTGAAACAAATTTCGTCTCCCTTGAGACAGTTGCCCTTGGAAATAAATTTTGTCTCTCTTGAGAC
AATTTCCCTTAAAACAAAATATTTGAATATGTTTTCT
Found at i:5863491 original size:65 final size:67
Alignment explanation
Indices: 5863387--5863546 Score: 207
Period size: 65 Copynumber: 2.4 Consensus size: 67
5863377 CAGTTTCTCT
* ** * * **
5863387 TAAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCC
1 TAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCC
5863450 CC
66 CC
*
5863452 TAAAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACACAAAATCTTCAAATTTATTTCC
1 TAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCC
*
5863517 CT
66 CC
*
5863519 TAAAACATAATTTTGTTTCCCTTGAGAC
1 TAAAACA-AATTTTGTCTCCCTTGAGAC
5863547 CGTTTCTCAT
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
65 32 0.39
66 2 0.02
67 29 0.35
68 19 0.23
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (67 bp):
TAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCC
CC
Found at i:5864395 original size:105 final size:106
Alignment explanation
Indices: 5864203--5864623 Score: 627
Period size: 105 Copynumber: 4.0 Consensus size: 106
5864193 GTGGCACTCG
* * *
5864203 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCCCAATTT
5864268 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTC
* *
5864309 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-AAACAACTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCCCAATTT
*
5864373 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTC
** *
5864414 AGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATCT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCCCAAT-T
*
5864478 T-AGAGCCAATTTCAACTTCACGACGAAGGATATTGGAC-TC
65 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTC
* * **
5864518 GAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCCCGGT
1 -AGACAACACAAGTTCAACTTCACAACGAAGGGACCG-CTGCTTGTCAACAAACAACTTCCCAAT
* * *
5864582 TCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGGACTT
64 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTT
5864624 GGAACAATGC
Statistics
Matches: 290, Mismatches: 18, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
104 3 0.01
105 194 0.67
106 92 0.32
107 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (106 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCCCAATTT
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTC
Found at i:5864616 original size:211 final size:211
Alignment explanation
Indices: 5864180--5864622 Score: 642
Period size: 211 Copynumber: 2.1 Consensus size: 211
5864170 TTAACTCCAT
* * *
5864180 AACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTT
1 AACGGAGGATAT--TGG-ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTT
*
5864245 GTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCA
63 GTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCA
* * *
5864310 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAAAACAACTTCCCAATTTCA
128 GACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAAAAACAACTTCCCAATTCCA
5864375 GAGCCAATTTCAACTTCAC
193 GAGCCAATTTCAACTTCAC
* ** *
5864394 AACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTC
1 AACGGAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTC
*
5864459 AAC-AACAACTTCCCAATCTT-AGAGCCAATTTCAACTTCACGACGAAGGATATTGGAC-TCGAG
66 AACAAACAACTTCCCAAT-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTC-AG
* * **
5864521 ACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCCCGGTTCC
129 ACAACACAAGTTCAACTTCACAACGAAGGGACCG-CTGCTTGTCAA-AAACAACTTCCCAATTCC
5864585 AGAGCCAATTTCAACTTCAC
192 AGAGCCAATTTCAACTTCAC
*
5864605 GACGGAGGATATTGGACT
1 AACGGAGGATATTGGACT
5864623 TGGAACAATG
Statistics
Matches: 207, Mismatches: 18, Indels: 11
0.88 0.08 0.05
Matches are distributed among these distances:
209 4 0.02
210 90 0.43
211 99 0.48
212 3 0.01
214 11 0.05
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (211 bp):
AACGGAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTC
AACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGAC
AACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAAAAACAACTTCCCAATTCCAGAG
CCAATTTCAACTTCAC
Found at i:5865214 original size:34 final size:37
Alignment explanation
Indices: 5865170--5865271 Score: 167
Period size: 34 Copynumber: 2.8 Consensus size: 37
5865160 TTTCGTCCTA
5865170 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
5865205 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
5865240 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
5865272 GTTCTACTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
33 1 0.02
34 29 0.47
35 3 0.05
37 28 0.45
38 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
Found at i:5865255 original size:37 final size:35
Alignment explanation
Indices: 5865170--5865305 Score: 168
Period size: 37 Copynumber: 3.8 Consensus size: 35
5865160 TTTCGTCCTA
5865170 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
5865205 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
*
5865240 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCT
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGAATT-T
* * * *
5865277 ACTAAGATTTAAATTCCTAAAGATAGGAT
1 -CTAGGATTCAAACTCCTAAAAATAGGAT
5865306 CCACAAGCAC
Statistics
Matches: 89, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
33 1 0.01
34 29 0.33
35 3 0.03
36 2 0.02
37 53 0.60
38 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:5865703 original size:18 final size:17
Alignment explanation
Indices: 5865664--5865706 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
5865654 ATTATATGAA
5865664 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
5865680 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
5865698 TATTATTAT
1 TATTATTAT
5865707 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:5865783 original size:58 final size:61
Alignment explanation
Indices: 5865671--5865790 Score: 176
Period size: 58 Copynumber: 2.0 Consensus size: 61
5865661 GAATATTTTA
* *
5865671 TTCATTTATTTTTATTATTCATGTTATTATTATTATATGTATATATATATATATAATTATT
1 TTCATTTATTTTTATTACTCATATTATTATTATTATATGTATATATATATATATAATTATT
*
5865732 TTCATTTATTTTT-TTACT-ATATT-TTATTATTATTAT-TATATATATATATATATTTATT
1 TTCATTTATTTTTATTACTCATATTATTATTATTA-TATGTATATATATATATATAATTATT
5865790 T
1 T
5865791 AATATTTTAC
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
58 31 0.56
59 7 0.13
60 4 0.07
61 13 0.24
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (61 bp):
TTCATTTATTTTTATTACTCATATTATTATTATTATATGTATATATATATATATAATTATT
Found at i:5866019 original size:21 final size:21
Alignment explanation
Indices: 5865966--5866020 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
5865956 CTTTATAACT
* * *
5865966 TTATATTATTTTTTATTATTT
1 TTATATTATTATTCATTATTA
* * *
5865987 TTGTTTTTTTATTCATTATTA
1 TTATATTATTATTCATTATTA
5866008 TTATATTATTATT
1 TTATATTATTATT
5866021 TTCTTTAAAA
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (21 bp):
TTATATTATTATTCATTATTA
Found at i:5868643 original size:20 final size:20
Alignment explanation
Indices: 5868618--5868751 Score: 142
Period size: 20 Copynumber: 6.6 Consensus size: 20
5868608 TAGTTGAAAA
5868618 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
5868638 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
5868659 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
5868679 TCGCGTTGCGATATTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
5868699 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
5868720 TCTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
5868740 TCGCGTTGCGAT
1 TCGCGTTGCGAT
5868752 AGTCTACAGT
Statistics
Matches: 89, Mismatches: 23, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
20 60 0.67
21 29 0.33
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:5868650 original size:41 final size:41
Alignment explanation
Indices: 5868593--5868691 Score: 189
Period size: 41 Copynumber: 2.4 Consensus size: 41
5868583 ATTCGCGTTG
*
5868593 CATTTCACGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
5868634 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
5868675 CATTTCGCGTTGCGATA
1 CATTTCGCGTTGCGATA
5868692 TTCCATTTCG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:5868696 original size:61 final size:61
Alignment explanation
Indices: 5868618--5868752 Score: 252
Period size: 61 Copynumber: 2.2 Consensus size: 61
5868608 TAGTTGAAAA
*
5868618 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATATTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
*
5868679 TCGCGTTGCGATATTCCATTTCGCGTTGCGATAGTTGAAAATCTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATATTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
5868740 TCGCGTTGCGATA
1 TCGCGTTGCGATA
5868753 GTCTACAGTT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 72 1.00
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (61 bp):
TCGCGTTGCGATATTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
Found at i:5868788 original size:61 final size:61
Alignment explanation
Indices: 5868618--5868773 Score: 206
Period size: 61 Copynumber: 2.5 Consensus size: 61
5868608 TAGTTGAAAA
* * * * *
5868618 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATATTACAGTTCGCGTTGCGATAGTTCAAAATCTCGTTGCGATTTTCCATT
* * *
5868679 TCGCGTTGCGATATTCCATTTCGCGTTGCGATAGTTGAAAATCTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATATTACAGTTCGCGTTGCGATAGTTCAAAATCTCGTTGCGATTTTCCATT
5868740 TCGCGTTGCGATAGTCTACAGTT-GTCGTTGCGAT
1 TCGCGTTGCGATA-T-TACAGTTCG-CGTTGCGAT
5868774 TTTCCAAATT
Statistics
Matches: 88, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
61 72 0.82
62 2 0.02
63 14 0.16
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (61 bp):
TCGCGTTGCGATATTACAGTTCGCGTTGCGATAGTTCAAAATCTCGTTGCGATTTTCCATT
Found at i:5868788 original size:102 final size:101
Alignment explanation
Indices: 5868593--5868793 Score: 289
Period size: 102 Copynumber: 2.0 Consensus size: 101
5868583 ATTCGCGTTG
5868593 CATTTCACGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 CATTTCACGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
*
5868658 ATCGCGTTGCGATTTTCCATTTCGCGTTGCGATATTC
66 ATCGCGTTGCGATTTTCCAATTC-CGTTGCGATATTC
* * *
5868695 CATTTCGCGTTGCGATAGTTGAAAATCTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-AC
1 CATTTCACGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAA
* * *
5868759 AGTTGTCGTTGCGATTTTCCAAATT-CGTTGTGATA
65 AATCG-CGTTGCGATTTTCC-AATTCCGTTGCGATA
5868794 GTTAAAAAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
102 71 0.80
103 15 0.17
104 3 0.03
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.38
Consensus pattern (101 bp):
CATTTCACGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
ATCGCGTTGCGATTTTCCAATTCCGTTGCGATATTC
Found at i:5873632 original size:17 final size:17
Alignment explanation
Indices: 5873610--5873643 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5873600 CACATCATTT
5873610 CCTTGATCAAAATAGCC
1 CCTTGATCAAAATAGCC
5873627 CCTTGATCAAAATAGCC
1 CCTTGATCAAAATAGCC
5873644 AAGCCTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (17 bp):
CCTTGATCAAAATAGCC
Found at i:5875548 original size:24 final size:24
Alignment explanation
Indices: 5875521--5875569 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
5875511 TGCATGACAT
*
5875521 TGTACATAGATGTTCTATACATCA
1 TGTACATAGATATTCTATACATCA
*
5875545 TGTACATAGATATTTTATACATCA
1 TGTACATAGATATTCTATACATCA
5875569 T
1 T
5875570 CAGGAAGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (24 bp):
TGTACATAGATATTCTATACATCA
Found at i:5876745 original size:54 final size:54
Alignment explanation
Indices: 5876663--5876765 Score: 161
Period size: 54 Copynumber: 1.9 Consensus size: 54
5876653 CCTCTTCCTC
* * * *
5876663 CTTCAGATGTCATTTTCACAGCCTGTTCCTCACTATTTCGTCTATGAAATTTTG
1 CTTCAGATGTCACTTTCAAAGCCTGTTCCTCACCATTTCATCTATGAAATTTTG
*
5876717 CTTCAGATGTCACTTTCAAAGCCTGTTCCTCACCATTTCATCTTTGAAA
1 CTTCAGATGTCACTTTCAAAGCCTGTTCCTCACCATTTCATCTATGAAA
5876766 CTTCTGATGC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (54 bp):
CTTCAGATGTCACTTTCAAAGCCTGTTCCTCACCATTTCATCTATGAAATTTTG
Found at i:5879925 original size:32 final size:32
Alignment explanation
Indices: 5879850--5879936 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 32
5879840 TGACATGACA
* * * * *
5879850 TGTCATGTCATCCAAAATAATTATGTGATATG
1 TGTCATGTCACCCAAAATGATTATATAACATG
* * *
5879882 TATTATATCACCCAAAATGATTATATAACATG
1 TGTCATGTCACCCAAAATGATTATATAACATG
*
5879914 TGTCATGTCACCCAAAGTGATTA
1 TGTCATGTCACCCAAAATGATTA
5879937 CATTGCATGT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (32 bp):
TGTCATGTCACCCAAAATGATTATATAACATG
Found at i:5881145 original size:15 final size:14
Alignment explanation
Indices: 5881125--5881176 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
5881115 TAACCCAACC
5881125 GAGTCAACCTAAATT
1 GAGTCAACCT-AATT
*
5881140 GAGTCAA-CTCATT
1 GAGTCAACCTAATT
*
5881153 CGAGTCAACCTGAACT
1 -GAGTCAACCT-AATT
5881169 GAGTCAAC
1 GAGTCAAC
5881177 TCGTTCAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 3 0.10
14 9 0.29
15 17 0.55
16 2 0.06
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (14 bp):
GAGTCAACCTAATT
Found at i:5881157 original size:29 final size:29
Alignment explanation
Indices: 5881124--5881190 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
5881114 TTAACCCAAC
*
5881124 CGAGTCAACCTAAATTGAGTCAACTCATT
1 CGAGTCAACCTAAACTGAGTCAACTCATT
* *
5881153 CGAGTCAACCTGAACTGAGTCAACTCGTT
1 CGAGTCAACCTAAACTGAGTCAACTCATT
*
5881182 CAAGTCAAC
1 CGAGTCAAC
5881191 TCGTTAGAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (29 bp):
CGAGTCAACCTAAACTGAGTCAACTCATT
Found at i:5881159 original size:14 final size:14
Alignment explanation
Indices: 5881140--5881205 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
5881130 AACCTAAATT
5881140 GAGTCAACTCATTC
1 GAGTCAACTCATTC
* *
5881154 GAGTCAACCTGA-AC
1 GAGTCAA-CTCATTC
*
5881168 TGAGTCAACTCGTTC
1 -GAGTCAACTCATTC
* * *
5881183 AAGTCAACTCGTTA
1 GAGTCAACTCATTC
5881197 GAGTCAACT
1 GAGTCAACT
5881206 TGTCCGAGAC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
14 30 0.73
15 11 0.27
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (14 bp):
GAGTCAACTCATTC
Found at i:5881218 original size:28 final size:28
Alignment explanation
Indices: 5881169--5881223 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
5881159 AACCTGAACT
* * *
5881169 GAGTCAACTCGTTCAAGTCAACTCGTTA
1 GAGTCAACTCGTCCAAGACAACCCGTTA
* *
5881197 GAGTCAACTTGTCCGAGACAACCCGTT
1 GAGTCAACTCGTCCAAGACAACCCGTT
5881224 GACTTTGACC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (28 bp):
GAGTCAACTCGTCCAAGACAACCCGTTA
Found at i:5883231 original size:22 final size:22
Alignment explanation
Indices: 5883203--5883244 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5883193 GTAGGCTCCA
*
5883203 AGGCCCCGAGAAACTTTCTTTG
1 AGGCCCCAAGAAACTTTCTTTG
5883225 AGGCCCCAAGAAACTTTCTT
1 AGGCCCCAAGAAACTTTCTT
5883245 GGGTAGGCTC
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:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (22 bp):
AGGCCCCAAGAAACTTTCTTTG
Found at i:5885718 original size:2 final size:2
Alignment explanation
Indices: 5885713--5885785 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
5885703 CTCATGTGTG
5885713 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
5885755 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5885786 GTGTGCGCGC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5885853 original size:17 final size:18
Alignment explanation
Indices: 5885831--5885870 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
5885821 GACTAATACG
*
5885831 TGTGTTTATATGGTA-TA
1 TGTGTTTATATGATATTA
5885848 TGTGTTTATATGATATTA
1 TGTGTTTATATGATATTA
5885866 TGTGT
1 TGTGT
5885871 GTGCTTACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (18 bp):
TGTGTTTATATGATATTA
Found at i:5887217 original size:20 final size:20
Alignment explanation
Indices: 5887192--5887540 Score: 436
Period size: 20 Copynumber: 17.4 Consensus size: 20
5887182 GATTTTCCAT
* ** *
5887192 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
5887212 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
5887232 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5887252 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
5887272 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
5887292 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5887312 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
5887332 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
5887352 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5887372 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
5887392 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5887412 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
5887432 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5887452 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
5887472 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
5887492 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
5887512 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
5887532 AATCACAAC
1 AATCGCAAC
5887541 ACTGAAATTT
Statistics
Matches: 289, Mismatches: 32, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
19 3 0.01
20 283 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:5888253 original size:24 final size:24
Alignment explanation
Indices: 5888214--5888260 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5888204 AAATTTGGTC
5888214 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
5888238 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
5888261 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:5888452 original size:12 final size:12
Alignment explanation
Indices: 5888435--5888459 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5888425 ATATAATCCT
5888435 GAAGAAGAAAAA
1 GAAGAAGAAAAA
5888447 GAAGAAGAAAAA
1 GAAGAAGAAAAA
5888459 G
1 G
5888460 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:5890763 original size:19 final size:19
Alignment explanation
Indices: 5890741--5891156 Score: 523
Period size: 19 Copynumber: 23.4 Consensus size: 19
5890731 CGGAAAATAC
*
5890741 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5890760 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
5890774 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
5890794 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
5890808 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5890827 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5890846 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
5890860 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5890879 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
5890893 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5890912 CATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5890931 AATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAA
5890950 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5890969 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5890988 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
5891002 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5891021 CATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5891040 AATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAA
5891059 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5891078 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5891097 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
5891111 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5891130 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5891149 AATCGCAA
1 AATCGCAA
5891157 CGAGATAATC
Statistics
Matches: 348, Mismatches: 18, Indels: 62
0.81 0.04 0.14
Matches are distributed among these distances:
14 60 0.17
15 4 0.01
16 15 0.04
17 14 0.04
18 5 0.01
19 237 0.68
20 13 0.04
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:5890793 original size:34 final size:33
Alignment explanation
Indices: 5890741--5891178 Score: 132
Period size: 33 Copynumber: 12.5 Consensus size: 33
5890731 CGGAAAATAC
*
5890741 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACGA-GAA
* *
5890774 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCCCAACGAGAA
*
5890808 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
* * * * *
5890846 AATCGCAACGAGAGAATCG-CAATGCGAA--ATGAA
1 AATCGCAATGCGA-AAT-GAAAATCCCAACGA-GAA
* * * * *
5890879 AATCGCAACGAGAGAATCG-CAATGCGAA--ATGAA
1 AATCGCAATGCGA-AAT-GAAAATCCCAACGA-GAA
* * *
5890912 CATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
*
5890950 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
* * * * *
5890988 AATCGCAACGAGAGAATCG-CAATGCGAA--ATGAA
1 AATCGCAATGCGA-AAT-GAAAATCCCAACGA-GAA
* * *
5891021 CATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
*
5891059 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
*
5891097 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
* *
5891130 AATCGCAATGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAA
5891163 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
5891179 TATAAACGCA
Statistics
Matches: 338, Mismatches: 37, Indels: 60
0.78 0.09 0.14
Matches are distributed among these distances:
31 2 0.01
32 16 0.05
33 134 0.40
34 30 0.09
35 9 0.03
36 8 0.02
37 1 0.00
38 120 0.36
39 16 0.05
40 2 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCCCAACGAGAA
Found at i:5890856 original size:52 final size:53
Alignment explanation
Indices: 5890769--5891156 Score: 387
Period size: 52 Copynumber: 7.2 Consensus size: 53
5890759 AAATCCCAAC
5890769 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAGAGAATCGCAATGCGAA
5890822 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAGAATCGCAATGCGAA
* *
5890874 ATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAACATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAGA-G-A-ATCGCAATGCGAA
* *
5890926 ATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAGAATCGCAATGCGAA
* *
5890983 ATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAACATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAGA-G-A-ATCGCAATGCGAA
* *
5891035 ATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAGAATCGCAATGCGAA
*
5891092 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAGAATCGCAATGCGAA
5891144 ATGAAAATCGCAA
1 ATGAAAATCGCAA
5891157 CGAGATAATC
Statistics
Matches: 297, Mismatches: 14, Indels: 49
0.82 0.04 0.14
Matches are distributed among these distances:
47 10 0.03
48 1 0.00
49 5 0.02
50 4 0.01
51 2 0.01
52 160 0.54
53 17 0.06
54 5 0.02
55 7 0.02
56 2 0.01
57 78 0.26
58 2 0.01
59 2 0.01
60 2 0.01
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAGAATCGCAATGCGAA
Found at i:5890865 original size:14 final size:14
Alignment explanation
Indices: 5890846--5890900 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
5890836 GCGAAATGAA
5890846 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
5890860 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
5890879 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5890893 AATCGCAA
1 AATCGCAA
5890901 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:5891012 original size:109 final size:109
Alignment explanation
Indices: 5890809--5891178 Score: 625
Period size: 109 Copynumber: 3.5 Consensus size: 109
5890799 CAACGAGAGA
* *
5890809 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAAT
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAATCGCAAT
5890869 GCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAC
66 GCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAC
5890913 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAATCGCAAT
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAATCGCAAT
5890978 GCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAC
66 GCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAC
5891022 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAATCGCAAT
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAATCGCAAT
* *
5891087 GCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAA
66 GCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAC
*
5891131 ATCGCAATGCGAAATGAAAATCGCAA--CGAGAT---AATCGCAATGCGAAAT
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAAT
5891179 TATAAACGCA
Statistics
Matches: 256, Mismatches: 5, Indels: 10
0.94 0.02 0.04
Matches are distributed among these distances:
104 60 0.23
106 2 0.01
107 5 0.02
108 1 0.00
109 188 0.73
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (109 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAATCGCAAT
GCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAC
Found at i:5891157 original size:52 final size:52
Alignment explanation
Indices: 5890808--5891178 Score: 509
Period size: 52 Copynumber: 6.9 Consensus size: 52
5890798 GCAACGAGAG
*
5890808 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
*
5890860 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
*
5890912 CATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA--G-AATCGCAATGCGAAATGAA
*
5890969 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
*
5891021 CATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA--G-AATCGCAATGCGAAATGAA
5891078 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
* *
5891130 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAAT
5891179 TATAAACGCA
Statistics
Matches: 293, Mismatches: 11, Indels: 30
0.88 0.03 0.09
Matches are distributed among these distances:
47 8 0.03
49 3 0.01
50 4 0.01
51 1 0.00
52 166 0.57
53 2 0.01
54 8 0.03
55 9 0.03
56 2 0.01
57 90 0.31
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
Found at i:5891275 original size:19 final size:19
Alignment explanation
Indices: 5891185--5891267 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
5891175 AAATTATAAA
5891185 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
5891204 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
5891224 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
5891240 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
5891257 CGCATTGCGAT
1 CGCATTGCGAT
5891268 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:5891393 original size:14 final size:14
Alignment explanation
Indices: 5891374--5891410 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5891364 CATCAATTAC
5891374 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5891388 ACAAATCATCTTTT
1 ACAAATCAACTTTT
5891402 ACAAATCAA
1 ACAAATCAA
5891411 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5893382 original size:14 final size:14
Alignment explanation
Indices: 5893363--5893419 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5893353 GCGAAATGAA
*
5893363 AATCGCAACGACAG
1 AATCGCAACGAAAG
5893377 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
5893394 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
5893410 AATCGCAACG
1 AATCGCAACG
5893420 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:5893390 original size:33 final size:33
Alignment explanation
Indices: 5893344--5893436 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
5893334 GCGAAACCAA
*
5893344 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
5893377 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
5893410 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
5893437 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:5893401 original size:19 final size:19
Alignment explanation
Indices: 5893307--5893441 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
5893297 TAGTTTACTT
* *
5893307 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
5893327 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
5893346 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5893365 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
5893379 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
5893398 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
5893412 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5893431 TCGCAATGCGA
1 TCGCAACGCGA
5893442 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:5893459 original size:19 final size:19
Alignment explanation
Indices: 5893437--5893565 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
5893427 AAAATCGCAA
5893437 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5893456 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
5893470 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5893489 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
5893503 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
5893522 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
5893541 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
5893561 TGCGA
1 TGCGA
5893566 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:5893479 original size:33 final size:33
Alignment explanation
Indices: 5893437--5893528 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
5893427 AAAATCGCAA
5893437 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
5893470 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
5893503 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
5893529 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:5893778 original size:92 final size:93
Alignment explanation
Indices: 5893609--5893987 Score: 726
Period size: 92 Copynumber: 4.1 Consensus size: 93
5893599 TTGAATGGAT
*
5893609 AAATTTACTTTCAACCAAAGGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5893674 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5893702 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5893766 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5893794 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5893858 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5893886 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
5893951 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5893979 AAATTTACT
1 AAATTTACT
5893988 AAGCAATCTA
Statistics
Matches: 283, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
92 184 0.65
93 99 0.35
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:5893939 original size:185 final size:185
Alignment explanation
Indices: 5893609--5893987 Score: 724
Period size: 185 Copynumber: 2.0 Consensus size: 185
5893599 TTGAATGGAT
*
5893609 AAATTTACTTTCAACCAAAGGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5893674 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
5893739 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
5893794 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5893858 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
5893923 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
5893979 AAATTTACT
1 AAATTTACT
5893988 AAGCAATCTA
Statistics
Matches: 191, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 92 0.48
185 99 0.52
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:5895712 original size:14 final size:14
Alignment explanation
Indices: 5895693--5895782 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
5895683 TTGAAATGAA
5895693 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5895707 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
5895724 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
5895740 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
5895759 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5895773 AATCGCAACG
1 AATCGCAACG
5895783 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:5895730 original size:33 final size:33
Alignment explanation
Indices: 5895685--5895799 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
5895675 TCTTTTGGTT
5895685 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
5895718 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
5895751 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
5895784 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
5895800 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:5895731 original size:19 final size:18
Alignment explanation
Indices: 5895692--5895804 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
5895682 GTTGAAATGA
5895692 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
5895707 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
5895724 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
5895740 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
5895757 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
5895773 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
5895790 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
5895805 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:5895835 original size:14 final size:14
Alignment explanation
Indices: 5895816--5895870 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
5895806 TTTGGTTTCG
5895816 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5895830 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
5895849 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5895863 CGTTGCGA
1 CGTTGCGA
5895871 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:5896033 original size:33 final size:33
Alignment explanation
Indices: 5895991--5896061 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
5895981 AATACTAACT
*
5895991 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
5896024 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
5896057 TGAAA
1 TGAAA
5896062 TCTAAGTGAA
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:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:5896294 original size:22 final size:22
Alignment explanation
Indices: 5896242--5896296 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
5896232 TGGTTGTGAG
**
5896242 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
5896264 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
5896286 GGATTTCTTCG
1 GGATTTCTTCG
5896297 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:5896467 original size:20 final size:20
Alignment explanation
Indices: 5896442--5896635 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
5896432 CTTTAAATAT
5896442 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5896462 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
5896484 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5896503 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
5896523 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
5896543 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5896563 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5896583 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
5896603 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
5896623 CGCGTTGCGATTT
1 CGCGTTGCGATTT
5896636 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:5896629 original size:60 final size:60
Alignment explanation
Indices: 5896442--5896635 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
5896432 CTTTAAATAT
**
5896442 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
5896503 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
5896563 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
5896623 CGCGTTGCGATTT
1 CGCGTTGCGATTT
5896636 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:5896652 original size:21 final size:20
Alignment explanation
Indices: 5896628--5896704 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
5896618 ATATTCGCGT
5896628 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
5896649 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
5896669 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
5896691 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
5896705 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:5896715 original size:20 final size:20
Alignment explanation
Indices: 5896690--5896741 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
5896680 AAGAATCGCG
*
5896690 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
5896710 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
5896730 TTGCGATTCTGG
1 TTGCGATTCTGG
5896742 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:5901056 original size:2 final size:2
Alignment explanation
Indices: 5901047--5901086 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
5901037 AAAATATAAA
5901047 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5901087 ATCGGGGCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5903096 original size:74 final size:74
Alignment explanation
Indices: 5902989--5903202 Score: 322
Period size: 74 Copynumber: 2.9 Consensus size: 74
5902979 ATTCAATCTT
* * *
5902989 TTTCACCTTTGATGAGGACACTCCCCAATGAGTAAGAATATGCATGAATCTCATTACCGCATTCA
1 TTTCACCTCTCATGAGGACACTCCCCAAGGAGTAAGAATATGCATGAATCTCATTACCGCATTCA
5903054 TTTAGACTC
66 TTTAGACTC
* * ** *
5903063 TTTCACCTCTCATGAGGACACTTCCCAAGGAGTAAGAATATGCATGACTAACATTACCACATTCA
1 TTTCACCTCTCATGAGGACACTCCCCAAGGAGTAAGAATATGCATGAATCTCATTACCGCATTCA
*
5903128 TTTAGACTT
66 TTTAGACTC
*
5903137 TTTCACCTCTCATGAGGACACTCCCCAAGGAGTAAGGATATGCATGAATCGT-ATTACCGCATTC
1 TTTCACCTCTCATGAGGACACTCCCCAAGGAGTAAGAATATGCATGAATC-TCATTACCGCATTC
5903201 AT
65 AT
5903203 GAAAACATTA
Statistics
Matches: 124, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
74 124 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29
Consensus pattern (74 bp):
TTTCACCTCTCATGAGGACACTCCCCAAGGAGTAAGAATATGCATGAATCTCATTACCGCATTCA
TTTAGACTC
Found at i:5906030 original size:24 final size:24
Alignment explanation
Indices: 5906003--5906054 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
5905993 AACGGATATA
*
5906003 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
5906027 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
5906051 TCAA
1 TCAA
5906055 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:5906055 original size:24 final size:24
Alignment explanation
Indices: 5906023--5906141 Score: 161
Period size: 24 Copynumber: 5.0 Consensus size: 24
5906013 AAACATAAAT
*
5906023 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
*
5906047 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
5906071 CAAGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
5906095 CATGTC-AGATATCAGATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
*
5906119 CATGTCAAGTATCAGATCAGAAT
1 CAGGTCAAGTATCAGATCAGAAT
5906142 TCAAATCGAA
Statistics
Matches: 87, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
23 5 0.06
24 80 0.92
25 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:5906157 original size:48 final size:48
Alignment explanation
Indices: 5906059--5906159 Score: 141
Period size: 48 Copynumber: 2.1 Consensus size: 48
5906049 GGTCAAGTAA
** *
5906059 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCATGTCAGATAT
1 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAAAT
* *
5906107 CAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAATC-GAAAAT
1 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAG-AAAT
5906155 CAGAT
1 CAGAT
5906160 AAAATATTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 1 0.02
48 46 0.98
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.23
Consensus pattern (48 bp):
CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAAAT
Found at i:5908650 original size:18 final size:18
Alignment explanation
Indices: 5908627--5908669 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
5908617 AATGGGTCAA
5908627 CGGGTCAGGTAAACGGAT
1 CGGGTCAGGTAAACGGAT
* * * *
5908645 CGGGTCGGGTCAATGGGT
1 CGGGTCAGGTAAACGGAT
5908663 CGGGTCA
1 CGGGTCA
5908670 ACGGGTAGGG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.44, T:0.19
Consensus pattern (18 bp):
CGGGTCAGGTAAACGGAT
Found at i:5908657 original size:31 final size:31
Alignment explanation
Indices: 5908620--5908685 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
5908610 AACGGTCAAT
*
5908620 GGGTCAACGGGTCAGGTAAACGGATCGGGTC
1 GGGTCAACGGGTCAGGTAAACGGATAGGGTC
* * * *
5908651 GGGTCAATGGGTCGGGTCAACGGGTAGGGTC
1 GGGTCAACGGGTCAGGTAAACGGATAGGGTC
5908682 GGGT
1 GGGT
5908686 TGTGACAGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.18, C:0.17, G:0.47, T:0.18
Consensus pattern (31 bp):
GGGTCAACGGGTCAGGTAAACGGATAGGGTC
Found at i:5908664 original size:13 final size:13
Alignment explanation
Indices: 5908645--5908681 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
5908635 GTAAACGGAT
5908645 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
5908658 TGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
5908671 CGGGTAGGGTC
1 CGGGTCGGGTC
5908682 GGGTTGTGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.14, C:0.19, G:0.49, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:5912552 original size:13 final size:13
Alignment explanation
Indices: 5912534--5912559 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5912524 AATTTATTAC
5912534 TTTTAATAATTTA
1 TTTTAATAATTTA
5912547 TTTTAATAATTTA
1 TTTTAATAATTTA
5912560 AAATTAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTAATAATTTA
Found at i:5913828 original size:32 final size:33
Alignment explanation
Indices: 5913752--5913859 Score: 91
Period size: 32 Copynumber: 3.4 Consensus size: 33
5913742 TTGGATTAGT
** * *
5913752 TTTGGTTTAGGTTAC-TTTCGGATCGAGTTAAA
1 TTTGGTTCGGGTTACTTTTCGGTTCTAGTTAAA
** * *
5913784 TTAAGTTTGGGTT-GTTTTCGGTTCTAGTTAAA
1 TTTGGTTCGGGTTACTTTTCGGTTCTAGTTAAA
5913816 TTTGGTTCGGGTTACTTTT-GGTT-TAGGTT-AA
1 TTTGGTTCGGGTTACTTTTCGGTTCTA-GTTAAA
5913847 TTTCGGTTCGGGT
1 TTT-GGTTCGGGT
5913860 CAAATTGGAT
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
31 7 0.11
32 51 0.82
33 4 0.06
ACGTcount: A:0.16, C:0.08, G:0.28, T:0.48
Consensus pattern (33 bp):
TTTGGTTCGGGTTACTTTTCGGTTCTAGTTAAA
Found at i:5913829 original size:16 final size:16
Alignment explanation
Indices: 5913810--5913865 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
5913800 TTCGGTTCTA
5913810 GTTAAATTTGGTTCGG
1 GTTAAATTTGGTTCGG
** **
5913826 GTTACTTTTGGTTTAG
1 GTTAAATTTGGTTCGG
5913842 GTT-AATTTCGGTTCGG
1 GTTAAATTT-GGTTCGG
*
5913858 GTCAAATT
1 GTTAAATT
5913866 GGATAAGGGT
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
15 3 0.10
16 22 0.76
17 4 0.14
ACGTcount: A:0.18, C:0.09, G:0.27, T:0.46
Consensus pattern (16 bp):
GTTAAATTTGGTTCGG
Found at i:5916004 original size:22 final size:20
Alignment explanation
Indices: 5915931--5915995 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
5915921 ATTCGATCCC
5915931 TTTTTCAGAATTAAGCTCCG
1 TTTTTCAGAATTAAGCTCCG
*
5915951 TTTTTCAGAATTAAGCTCTG
1 TTTTTCAGAATTAAGCTCCG
*
5915971 TTTTTCAGAATTAATCTCCG
1 TTTTTCAGAATTAAGCTCCG
5915991 TTTTT
1 TTTTT
5915996 TATGTAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.48
Consensus pattern (20 bp):
TTTTTCAGAATTAAGCTCCG
Found at i:5928630 original size:21 final size:22
Alignment explanation
Indices: 5928606--5928664 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
5928596 CATTGTAAGA
* *
5928606 AAGGGATCGATCATTTTTGT-G
1 AAGGGATCGATCCTTTTTCTCG
* *
5928627 AAGGAAT-GATCCTTTTACTCG
1 AAGGGATCGATCCTTTTTCTCG
5928648 -AGGGATCGATCCTTTTT
1 AAGGGATCGATCCTTTTT
5928665 ATAAAAGGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (22 bp):
AAGGGATCGATCCTTTTTCTCG
Found at i:5928744 original size:21 final size:22
Alignment explanation
Indices: 5928715--5928755 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5928705 TGATCATTTT
* *
5928715 TCAAGGGGATTGA-TCCTTTGG
1 TCAAAGGGATCGATTCCTTTGG
5928736 TCAAAGGGATCGATTCCTTT
1 TCAAAGGGATCGATTCCTTT
5928756 TCCAATAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (22 bp):
TCAAAGGGATCGATTCCTTTGG
Found at i:5928825 original size:25 final size:25
Alignment explanation
Indices: 5928797--5928848 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
5928787 CTTGGAAACT
*
5928797 AGACTTTAAAGCGTAAAAATGATCG
1 AGACTTTAAAGCGTAAAAAAGATCG
5928822 AGACTTTAAAGCGTAAAAAAGATCG
1 AGACTTTAAAGCGTAAAAAAGATCG
5928847 AG
1 AG
5928849 TATGTTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (25 bp):
AGACTTTAAAGCGTAAAAAAGATCG
Found at i:5932685 original size:12 final size:12
Alignment explanation
Indices: 5932639--5932688 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
5932629 GCAACACCAA
5932639 CTTTCTTTT-TGT
1 CTTTCTTTTCT-T
5932651 -TTTC-TTTCTTT
1 CTTTCTTTTC-TT
*
5932662 CTTTCTTCTCTT
1 CTTTCTTTTCTT
5932674 CTTTCTTTTCTT
1 CTTTCTTTTCTT
5932686 CTT
1 CTT
5932689 CCTGCTCCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
10 3 0.09
11 5 0.16
12 21 0.66
13 3 0.09
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (12 bp):
CTTTCTTTTCTT
Found at i:5932689 original size:20 final size:20
Alignment explanation
Indices: 5932639--5932681 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
5932629 GCAACACCAA
* *
5932639 CTTTCTTT-TTGTTTTCTTT
1 CTTTCTTTCTTCTCTTCTTT
5932658 CTTTCTTTCTTCTCTTCTTT
1 CTTTCTTTCTTCTCTTCTTT
5932678 CTTT
1 CTTT
5932682 TCTTCTTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.74
Consensus pattern (20 bp):
CTTTCTTTCTTCTCTTCTTT
Found at i:5933574 original size:68 final size:68
Alignment explanation
Indices: 5933440--5933573 Score: 234
Period size: 68 Copynumber: 2.0 Consensus size: 68
5933430 TCAACCGAAT
*
5933440 AACGCCAAGATGAGGTGAATTGACTTTTTAAGAATTTGGTGGAAGCAATAGAAAAAATAAAATTT
1 AACGCCAAGAGGAGGTGAATTGACTTTTTAAGAATTTGGTGGAAGCAATAGAAAAAATAAAATTT
5933505 TTG
66 TTG
* *
5933508 AACGCCAAGAGGGGGTGAATTGACTTTTTAAGAATTTGGTGGAAGCAATA-AAAAAATAAACTTT
1 AACGCCAAGAGGAGGTGAATTGACTTTTTAAGAATTTGGTGGAAGCAATAGAAAAAATAAAATTT
5933572 TT
66 TT
5933574 TCATGCAAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
67 15 0.24
68 48 0.76
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.29
Consensus pattern (68 bp):
AACGCCAAGAGGAGGTGAATTGACTTTTTAAGAATTTGGTGGAAGCAATAGAAAAAATAAAATTT
TTG
Found at i:5934217 original size:21 final size:21
Alignment explanation
Indices: 5934188--5934255 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
5934178 CAATCATTTT
*
5934188 TCAAGGGGATCGATCCTTTGG
1 TCAAAGGGATCGATCCTTTGG
** *
5934209 TCAAAGGGATTAATCCTTT-T
1 TCAAAGGGATCGATCCTTTGG
*
5934229 TCAAGGGGATCGATCCTTTGG
1 TCAAAGGGATCGATCCTTTGG
5934250 TCAAAG
1 TCAAAG
5934256 AAAAGCTTGA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 16 0.43
21 21 0.57
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (21 bp):
TCAAAGGGATCGATCCTTTGG
Done.