Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 51
Found at i:3818267 original size:22 final size:22
Alignment explanation
Indices: 3818242--3818284 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3818232 GTAATTTATA
**
3818242 ATGTTATCATTTATATATATTG
1 ATGTTATCAAATATATATATTG
*
3818264 ATGTTGTCAAATATATATATT
1 ATGTTATCAAATATATATATT
3818285 TATAATATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (22 bp):
ATGTTATCAAATATATATATTG
Found at i:3838057 original size:20 final size:20
Alignment explanation
Indices: 3838032--3838074 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
3838022 TATAAAAGCC
*
3838032 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
3838052 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
3838072 CAT
1 CAT
3838075 GTGGTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:3843338 original size:14 final size:14
Alignment explanation
Indices: 3843318--3843352 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
3843308 CCACTTTATA
3843318 AAAAAAAGAGAAAAG
1 AAAAAAAGA-AAAAG
3843333 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
3843347 AAAAAA
1 AAAAAA
3843353 TGAAGCTGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:3843989 original size:20 final size:20
Alignment explanation
Indices: 3843964--3844006 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
3843954 TCTAAAAGCC
*
3843964 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
3843984 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
3844004 CAT
1 CAT
3844007 GTGGTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:3848629 original size:23 final size:23
Alignment explanation
Indices: 3848603--3848673 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
3848593 TCGATATACA
3848603 TTCAAGGAATGCATCGGTGCAAT
1 TTCAAGGAATGCATCGGTGCAAT
* *
3848626 TTCACA-G--TGTATCGATGCACAT
1 TTCA-AGGAATGCATCGGTGCA-AT
* *
3848648 TT-AAGGAATGCATCGGTACACT
1 TTCAAGGAATGCATCGGTGCAAT
3848670 TTCA
1 TTCA
3848674 TAGTGTATCG
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
20 1 0.03
21 12 0.33
22 7 0.19
23 15 0.42
24 1 0.03
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (23 bp):
TTCAAGGAATGCATCGGTGCAAT
Found at i:3848686 original size:44 final size:44
Alignment explanation
Indices: 3848587--3848686 Score: 146
Period size: 44 Copynumber: 2.3 Consensus size: 44
3848577 TACACTCTTG
** *
3848587 AGTGTATCGATATACATTCAAGGAATGCATCGGTGCAATTTCAC
1 AGTGTATCGATGCACATTCAAGGAATGCATCGGTACAATTTCAC
* * *
3848631 AGTGTATCGATGCACATTTAAGGAATGCATCGGTACACTTTCAT
1 AGTGTATCGATGCACATTCAAGGAATGCATCGGTACAATTTCAC
3848675 AGTGTATCGATG
1 AGTGTATCGATG
3848687 GACTTTACAC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (44 bp):
AGTGTATCGATGCACATTCAAGGAATGCATCGGTACAATTTCAC
Found at i:3852637 original size:2 final size:2
Alignment explanation
Indices: 3852630--3852655 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3852620 AATTCATTTA
3852630 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3852656 GAAATTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3854233 original size:3 final size:3
Alignment explanation
Indices: 3854225--3854267 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
3854215 AGTATTTTAT
* **
3854225 ATA ATA ATA ATA ATA ATA ATA GTA GCA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3854268 ACAATTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:3866126 original size:39 final size:39
Alignment explanation
Indices: 3866057--3866146 Score: 108
Period size: 39 Copynumber: 2.3 Consensus size: 39
3866047 ATGGTGCGTA
* * *
3866057 GTAAGGACTTACCCTATGCACAAAGCAGAGGAGTCTGCG
1 GTAAGGACTTACCCTATGCAAAAAGCAGAGGACTCTACG
* * * *
3866096 GTAAGGACTTACCTTGTGCAAAAAGTAGAGGACTCTATG
1 GTAAGGACTTACCCTATGCAAAAAGCAGAGGACTCTACG
*
3866135 GTAAGGTCTTAC
1 GTAAGGACTTAC
3866147 AAGTCATAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (39 bp):
GTAAGGACTTACCCTATGCAAAAAGCAGAGGACTCTACG
Found at i:3868742 original size:35 final size:35
Alignment explanation
Indices: 3868678--3868745 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 35
3868668 ACCTAGGTCC
*
3868678 ATAAGGAATTACCAGTTCGATCGGCCTGAACCTAT
1 ATAAGGAATTACCAGTTCGACCGGCCTGAACCTAT
3868713 ATAAGGAATTACCAGCTT-GACCGAG-CTGAACCT
1 ATAAGGAATTACCAG-TTCGACCG-GCCTGAACCT
3868746 GCAGTGACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 27 0.90
36 3 0.10
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (35 bp):
ATAAGGAATTACCAGTTCGACCGGCCTGAACCTAT
Found at i:3868865 original size:8 final size:8
Alignment explanation
Indices: 3868852--3868880 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
3868842 ATTCAGTAAT
3868852 ATCAGACA
1 ATCAGACA
3868860 ATCAGACA
1 ATCAGACA
3868868 ATCAGACA
1 ATCAGACA
3868876 ATCAG
1 ATCAG
3868881 GCTTAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.14, T:0.14
Consensus pattern (8 bp):
ATCAGACA
Found at i:3891759 original size:55 final size:55
Alignment explanation
Indices: 3891618--3891958 Score: 411
Period size: 55 Copynumber: 6.2 Consensus size: 55
3891608 TTCATTAGGA
* * * * * *
3891618 TGCACACATAGTGCCTATATGGTAATTTATCAACTCATGATGAA-TCTCGTGG-GT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTC-CGTGGATT
* ** *
3891672 TGCACACATAATGCATGTAATGTTATTAATCAACTCATGATGAA-TCCTGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCC-GTGGATT
* * * *
3891727 TGCACAAAAAGTG-ACTGTACGATTATTCATCAACTCATGATGAATTCTGTGGATT
1 TGCACACATAGTGCA-TGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * *
3891782 TACACACATAGTGCATATACGGTTATTCATCAAATCATGATGAATTCCGTTGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * *
3891837 TACATACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
*
3891892 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATAAATTCCGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* *
3891947 TGTACAGATAGT
1 TGCACACATAGT
3891959 ACCTGTAGTA
Statistics
Matches: 247, Mismatches: 35, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
53 1 0.00
54 44 0.18
55 199 0.81
56 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (55 bp):
TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
Found at i:3892335 original size:22 final size:22
Alignment explanation
Indices: 3892304--3892346 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3892294 TATCGATATT
*
3892304 CATACCATGGTATCGATACTAC
1 CATACCATGGTACCGATACTAC
* *
3892326 CATACTATGGTACCGCTACTA
1 CATACCATGGTACCGATACTA
3892347 TGCAATGGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (22 bp):
CATACCATGGTACCGATACTAC
Found at i:3893381 original size:14 final size:15
Alignment explanation
Indices: 3893350--3893382 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3893340 ATCTAATTAG
3893350 CTTCTTTTTCAACTTT
1 CTTCTTTTTC-ACTTT
3893366 CTTCTTTTTC-CTTT
1 CTTCTTTTTCACTTT
3893380 CTT
1 CTT
3893383 AAATACCCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
16 10 0.59
ACGTcount: A:0.06, C:0.27, G:0.00, T:0.67
Consensus pattern (15 bp):
CTTCTTTTTCACTTT
Found at i:3894851 original size:2 final size:2
Alignment explanation
Indices: 3894841--3894886 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
3894831 ATTTGTTACA
3894841 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
3894883 AT AT
1 AT AT
3894887 GTTAGCAGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3894986 original size:29 final size:29
Alignment explanation
Indices: 3894941--3894999 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
3894931 ATAATATTGA
* * *
3894941 TATTTTTTAAATTTGACATTATTTTATAT
1 TATTTTTTAAATATGACATTAGTTCATAT
3894970 TATTTTTT-AATCATGACATTAGTTCATAT
1 TATTTTTTAAAT-ATGACATTAGTTCATAT
3894999 T
1 T
3895000 CAATATATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 3 0.12
29 23 0.88
ACGTcount: A:0.31, C:0.07, G:0.05, T:0.58
Consensus pattern (29 bp):
TATTTTTTAAATATGACATTAGTTCATAT
Found at i:3897654 original size:14 final size:14
Alignment explanation
Indices: 3897630--3897676 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 14
3897620 AGTTTGTGAC
3897630 TTATT-TATAATTA
1 TTATTATATAATTA
3897643 TTATTATAT-A--A
1 TTATTATATAATTA
3897654 TTATTATATAATTA
1 TTATTATATAATTA
3897668 TTTATTATA
1 -TTATTATA
3897677 AATAATGGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 10 0.34
12 1 0.03
13 6 0.21
14 4 0.14
15 8 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATTATATAATTA
Found at i:3902876 original size:21 final size:21
Alignment explanation
Indices: 3902852--3902916 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
3902842 ATATGATCAA
*
3902852 TAATTTTTCAAATTGGCCATT
1 TAATTTTTCAAATTGACCATT
*
3902873 TAATTTTTCAAATTGACCTTT
1 TAATTTTTCAAATTGACCATT
*
3902894 TAACTTTTCAAATTGACCATT
1 TAATTTTTCAAATTGACCATT
3902915 TA
1 TA
3902917 TTATAGAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.48
Consensus pattern (21 bp):
TAATTTTTCAAATTGACCATT
Found at i:3904295 original size:12 final size:12
Alignment explanation
Indices: 3904278--3904302 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3904268 TTGCACTTTG
3904278 GTTATTTATTTT
1 GTTATTTATTTT
3904290 GTTATTTATTTT
1 GTTATTTATTTT
3904302 G
1 G
3904303 AATATGCATA
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:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (12 bp):
GTTATTTATTTT
Found at i:3904622 original size:25 final size:26
Alignment explanation
Indices: 3904585--3904633 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
3904575 TATTTTATTT
* *
3904585 TTATTTGGTTGTTTTTACTATTTTTA
1 TTATTTGGATGTTTTAACTATTTTTA
*
3904611 TTATTT-GATGTTTTAATTATTTT
1 TTATTTGGATGTTTTAACTATTTT
3904634 AATTTAGTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.18, C:0.02, G:0.10, T:0.69
Consensus pattern (26 bp):
TTATTTGGATGTTTTAACTATTTTTA
Found at i:3906575 original size:149 final size:149
Alignment explanation
Indices: 3906293--3906580 Score: 350
Period size: 149 Copynumber: 1.9 Consensus size: 149
3906283 AGTAGCGTCA
* *
3906293 AGAGGTAGTCTACCTACCAAGGAGATGAGCCTGACATCTGTCTGCTGAGGTAACAAGTTAGACTC
1 AGAGGGAGTCTACCTACCAAGGAGATGAGCCTGACATCTGTCTACTGAGGTAACAAGTTAGACTC
** * * * * *
3906358 GAGATGATTTGATGTTGAAGCCAACAGTTAAAGATCACGAACCAGCTCAAACAATTTCTGGAAAT
66 GAGACAATTTGACGCTGAAGCCAACAGTTAAAGATCAAGAACCAGCTCAAACAACTTCTGAAAAT
3906423 AGGAGATGAAGCAGGAGCT
131 AGGAGATGAAGCAGGAGCT
* ** * *
3906442 AGAGGGAGTCTATCTACCAAGGAGATG-TTCTAGACAT-TTTCCTACTGAGGTAACAAGTTGGAC
1 AGAGGGAGTCTACCTACCAAGGAGATGAGCCT-GACATCTGT-CTACTGAGGTAACAAGTTAGAC
* * * *
3906505 TCGAGACAATTTGACGCTGAATCCAACAGTTGAAGATGAAGAACCAGCTCGAAA-GACTTCT-AA
64 TCGAGACAATTTGACGCTGAAGCCAACAGTTAAAGATCAAGAACCAGCTC-AAACAACTTCTGAA
3906568 AAGTAGGAGATGA
128 AA-TAGGAGATGA
3906581 GGTAGAAGCT
Statistics
Matches: 117, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
148 7 0.06
149 107 0.91
150 3 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.23
Consensus pattern (149 bp):
AGAGGGAGTCTACCTACCAAGGAGATGAGCCTGACATCTGTCTACTGAGGTAACAAGTTAGACTC
GAGACAATTTGACGCTGAAGCCAACAGTTAAAGATCAAGAACCAGCTCAAACAACTTCTGAAAAT
AGGAGATGAAGCAGGAGCT
Found at i:3909328 original size:101 final size:104
Alignment explanation
Indices: 3909153--3909337 Score: 261
Period size: 101 Copynumber: 1.8 Consensus size: 104
3909143 CTTGATACAC
* * * * **
3909153 TTTCTTTCAAAACAATTTTCGTCTCACTTGAGACATTTTTTTCCTATGAGATGCAAATTCTGAGT
1 TTTCTTTCAAAACAAGTTTCGTCTCACTAGAGACATTTTTTTCCTATAAAATGCAAATTCTGAAA
*
3909218 TTGTTTCACTTA-AAACAAAGCTGGTCTCACTTGAGATTG
66 TTATTTCAC-TAGAAACAAAGCTGGTCTCACTTGAGATTG
*
3909257 TTTCTTTCAAAAC-AGTTTCGTCTCACTAGAGAC-TTTTTTT-CTTTAAAATGCAAATTCTGAAA
1 TTTCTTTCAAAACAAGTTTCGTCTCACTAGAGACATTTTTTTCCTATAAAATGCAAATTCTGAAA
3909319 TTATTTCACTAGAAACAAA
66 TTATTTCACTAGAAACAAA
3909338 ATTGATAAAC
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
100 2 0.03
101 32 0.44
102 7 0.10
103 18 0.25
104 13 0.18
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (104 bp):
TTTCTTTCAAAACAAGTTTCGTCTCACTAGAGACATTTTTTTCCTATAAAATGCAAATTCTGAAA
TTATTTCACTAGAAACAAAGCTGGTCTCACTTGAGATTG
Found at i:3909353 original size:101 final size:104
Alignment explanation
Indices: 3909153--3909362 Score: 250
Period size: 101 Copynumber: 2.0 Consensus size: 104
3909143 CTTGATACAC
* * * * **
3909153 TTTCTTTCAAAACAATTTTCGTCTCACTTGAGACATTTTTTTCCTATGAGATGCAAATTCTGAGT
1 TTTCTTTCAAAACAAGTTTCGTCTCACTAGAGACATTTTTTTCCTATAAAATGCAAATTCTGAAA
* * * **
3909218 TTGTTTCACTTAAAACAAAGCTGGTCTCACTTGAGATTG
66 TTATTTCACTTAAAACAAAACTGATCAAACTTGAGATTG
*
3909257 TTTCTTTCAAAAC-AGTTTCGTCTCACTAGAGAC-TTTTTTT-CTTTAAAATGCAAATTCTGAAA
1 TTTCTTTCAAAACAAGTTTCGTCTCACTAGAGACATTTTTTTCCTATAAAATGCAAATTCTGAAA
*
3909319 TTATTTCAC-TAGAAACAAAATTGAT-AAACTTTGAGATTG
66 TTATTTCACTTA-AAACAAAACTGATCAAAC-TTGAGATTG
3909358 TTTCT
1 TTTCT
3909363 CTATAAAAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
100 4 0.04
101 49 0.54
102 7 0.08
103 18 0.20
104 13 0.14
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (104 bp):
TTTCTTTCAAAACAAGTTTCGTCTCACTAGAGACATTTTTTTCCTATAAAATGCAAATTCTGAAA
TTATTTCACTTAAAACAAAACTGATCAAACTTGAGATTG
Found at i:3909556 original size:64 final size:65
Alignment explanation
Indices: 3909395--3909575 Score: 238
Period size: 65 Copynumber: 2.8 Consensus size: 65
3909385 CTTGAGATCA
* * * *
3909395 TTTCCCTTGAAATGAATTTTGTCTCTTTTAAGACAGTTTCTCTTGAAACATAAATTTTGAAAACG
1 TTTCCCTTGAAACGAATTTTGTCTCTTTTGAGACATTTTCTCTTGAAACATAAACTTTGAAAACG
* **
3909460 CTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACATTTTCTCTTGAAACATAAACTTTG-AAACG
1 TTTCCCTTGAAACGAATTTTGTCTCTTTTGAGACATTTTCTCTTGAAACATAAACTTTGAAAACG
* ** * * *
3909524 TTTCACTTGAAACGAATTTCATCTCTTTTGAGATATTTTCCCTTCAAACATA
1 TTTCCCTTGAAACGAATTTTGTCTCTTTTGAGACATTTTCTCTTGAAACATA
3909576 GTTTTGTCTC
Statistics
Matches: 100, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
64 48 0.48
65 52 0.52
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (65 bp):
TTTCCCTTGAAACGAATTTTGTCTCTTTTGAGACATTTTCTCTTGAAACATAAACTTTGAAAACG
Found at i:3909992 original size:37 final size:37
Alignment explanation
Indices: 3909951--3910067 Score: 121
Period size: 37 Copynumber: 3.2 Consensus size: 37
3909941 ACCAACTTCG
*
3909951 TCTCACTTGAGACAATTTTCCCTTGAAACAAAATGTA
1 TCTCACTTGAGACAGTTTTCCCTTGAAACAAAATGTA
** * * ** *
3909988 TCTCACTTGAGATGGTTTT-TCTTAAAATCAACTTG-G
1 TCTCACTTGAGACAGTTTTCCCTTGAAA-CAAAATGTA
* *
3910024 TCTCACTTGAGACAGTTTTCCCTCGAAACAAAATTTA
1 TCTCACTTGAGACAGTTTTCCCTTGAAACAAAATGTA
3910061 TCTCACT
1 TCTCACT
3910068 CAAGAGAGCT
Statistics
Matches: 60, Mismatches: 17, Indels: 6
0.72 0.20 0.07
Matches are distributed among these distances:
36 27 0.45
37 33 0.55
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (37 bp):
TCTCACTTGAGACAGTTTTCCCTTGAAACAAAATGTA
Found at i:3910035 original size:36 final size:34
Alignment explanation
Indices: 3909916--3910035 Score: 105
Period size: 37 Copynumber: 3.4 Consensus size: 34
3909906 AGAAATTTTA
* *
3909916 TCTCACTCGAGATGTTTTTCTTAAAACCAACTTCG
1 TCTCACTTGAGATGTTTTTCTTAAAA-CAACTTGG
** * * ** *
3909951 TCTCACTTGAGACAATTTTCCCTTGAAACAAAATGTA
1 TCTCACTTGAGA-TGTTTT-TCTTAAAACAACTTG-G
3909988 TCTCACTTGAGATGGTTTTTCTTAAAATCAACTTGG
1 TCTCACTTGAGAT-GTTTTTCTTAAAA-CAACTTGG
3910024 TCTCACTTGAGA
1 TCTCACTTGAGA
3910036 CAGTTTTCCC
Statistics
Matches: 64, Mismatches: 16, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
35 11 0.17
36 26 0.41
37 27 0.42
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (34 bp):
TCTCACTTGAGATGTTTTTCTTAAAACAACTTGG
Found at i:3910042 original size:36 final size:35
Alignment explanation
Indices: 3909916--3910042 Score: 112
Period size: 36 Copynumber: 3.5 Consensus size: 35
3909906 AGAAATTTTA
* * *
3909916 TCTCACTCGAGA-TGTTTTTCTTAAAACCAACTTCG
1 TCTCACTTGAGACAGTTTTTCTTAAAA-CAACTTGG
* * * ** *
3909951 TCTCACTTGAGACAATTTTCCCTTGAAACAAAATGTA
1 TCTCACTTGAGACAGTTTT-TCTTAAAACAACTTG-G
**
3909988 TCTCACTTGAGATGGTTTTTCTTAAAATCAACTTGG
1 TCTCACTTGAGACAGTTTTTCTTAAAA-CAACTTGG
3910024 TCTCACTTGAGACAGTTTT
1 TCTCACTTGAGACAGTTTT
3910043 CCCTCGAAAC
Statistics
Matches: 69, Mismatches: 19, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
35 11 0.16
36 31 0.45
37 27 0.39
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (35 bp):
TCTCACTTGAGACAGTTTTTCTTAAAACAACTTGG
Found at i:3910087 original size:73 final size:75
Alignment explanation
Indices: 3909654--3910068 Score: 458
Period size: 73 Copynumber: 5.6 Consensus size: 75
3909644 ACAAATTTCA
* *
3909654 TCTCACTTGAGACAG-TTTCCCTCGAAACAAGAAATTTTATCTCACTCAAGATGGTTTTTCTTAA
1 TCTCACTTGAGACAGTTTTCCCTTGAAACAAGAAA-TTTATCTCACTCGAGATGGTTTTTCTTAA
3909718 AACCAACTTCG
65 AACCAACTTCG
* ** * * * * * *
3909729 TCTCACTTGAGACATTTTTCGTTTGCAA-TA-AAATTTACCTCACTTGAGATTGTTTTTCTCAAA
1 TCTCACTTGAGACAGTTTTCCCTTGAAACAAGAAATTTATCTCACTCGAGATGGTTTTTCTTAAA
* *
3909792 A-GAAGTTTCG
66 ACCAA-CTTCG
* * * *
3909802 TCCCA-TTGGAGACA-ATTTCCCTAGAAACAAGAAATCTTATCTCACTTGAGATGGTTTTTCTTA
1 TCTCACTT-GAGACAGTTTTCCCTTGAAACAAGAAAT-TTATCTCACTCGAGATGGTTTTTCTTA
* *
3909865 AAACCAATTTCC
64 AAACCAACTTCG
* *
3909877 TCTCACTGGACACAG-TTTCCCTTGAAACAAGAAATTTTATCTCACTCGAGAT-GTTTTTCTTAA
1 TCTCACTTGAGACAGTTTTCCCTTGAAACAAGAAA-TTTATCTCACTCGAGATGGTTTTTCTTAA
3909940 AACCAACTTCG
65 AACCAACTTCG
* * *
3909951 TCTCACTTGAGACAATTTTCCCTTGAAAC-A-AAATGTATCTCACTTGAGATGGTTTTTCTTAAA
1 TCTCACTTGAGACAGTTTTCCCTTGAAACAAGAAATTTATCTCACTCGAGATGGTTTTTCTTAAA
* *
3910014 ATCAACTTGG
66 ACCAACTTCG
*
3910024 TCTCACTTGAGACAGTTTTCCCTCGAAAC-A-AAATTTATCTCACTC
1 TCTCACTTGAGACAGTTTTCCCTTGAAACAAGAAATTTATCTCACTC
3910069 AAGAGAGCTT
Statistics
Matches: 285, Mismatches: 43, Indels: 26
0.81 0.12 0.07
Matches are distributed among these distances:
72 27 0.09
73 105 0.37
74 40 0.14
75 101 0.35
76 12 0.04
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.35
Consensus pattern (75 bp):
TCTCACTTGAGACAGTTTTCCCTTGAAACAAGAAATTTATCTCACTCGAGATGGTTTTTCTTAAA
ACCAACTTCG
Found at i:3910116 original size:147 final size:146
Alignment explanation
Indices: 3909654--3910087 Score: 348
Period size: 148 Copynumber: 2.9 Consensus size: 146
3909644 ACAAATTTCA
* * * * **
3909654 TCTCACTTGAGAC-AGTTTCCCTCGAAACAAGAAATTTTATCTCACTCAAGATGGTTTTTCTTAA
1 TCTCACTTCAGACAATTTTCCCTTGAAAC-A-AAA-TGTATCTCACTTGAGATGGTTTTTCTTAA
* * * * *** * * * *
3909718 AACCAACTTCGTCTCACTTGAGACA-TTT--TTCGTTTGCAATAAAATTTACCTCACTTGAGATT
63 AACCAACTTCCTCTCACTGGACACAGTTTCCCTCG-AAACAAGAAATTTTATCTCACTCGAGA-T
* * * * *
3909780 GTTTTTCTCAAAAGAAGTTTCG
126 GCTTCTCTTAAAACAA-CTTCG
* * * *
3909802 TCCCA-TTGGAGACAA-TTTCCCTAGAAACAAGAAATCTTATCTCACTTGAGATGGTTTTTCTTA
1 TCTCACTT-CAGACAATTTTCCCTTGAAAC-A-AAAT-GTATCTCACTTGAGATGGTTTTTCTTA
* *
3909865 AAACCAATTTCCTCTCACTGGACACAGTTTCCCTTGAAACAAGAAATTTTATCTCACTCGAGATG
62 AAACCAACTTCCTCTCACTGGACACAGTTTCCCTCGAAACAAGAAATTTTATCTCACTCGAGATG
* *
3909930 TTTTTCTTAAAACCAACTTCG
127 CTTCTCTTAAAA-CAACTTCG
* *
3909951 TCTCACTTGAGACAATTTTCCCTTGAAACAAAATGTATCTCACTTGAGATGGTTTTTCTTAAAAT
1 TCTCACTTCAGACAATTTTCCCTTGAAACAAAATGTATCTCACTTGAGATGGTTTTTCTTAAAAC
** * *
3910016 CAACTTGGTCTCACTTGAGACAGTTTTCCCTCGAAAC-A-AAA-TTTATCTCACTCAAGAGA-GC
66 CAACTTCCTCTCACTGGACACAG-TTTCCCTCGAAACAAGAAATTTTATCTCACTC--GAGATGC
3910077 TTCTCTTAAAA
128 TTCTCTTAAAA
3910088 AATTTCTTAT
Statistics
Matches: 242, Mismatches: 32, Indels: 26
0.81 0.11 0.09
Matches are distributed among these distances:
145 12 0.05
146 14 0.06
147 55 0.23
148 90 0.37
149 33 0.14
150 36 0.15
151 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.35
Consensus pattern (146 bp):
TCTCACTTCAGACAATTTTCCCTTGAAACAAAATGTATCTCACTTGAGATGGTTTTTCTTAAAAC
CAACTTCCTCTCACTGGACACAGTTTCCCTCGAAACAAGAAATTTTATCTCACTCGAGATGCTTC
TCTTAAAACAACTTCG
Found at i:3910501 original size:91 final size:91
Alignment explanation
Indices: 3910341--3910801 Score: 633
Period size: 91 Copynumber: 5.1 Consensus size: 91
3910331 AATGAAGATA
* * * * *
3910341 AACCTTGCATCAGCATTTCCAGTGGAGAGTTCCA-AATAAGAAGAACTC-GCCAAAAGAGGAAGA
1 AACCTTGCATCAACATTTCCAGTGGAGAGTT-CATAATGAGAAGAACTCATCC-AACGAGGGAGA
* *
3910404 ATAAGTTCATAGTGAGAAGAACTTGTTC
64 AGAAGTTCATAATGAGAAGAACTTGTTC
* * *
3910432 AACCTT-CGTTCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGTGAGAA
1 AACCTTGC-ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAA
*
3910496 GAAGTTCATAATGAGAAAAACTTGTTC
65 GAAGTTCATAATGAGAAGAACTTGTTC
* * * * * **
3910523 AACCTTGCATCAACGTTTCCAGTGGGGAGTTTATAATGAGAAGAACTCATCCGATGAGAAAGAAG
1 AACCTTGCATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAG
3910588 AAGTTCATAATGAGAAGAACTTGTTC
66 AAGTTCATAATGAGAAGAACTTGTTC
* *
3910614 AACCTTGCATCAACATTTCCAGCGGGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAG
1 AACCTTGCATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAG
*
3910679 AAGTTCATAATGAGAAGAATTTGTTC
66 AAGTTCATAATGAGAAGAACTTGTTC
* *
3910705 AACCTTG-ACTCAATATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGGGGGAGAA
1 AACCTTGCA-TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAA
* *
3910769 AAAGTTCATATTGAGAAGAACTTGTTC
65 GAAGTTCATAATGAGAAGAACTTGTTC
3910796 AACCTT
1 AACCTT
3910802 AGCTTGATTC
Statistics
Matches: 331, Mismatches: 34, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
90 4 0.01
91 324 0.98
92 3 0.01
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (91 bp):
AACCTTGCATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAG
AAGTTCATAATGAGAAGAACTTGTTC
Found at i:3911134 original size:21 final size:20
Alignment explanation
Indices: 3911110--3911149 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3911100 TAAACACCAT
*
3911110 TTTTTATTATTATTTATTTTC
1 TTTTTATTATCA-TTATTTTC
*
3911131 TTTTTGTTATCATTATTTT
1 TTTTTATTATCATTATTTT
3911150 ATTATGCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (20 bp):
TTTTTATTATCATTATTTTC
Found at i:3914119 original size:14 final size:14
Alignment explanation
Indices: 3914096--3914125 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3914086 CAGTTTATGC
*
3914096 AAATAGTGTAATTT
1 AAATACTGTAATTT
3914110 AAATACTGTAATTT
1 AAATACTGTAATTT
3914124 AA
1 AA
3914126 CTTAAGCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (14 bp):
AAATACTGTAATTT
Found at i:3914909 original size:24 final size:24
Alignment explanation
Indices: 3914882--3914934 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
3914872 ATTCTTTTTA
*
3914882 ATTGGTTTTAGATT-ACTTTTTTCT
1 ATTGATTTTAGATTGA-TTTTTTCT
* *
3914906 ATTGATTTTAGGTTGATTTTTTTT
1 ATTGATTTTAGATTGATTTTTTCT
3914930 ATTGA
1 ATTGA
3914935 AAGTAATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.19, C:0.04, G:0.15, T:0.62
Consensus pattern (24 bp):
ATTGATTTTAGATTGATTTTTTCT
Found at i:3915853 original size:15 final size:16
Alignment explanation
Indices: 3915833--3915863 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3915823 TATTGCTCGA
3915833 TTTTGAAAAA-TATTT
1 TTTTGAAAAAGTATTT
3915848 TTTTGAAAAAGTATTT
1 TTTTGAAAAAGTATTT
3915864 ATTACTACCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (16 bp):
TTTTGAAAAAGTATTT
Found at i:3919250 original size:24 final size:24
Alignment explanation
Indices: 3919180--3919238 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
3919170 ATTTCCAATT
* *
3919180 TGAATTATGTTCTGATACCTGATC
1 TGAATTATGTTATGATATCTGATC
*
3919204 TGAATTCTGTTATGATATCTGATC
1 TGAATTATGTTATGATATCTGATC
3919228 TGAATTATGTT
1 TGAATTATGTT
3919239 TGGATTTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (24 bp):
TGAATTATGTTATGATATCTGATC
Found at i:3921729 original size:75 final size:75
Alignment explanation
Indices: 3921631--3921860 Score: 268
Period size: 75 Copynumber: 3.0 Consensus size: 75
3921621 AACTTAAATA
* *
3921631 CTAATTAAAACACTTAAAACTATTTAAACTAAAAGACCTAAAACAAAA-ATAATATTTAAAATAT
1 CTAATTAAAATAC-TAAAACTATTTAAACTAAAATACCTAAAACAAAATATAATATTTAAAATAT
3921695 TATCCTAAAAC
65 TATCCTAAAAC
*
3921706 TTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAATATTTA
1 CTAATTAAAATACTAAAA-CTATTTAAACTAAAATACCTAAAAC------AAAATATAATATTTA
*
3921771 AAATATTATCCTAAATC
59 AAATATTATCCTAAAAC
* * * * *
3921788 CTAATTGAAATGCTAACATCTATTTAAACTAAAATA-C-AAAGATAAAATATAATGTTTAAAATA
1 CTAATTAAAATACTAA-AACTATTTAAACTAAAATACCTAAA-ACAAAATATAATATTTAAAATA
3921851 TTATCCTAAA
64 TTATCCTAAA
3921861 CTTGAGTTTA
Statistics
Matches: 135, Mismatches: 10, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
74 5 0.04
75 64 0.47
80 3 0.02
81 6 0.04
82 56 0.41
83 1 0.01
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.31
Consensus pattern (75 bp):
CTAATTAAAATACTAAAACTATTTAAACTAAAATACCTAAAACAAAATATAATATTTAAAATATT
ATCCTAAAAC
Found at i:3926353 original size:22 final size:22
Alignment explanation
Indices: 3926325--3926374 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
3926315 GGACTTACTC
3926325 AATTACTATATGATATTGGATA
1 AATTACTATATGATATTGGATA
*
3926347 AATTACTATCTGATATTGGATA
1 AATTACTATATGATATTGGATA
*
3926369 GATTAC
1 AATTAC
3926375 GTCAGCATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (22 bp):
AATTACTATATGATATTGGATA
Found at i:3935940 original size:178 final size:178
Alignment explanation
Indices: 3935609--3935942 Score: 415
Period size: 178 Copynumber: 1.9 Consensus size: 178
3935599 TTAGTATGTA
* * * *
3935609 GCATAATATAGTACATGGTGCATAACGTACTTTCAGGATACATTATGTGGCACAAAATAGTACAT
1 GCATAACATAGTACATGGTGCAAAACGTACTTTCAGAATACATTATATGGCACAAAATAGTACAT
* * * * *
3935674 GGTGCCTGCACAATATAGTAGATGGTGTAATGTATCATTCATTATTGATACAGAGATGTTGTGTT
66 GGTGCCTACACAATATAATAGATGGTGCAATGTATCATTCATTATGGATACACAGATGTTGTGTT
* * *
3935739 CTACAGTACATGTATATTCTATATGGAACAATATAGTATATGGTGTCT
131 CTACAGCACATATATACTCTATATGGAACAATATAGTATATGGTGTCT
** * * *
3935787 GCATAACATAGTACATGGTGCAAAACGTA-TGTTTTGAATGCATTATATGGCACAACATAGTATA
1 GCATAACATAGTACATGGTGCAAAACGTACT-TTCAGAATACATTATATGGCACAAAATAGTACA
* * *
3935851 TGGTGTCTACACAATATAATATATGGTGCAATGTATTC-TTTATTATGGATACATCA-ATGTTGT
65 TGGTGCCTACACAATATAATAGATGGTGCAATGTA-TCATTCATTATGGATACA-CAGATGTTGT
*
3935914 GTTTTACAGCAGC-TATATACTCTATATGG
128 GTTCTACAGCA-CATATATACTCTATATGG
3935943 CACTATATGA
Statistics
Matches: 131, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
177 1 0.01
178 126 0.96
179 4 0.03
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (178 bp):
GCATAACATAGTACATGGTGCAAAACGTACTTTCAGAATACATTATATGGCACAAAATAGTACAT
GGTGCCTACACAATATAATAGATGGTGCAATGTATCATTCATTATGGATACACAGATGTTGTGTT
CTACAGCACATATATACTCTATATGGAACAATATAGTATATGGTGTCT
Found at i:3937764 original size:19 final size:20
Alignment explanation
Indices: 3937728--3937766 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
3937718 ATGCTCGGAT
3937728 GGTACCGATACCCCCTCAGGA
1 GGTACCGATA-CCCCTCAGGA
3937749 GGTACCGATA-CCCTCAGG
1 GGTACCGATACCCCTCAGG
3937767 CATATAACGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.23, C:0.36, G:0.26, T:0.15
Consensus pattern (20 bp):
GGTACCGATACCCCTCAGGA
Found at i:3944404 original size:308 final size:307
Alignment explanation
Indices: 3943809--3944428 Score: 1215
Period size: 308 Copynumber: 2.0 Consensus size: 307
3943799 TTCTAATATT
3943809 ACAAACAATGAGTTACATCTAGCAATATATCATTGTTACCTAAGTTACAAGAAGTCATGATTCGA
1 ACAAACAATGAGTTACATCTAGCAATATATCATTGTTACCTAAGTTACAAGAAGTCATGATTCGA
3943874 CATAACATATTCATGACTAACTCTTTTAATGTATTATATTCTTTTGTCCTTTATATGTATAATAG
66 CATAACATATTCATGACTAACTCTTTTAATGTATTATATTCTTTTGTCCTTTATATGTATAATAG
3943939 GCACAAGTCTTCGAAAAGCCAGCTAGTATAGCCATCTATTATTTCTTGATATCTAGAGTAGACTA
131 GCACAAGTCTTCGAAAAGCCAGCTAGTATAGCCATCTATTATTTCTTGATATCTAGAGTAGACTA
3944004 TGATAAACGAATAATTTGTGATATCTCATATCAACTTATTCGAGCATTGCCATGCATTTCTAGTC
196 TGATAAACGAATAATTTGTGATATCTCATATCAACTTATTCGAGCATTGCCATGCATTTCTAGTC
3944069 TCGCTCAATCAAGTGGCTTGTGATATATTTCCTATTATGTAGGAAGG
261 TCGCTCAATCAAGTGGCTTGTGATATATTTCCTATTATGTAGGAAGG
3944116 ACAAACAATGAGTTACATCTAGC-ATATATCATTGTTACCTAAGTTACAAGAAGTCATGATTCGA
1 ACAAACAATGAGTTACATCTAGCAATATATCATTGTTACCTAAGTTACAAGAAGTCATGATTCGA
3944180 CATAACATATTCATGACTAACTCTTTTAATGTATTATATTCTTTTGTCCTTTATATGTATAATAG
66 CATAACATATTCATGACTAACTCTTTTAATGTATTATATTCTTTTGTCCTTTATATGTATAATAG
3944245 GCACAAGTCTTCGAAAAGCCATGCTAGTATAGCCCATCTATTATTTCTTGATATCTAGAGTAGAC
131 GCACAAGTCTTCGAAAAGCCA-GCTAGTATAG-CCATCTATTATTTCTTGATATCTAGAGTAGAC
3944310 TATGATAAACGAATAATTTGTGATATCTCATATCAACTTATTCGAGCATTGCCATGCATTTCTAG
194 TATGATAAACGAATAATTTGTGATATCTCATATCAACTTATTCGAGCATTGCCATGCATTTCTAG
3944375 TCTCGCTCAATCAAGTGGCTTGTGATATATTTCCTATTATGTAGGAAGG
259 TCTCGCTCAATCAAGTGGCTTGTGATATATTTCCTATTATGTAGGAAGG
3944424 ACAAA
1 ACAAA
3944429 TCATATCTCG
Statistics
Matches: 311, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
306 127 0.41
307 33 0.11
308 151 0.49
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (307 bp):
ACAAACAATGAGTTACATCTAGCAATATATCATTGTTACCTAAGTTACAAGAAGTCATGATTCGA
CATAACATATTCATGACTAACTCTTTTAATGTATTATATTCTTTTGTCCTTTATATGTATAATAG
GCACAAGTCTTCGAAAAGCCAGCTAGTATAGCCATCTATTATTTCTTGATATCTAGAGTAGACTA
TGATAAACGAATAATTTGTGATATCTCATATCAACTTATTCGAGCATTGCCATGCATTTCTAGTC
TCGCTCAATCAAGTGGCTTGTGATATATTTCCTATTATGTAGGAAGG
Found at i:3944616 original size:24 final size:24
Alignment explanation
Indices: 3944589--3944643 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
3944579 TACATATAGT
*
3944589 TGTCACCATGATCAATATTGTGAC
1 TGTCACAATGATCAATATTGTGAC
3944613 TGTCACAATGATCAATATTGTGAC
1 TGTCACAATGATCAATATTGTGAC
3944637 TGTCACA
1 TGTCACA
3944644 TAATAATCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (24 bp):
TGTCACAATGATCAATATTGTGAC
Found at i:3946729 original size:38 final size:38
Alignment explanation
Indices: 3946640--3946730 Score: 121
Period size: 38 Copynumber: 2.4 Consensus size: 38
3946630 ATTGTAATTG
* * * *
3946640 AAAATCTGGTTTCAATTTGAAAAATTAGGTTACAACCT
1 AAAATCTGGTTTCCATATGAAAAATCAGGGTACAACCT
*
3946678 AAAATCTGGTTTCCATATGAAAAATCAGGGTGCAACCT
1 AAAATCTGGTTTCCATATGAAAAATCAGGGTACAACCT
3946716 ATAAA-CTGGTTTCCA
1 A-AAATCTGGTTTCCA
3946731 AACTAATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 44 0.94
39 3 0.06
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.31
Consensus pattern (38 bp):
AAAATCTGGTTTCCATATGAAAAATCAGGGTACAACCT
Found at i:3952008 original size:26 final size:26
Alignment explanation
Indices: 3951967--3952016 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
3951957 TTTGCTAAAA
*
3951967 ATCAAAAGATGGGAAAAAAGAATAAG
1 ATCAAAAGATAGGAAAAAAGAATAAG
* *
3951993 ATCAAAAGATATGAAAAAATAATA
1 ATCAAAAGATAGGAAAAAAGAATA
3952017 TTTTTTTGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.64, C:0.04, G:0.16, T:0.16
Consensus pattern (26 bp):
ATCAAAAGATAGGAAAAAAGAATAAG
Found at i:3952468 original size:20 final size:20
Alignment explanation
Indices: 3952445--3952486 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3952435 GTTTTATGGA
*
3952445 ATTTTGTTTTTTT-TTTGTTT
1 ATTTGGTTTTTTTATTT-TTT
3952465 ATTTGGTTTTTTTATTTTTT
1 ATTTGGTTTTTTTATTTTTT
3952485 AT
1 AT
3952487 GAAAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.81
Consensus pattern (20 bp):
ATTTGGTTTTTTTATTTTTT
Found at i:3961039 original size:21 final size:22
Alignment explanation
Indices: 3960989--3961050 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
3960979 ATACCCCCAT
3960989 AAGGGAACCGATTCCCCCTTTG
1 AAGGGAACCGATTCCCCCTTTG
*
3961011 AATTGGAACCGATTCCCTCC-TTG
1 AA-GGGAACCGATTCCC-CCTTTG
* *
3961034 -AGGGAATCGATACCCCC
1 AAGGGAACCGATTCCCCC
3961051 CACGGGTTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 2 0.06
21 11 0.32
22 3 0.09
23 16 0.47
24 2 0.06
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (22 bp):
AAGGGAACCGATTCCCCCTTTG
Found at i:3968542 original size:21 final size:22
Alignment explanation
Indices: 3968492--3968553 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
3968482 ATACCCCCAT
3968492 AAGGGAACCGATTCCCCCTTTG
1 AAGGGAACCGATTCCCCCTTTG
*
3968514 AATTGGAACCGATTCCCTCC-TTG
1 AA-GGGAACCGATTCCC-CCTTTG
* *
3968537 -AGGGAATCGATACCCCC
1 AAGGGAACCGATTCCCCC
3968554 CACGGGTTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 2 0.06
21 11 0.32
22 3 0.09
23 16 0.47
24 2 0.06
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (22 bp):
AAGGGAACCGATTCCCCCTTTG
Found at i:3973631 original size:61 final size:64
Alignment explanation
Indices: 3973520--3973664 Score: 188
Period size: 61 Copynumber: 2.3 Consensus size: 64
3973510 TCAGGTTTAT
* * * *
3973520 ATTAGCACTAGTGTGTAAGGACACTAAGTGTAGGTGGAGGGCACAACCTTATGTCTCATATCCGG
1 ATTAGCACTAGAGTGTAA-GACACTAAGTGTAGGTGGAGGGAACAACCTTATGTATCATAACCGG
* * *
3973585 ATTAGCACTAGAGTGTAA-AC-CT-AGTGTAGGTGGTGGGAACGACCTTATGTATCATAACTGG
1 ATTAGCACTAGAGTGTAAGACACTAAGTGTAGGTGGAGGGAACAACCTTATGTATCATAACCGG
*
3973646 ATTAGCACTAGAGCGTAAG
1 ATTAGCACTAGAGTGTAAG
3973665 CTTAGTACAT
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
61 50 0.70
62 2 0.03
63 2 0.03
65 17 0.24
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.26
Consensus pattern (64 bp):
ATTAGCACTAGAGTGTAAGACACTAAGTGTAGGTGGAGGGAACAACCTTATGTATCATAACCGG
Found at i:3977135 original size:3 final size:3
Alignment explanation
Indices: 3977127--3977214 Score: 148
Period size: 3 Copynumber: 30.7 Consensus size: 3
3977117 TCTACAAAAA
3977127 TAT TAT TAT TAT TA- TAT T-T TAT TAT TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3977172 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3977215 CATGGTTACA
Statistics
Matches: 81, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
2 8 0.10
3 73 0.90
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3978382 original size:30 final size:28
Alignment explanation
Indices: 3978348--3978476 Score: 118
Period size: 30 Copynumber: 4.4 Consensus size: 28
3978338 GTAATCACTG
*
3978348 TTTAGTCCTTTAAGTTTATATTTTTCCTA
1 TTTAGTCCTTTAAGTTTTTATTTTT-CTA
* *
3978377 TTTTAGTCCTTTATGTTTTTGTTTGTAT-TA
1 -TTTAGTCCTTTAAGTTTTTATTT-T-TCTA
*
3978407 TTTACGTCCCTTAAGTTTTTATTTTTGCTA
1 TTTA-GTCCTTTAAGTTTTTATTTTT-CTA
* * *
3978437 TTTCAGTCCTGTAAATTTCTATTTTT-TA
1 TTT-AGTCCTTTAAGTTTTTATTTTTCTA
3978465 TTTAGTCCTTTA
1 TTTAGTCCTTTA
3978477 TTTTACTAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
27 8 0.10
28 6 0.07
29 5 0.06
30 60 0.73
31 2 0.02
32 1 0.01
ACGTcount: A:0.18, C:0.13, G:0.09, T:0.60
Consensus pattern (28 bp):
TTTAGTCCTTTAAGTTTTTATTTTTCTA
Found at i:3984062 original size:32 final size:32
Alignment explanation
Indices: 3984020--3984082 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
3984010 CAAGAATGAT
3984020 GAATGATGGGGCATCTTTG-GAGATTCAACATC
1 GAATGATGGGGCATCTTTGAG-GATTCAACATC
*
3984052 GAATGTTGGGGCATCTTTGAGGATTCAACAT
1 GAATGATGGGGCATCTTTGAGGATTCAACAT
3984083 ATTGATGCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (32 bp):
GAATGATGGGGCATCTTTGAGGATTCAACATC
Found at i:3984246 original size:61 final size:63
Alignment explanation
Indices: 3984152--3984293 Score: 173
Period size: 61 Copynumber: 2.2 Consensus size: 63
3984142 TATCAGTATC
* * * *
3984152 CTTTGAGTTGTTTCTTTTGAAACAAATTTTGTCTCTC-GAGATAGTTTCTTTT-G-AAAAAAT
1 CTTTGAGTTGTTTCTCTGGAAACAAATTTTGTCTCTCTGAGACAATTTCTTTTAGAAAAAAAT
*
3984212 CTTTGAGTTTGTTTCTCTGGAAATAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAAAAA
1 CTTTGAG-TTGTTTCTCTGGAAACAAATTTTGTCTCTC-TGAGACAATTTCTTTT-AG-AAAAAA
3984277 AT
62 AT
3984279 CTTTGAGATTGTTTC
1 CTTTGAG-TTGTTTC
3984294 CAATGAAACA
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
60 7 0.10
61 27 0.39
63 13 0.19
65 1 0.01
67 21 0.30
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (63 bp):
CTTTGAGTTGTTTCTCTGGAAACAAATTTTGTCTCTCTGAGACAATTTCTTTTAGAAAAAAAT
Found at i:3984680 original size:130 final size:128
Alignment explanation
Indices: 3984377--3984757 Score: 422
Period size: 130 Copynumber: 2.9 Consensus size: 128
3984367 TTGATATATT
* * *
3984377 ATCCCTAAAGATGGACTGCCATCATCATCACATAAGAACCGTGTCATCCCCCGACCAGGCCTCCT
1 ATCCCTAAAGATGGACTGCCATCCTCATCACATAGGAACTGTGTCATCCCCCGACCA-GCCTCCT
* ** ** * *
3984442 CATCACGTATGAGTTATGTCAACCTCAAATAACCAGTCGTCCTCATCACGTAGGAATCGTATTAT
65 CATCACGTAGGAGTCGTGTC-ACC-CTGATAACCAGCCGTCCTCATCACGTAGGAACCGTATTAT
*
3984507 T
128 C
* * * * *
3984508 ATCCTTAAAGATGGCCTGCTATCCTCATCACGTAGG-ACTGTGTCATCCCCCGACCATACCTCCT
1 ATCCCTAAAGATGGACTGCCATCCTCATCACATAGGAACTGTGTCATCCCCCGACCA-GCCTCCT
* *
3984572 CATCACGTAGGAGTCGTGTCACTCCTGATAACCAGCCGTCCTCATCACGTATGAACCGTGTTATC
65 CATCACGTAGGAGTCGTGTCAC-CCTGATAACCAGCCGTCCTCATCACGTAGGAACCGTATTATC
* ** * * *
3984637 ATCCCTAAATATGTTCTGCCATCCTCATCACATAGGAAATGTGTCATCCACAGACCAGCCTTCCT
1 ATCCCTAAAGATGGACTGCCATCCTCATCACATAGGAACTGTGTCATCCCCCGACCAGCC-TCCT
** ** *
3984702 CATCACGTAGGAGTCGCATCACCCCTAGATAACCAGCTATCCTCATTACGTAGGAA
65 CATCACGTAGGAGTCGTGTCA-CCCT-GATAACCAGCCGTCCTCATCACGTAGGAA
3984758 TCATGTTTCG
Statistics
Matches: 210, Mismatches: 35, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
129 68 0.32
130 86 0.41
131 56 0.27
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.25
Consensus pattern (128 bp):
ATCCCTAAAGATGGACTGCCATCCTCATCACATAGGAACTGTGTCATCCCCCGACCAGCCTCCTC
ATCACGTAGGAGTCGTGTCACCCTGATAACCAGCCGTCCTCATCACGTAGGAACCGTATTATC
Found at i:3984780 original size:180 final size:180
Alignment explanation
Indices: 3984585--3984944 Score: 720
Period size: 180 Copynumber: 2.0 Consensus size: 180
3984575 CACGTAGGAG
3984585 TCGTGTCACTCCTGATAACCAGCCGTCCTCATCACGTATGAACCGTGTTATCATCCCTAAATATG
1 TCGTGTCACTCCTGATAACCAGCCGTCCTCATCACGTATGAACCGTGTTATCATCCCTAAATATG
3984650 TTCTGCCATCCTCATCACATAGGAAATGTGTCATCCACAGACCAGCCTTCCTCATCACGTAGGAG
66 TTCTGCCATCCTCATCACATAGGAAATGTGTCATCCACAGACCAGCCTTCCTCATCACGTAGGAG
3984715 TCGCATCACCCCTAGATAACCAGCTATCCTCATTACGTAGGAATCATGTT
131 TCGCATCACCCCTAGATAACCAGCTATCCTCATTACGTAGGAATCATGTT
3984765 TCGTGTCACTCCTGATAACCAGCCGTCCTCATCACGTATGAACCGTGTTATCATCCCTAAATATG
1 TCGTGTCACTCCTGATAACCAGCCGTCCTCATCACGTATGAACCGTGTTATCATCCCTAAATATG
3984830 TTCTGCCATCCTCATCACATAGGAAATGTGTCATCCACAGACCAGCCTTCCTCATCACGTAGGAG
66 TTCTGCCATCCTCATCACATAGGAAATGTGTCATCCACAGACCAGCCTTCCTCATCACGTAGGAG
3984895 TCGCATCACCCCTAGATAACCAGCTATCCTCATTACGTAGGAATCATGTT
131 TCGCATCACCCCTAGATAACCAGCTATCCTCATTACGTAGGAATCATGTT
3984945 ATCACCCTCC
Statistics
Matches: 180, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
180 180 1.00
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (180 bp):
TCGTGTCACTCCTGATAACCAGCCGTCCTCATCACGTATGAACCGTGTTATCATCCCTAAATATG
TTCTGCCATCCTCATCACATAGGAAATGTGTCATCCACAGACCAGCCTTCCTCATCACGTAGGAG
TCGCATCACCCCTAGATAACCAGCTATCCTCATTACGTAGGAATCATGTT
Found at i:3984884 original size:88 final size:88
Alignment explanation
Indices: 3984602--3984890 Score: 313
Period size: 88 Copynumber: 3.2 Consensus size: 88
3984592 ACTCCTGATA
3984602 ACCAGCCGTCCTCATCACGTATGAACCGTGTTATCATCCCTAAATATGTTCTGCCATCCTCATCA
1 ACCAGCCGTCCTCATCACGTATGAACCGTGTTATCATCCCTAAATATGTTCTGCCATCCTCATCA
3984667 CATAGGAAATGTGTCATCCACAG
66 CATAGGAAATGTGTCATCCACAG
* * * * * ** * * *
3984690 ACCAGCCTTCCTCATCACGTA-GGA--GTCG-CATCACCCCTAGATA--ACCAGCTATCCTCATT
1 ACCAGCCGTCCTCATCACGTATGAACCGT-GTTATCATCCCTAAATATGTTCTGCCATCCTCATC
* *
3984749 ACGTAGGAATCATGTTTCGTGTCACTCCTGATA-
65 ACATAGGAA--A----T-GTGTCA-TCC--ACAG
3984782 ACCAGCCGTCCTCATCACGTATGAACCGTGTTATCATCCCTAAATATGTTCTGCCATCCTCATCA
1 ACCAGCCGTCCTCATCACGTATGAACCGTGTTATCATCCCTAAATATGTTCTGCCATCCTCATCA
3984847 CATAGGAAATGTGTCATCCACAG
66 CATAGGAAATGTGTCATCCACAG
*
3984870 ACCAGCCTTCCTCATCACGTA
1 ACCAGCCGTCCTCATCACGTA
3984891 GGAGTCGCAT
Statistics
Matches: 158, Mismatches: 25, Indels: 36
0.72 0.11 0.16
Matches are distributed among these distances:
83 19 0.12
85 15 0.09
86 1 0.01
87 4 0.03
88 40 0.25
89 4 0.03
90 12 0.08
91 4 0.03
92 20 0.13
93 4 0.03
94 1 0.01
95 15 0.09
97 19 0.12
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (88 bp):
ACCAGCCGTCCTCATCACGTATGAACCGTGTTATCATCCCTAAATATGTTCTGCCATCCTCATCA
CATAGGAAATGTGTCATCCACAG
Found at i:3985166 original size:3 final size:3
Alignment explanation
Indices: 3985151--3985249 Score: 164
Period size: 3 Copynumber: 32.7 Consensus size: 3
3985141 TTTACAAAAA
3985151 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TATT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
*
3985197 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3985245 TAT TA
1 TAT TA
3985250 CATATTTTGT
Statistics
Matches: 91, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
2 1 0.01
3 86 0.95
4 4 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3986710 original size:30 final size:29
Alignment explanation
Indices: 3986671--3986763 Score: 89
Period size: 30 Copynumber: 3.1 Consensus size: 29
3986661 AAGTTTCTAT
*
3986671 TTTTCCTATTTTAGTCATTTAAATTTTTG
1 TTTTGCTATTTTAGTCATTTAAATTTTTG
** **
3986700 TTTGTGCTA-TTTACGTCCCTTATGTTTTTGG
1 TTT-TGCTATTTTA-GTCATTTAAATTTTT-G
* *
3986731 TTTTGCTATTTCAGTCATGTAAATTTTTG
1 TTTTGCTATTTTAGTCATTTAAATTTTTG
3986760 TTTT
1 TTTT
3986764 TTTTTTTTTG
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
29 12 0.24
30 30 0.61
31 7 0.14
ACGTcount: A:0.16, C:0.12, G:0.13, T:0.59
Consensus pattern (29 bp):
TTTTGCTATTTTAGTCATTTAAATTTTTG
Found at i:3992538 original size:33 final size:31
Alignment explanation
Indices: 3992462--3992540 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 31
3992452 TATATTTTAC
* *
3992462 ATATAAAAATAAATTCAAAATTAAAATTTAAT
1 ATATAAATATATATT-AAAATTAAAATTTAAT
3992494 ATATAAATATATATTAAAATCTAAAATTTATAT
1 ATATAAATATATATTAAAAT-TAAAATTTA-AT
* *
3992527 GTATAATTATATAT
1 ATATAAATATATAT
3992541 AGGGTCGGTC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
31 5 0.12
32 22 0.54
33 14 0.34
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.41
Consensus pattern (31 bp):
ATATAAATATATATTAAAATTAAAATTTAAT
Found at i:3995184 original size:12 final size:12
Alignment explanation
Indices: 3995167--3995191 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3995157 AATCACTATT
3995167 TGACATTATTCA
1 TGACATTATTCA
3995179 TGACATTATTCA
1 TGACATTATTCA
3995191 T
1 T
3995192 ACGAGGGTAC
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:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (12 bp):
TGACATTATTCA
Found at i:3998168 original size:21 final size:21
Alignment explanation
Indices: 3998139--3998187 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
3998129 AGTTTGAGTT
*
3998139 GACACGATATCCTGATGAATC
1 GACATGATATCCTGATGAATC
3998160 GACATGATATCCTGATGAATC
1 GACATGATATCCTGATGAATC
3998181 GACATGA
1 GACATGA
3998188 ATCTTGAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (21 bp):
GACATGATATCCTGATGAATC
Found at i:4000787 original size:13 final size:13
Alignment explanation
Indices: 4000769--4000793 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4000759 AATTTATTAC
4000769 TTTTAATAATTTA
1 TTTTAATAATTTA
4000782 TTTTAATAATTT
1 TTTTAATAATTT
4000794 GAAAATAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTAATAATTTA
Found at i:4003022 original size:19 final size:17
Alignment explanation
Indices: 4002998--4003042 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
4002988 TTTAAAAGTG
*
4002998 AATAAAATTAAATAACAAA
1 AATAAAATGAAAT-A-AAA
*
4003017 AATAAAATGCAATAAAA
1 AATAAAATGAAATAAAA
4003034 AATAAAATG
1 AATAAAATG
4003043 TTAGTGTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 12 0.50
18 1 0.04
19 11 0.46
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.20
Consensus pattern (17 bp):
AATAAAATGAAATAAAA
Found at i:4003203 original size:16 final size:16
Alignment explanation
Indices: 4003178--4003220 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
4003168 CAATTAGTAA
*
4003178 TTAGTGGTTAGAAAGG
1 TTAGTGGTTAGAAAAG
*
4003194 TTAGTTGTTAGAAAAG
1 TTAGTGGTTAGAAAAG
*
4003210 TTAGCGGTTAG
1 TTAGTGGTTAG
4003221 TGGTTAACAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.33, T:0.35
Consensus pattern (16 bp):
TTAGTGGTTAGAAAAG
Found at i:4003249 original size:16 final size:16
Alignment explanation
Indices: 4003184--4003253 Score: 56
Period size: 16 Copynumber: 4.5 Consensus size: 16
4003174 GTAATTAGTG
* *
4003184 GTTAGAAAGGTTAGTT
1 GTTAGAAATGTTAGCT
* *
4003200 GTTAGAAAAGTTAGCG
1 GTTAGAAATGTTAGCT
* *
4003216 GTTAG---TGGTTAACA
1 GTTAGAAAT-GTTAGCT
4003230 GTTAGAAATGTTAGCT
1 GTTAGAAATGTTAGCT
4003246 GTTAGAAA
1 GTTAGAAA
4003254 AATTAACGGT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
14 10 0.24
16 31 0.74
17 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (16 bp):
GTTAGAAATGTTAGCT
Found at i:4003268 original size:46 final size:46
Alignment explanation
Indices: 4003184--4003272 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
4003174 GTAATTAGTG
* * *
4003184 GTTAGAAAGGTTAGTTGTTAGAAAAGTTAGCGGTTAGTGGTTAACA
1 GTTAGAAAGGTTAGCTGTTAGAAAAATTAACGGTTAGTGGTTAACA
*
4003230 GTTAGAAATGTTAGCTGTTAGAAAAATTAACGGTTAGTGGTTA
1 GTTAGAAAGGTTAGCTGTTAGAAAAATTAACGGTTAGTGGTTA
4003273 GCAGAGTCTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (46 bp):
GTTAGAAAGGTTAGCTGTTAGAAAAATTAACGGTTAGTGGTTAACA
Found at i:4003432 original size:28 final size:28
Alignment explanation
Indices: 4003401--4003485 Score: 65
Period size: 28 Copynumber: 3.1 Consensus size: 28
4003391 AGTTAACTAG
4003401 AAATAAATAACATAGCAGAATAGTGACC
1 AAATAAATAACATAGCAGAATAGTGACC
* ** *
4003429 AAATTAA-AAGTTAGTAGTTAACT--TG---
1 AAATAAATAACATAGCAG--AA-TAGTGACC
4003454 AAATAAATAACATAGCAGAATAGTGACC
1 AAATAAATAACATAGCAGAATAGTGACC
4003482 AAAT
1 AAAT
4003486 TAAAAGTTAG
Statistics
Matches: 40, Mismatches: 8, Indels: 18
0.61 0.12 0.27
Matches are distributed among these distances:
23 1 0.03
24 2 0.05
25 8 0.20
26 7 0.17
27 7 0.17
28 12 0.30
29 2 0.05
30 1 0.03
ACGTcount: A:0.52, C:0.11, G:0.14, T:0.24
Consensus pattern (28 bp):
AAATAAATAACATAGCAGAATAGTGACC
Found at i:4003437 original size:53 final size:53
Alignment explanation
Indices: 4003375--4003497 Score: 228
Period size: 53 Copynumber: 2.3 Consensus size: 53
4003365 TAAAATGTAA
*
4003375 CAAAATAAAAGTTAGTAGTTAACTAGAAATAAATAACATAGCAGAATAGTGAC
1 CAAATTAAAAGTTAGTAGTTAACTAGAAATAAATAACATAGCAGAATAGTGAC
*
4003428 CAAATTAAAAGTTAGTAGTTAACTTGAAATAAATAACATAGCAGAATAGTGAC
1 CAAATTAAAAGTTAGTAGTTAACTAGAAATAAATAACATAGCAGAATAGTGAC
4003481 CAAATTAAAAGTTAGTA
1 CAAATTAAAAGTTAGTA
4003498 AAATTAGTAT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 68 1.00
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.25
Consensus pattern (53 bp):
CAAATTAAAAGTTAGTAGTTAACTAGAAATAAATAACATAGCAGAATAGTGAC
Found at i:4008267 original size:34 final size:34
Alignment explanation
Indices: 4008219--4008295 Score: 118
Period size: 34 Copynumber: 2.2 Consensus size: 34
4008209 TAACGTGACA
*
4008219 CTTTTTTTCATTTCTTCGTTTAGTGATTAATGTT
1 CTTTTTTTCATTTCTTCATTTAGTGATTAATGTT
*
4008253 CTTTTTTTCGTTTCTTCATTTAGTGATTAATGTT
1 CTTTTTTTCATTTCTTCATTTAGTGATTAATGTT
*
4008287 GTTTCTTTT
1 CTTT-TTTT
4008296 ATGACGATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 35 0.90
35 4 0.10
ACGTcount: A:0.13, C:0.12, G:0.12, T:0.64
Consensus pattern (34 bp):
CTTTTTTTCATTTCTTCATTTAGTGATTAATGTT
Found at i:4012791 original size:27 final size:28
Alignment explanation
Indices: 4012761--4012821 Score: 106
Period size: 27 Copynumber: 2.2 Consensus size: 28
4012751 ATAAACCTTA
*
4012761 TAATTTTGCGTCATTAGTGT-AATATGG
1 TAATTTTGCGCCATTAGTGTAAATATGG
4012788 TAATTTTGCGCCATTAGTGTAAATATGG
1 TAATTTTGCGCCATTAGTGTAAATATGG
4012816 TAATTT
1 TAATTT
4012822 ATCAACTCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 19 0.59
28 13 0.41
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (28 bp):
TAATTTTGCGCCATTAGTGTAAATATGG
Found at i:4012910 original size:55 final size:55
Alignment explanation
Indices: 4012822--4013193 Score: 440
Period size: 55 Copynumber: 6.8 Consensus size: 55
4012812 ATGGTAATTT
* * * * *
4012822 ATCAACTCATGATGAATTACGTGGTTTTACACACATATTGCTTGTACGATTATTC
1 ATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCTTGTACGACTATTC
** * * * *
4012877 ATCAACTCATGATGAATTTTGTGGAATTGCACACATAATGCTTGAACGAATATTC
1 ATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCTTGTACGACTATTC
* * *
4012932 AACAACTCATGATGAATTCCGTGGATTTGCATACATAGTGCTTGTACGGCTATTC
1 ATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCTTGTACGACTATTC
* * *
4012987 ATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATATACAACTATTC
1 ATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCTTGTACGACTATTC
* * **
4013042 ATCAACTCATGATGAATTTCGTTGATTTGCACACATAGTGCTTGTACGGTTATTC
1 ATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCTTGTACGACTATTC
** * * * * * *
4013097 ATCAACT-ATTGATGAATTCTATGGAATTGCACAAATAGTTCCTATACGGCTATTC
1 ATCAACTCA-TGATGAATTCCGTGGATTTGCACACATAGTGCTTGTACGACTATTC
* * *
4013152 ATCAACTCATGATGAATTCTGTGGCTTTGCACACATAATGCT
1 ATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCT
4013194 GGTAGTACAC
Statistics
Matches: 268, Mismatches: 47, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
54 1 0.00
55 266 0.99
56 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (55 bp):
ATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCTTGTACGACTATTC
Found at i:4013546 original size:20 final size:20
Alignment explanation
Indices: 4013521--4013570 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
4013511 TGGCTCTATA
4013521 GTATCGATACCCCTACCATG
1 GTATCGATACCCCTACCATG
4013541 GTATCGATACCCCTACCATG
1 GTATCGATACCCCTACCATG
*
4013561 GTATCTATAC
1 GTATCGATAC
4013571 TACTATACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28
Consensus pattern (20 bp):
GTATCGATACCCCTACCATG
Found at i:4013673 original size:20 final size:20
Alignment explanation
Indices: 4013650--4013705 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
4013640 TCTATACCTT
4013650 CCCTTTGGTATCGATAATCC
1 CCCTTTGGTATCGATAATCC
*
4013670 CCCTTCGGTATCGATAATCC
1 CCCTTTGGTATCGATAATCC
4013690 CCCTTTGGTATCGATA
1 CCCTTTGGTATCGATA
4013706 CTGATTGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.34
Consensus pattern (20 bp):
CCCTTTGGTATCGATAATCC
Found at i:4014038 original size:16 final size:16
Alignment explanation
Indices: 4014017--4014049 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4014007 CTAATATCTC
4014017 ATTTACCTCTTTGACA
1 ATTTACCTCTTTGACA
4014033 ATTTACCTCTTTGACA
1 ATTTACCTCTTTGACA
4014049 A
1 A
4014050 GTTAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.24, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTACCTCTTTGACA
Found at i:4019592 original size:15 final size:16
Alignment explanation
Indices: 4019567--4019596 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4019557 AGTTTGTATT
4019567 TAAACTACACGTTAAA
1 TAAACTACACGTTAAA
4019583 TAAA-TACACGTTAA
1 TAAACTACACGTTAA
4019597 TTATTACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.27
Consensus pattern (16 bp):
TAAACTACACGTTAAA
Found at i:4020170 original size:55 final size:54
Alignment explanation
Indices: 4019775--4020164 Score: 492
Period size: 55 Copynumber: 7.1 Consensus size: 54
4019765 AATGCACGAT
* * * *
4019775 TAGTGCCTATACGGTAATTCATCAACTCATGATGAATTCCGTTGTTTTGCACACA
1 TAGTGCCTGTACGCT-ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
* * * * *
4019830 TAGTACCTATACGACTATTCATCAACTCATGATGTATTCCGTTGAATTGCACACA
1 TAGTGCCTGTACG-CTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
* * *
4019885 TAGTTCCTGTACGGCTATTCATCAAATCATGATGAATTCCGTGGATTTACACACA
1 TAGTGCCTGTAC-GCTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
*
4019940 TAGTGCCTGTACGACTATTCATCAACTCATGATGAATTCTGTGGATTTGCACACA
1 TAGTGCCTGTACG-CTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
* * *
4019995 TAGTGCCTGTAAGGCTATTCATCAACTCATGATGAATTCCATGGATTTGCATACA
1 TAGTGCCTGT-ACGCTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
** * * *
4020050 TAGTGATTGTATGGCTATTCATCAACTCATAATGAATTCCGTGGAATTGCACACA
1 TAGTGCCTGTA-CGCTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
** * *
4020105 TAGTGTTTGTACTGCTATTCATCAACTCATAATGAATTCTGTGGATTTGCACACA
1 TAGTGCCTGTAC-GCTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
4020160 TAGTG
1 TAGTG
4020165 TTTGTAGTAC
Statistics
Matches: 299, Mismatches: 30, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
54 2 0.01
55 293 0.98
56 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.34
Consensus pattern (54 bp):
TAGTGCCTGTACGCTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
Found at i:4020559 original size:19 final size:19
Alignment explanation
Indices: 4020494--4020564 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 19
4020484 TGGTTCCATA
* *
4020494 GTATCGATACCCCTACCATG
1 GTATCGATA-CTCTACTATG
4020514 GTATCGATACTACTA-TATTAG
1 GTATCGATACT-CTACTA-T-G
4020535 GATATCGATACTCTACTATG
1 G-TATCGATACTCTACTATG
4020555 GTATCGATAC
1 GTATCGATAC
4020565 CAATTTTGCA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
19 11 0.25
20 15 0.34
21 6 0.14
22 12 0.27
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (19 bp):
GTATCGATACTCTACTATG
Found at i:4031542 original size:36 final size:36
Alignment explanation
Indices: 4031476--4031546 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
4031466 ACCTTTGGTC
*
4031476 TATAAGGAATTACCACCTTGATCAGTGTTGAACCTA
1 TATAAGGAATTACCACCTTGATCAGAGTTGAACCTA
* **
4031512 TATAAGGAATTATCAGTTTGATC-GAAGTTGAACCT
1 TATAAGGAATTACCACCTTGATCAG-AGTTGAACCT
4031547 GTAGAGACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 1 0.03
36 29 0.97
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (36 bp):
TATAAGGAATTACCACCTTGATCAGAGTTGAACCTA
Found at i:4048702 original size:318 final size:318
Alignment explanation
Indices: 4048125--4048761 Score: 1265
Period size: 318 Copynumber: 2.0 Consensus size: 318
4048115 CATATTTACC
4048125 ATCAAAACAAGAAACCTCAACCTTATAATCTTCCTAAAGTCAAAGATGAACAAAAAATTCTTACT
1 ATCAAAACAAGAAACCTCAACCTTATAATCTTCCTAAAGTCAAAGATGAACAAAAAATTCTTACT
4048190 TTATCGATTTACCCTTGCATTTTTCCAAATATTGCAATCTTGTCACTTTAATCCAATAGTCAAAA
66 TTATCGATTTACCCTTGCATTTTTCCAAATATTGCAATCTTGTCACTTTAATCCAATAGTCAAAA
4048255 TTCAACATGGAATTAAATCCTCAATTCCAAATATTTATATTGTTTTCCAACATATTAAAATGCGG
131 TTCAACATGGAATTAAATCCTCAATTCCAAATATTTATATTGTTTTCCAACATATTAAAATGCGG
4048320 AAATAGTGTTTTTAGGTCTAATTTATCATCCTTCAGATTTTCCTGAAATTTATATTCGAACTGAT
196 AAATAGTGTTTTTAGGTCTAATTTATCATCCTTCAGATTTTCCTGAAATTTATATTCGAACTGAT
4048385 TTACCGAATTTTTCCTCAACTTTATCGCTTTATAATTTTTAATACAAAATTCGGACAA
261 TTACCGAATTTTTCCTCAACTTTATCGCTTTATAATTTTTAATACAAAATTCGGACAA
4048443 ATCAAAACAAGAAACCTCAACCTTATAATCTTCCTAAAGTCAAAGATGAACAAAAAATTCTTACT
1 ATCAAAACAAGAAACCTCAACCTTATAATCTTCCTAAAGTCAAAGATGAACAAAAAATTCTTACT
4048508 TTATCGATTTACCCTTGCATTTTTCCAAATATTGCAATCTTGTCACTTTAATCCAATAGTCAAAA
66 TTATCGATTTACCCTTGCATTTTTCCAAATATTGCAATCTTGTCACTTTAATCCAATAGTCAAAA
*
4048573 TTCAACATGGAATTAAATCCTCAATTTCAAATATTTATATTGTTTTCCAACATATTAAAATGCGG
131 TTCAACATGGAATTAAATCCTCAATTCCAAATATTTATATTGTTTTCCAACATATTAAAATGCGG
4048638 AAATAGTGTTTTTAGGTCTAATTTATCATCCTTCAGATTTTCCTGAAATTTATATTCGAACTGAT
196 AAATAGTGTTTTTAGGTCTAATTTATCATCCTTCAGATTTTCCTGAAATTTATATTCGAACTGAT
4048703 TTACCGAATTTTTCCTCAACTTTATCGCTTTATAATTTTTAATACAAAATTCGGACAA
261 TTACCGAATTTTTCCTCAACTTTATCGCTTTATAATTTTTAATACAAAATTCGGACAA
4048761 A
1 A
4048762 ATTATGATTC
Statistics
Matches: 318, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
318 318 1.00
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (318 bp):
ATCAAAACAAGAAACCTCAACCTTATAATCTTCCTAAAGTCAAAGATGAACAAAAAATTCTTACT
TTATCGATTTACCCTTGCATTTTTCCAAATATTGCAATCTTGTCACTTTAATCCAATAGTCAAAA
TTCAACATGGAATTAAATCCTCAATTCCAAATATTTATATTGTTTTCCAACATATTAAAATGCGG
AAATAGTGTTTTTAGGTCTAATTTATCATCCTTCAGATTTTCCTGAAATTTATATTCGAACTGAT
TTACCGAATTTTTCCTCAACTTTATCGCTTTATAATTTTTAATACAAAATTCGGACAA
Found at i:4050470 original size:26 final size:25
Alignment explanation
Indices: 4050403--4050472 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
4050393 ATTTATGTAC
*
4050403 TCTTTAATATATAAT-AAAAA-TTT
1 TCTTTAATATATATTAAAAAATTTT
* *
4050426 TCTTTAATATGTATGAAAAGAATTTT
1 TCTTTAATATATATTAAAA-AATTTT
*
4050452 TCTTTAATATATGTTAAAAAA
1 TCTTTAATATATATTAAAAAA
4050473 ATTCTTTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
23 12 0.32
24 3 0.08
25 4 0.11
26 19 0.50
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (25 bp):
TCTTTAATATATATTAAAAAATTTT
Found at i:4054423 original size:21 final size:21
Alignment explanation
Indices: 4054397--4054447 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
4054387 GTTATCCAAT
*
4054397 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
4054418 AAACTTGAAATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
*
4054439 CAACTTGAA
1 AAACTTGAA
4054448 CTCAATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.49, C:0.25, G:0.06, T:0.20
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:4054455 original size:21 final size:21
Alignment explanation
Indices: 4054397--4054455 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
4054387 GTTATCCAAT
* *
4054397 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCAATAACAAC
*
4054418 AAACTTGAAATCCATAACAAC
1 AAACTTGAAATCAATAACAAC
* *
4054439 CAACTTGAACTCAATAA
1 AAACTTGAAATCAATAA
4054456 TAAGTCAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.49, C:0.25, G:0.05, T:0.20
Consensus pattern (21 bp):
AAACTTGAAATCAATAACAAC
Found at i:4055184 original size:306 final size:306
Alignment explanation
Indices: 4054624--4055244 Score: 908
Period size: 306 Copynumber: 2.0 Consensus size: 306
4054614 CAAGTCTTAT
4054624 CATCTAAGTGTGCAATTTCAACTTTGTCGAGTGGTTCACAATAACTTCCAAACAAATAAGTCTCA
1 CATCTAAGTGTGCAATTTCAACTTTGTCGAGTGGTTCACAATAACTTCCAAACAAATAAGTCTCA
* *
4054689 GCTAAGTCATTAGTACTGAACAAGTCATTTATATTTGATATATTCAATCTTGTTTGAACATCTAC
66 GCTAAGTCATCAGTACTGAACAAGTCATTTATATTTGATATATTCAATCTTGTTTCAACATCTAC
* * *
4054754 CAAATATCTAGAGCAAAAATTCATACATTCCTCTTCAAAATACCCTTAAGCAATTAATCCTTCAG
131 CAAATATCTAGAGAAAAAATTCATACATACCTCTTCAAAATACCCTTAAGCAATCAATCCTTCAG
* *
4054819 GATAACGCTTATTACGACAATAAGACTTCAACTTGCACAGTAACCTAGACACGAAACAAAATAGT
196 GATAACGCTTATTACGACAATAAGACTTCAACTTGCACAGTAACCTAGACACAAAACAAAATAAT
* *
4054884 ATTTAAATAGTTGTAATGAAAAGGTATAATCCCTATTCATTTAATA
261 ATGTAAATAGTTGTAATGAAAAGGTATAATCCCTAGTCATTTAATA
* * * *
4054930 CATCTAAGTGTGCAATTTCAACTTTGTTGAGTGGTTCACCATATCTTCCAAACAAATAAGTTTCA
1 CATCTAAGTGTGCAATTTCAACTTTGTCGAGTGGTTCACAATAACTTCCAAACAAATAAGTCTCA
* * * * * * * *
4054995 GCTAATTCATCAGTACTTAACACA-TTATTTCTATTTGGTCTATTCAATCTTGTTTCAACATTTT
66 GCTAAGTCATCAGTACTGAACA-AGTCATTTATATTTGATATATTCAATCTTGTTTCAACATCTA
* * *
4055059 CCAAATATCTAGAGAAAAAATTCTTACATACCTCTGTC-AAATACCCTTCAGCAATCGATCCTTC
130 CCAAATATCTAGAGAAAAAATTCATACATACCTCT-TCAAAATACCCTTAAGCAATCAATCCTT-
* *
4055123 CA-GATAATGCTTATTACGACATTAAGACTTCAACTTGCACAAG-AACCTAGACACAAAACAAAA
193 CAGGATAACGCTTATTACGACAATAAGACTTCAACTTGCAC-AGTAACCTAGACACAAAACAAAA
* * *
4055186 TAATATGTAAATAGTTGTGATGAAAAGGTATAATCTCTAGTCATTTAATG
257 TAATATGTAAATAGTTGTAATGAAAAGGTATAATCCCTAGTCATTTAATA
*
4055236 CATATAAGT
1 CATCTAAGT
4055245 CAATTAACGC
Statistics
Matches: 281, Mismatches: 30, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
306 274 0.98
307 7 0.02
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (306 bp):
CATCTAAGTGTGCAATTTCAACTTTGTCGAGTGGTTCACAATAACTTCCAAACAAATAAGTCTCA
GCTAAGTCATCAGTACTGAACAAGTCATTTATATTTGATATATTCAATCTTGTTTCAACATCTAC
CAAATATCTAGAGAAAAAATTCATACATACCTCTTCAAAATACCCTTAAGCAATCAATCCTTCAG
GATAACGCTTATTACGACAATAAGACTTCAACTTGCACAGTAACCTAGACACAAAACAAAATAAT
ATGTAAATAGTTGTAATGAAAAGGTATAATCCCTAGTCATTTAATA
Found at i:4060195 original size:16 final size:16
Alignment explanation
Indices: 4060145--4060203 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
4060135 AACTGGTATT
*
4060145 ACCTGACCTATTTTCA
1 ACCTGACCTGTTTTCA
* ** *
4060161 ACCTGACATGTGATGA
1 ACCTGACCTGTTTTCA
*
4060177 ACCTGACCTGTTTTTA
1 ACCTGACCTGTTTTCA
*
4060193 ACCTAACCTGT
1 ACCTGACCTGT
4060204 AAATGATCCG
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (16 bp):
ACCTGACCTGTTTTCA
Found at i:4060772 original size:21 final size:21
Alignment explanation
Indices: 4060746--4060814 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
4060736 TTTACAATAT
*
4060746 GGTTTAGGGTTT-GAGGTTTGA
1 GGTTTAGGGTTTAG-GGTTTAA
**
4060767 GGTTTAGTATTTAGGGTTTAA
1 GGTTTAGGGTTTAGGGTTTAA
* **
4060788 AGTTTAGGGTTTAGAATTTAA
1 GGTTTAGGGTTTAGGGTTTAA
4060809 GGTTTA
1 GGTTTA
4060815 TATAAACTAT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 37 0.97
22 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (21 bp):
GGTTTAGGGTTTAGGGTTTAA
Found at i:4060784 original size:14 final size:14
Alignment explanation
Indices: 4060767--4060814 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
4060757 TGAGGTTTGA
*
4060767 GGTTTAGTATTTAG
1 GGTTTAGAATTTAG
4060781 GGTTTA-AAGTTTAG
1 GGTTTAGAA-TTTAG
*
4060795 GGTTTAGAATTTAA
1 GGTTTAGAATTTAG
4060809 GGTTTA
1 GGTTTA
4060815 TATAAACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 1 0.03
14 27 0.90
15 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (14 bp):
GGTTTAGAATTTAG
Found at i:4060792 original size:28 final size:28
Alignment explanation
Indices: 4060748--4060814 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
4060738 TACAATATGG
* * *
4060748 TTTAGGGTTTGAGGTTT-GAGGTTTAGTA
1 TTTAGGGTTTAAAGTTTAG-GGTTTAGAA
4060776 TTTAGGGTTTAAAGTTTAGGGTTTAGAA
1 TTTAGGGTTTAAAGTTTAGGGTTTAGAA
*
4060804 TTTAAGGTTTA
1 TTTAGGGTTTA
4060815 TATAAACTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 33 0.97
29 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (28 bp):
TTTAGGGTTTAAAGTTTAGGGTTTAGAA
Found at i:4061002 original size:4 final size:4
Alignment explanation
Indices: 4060993--4061603 Score: 1060
Period size: 4 Copynumber: 152.8 Consensus size: 4
4060983 TATAGTTTAT
4060993 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4061041 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4061089 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4061137 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* **
4061185 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATAC ATGT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * * * * *
4061233 ATGC ATGC ATGC ATGC ATAC ATGC ATGC ATGC ATGC ATAC ATGC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * *
4061281 ATGC ATGC ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATGC ATGC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4061329 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4061377 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4061425 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4061473 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4061521 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4061569 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
4061604 TACATATACA
Statistics
Matches: 593, Mismatches: 14, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 593 1.00
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:4061877 original size:19 final size:20
Alignment explanation
Indices: 4061838--4061885 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
4061828 AATTTTTCTA
* *
4061838 TTCCCTCTAAATTTTCCAAT
1 TTCCCTATAAATTTCCCAAT
4061858 TTCCCTATAAA-TTCCCAAT
1 TTCCCTATAAATTTCCCAAT
4061877 TTCCCTATA
1 TTCCCTATA
4061886 TTCTCAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.42
Consensus pattern (20 bp):
TTCCCTATAAATTTCCCAAT
Found at i:4062016 original size:2 final size:2
Alignment explanation
Indices: 4062009--4062061 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
4061999 ACATACATAC
4062009 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4062051 AT AT AT AT AT A
1 AT AT AT AT AT A
4062062 ATTAAACATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4062547 original size:13 final size:13
Alignment explanation
Indices: 4062531--4062560 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4062521 CTATATAGTT
4062531 TATATATAATATA
1 TATATATAATATA
*
4062544 TATATATTATATA
1 TATATATAATATA
4062557 TATA
1 TATA
4062561 AACTATTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATATATAATATA
Found at i:4062560 original size:11 final size:11
Alignment explanation
Indices: 4062522--4062560 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
4062512 TTAAAAAAAC
4062522 TATATAGTT-TA
1 TATATA-TTATA
*
4062533 TATATAATATA
1 TATATATTATA
4062544 TATATATTATA
1 TATATATTATA
4062555 TATATA
1 TATATA
4062561 AACTATTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 1 0.04
11 24 0.96
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (11 bp):
TATATATTATA
Found at i:4064713 original size:41 final size:41
Alignment explanation
Indices: 4064668--4064781 Score: 99
Period size: 41 Copynumber: 2.8 Consensus size: 41
4064658 TTTTTGTGGC
* *
4064668 GTTTGTTGAAAAAAGACACTATAGATGAACCCTATTGCGGT
1 GTTTGTTGAAAAAAGACACTATAGATGAACCCTATTACAGT
* * * * *
4064709 GTTTGTAT-AAAAACGCCGCTAAAG-T-ACTACTCTATTACAGT
1 GTTTGT-TGAAAAAAGACACTATAGATGA--ACCCTATTACAGT
*
4064750 GTTTGTTGAAAAAACACCACTATAGATGAACC
1 GTTTGTTGAAAAAAGA-CACTATAGATGAACC
4064782 GTCTAGCAAC
Statistics
Matches: 53, Mismatches: 13, Indels: 13
0.67 0.16 0.16
Matches are distributed among these distances:
39 1 0.02
40 2 0.04
41 39 0.74
42 9 0.17
43 1 0.02
44 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (41 bp):
GTTTGTTGAAAAAAGACACTATAGATGAACCCTATTACAGT
Found at i:4064719 original size:82 final size:83
Alignment explanation
Indices: 4064627--4064781 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 83
4064617 CTATAGTGAC
* * * *** *
4064627 GTTTGAATAAAAACGCAC-CTAAAGTACTCCTTTTTTGTGGCGTTTGTTGAAAAAAGA-CACTAT
1 GTTTGAATAAAAACGC-CGCTAAAGTACTACTCTATTACAGCGTTTGTTGAAAAAACACCACTAT
4064690 AGATGAACCCTATTGCGGT
65 AGATGAACCCTATTGCGGT
* *
4064709 GTTTGTATAAAAACGCCGCTAAAGTACTACTCTATTACAGTGTTTGTTGAAAAAACACCACTATA
1 GTTTGAATAAAAACGCCGCTAAAGTACTACTCTATTACAGCGTTTGTTGAAAAAACACCACTATA
4064774 GATGAACC
66 GATGAACC
4064782 GTCTAGCAAC
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
81 1 0.02
82 46 0.74
83 15 0.24
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (83 bp):
GTTTGAATAAAAACGCCGCTAAAGTACTACTCTATTACAGCGTTTGTTGAAAAAACACCACTATA
GATGAACCCTATTGCGGT
Found at i:4064996 original size:83 final size:83
Alignment explanation
Indices: 4064809--4064999 Score: 217
Period size: 83 Copynumber: 2.3 Consensus size: 83
4064799 TAAAAGAGCT
* * *
4064809 ATTTGTATAAAAGCGCCGCTAACA-TACTACTCTGTTGCGGCGTTTGTTGAAAAAATGCTACTAT
1 ATTTGTATAAAAACGCTGCTAA-AGTACTACTCTGTTGCGGCGTTTGCTGAAAAAATGCTACTAT
*
4064873 AGATTAACCCTATTGCGGC
65 AGATGAACCCTATTGCGGC
* * * * * *
4064892 ATTTGTGTTAAAAC-ATGGCTAAAGTACTCCTCTTTTGCGGCGTTTGCTGAAAAAATG-TCACTG
1 ATTTGTATAAAAACGCT-GCTAAAGTACTACTCTGTTGCGGCGTTTGCTGAAAAAATGCT-ACTA
* *
4064955 TAGATGAATCTTATTGCGGC
64 TAGATGAACCCTATTGCGGC
*
4064975 GTTTGTATAAAAACGCTGCTAAAGT
1 ATTTGTATAAAAACGCTGCTAAAGT
4065000 TACCATTTTG
Statistics
Matches: 88, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
82 2 0.02
83 85 0.97
84 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (83 bp):
ATTTGTATAAAAACGCTGCTAAAGTACTACTCTGTTGCGGCGTTTGCTGAAAAAATGCTACTATA
GATGAACCCTATTGCGGC
Found at i:4066394 original size:2 final size:2
Alignment explanation
Indices: 4066342--4066381 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4066332 GCTTAATAGA
4066342 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4066382 CAAATGGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4066394 original size:13 final size:13
Alignment explanation
Indices: 4066376--4066403 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4066366 ATATATATAT
4066376 ATATATCAAATGG
1 ATATATCAAATGG
4066389 ATATATCAAATGG
1 ATATATCAAATGG
4066402 AT
1 AT
4066404 TTTTGAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.32
Consensus pattern (13 bp):
ATATATCAAATGG
Found at i:4069037 original size:18 final size:18
Alignment explanation
Indices: 4069009--4069051 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
4068999 TCTTCTTATT
*
4069009 TTTACTTTAATTACTTTTA
1 TTTA-TTTAATCACTTTTA
*
4069028 TTTATTTAATCGCTTTTA
1 TTTATTTAATCACTTTTA
4069046 -TTATTT
1 TTTATTT
4069052 TAATATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 12 0.55
19 4 0.18
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTTAATCACTTTTA
Found at i:4073020 original size:18 final size:19
Alignment explanation
Indices: 4072989--4073032 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
4072979 TATTCTCTTA
* *
4072989 TTTTTTTTACTTTAATTGC
1 TTTTATTTACTTTAATCGC
*
4073008 TTTTATTTA-TTTAATCGT
1 TTTTATTTACTTTAATCGC
4073026 TTTTATT
1 TTTTATT
4073033 ACTACTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.18, C:0.07, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTATTTACTTTAATCGC
Found at i:4078736 original size:18 final size:19
Alignment explanation
Indices: 4078708--4078746 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
4078698 TCTCTTATTT
*
4078708 TTTACTTTAATTGCTTTTA
1 TTTACTTTAATCGCTTTTA
*
4078727 TTTA-TTTAATCGTTTTTA
1 TTTACTTTAATCGCTTTTA
4078745 TT
1 TT
4078747 ACTATTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTACTTTAATCGCTTTTA
Found at i:4082761 original size:17 final size:17
Alignment explanation
Indices: 4082727--4082772 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
4082717 AAAGCAAGAA
4082727 GAAAAAAAACAGCAGTTC
1 GAAAAAAAA-AGCAGTTC
**
4082745 GAAAAAAAAAGTTGTTC
1 GAAAAAAAAAGCAGTTC
*
4082762 GAAAGAAAAAG
1 GAAAAAAAAAG
4082773 AGAGAGAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.59, C:0.09, G:0.20, T:0.13
Consensus pattern (17 bp):
GAAAAAAAAAGCAGTTC
Found at i:4087059 original size:31 final size:31
Alignment explanation
Indices: 4087021--4087092 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
4087011 GCGGGATTTA
4087021 TGTTGAAATTAAGAAGGGTCAATAGTTCAAT
1 TGTTGAAATTAAGAAGGGTCAATAGTTCAAT
4087052 TGTTGAAATTAAGAAGGGTCAATAGTTCAAT
1 TGTTGAAATTAAGAAGGGTCAATAGTTCAAT
4087083 TGTTGAAATT
1 TGTTGAAATT
4087093 TGGGGGGCTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.35
Consensus pattern (31 bp):
TGTTGAAATTAAGAAGGGTCAATAGTTCAAT
Found at i:4093800 original size:23 final size:23
Alignment explanation
Indices: 4093773--4093848 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
4093763 TGCATCGTTA
*
4093773 TTCATGTTTATTTATGGCATCCT
1 TTCATGTTCATTTATGGCATCCT
* * * *
4093796 TTCATGCTGA-TAAT-GCATCGTT
1 TTCATGTTCATTTATGGCATC-CT
4093818 ATTCATGTTCATTTATGGCATCCT
1 -TTCATGTTCATTTATGGCATCCT
4093842 TTCATGT
1 TTCATGT
4093849 CGATAATGCA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
21 5 0.12
22 4 0.10
23 23 0.56
24 4 0.10
25 5 0.12
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.47
Consensus pattern (23 bp):
TTCATGTTCATTTATGGCATCCT
Found at i:4093815 original size:46 final size:46
Alignment explanation
Indices: 4093713--4094288 Score: 727
Period size: 46 Copynumber: 12.6 Consensus size: 46
4093703 TATATGTCGT
* * * * * *
4093713 TAATACACCGTTATGTAATTTCATTTATGGCATTTCTTTCGTGCCAA
1 TAATGCACCGTTATGCATTTTCATTTATGGCA-TCCTTTCATGCCGA
* * * *
4093760 TTATGCATCGTTATTCATGTTT-ATTTATGGCATCCTTTCATGCTGA
1 TAATGCACCGTTATGCAT-TTTCATTTATGGCATCCTTTCATGCCGA
* * * *
4093806 TAATGCATCGTTATTCATGTTCATTTATGGCATCCTTTCATGTCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
4093852 TAATGCACCGTTATGCATTTTCATTTGA-GGCATCCTTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTT-ATGGCATCCTTTCATGCCGA
* * * *
4093898 TATTACACCGTTATGCATTTTTATTTATGGCATCCTTTCATGCCAA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
*
4093944 TAATGCACCGTTATGTATTTTCATTTATGGCATCCTTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* * *
4093990 TGATGCACCATTATCCATTTTCATTTATGGCATCCTTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* * * * *
4094036 TAATGCACCGTTATGCATTTTAAGTTATGGCGTTCTTTCATGCCAA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* *
4094082 TAATGCACTGTTATGCATTTTCATTTATGGCATCC-AT-AT--CGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
*
4094124 TAATGCACCGTTATGCATTTTCATTTATGGCATCCGTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* * * *
4094170 TAATGCACCATTATGCATTTTCATTGATGGAATCCTTTCAT-CTCAA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGC-CGA
* *
4094216 TAATGCATCGTTATGCATTTT-ATTTATGGCATCCTTTCATGTCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
*
4094261 TAATGCACCGTTATGTATTTTCATTTAT
1 TAATGCACCGTTATGCATTTTCATTTAT
4094289 TTATTCATTT
Statistics
Matches: 457, Mismatches: 61, Indels: 23
0.84 0.11 0.04
Matches are distributed among these distances:
42 36 0.08
43 1 0.00
44 4 0.01
45 43 0.09
46 347 0.76
47 23 0.05
48 3 0.01
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (46 bp):
TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
Found at i:4098101 original size:43 final size:47
Alignment explanation
Indices: 4098053--4098159 Score: 123
Period size: 48 Copynumber: 2.3 Consensus size: 47
4098043 GTAAGTATGC
*
4098053 AAATAAGCTTACGAGCATAT-GAA-T-AATGGCAAGTA-TATTGATA
1 AAATAAGCTTACGAGCATATGGAATTAAATGGCAAATATTATTGATA
* * * * *
4098096 AAATAAGCTTACGAACTTATGGAATTTAAATGGTAAATATTTTTGGTA
1 AAATAAGCTTACGAGCATATGGAA-TTAAATGGCAAATATTATTGATA
4098144 AAATAAGCTTACGAGC
1 AAATAAGCTTACGAGC
4098160 TTATAGGATA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
43 18 0.35
44 3 0.06
46 1 0.02
47 9 0.17
48 21 0.40
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (47 bp):
AAATAAGCTTACGAGCATATGGAATTAAATGGCAAATATTATTGATA
Found at i:4100067 original size:20 final size:20
Alignment explanation
Indices: 4100042--4100081 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4100032 GTCTACAAGT
4100042 ACTTTAGGCTTTTGTAATTA
1 ACTTTAGGCTTTTGTAATTA
4100062 ACTTTAGGCTTTTGTAATTA
1 ACTTTAGGCTTTTGTAATTA
4100082 GCACAACTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (20 bp):
ACTTTAGGCTTTTGTAATTA
Found at i:4103044 original size:23 final size:23
Alignment explanation
Indices: 4103018--4103139 Score: 83
Period size: 23 Copynumber: 5.3 Consensus size: 23
4103008 TGCACCTTTA
4103018 TTCATGTTCATTTATGGCATCCT
1 TTCATGTTCATTTATGGCATCCT
* * * *
4103041 TTCATGCTGA-TAAT-GCATTCTT
1 TTCATGTTCATTTATGGCA-TCCT
4103063 ATTCATGTTCATTTATGGCATCCT
1 -TTCATGTTCATTTATGGCATCCT
* * *
4103087 TTCATG-CCGA-TAAT-GCACCGCT
1 TTCATGTTC-ATTTATGGCATC-CT
* *
4103109 ATGCATTTTCATTTATGGCATCCT
1 -TTCATGTTCATTTATGGCATCCT
4103133 TTCATGT
1 TTCATGT
4103140 CGATAATGCA
Statistics
Matches: 71, Mismatches: 18, Indels: 20
0.65 0.17 0.18
Matches are distributed among these distances:
21 7 0.10
22 12 0.17
23 33 0.46
24 12 0.17
25 7 0.10
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.43
Consensus pattern (23 bp):
TTCATGTTCATTTATGGCATCCT
Found at i:4103045 original size:46 final size:46
Alignment explanation
Indices: 4102958--4103538 Score: 743
Period size: 46 Copynumber: 12.6 Consensus size: 46
4102948 TATATGTCGT
* * * * * * *
4102958 TAATACACCGTTATGTAATTTCATTTGTGGTAATTCTTTCATGCCAA
1 TAATGCACCGTTATGCATTTTCATTTATGG-CATCCTTTCATGCCGA
* * * * *
4103005 TTATGCACCTTTATTCATGTTCATTTATGGCATCCTTTCATGCTGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* * *
4103051 TAATGCATTC-TTATTCATGTTCATTTATGGCATCCTTTCATGCCGA
1 TAATGCA-CCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* *
4103097 TAATGCACCGCTATGCATTTTCATTTATGGCATCCTTTCATGTCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* * *
4103143 TAATGCAACGTTATGCATTTTCATTTATGGAATCCTTTCATGCAGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* * *
4103189 TAATGCATCGTTATGTATTTTCATTTATGGCATCCTTTCATACCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
** * *
4103235 TAATGCACCGTTATATATTTTCATTTTTGGAATCCTTTCATAG-CGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCAT-GCCGA
* * **
4103281 TAATGCATCGTTATGCATTTTCATTTATGTCATCCTTTCATGTTGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* * * * * *
4103327 TAATGCATCGTTATACATTTTCATTCATTGTATCTTTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
4103373 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
*
4103419 TAATGCACCATTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* *
4103465 TAATGCACTGTTATGCATTTTCATTTATGGCATCCTTTCATGTCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* *
4103511 TAATGCACTGTTATGTATTTTCATTTAT
1 TAATGCACCGTTATGCATTTTCATTTAT
4103539 TCATTCATTT
Statistics
Matches: 469, Mismatches: 61, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
45 2 0.00
46 444 0.95
47 23 0.05
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (46 bp):
TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
Found at i:4121087 original size:21 final size:20
Alignment explanation
Indices: 4121044--4121093 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
4121034 TTAAAATGGC
* *
4121044 ATCGATACCTCCCATTTGGT
1 ATCGATACCCCCCATTAGGT
*
4121064 ATCGATACTCCCCCCTTAGGT
1 ATCGATAC-CCCCCATTAGGT
4121085 ATCGATACC
1 ATCGATACC
4121094 ATGCGGTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.22, C:0.34, G:0.14, T:0.30
Consensus pattern (20 bp):
ATCGATACCCCCCATTAGGT
Found at i:4122777 original size:60 final size:55
Alignment explanation
Indices: 4122681--4122825 Score: 227
Period size: 60 Copynumber: 2.5 Consensus size: 55
4122671 TTACACTATA
4122681 ATATTCTATAGTAGTATATGAGCATGTAGTTCAAATTATAAGATATATATACATATTTC
1 ATATTCTATAGTAGTATATGAGCATGTAGTTCAAATTATAAG--ATATAT--ATATTTC
*
4122740 ATATTTCTATAATAGTATATGAGCATGTAGTTCAAATTATAAGATATATATATTTC
1 ATA-TTCTATAGTAGTATATGAGCATGTAGTTCAAATTATAAGATATATATATTTC
*
4122796 ATATTCTATAGTAGCATATGAGCATGTAGT
1 ATATTCTATAGTAGTATATGAGCATGTAGT
4122826 ATATATGTTT
Statistics
Matches: 82, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
55 25 0.30
56 10 0.12
58 6 0.07
59 3 0.04
60 38 0.46
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (55 bp):
ATATTCTATAGTAGTATATGAGCATGTAGTTCAAATTATAAGATATATATATTTC
Found at i:4122792 original size:33 final size:33
Alignment explanation
Indices: 4122695--4122792 Score: 86
Period size: 33 Copynumber: 3.2 Consensus size: 33
4122685 TCTATAGTAG
4122695 TATATGAGCATGTAGTTCAAATTATAAG--ATA
1 TATATGAGCATGTAGTTCAAATTATAAGATATA
* * * *
4122726 TATAT-A-CA--TATTTCATATTTCTATA-ATA-G
1 TATATGAGCATGTAGTTCA-AATTATA-AGATATA
4122755 TATATGAGCATGTAGTTCAAATTATAAGATATA
1 TATATGAGCATGTAGTTCAAATTATAAGATATA
4122788 TATAT
1 TATAT
4122793 TTCATATTCT
Statistics
Matches: 49, Mismatches: 8, Indels: 18
0.65 0.11 0.24
Matches are distributed among these distances:
27 6 0.12
28 5 0.10
29 8 0.16
30 3 0.06
31 8 0.16
32 8 0.16
33 11 0.22
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (33 bp):
TATATGAGCATGTAGTTCAAATTATAAGATATA
Found at i:4122841 original size:41 final size:41
Alignment explanation
Indices: 4122784--4122866 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
4122774 AATTATAAGA
4122784 TATATATATTTCATATTCTATAGTAGCATATGAGCATGTAG
1 TATATATATTTCATATTCTATAGTAGCATATGAGCATGTAG
* *
4122825 TATATATGTTTCATATTCTATAGTAGTATATGAGCATGTAG
1 TATATATATTTCATATTCTATAGTAGCATATGAGCATGTAG
4122866 T
1 T
4122867 TCAAATTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (41 bp):
TATATATATTTCATATTCTATAGTAGCATATGAGCATGTAG
Found at i:4123396 original size:308 final size:308
Alignment explanation
Indices: 4122838--4123423 Score: 1102
Period size: 308 Copynumber: 1.9 Consensus size: 308
4122828 ATATGTTTCA
*
4122838 TATTCTATAGTAGTATATGAGCATGTAGTTCAAATTATAAGATATATATTTCATATTCTTTTTAT
1 TATTCTATAGTAGTATATGAGCATGTAGTTCAAATTATAAGATATATATTTCATATTATTTTTAT
**
4122903 ACTATAATATTATTTAATATATTAAATGTAATCTAAAATTATAAATTATATTTGTAATATTATAT
66 ACTATAATATTATTTAATATATTAAAAATAATCTAAAATTATAAATTATATTTGTAATATTATAT
4122968 TTTTGTTATTTTGGAAGTAAAATATTAATGAGAGTATATAAGAGTCAAGAAATTAATAGGAAGAA
131 TTTTGTTATTTTGGAAGTAAAATATTAATGAGAGTATATAAGAGTCAAGAAATTAATAGGAAGAA
*
4123033 AGAATTTGTAAACAATTGTTTACAAAAGATCAAATTGAGTAAAATATAATGTTAAGGTTTTAAAT
196 AGAATTTGTAAACAATTGTTTACAAAAGATCAAATTGAGTAAAATATAATGTTAAGGGTTTAAAT
4123098 AAAAAAGTGTATATTTTTAATAAAAATTAAGAATTGAAACTATATAGG
261 AAAAAAGTGTATATTTTTAATAAAAATTAAGAATTGAAACTATATAGG
4123146 TATTCTATAGTAGTATATGAGCATGTAGTTCAAATTATAAGATATATATTTCATATTATTTTTAC
1 TATTCTATAGTAGTATATGAGCATGTAGTTCAAATTATAAGATATATATTTCATATTATTTTTA-
4123211 T-CTATAATATTATTTAATATATTAAAAATAATCTAAAATTATAAATTATATTTGTAATATTATA
65 TACTATAATATTATTTAATATATTAAAAATAATCTAAAATTATAAATTATATTTGTAATATTATA
*
4123275 TTTTTGTTCTTTTGGAAGTAAAATATTAATGAGAGTATATAAGAGTCAAGAAATTAATAGGAAGA
130 TTTTTGTTATTTTGGAAGTAAAATATTAATGAGAGTATATAAGAGTCAAGAAATTAATAGGAAGA
*
4123340 AAGAATTTGTAAACAATTGTTTACAAGAGATCAAATTGAGTAAAATATAATGTTAAGGGTTTAAA
195 AAGAATTTGTAAACAATTGTTTACAAAAGATCAAATTGAGTAAAATATAATGTTAAGGGTTTAAA
4123405 TAAAAAAGTGTATATTTTT
260 TAAAAAAGTGTATATTTTT
4123424 TAGATTCTCT
Statistics
Matches: 271, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
308 270 1.00
309 1 0.00
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (308 bp):
TATTCTATAGTAGTATATGAGCATGTAGTTCAAATTATAAGATATATATTTCATATTATTTTTAT
ACTATAATATTATTTAATATATTAAAAATAATCTAAAATTATAAATTATATTTGTAATATTATAT
TTTTGTTATTTTGGAAGTAAAATATTAATGAGAGTATATAAGAGTCAAGAAATTAATAGGAAGAA
AGAATTTGTAAACAATTGTTTACAAAAGATCAAATTGAGTAAAATATAATGTTAAGGGTTTAAAT
AAAAAAGTGTATATTTTTAATAAAAATTAAGAATTGAAACTATATAGG
Found at i:4123596 original size:33 final size:33
Alignment explanation
Indices: 4123493--4123596 Score: 97
Period size: 33 Copynumber: 3.2 Consensus size: 33
4123483 TCTATAGTAG
4123493 TATATGAGCATGTAGTTCAAATTATAAGATATA
1 TATATGAGCATGTAGTTCAAATTATAAGATATA
** * * * * *
4123526 TATAT-ATATATATATTTCATATTTCTATA-ATA-G
1 TATATGA-GCATGTAGTTCA-AATTATA-AGATATA
4123559 TATATGAGCATGTAGTTCAAATTATAAGATATA
1 TATATGAGCATGTAGTTCAAATTATAAGATATA
4123592 TATAT
1 TATAT
4123597 TTCATATTCT
Statistics
Matches: 51, Mismatches: 14, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
31 1 0.02
32 9 0.18
33 31 0.61
34 9 0.18
35 1 0.02
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.42
Consensus pattern (33 bp):
TATATGAGCATGTAGTTCAAATTATAAGATATA
Found at i:4123645 original size:41 final size:41
Alignment explanation
Indices: 4123588--4123670 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
4123578 AATTATAAGA
4123588 TATATATATTTCATATTCTATAGTAGCATATGAGCATGTAG
1 TATATATATTTCATATTCTATAGTAGCATATGAGCATGTAG
* *
4123629 TATATATGTTTCATATTCTATAGTAGTATATGAGCATGTAG
1 TATATATATTTCATATTCTATAGTAGCATATGAGCATGTAG
4123670 T
1 T
4123671 TCAAATTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (41 bp):
TATATATATTTCATATTCTATAGTAGCATATGAGCATGTAG
Found at i:4123910 original size:804 final size:793
Alignment explanation
Indices: 4122078--4123919 Score: 3472
Period size: 794 Copynumber: 2.3 Consensus size: 793
4122068 TTCTCTAATC
* * *
4122078 TTATAAGATATATATATCATATTCTTTTTACACTATAATATTATTTAATATATTAAATATAATCT
1 TTATAAGATATATATTTCATATTCTTTTTATACTATAATATTATTTAATATATTAAATGTAATCT
4122143 AAAATTATAAATTATATTTGTAATATTATATTTTTGTTATTTTGGAAGTAAAATATTAATGAGAG
66 AAAATTATAAATTATATTTGTAATATTATATTTTTGTTATTTTGGAAGTAAAATATTAATGAGAG
4122208 TATATAAGAGTCAAGAAATTAATAGGAAGAAAGAATTTGTAAACAATTGTTTACAAAAGATCAAA
131 TATATAAGAGTCAAGAAATTAATAGGAAGAAAGAATTTGTAAACAATTGTTTACAAAAGATCAAA
*
4122273 TTGAGTAAAATATAATGTTAAGGTTTTAAATAAAAAAGTGTATATTTTTAGTAAAAATTAAGAAT
196 TTGAGTAAAATATAATGTTAAGGTTTTAAATAAAAAAGTGTATATTTTTAATAAAAATTAAGAAT
4122338 TGAAACTATATAGGTATTCTATAGTAGTATATGAGCATGTAGTTCAAATTATAAGATATATATTT
261 TGAAACTATATAGGTATTCTATAGTAGTATATGAGCATGTAGTTCAAATTATAAGATATATATTT
*
4122403 CATATTATTTTTACTCTATAATATTATTTAATATTAAAATTAATCTAAAATTATAAATATTGTAA
326 CATATTATTTTTACTCTATAATATTATTTAATATTAAAAATAATCTAAAATTATAAATATTGTAA
4122468 TATTATATTTTTGTTATTTTGGAAGTAAAATATTAATGAGAGTATATAAGAGTCAAGAAATTAAT
391 TATTATATTTTTGTTATTTTGGAAGTAAAATATTAATGAGAGTATATAAGAGTCAAGAAATTAAT
4122533 AGGAAGAAAGAATTTGTAAACAATTGTTTACAAGAGATCAAATTGAGTAAAATATAATGTTAAGG
456 AGGAAGAAAGAATTTGTAAACAATTGTTTACAAGAGATCAAATTGAGTAAAATATAATGTTAAGG
4122598 GTTTAAATAAAAAAGTGTATATTTTTTAGATTCTCTAATCTTATAAGATATATATATATATTTCA
521 GTTTAAATAAAAAAGTGTATATTTTTTAGATTCTCTAATCTTATAAGA-ATATATATATATTTCA
4122663 TATTCTTTTTACACTATAATATTCTATAGTAGTATATGAGCATGTAGTTCAAATTATAAGATATA
585 TATTCTTTTTACACTATAATATTCTATAGTAGTATATGAGCATGTAGTTCAAATTATAAGATATA
4122728 TATACATATTTCATATTTCTATAATAGTATATGAGCATGTAGTTCAAATTATAAGATATATATAT
650 TATACATATTTCATATTTCTATAATAGTATATGAGCATGTAGTTCAAATTATAAGATATATATAT
4122793 TTCATATTCTATAGTAGCATATGAGCATGTAGTATATATGTTTCATATTCTATAGTAGTATATGA
715 TTCATATTCTATAGTAGCATATGAGCATGTAGTATATATGTTTCATATTCTATAGTAGTATATGA
4122858 GCATGTAGTTCAAA
780 GCATGTAGTTCAAA
4122872 TTATAAGATATATATTTCATATTCTTTTTATACTATAATATTATTTAATATATTAAATGTAATCT
1 TTATAAGATATATATTTCATATTCTTTTTATACTATAATATTATTTAATATATTAAATGTAATCT
4122937 AAAATTATAAATTATATTTGTAATATTATATTTTTGTTATTTTGGAAGTAAAATATTAATGAGAG
66 AAAATTATAAATTATATTTGTAATATTATATTTTTGTTATTTTGGAAGTAAAATATTAATGAGAG
4123002 TATATAAGAGTCAAGAAATTAATAGGAAGAAAGAATTTGTAAACAATTGTTTACAAAAGATCAAA
131 TATATAAGAGTCAAGAAATTAATAGGAAGAAAGAATTTGTAAACAATTGTTTACAAAAGATCAAA
4123067 TTGAGTAAAATATAATGTTAAGGTTTTAAATAAAAAAGTGTATATTTTTAATAAAAATTAAGAAT
196 TTGAGTAAAATATAATGTTAAGGTTTTAAATAAAAAAGTGTATATTTTTAATAAAAATTAAGAAT
4123132 TGAAACTATATAGGTATTCTATAGTAGTATATGAGCATGTAGTTCAAATTATAAGATATATATTT
261 TGAAACTATATAGGTATTCTATAGTAGTATATGAGCATGTAGTTCAAATTATAAGATATATATTT
4123197 CATATTATTTTTACTCTATAATATTATTTAATATATTAAAAATAATCTAAAATTATAAATTATAT
326 CATATTATTTTTACTCTATAATATTATTT-A-ATATTAAAAATAATCTAAAATTAT-AA--ATA-
*
4123262 TTGTAATATTATATTTTTGTTCTTTTGGAAGTAAAATATTAATGAGAGTATATAAGAGTCAAGAA
385 TTGTAATATTATATTTTTGTTATTTTGGAAGTAAAATATTAATGAGAGTATATAAGAGTCAAGAA
4123327 ATTAATAGGAAGAAAGAATTTGTAAACAATTGTTTACAAGAGATCAAATTGAGTAAAATATAATG
450 ATTAATAGGAAGAAAGAATTTGTAAACAATTGTTTACAAGAGATCAAATTGAGTAAAATATAATG
4123392 TTAAGGGTTTAAATAAAAAAGTGTATATTTTTTAGATTCTCTAATCTTATAAG-ATATATATATA
515 TTAAGGGTTTAAATAAAAAAGTGTATATTTTTTAGATTCTCTAATCTTATAAGAATATATATATA
4123456 TTTCATATTCTTTTTACACTATAATATTCTATAGTAGTATATGAGCATGTAGTTCAAATTATAAG
580 TTTCATATTCTTTTTACACTATAATATTCTATAGTAGTATATGAGCATGTAGTTCAAATTATAAG
*
4123521 ATATATATATATATATATATTTCATATTTCTATAATAGTATATGAGCATGTAGTTCAAATTATAA
645 ------ATATATATACATATTTCATATTTCTATAATAGTATATGAGCATGTAGTTCAAATTATAA
4123586 GATATATATATTTCATATTCTATAGTAGCATATGAGCATGTAGTATATATGTTTCATATTCTATA
704 GATATATATATTTCATATTCTATAGTAGCATATGAGCATGTAGTATATATGTTTCATATTCTATA
4123651 GTAGTATATGAGCATGTAGTTCAAA
769 GTAGTATATGAGCATGTAGTTCAAA
4123676 TTATAAGATATATATTTCATATTCTTTTTATACTATAATATTATTTAATATATTAAATGTAATCT
1 TTATAAGATATATATTTCATATTCTTTTTATACTATAATATTATTTAATATATTAAATGTAATCT
4123741 AAAATTATAAATTATATTTGTAATATTATATTTTT-TTATTTTGGAAGTAAAATATTAATGAGAG
66 AAAATTATAAATTATATTTGTAATATTATATTTTTGTTATTTTGGAAGTAAAATATTAATGAGAG
4123805 TATATAAGAGTCAAGAAATTAATAGGAAGAAAGAATTTGTAAACAATTGTTTACAAAAGATCAAA
131 TATATAAGAGTCAAGAAATTAATAGGAAGAAAGAATTTGTAAACAATTGTTTACAAAAGATCAAA
*
4123870 TTGAGTAAAATATAATGTTAAGGGTTTAAATAAAAAAAGTGTATATTTTT
196 TTGAGTAAAATATAATGTTAAGGTTTTAAAT-AAAAAAGTGTATATTTTT
4123920 TACATTCTCT
Statistics
Matches: 1027, Mismatches: 8, Indels: 16
0.98 0.01 0.02
Matches are distributed among these distances:
794 350 0.34
795 1 0.00
796 23 0.02
797 2 0.00
798 76 0.07
799 3 0.00
800 182 0.18
803 124 0.12
804 266 0.26
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (793 bp):
TTATAAGATATATATTTCATATTCTTTTTATACTATAATATTATTTAATATATTAAATGTAATCT
AAAATTATAAATTATATTTGTAATATTATATTTTTGTTATTTTGGAAGTAAAATATTAATGAGAG
TATATAAGAGTCAAGAAATTAATAGGAAGAAAGAATTTGTAAACAATTGTTTACAAAAGATCAAA
TTGAGTAAAATATAATGTTAAGGTTTTAAATAAAAAAGTGTATATTTTTAATAAAAATTAAGAAT
TGAAACTATATAGGTATTCTATAGTAGTATATGAGCATGTAGTTCAAATTATAAGATATATATTT
CATATTATTTTTACTCTATAATATTATTTAATATTAAAAATAATCTAAAATTATAAATATTGTAA
TATTATATTTTTGTTATTTTGGAAGTAAAATATTAATGAGAGTATATAAGAGTCAAGAAATTAAT
AGGAAGAAAGAATTTGTAAACAATTGTTTACAAGAGATCAAATTGAGTAAAATATAATGTTAAGG
GTTTAAATAAAAAAGTGTATATTTTTTAGATTCTCTAATCTTATAAGAATATATATATATTTCAT
ATTCTTTTTACACTATAATATTCTATAGTAGTATATGAGCATGTAGTTCAAATTATAAGATATAT
ATACATATTTCATATTTCTATAATAGTATATGAGCATGTAGTTCAAATTATAAGATATATATATT
TCATATTCTATAGTAGCATATGAGCATGTAGTATATATGTTTCATATTCTATAGTAGTATATGAG
CATGTAGTTCAAA
Found at i:4124146 original size:262 final size:257
Alignment explanation
Indices: 4123676--4124180 Score: 893
Period size: 262 Copynumber: 1.9 Consensus size: 257
4123666 GTAGTTCAAA
* *
4123676 TTATAAGATATATATTTCATATTCTTTTTATACTATAATATTATTTAATATATTAAATGTAATCT
1 TTATAAGATATATATTTCATATTCTTTTTACACTATAATATTATTTAATATATTAAATATAATCT
*
4123741 AAAATTATAAATTATATTTGTAATATTATATTTTTTTATTTTGGAAGTAAAATATTAATGAGAGT
66 AAAATTATAAATTATATTTGTAATATTATATTTTTTTATTTTGGAAGTAAAATATCAATGAGAGT
* * * *
4123806 ATATAAGAGTCAAGAAATTAATAGGAAGAAAGAATTTGTAAACAATTGTTTACAAAAGATCAAAT
131 ACATAAGAGTAAAGAAAATAATAGGAAGAAAGAATTTGTAAACAACTGTTTACAAAAGATCAAAT
*
4123871 TGAGTAAAATATAATGTTAAGGGTTTAAATAAAAAAAGTGTATATTTTTTACATTCTCTAATC
196 TGAGTAAAATATAACGTTAAGGGTTTAAAT-AAAAAAGTGTATATTTTTTACATTCTCTAATC
4123934 TTATAAGATATATATATTTCATATTCTTTTTACACTATAATATTATTTAATATATTAAATATAAT
1 TTATAAG--ATATATATTTCATATTCTTTTTACACTATAATATTATTTAATATATTAAATATAAT
4123999 CTAAAATTATAAATTATATTTGTAATATTATATTTTTGTTATTTTTGGAAGTAAAATATCAATGA
64 CTAAAATTATAAATTATATTTGTAATATTATATTTTT-TTA-TTTTGGAAGTAAAATATCAATGA
4124064 GAGTACATAAGAGTAAAGAAAATAATAGGAAGAAAGAATTTGTAAACAACTGTTTACAAAAGATC
127 GAGTACATAAGAGTAAAGAAAATAATAGGAAGAAAGAATTTGTAAACAACTGTTTACAAAAGATC
4124129 AAATTGAGTAAAATATAACGTTAAGGGTTTAAATAAAAAAGTGTATATTTTT
192 AAATTGAGTAAAATATAACGTTAAGGGTTTAAATAAAAAAGTGTATATTTTT
4124181 AATAAAAATT
Statistics
Matches: 235, Mismatches: 8, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
258 7 0.03
260 91 0.39
261 21 0.09
262 116 0.49
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (257 bp):
TTATAAGATATATATTTCATATTCTTTTTACACTATAATATTATTTAATATATTAAATATAATCT
AAAATTATAAATTATATTTGTAATATTATATTTTTTTATTTTGGAAGTAAAATATCAATGAGAGT
ACATAAGAGTAAAGAAAATAATAGGAAGAAAGAATTTGTAAACAACTGTTTACAAAAGATCAAAT
TGAGTAAAATATAACGTTAAGGGTTTAAATAAAAAAGTGTATATTTTTTACATTCTCTAATC
Found at i:4128432 original size:16 final size:17
Alignment explanation
Indices: 4128404--4128435 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4128394 ATCACCGACA
4128404 AAATTTAACTATTCACG
1 AAATTTAACTATTCACG
4128421 AAATTT-ACTATTCAC
1 AAATTTAACTATTCAC
4128436 ATGAATAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.41, C:0.19, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATTTAACTATTCACG
Found at i:4132424 original size:9 final size:10
Alignment explanation
Indices: 4132402--4132436 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
4132392 TTAGGCGTTC
*
4132402 TTTTATTAGT
1 TTTTTTTAGT
4132412 TTTTTTTAGT
1 TTTTTTTAGT
4132422 TTTTTTTA-T
1 TTTTTTTAGT
4132431 TTTTTT
1 TTTTTT
4132437 ATTCTAATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.11, C:0.00, G:0.06, T:0.83
Consensus pattern (10 bp):
TTTTTTTAGT
Found at i:4133400 original size:17 final size:16
Alignment explanation
Indices: 4133378--4133423 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
4133368 GATGTTGGAG
4133378 AGTATTGATACTATAAC
1 AGTATTGATACTA-AAC
*
4133395 AGTATTGGTAC--AAC
1 AGTATTGATACTAAAC
*
4133409 AATATTGATACTAAA
1 AGTATTGATACTAAA
4133424 ATAATATCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
14 12 0.50
16 2 0.08
17 10 0.42
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (16 bp):
AGTATTGATACTAAAC
Found at i:4139254 original size:29 final size:29
Alignment explanation
Indices: 4139222--4139295 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
4139212 CCTGATGTTG
* *
4139222 CATGAGATTATATCTCCATCCTGATTCTA
1 CATGGGATTATATCTCCATCCTAATTCTA
*
4139251 CATGGGATTGA-ATCCCCATCCTAATTCTA
1 CATGGGATT-ATATCTCCATCCTAATTCTA
4139280 CATGGGATTATATCTC
1 CATGGGATTATATCTC
4139296 GTCTTATTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 37 0.95
30 1 0.03
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (29 bp):
CATGGGATTATATCTCCATCCTAATTCTA
Found at i:4140391 original size:28 final size:28
Alignment explanation
Indices: 4140359--4140417 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
4140349 TTAAATCTCC
4140359 TATTGTGGTTCATTTACAATAGCAATCA
1 TATTGTGGTTCATTTACAATAGCAATCA
4140387 TATTGTGGTTCATTTACAATAGCAATCA
1 TATTGTGGTTCATTTACAATAGCAATCA
4140415 TAT
1 TAT
4140418 ATGTTTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (28 bp):
TATTGTGGTTCATTTACAATAGCAATCA
Done.