Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 343 of 770
Found at i:105168784 original size:66 final size:68
Alignment explanation
Indices: 105168703--105168858 Score: 280
Period size: 66 Copynumber: 2.3 Consensus size: 68
105168693 GTCACTTGGA
* *
105168703 ATCACGCATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACAT-GG-TACATCT
1 ATCACACATGTGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGGATACATCT
105168766 CGT
66 CGT
105168769 ATCACACATGTGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGGATACATCT
1 ATCACACATGTGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGGATACATCT
105168834 CGT
66 CGT
105168837 ATCACACATGTGACCTAGCTAC
1 ATCACACATGTGACCTAGCTAC
105168859 TACAGGGTGT
Statistics
Matches: 86, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
66 52 0.60
67 2 0.02
68 32 0.37
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (68 bp):
ATCACACATGTGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGGATACATCT
CGT
Found at i:105168875 original size:68 final size:67
Alignment explanation
Indices: 105168661--105168926 Score: 225
Period size: 68 Copynumber: 3.9 Consensus size: 67
105168651 CTAGCCGATT
* * * * * * *
105168661 TGTCTCGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCTAGCTACA
1 TGTCACGTAGCTCTCTTGTCTACATGG-GTACAT--C-TCGTATCACACATGTGACCTAGCTACA
** *
105168726 TTTATC
62 TACAGC
* **
105168732 TTTCACGTAGCTCTCTTGTCTACAT-GGTACATCTCGTATCACACATGTGACCTAGCTACATTTA
1 TGTCACGTAGCTCTCTTGTCTACATGGGTACATCTCGTATCACACATGTGACCTAGCTACATACA
*
105168796 TC
66 GC
*
105168798 TTTCACGTAGCTCTCTTGTCTACATGGGATACATCTCGTATCACACATGTGACCTAGCTAC-TAC
1 TGTCACGTAGCTCTCTTGTCTACATGGG-TACATCTCGTATCACACATGTGACCTAGCTACATAC
*
105168862 AGGG
65 A-GC
* * * * * *
105168866 TGTCTCGTAGCTTTCTTGTAC-ACATGATGTGCA-CTCGGCATCATACATGTGACCTAGCTAC
1 TGTCACGTAGCTCTCTTGT-CTACATG-GGTACATCTC-GTATCACACATGTGACCTAGCTAC
105168927 GCTCCATCTA
Statistics
Matches: 170, Mismatches: 19, Indels: 15
0.83 0.09 0.07
Matches are distributed among these distances:
66 54 0.32
67 8 0.05
68 78 0.46
69 6 0.04
70 1 0.01
71 23 0.14
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.33
Consensus pattern (67 bp):
TGTCACGTAGCTCTCTTGTCTACATGGGTACATCTCGTATCACACATGTGACCTAGCTACATACA
GC
Found at i:105170268 original size:38 final size:38
Alignment explanation
Indices: 105170226--105170301 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
105170216 CCAATCTCAA
* *
105170226 TCAT-ACACTGGGCTGTAGCCCTTTTCATATTTCATATT
1 TCATAACACTGGGCCGAAG-CCTTTTCATATTTCATATT
*
105170264 TCATAATACTGGGCCGAAGCCTTTTCATATTTCATATT
1 TCATAACACTGGGCCGAAGCCTTTTCATATTTCATATT
105170302 ACTGGGCCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 23 0.68
39 11 0.32
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (38 bp):
TCATAACACTGGGCCGAAGCCTTTTCATATTTCATATT
Found at i:105170290 original size:31 final size:31
Alignment explanation
Indices: 105170255--105170318 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
105170245 CCTTTTCATA
105170255 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
*
105170286 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
105170317 TT
1 TT
105170319 ACTGTAAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Found at i:105170561 original size:24 final size:24
Alignment explanation
Indices: 105170510--105170676 Score: 248
Period size: 24 Copynumber: 7.0 Consensus size: 24
105170500 GCTTTATCAT
* *
105170510 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTG
* **
105170535 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTG
*
105170559 ATAACTAGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTG
105170582 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
105170606 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
105170630 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
105170654 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
105170677 TCACTTCCTC
Statistics
Matches: 133, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
23 22 0.17
24 99 0.74
25 12 0.09
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:105170752 original size:20 final size:20
Alignment explanation
Indices: 105170727--105170786 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
105170717 TATGATTACC
* *
105170727 TCATGTGCATATTATATATA
1 TCATGTGCATATCATACATA
*
105170747 TCATGTGCATATCATACATT
1 TCATGTGCATATCATACATA
105170767 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
105170787 CCATATTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:105170861 original size:25 final size:25
Alignment explanation
Indices: 105170829--105170876 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
105170819 ATACATAAAC
* * *
105170829 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
105170854 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
105170877 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:105182379 original size:22 final size:22
Alignment explanation
Indices: 105182325--105182379 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
105182315 ATATAATCTC
*
105182325 ATATACACATA-CTAATCATAT
1 ATATACAAATATCTAATCATAT
*
105182346 A-AT-CGAATATATCTTATCATAT
1 ATATAC-AA-ATATCTAATCATAT
105182368 ATATACAAATAT
1 ATATACAAATAT
105182380 AAGGACTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
19 1 0.04
20 3 0.11
21 4 0.15
22 14 0.52
23 4 0.15
24 1 0.04
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.36
Consensus pattern (22 bp):
ATATACAAATATCTAATCATAT
Found at i:105182512 original size:24 final size:24
Alignment explanation
Indices: 105182480--105182528 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
105182470 TAACAAATAG
105182480 CCAAGGTACTTACTTACCTTACAT
1 CCAAGGTACTTACTTACCTTACAT
105182504 CCAAGGTACTTACTTACCTTACAT
1 CCAAGGTACTTACTTACCTTACAT
105182528 C
1 C
105182529 AAATAGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.33
Consensus pattern (24 bp):
CCAAGGTACTTACTTACCTTACAT
Found at i:105188947 original size:28 final size:28
Alignment explanation
Indices: 105188908--105188970 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
105188898 TTTAAAACCC
105188908 TAAGGGT-ATATCGGTAATTTTACTCTT
1 TAAGGGTAATATCGGTAATTTTACTCTT
*
105188935 TAAGGGTAATATCGGTAATTTTGCTCTT
1 TAAGGGTAATATCGGTAATTTTACTCTT
*
105188963 TAGGGGTA
1 TAAGGGTA
105188971 GTTTCGTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
27 7 0.21
28 26 0.79
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.41
Consensus pattern (28 bp):
TAAGGGTAATATCGGTAATTTTACTCTT
Found at i:105190626 original size:20 final size:20
Alignment explanation
Indices: 105190603--105190640 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
105190593 CACATCCAAA
*
105190603 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
105190623 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
105190641 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:105200001 original size:29 final size:29
Alignment explanation
Indices: 105199922--105200037 Score: 112
Period size: 29 Copynumber: 4.1 Consensus size: 29
105199912 ACCCCTACAT
*
105199922 ACATGCATATGGCCCACTT-GGCCC--ATC
1 ACATTCATATGGCCCA-TTAGGCCCAAATC
* * * *
105199949 TCATTCATATGGCCCATCACGCCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAAATC
*
105199978 ACATTCATATGGCCTATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
* * * *
105200007 ACCTTTATGTGGCCCGTTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
105200036 AC
1 AC
105200038 CTTATATTCA
Statistics
Matches: 71, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
26 1 0.01
27 18 0.25
29 52 0.73
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.26
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAAATC
Found at i:105207517 original size:30 final size:30
Alignment explanation
Indices: 105207483--105207541 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
105207473 CACAGCCATG
* *
105207483 ACACACGGGCGTGTGG-TCTACTCGTGTGGC
1 ACACACGGGCATGTGGATC-ACCCGTGTGGC
105207513 ACACACGGGCATGTGGATCACCCGTGTGG
1 ACACACGGGCATGTGGATCACCCGTGTGG
105207542 AAGTGCCTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.17, C:0.27, G:0.36, T:0.20
Consensus pattern (30 bp):
ACACACGGGCATGTGGATCACCCGTGTGGC
Found at i:105219735 original size:55 final size:55
Alignment explanation
Indices: 105219640--105219745 Score: 142
Period size: 55 Copynumber: 1.9 Consensus size: 55
105219630 TAGGCCCACG
* **
105219640 CCCGTGTTAATTTAACAGGTTCACCCATGGTTGCTTGGCACGGGCGTGTCGTACA
1 CCCGTGTTAATTTAACAGGTTCACCCAGGGTTGCAAGGCACGGGCGTGTCGTACA
* * *
105219695 CCCGTGTTAATTTGACATGTTCAGCCACGGGTT-CAAGGCACGGGCGTGTCG
1 CCCGTGTTAATTTAACAGGTTCACCCA-GGGTTGCAAGGCACGGGCGTGTCG
105219746 CACGCCTGTG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
55 40 0.91
56 4 0.09
ACGTcount: A:0.18, C:0.25, G:0.29, T:0.27
Consensus pattern (55 bp):
CCCGTGTTAATTTAACAGGTTCACCCAGGGTTGCAAGGCACGGGCGTGTCGTACA
Found at i:105219772 original size:55 final size:55
Alignment explanation
Indices: 105219640--105219779 Score: 138
Period size: 55 Copynumber: 2.5 Consensus size: 55
105219630 TAGGCCCACG
* * * ** *
105219640 CCCGTGTTAATTTAACAGGTTCACCCA-TGGTTGCTTGGCACGGGCGTGTCGTACA
1 CCCGTGCTAATTTGACAGGTTCACCCACGGGTT-CAAGGCACGGGCGTGTCGCACA
* * * *
105219695 CCCGTGTTAATTTGACATGTTCAGCCACGGGTTCAAGGCACGGGCGTGTCGCACG
1 CCCGTGCTAATTTGACAGGTTCACCCACGGGTTCAAGGCACGGGCGTGTCGCACA
* ** *
105219750 CCTGTGCTGTTTTGGCAGGTTCACCCACGG
1 CCCGTGCTAATTTGACAGGTTCACCCACGG
105219780 CCATGTCGAA
Statistics
Matches: 69, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
55 65 0.94
56 4 0.06
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.27
Consensus pattern (55 bp):
CCCGTGCTAATTTGACAGGTTCACCCACGGGTTCAAGGCACGGGCGTGTCGCACA
Found at i:105221872 original size:25 final size:25
Alignment explanation
Indices: 105221819--105221872 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
105221809 AATTTTATTT
* *
105221819 AATTATTTAATTTTTCATATTATTG
1 AATTATTTAATTTTTCATATAATTA
105221844 AATTA-TTAATATTTT-ATACTAATTA
1 AATTATTTAAT-TTTTCATA-TAATTA
105221869 AATT
1 AATT
105221873 TATCTGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (25 bp):
AATTATTTAATTTTTCATATAATTA
Found at i:105226499 original size:24 final size:23
Alignment explanation
Indices: 105226472--105226517 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
105226462 ATCCACACTG
*
105226472 GAGTGTAGGTTTGGATGAGATACA
1 GAGTGTAGGGTTGGATG-GATACA
*
105226496 GAGTGTAGGGTTGGTTGGATAC
1 GAGTGTAGGGTTGGATGGATAC
105226518 TTGTGCATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.24, C:0.04, G:0.41, T:0.30
Consensus pattern (23 bp):
GAGTGTAGGGTTGGATGGATACA
Found at i:105229227 original size:3 final size:3
Alignment explanation
Indices: 105229219--105229270 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
105229209 GCTCATGAAA
*
105229219 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
105229267 AAG A
1 AAG A
105229271 GCATATGTAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:105234430 original size:38 final size:38
Alignment explanation
Indices: 105234371--105234754 Score: 588
Period size: 38 Copynumber: 10.1 Consensus size: 38
105234361 AGGCCCGAAT
* * *
105234371 TAATACCAGCACTAGGGCTGCGGGATTTAACCCGGATA
1 TAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATA
** * *
105234409 TTTTACCAGCACGAAGCCTGCGGGTCTTTAAGTCCGGATA
1 TAATACCAGCACGAAGCCTGCGGG-ATTTAA-CCCGGATA
* *
105234449 TAATACCAGCACGAAGCCTGTGAGATTTAACCCGGATA
1 TAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATA
*
105234487 TAATACCAGCACGAAGCCTGCGGGATTTAACCTGGATA
1 TAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATA
* *
105234525 TATTACCAGCACGAAGCCTGCGGGATTTAACCCAGATA
1 TAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATA
*
105234563 TAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATG
1 TAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATA
* *
105234601 TATTACCAACACGAAGCCTGCGGGATTTAACCCGGATA
1 TAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATA
105234639 TAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATA
1 TAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATA
* * *
105234677 TATTACCAGCACGAAGCCTGCAGGATTTCACCCGGATA
1 TAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATA
105234715 TAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATA
1 TAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATA
105234753 TA
1 TA
105234755 CATCGAATAT
Statistics
Matches: 311, Mismatches: 33, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
38 274 0.88
39 10 0.03
40 27 0.09
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (38 bp):
TAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATA
Found at i:105236919 original size:40 final size:40
Alignment explanation
Indices: 105236849--105237026 Score: 218
Period size: 40 Copynumber: 4.5 Consensus size: 40
105236839 AAGCCAGGTA
* * * *
105236849 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
105236888 CCTTCGGGACATAGCCCGGATTTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
105236928 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
105236968 CCTTCGGGACTTAGTCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
105237008 CCTTCAGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
105237027 TTATCATCCG
Statistics
Matches: 122, Mismatches: 14, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
39 13 0.11
40 109 0.89
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:105240770 original size:40 final size:40
Alignment explanation
Indices: 105240725--105240854 Score: 174
Period size: 40 Copynumber: 3.2 Consensus size: 40
105240715 CGGAATACAA
105240725 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* * *
105240765 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
105240805 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
105240845 CCGGATATAA
1 CCGGATATAA
105240855 TTTCCAGCAT
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 3 0.04
40 75 0.96
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:105248725 original size:40 final size:40
Alignment explanation
Indices: 105248680--105248808 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
105248670 TCGGAATACA
105248680 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* * *
105248720 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
105248760 CCGGATGTAGCC-CTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
105248799 CCGGATATAA
1 CCGGATATAA
105248809 TTTCCAGCAT
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.03
39 31 0.40
40 44 0.57
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.22
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:105248802 original size:39 final size:40
Alignment explanation
Indices: 105248696--105248805 Score: 145
Period size: 39 Copynumber: 2.8 Consensus size: 40
105248686 ATAACCACGT
*
105248696 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTC
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTA
* *
105248736 GCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTA-GCCCTA
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACG-ACTA
*
105248775 GCAC-AATTGCCTTCGGGTCTTAACCCGGATA
1 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATA
105248806 TAATTTCCAG
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
38 3 0.05
39 30 0.48
40 30 0.48
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (40 bp):
GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTA
Found at i:105250189 original size:28 final size:27
Alignment explanation
Indices: 105250126--105250195 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
105250116 ATAGTGAGTC
105250126 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
* *
105250153 AGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
105250181 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
105250196 GTACAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:105254462 original size:49 final size:52
Alignment explanation
Indices: 105254390--105254558 Score: 181
Period size: 52 Copynumber: 3.3 Consensus size: 52
105254380 ACTAGTGACT
* *
105254390 CAAGTGTAGTACTATCTGAAGGCCACTTTGA-GAAG-AGATAG-GTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGATGAAGAAGATAGCGTTGGTCA
* *
105254439 CAAGTGTGGTACTATGTGAAGGCCA-TTTTATGAAGAAAGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGATGAAG-AAGATAGCGTTGGTCA
* * * * *
105254491 CATGTGTGGTACTATGTGAAGGCCACTTTG-TGAAAAAGGTAGC-TTTGACTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGATGAAGAAGATAGCGTTGGTC-A
105254542 CAAG-GATGGTACTATGT
1 CAAGTG-TGGTACTATGT
105254559 ACAGGCTACC
Statistics
Matches: 102, Mismatches: 11, Indels: 12
0.82 0.09 0.10
Matches are distributed among these distances:
48 4 0.04
49 27 0.26
50 5 0.05
51 28 0.27
52 35 0.34
53 3 0.03
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.30
Consensus pattern (52 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGATGAAGAAGATAGCGTTGGTCA
Found at i:105259782 original size:25 final size:25
Alignment explanation
Indices: 105259748--105259797 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
105259738 GTTAATATAC
105259748 GTGGGTGTTATGTAAGTCCTAAGCT
1 GTGGGTGTTATGTAAGTCCTAAGCT
105259773 GTGGGTGTTATGTAAGTCCTAAGCT
1 GTGGGTGTTATGTAAGTCCTAAGCT
105259798 AACTCTTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.12, G:0.32, T:0.36
Consensus pattern (25 bp):
GTGGGTGTTATGTAAGTCCTAAGCT
Found at i:105261364 original size:2 final size:2
Alignment explanation
Indices: 105261357--105261388 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
105261347 AGTGTAATTC
105261357 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
105261389 TTGTATACCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:105262649 original size:24 final size:24
Alignment explanation
Indices: 105262617--105262664 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
105262607 ATTTATACTA
105262617 AAAAACTTCCTAAAATAACTTAAC
1 AAAAACTTCCTAAAATAACTTAAC
105262641 AAAAACTTCCTAAAATAACTTAAC
1 AAAAACTTCCTAAAATAACTTAAC
105262665 TACTTTGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAAACTTCCTAAAATAACTTAAC
Found at i:105266100 original size:22 final size:21
Alignment explanation
Indices: 105266067--105266111 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
105266057 TTGACAAAAA
105266067 AACAGAAAAAATAAATAAAGC
1 AACAGAAAAAATAAATAAAGC
* *
105266088 AACATAAATAAATAATTAAAGC
1 AACAGAAA-AAATAAATAAAGC
105266110 AA
1 AA
105266112 AACTTGTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.69, C:0.09, G:0.07, T:0.16
Consensus pattern (21 bp):
AACAGAAAAAATAAATAAAGC
Found at i:105269067 original size:21 final size:21
Alignment explanation
Indices: 105269025--105269067 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
105269015 GTGTTGTGTC
*
105269025 TAATTTATCTCATATTTCATA
1 TAATTTATCTCATAATTCATA
*
105269046 TAATTTGTCATCATAATT-ATA
1 TAATTTATC-TCATAATTCATA
105269067 T
1 T
105269068 TTATTAAGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (21 bp):
TAATTTATCTCATAATTCATA
Found at i:105277787 original size:25 final size:26
Alignment explanation
Indices: 105277759--105277811 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
105277749 GCCTAGCCTC
105277759 TTTTAATAAA-TGGGGCAAAGCCCTT
1 TTTTAATAAACTGGGGCAAAGCCCTT
**
105277784 TTTTGGTAAACTGGGGCAAAGCCCTT
1 TTTTAATAAACTGGGGCAAAGCCCTT
105277810 TT
1 TT
105277812 CGCACTTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (26 bp):
TTTTAATAAACTGGGGCAAAGCCCTT
Found at i:105277886 original size:21 final size:21
Alignment explanation
Indices: 105277859--105277919 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
105277849 TATAATGAGT
105277859 ATATCATAGCATATCATGTGC
1 ATATCATAGCATATCATGTGC
* *
105277880 ATCTCATAACATATCATGTGC
1 ATATCATAGCATATCATGTGC
105277901 ATATCAT-GTCATATCATGT
1 ATATCATAG-CATATCATGT
105277920 ATAATAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (21 bp):
ATATCATAGCATATCATGTGC
Found at i:105277918 original size:10 final size:10
Alignment explanation
Indices: 105277859--105277919 Score: 61
Period size: 10 Copynumber: 5.9 Consensus size: 10
105277849 TATAATGAGT
105277859 ATATCATAG-C
1 ATATCAT-GTC
105277869 ATATCATGTGC
1 ATATCATGT-C
* **
105277880 ATCTCATAAC
1 ATATCATGTC
105277890 ATATCATGTGC
1 ATATCATGT-C
105277901 ATATCATGTC
1 ATATCATGTC
105277911 ATATCATGT
1 ATATCATGT
105277920 ATAATAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 1 0.02
10 24 0.57
11 17 0.40
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (10 bp):
ATATCATGTC
Found at i:105281748 original size:29 final size:29
Alignment explanation
Indices: 105281706--105281805 Score: 200
Period size: 29 Copynumber: 3.4 Consensus size: 29
105281696 GACGAGATTA
105281706 GCACTAAGTGTGCATGCTGGAAATATATG
1 GCACTAAGTGTGCATGCTGGAAATATATG
105281735 GCACTAAGTGTGCATGCTGGAAATATATG
1 GCACTAAGTGTGCATGCTGGAAATATATG
105281764 GCACTAAGTGTGCATGCTGGAAATATATG
1 GCACTAAGTGTGCATGCTGGAAATATATG
105281793 GCACTAAGTGTGC
1 GCACTAAGTGTGC
105281806 GAGCTCGAAG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 71 1.00
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (29 bp):
GCACTAAGTGTGCATGCTGGAAATATATG
Found at i:105281821 original size:29 final size:30
Alignment explanation
Indices: 105281706--105281865 Score: 188
Period size: 29 Copynumber: 5.5 Consensus size: 30
105281696 GACGAGATTA
105281706 GCACTAAGTGTGC-ATGCTGGAAATATATG
1 GCACTAAGTGTGCGATGCTGGAAATATATG
105281735 GCACTAAGTGTGC-ATGCTGGAAATATATG
1 GCACTAAGTGTGCGATGCTGGAAATATATG
105281764 GCACTAAGTGTGC-ATGCTGGAAATATATG
1 GCACTAAGTGTGCGATGCTGGAAATATATG
* ***
105281793 GCACTAAGTGTGCGA-GCTCGAAGGGTATG
1 GCACTAAGTGTGCGATGCTGGAAATATATG
* * * **
105281822 GCACTATGTGTGCG-GGCT-TAAATCGCATG
1 GCACTAAGTGTGCGATGCTGGAAAT-ATATG
105281851 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
105281866 AATCGAGTAT
Statistics
Matches: 117, Mismatches: 10, Indels: 7
0.87 0.07 0.05
Matches are distributed among these distances:
28 2 0.02
29 114 0.97
30 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.26
Consensus pattern (30 bp):
GCACTAAGTGTGCGATGCTGGAAATATATG
Found at i:105281903 original size:2 final size:2
Alignment explanation
Indices: 105281898--105281924 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
105281888 GTGCGTACTC
105281898 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
105281925 CTCCAATCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:105287233 original size:39 final size:39
Alignment explanation
Indices: 105287183--105287291 Score: 137
Period size: 39 Copynumber: 2.8 Consensus size: 39
105287173 GGATACTAAT
* * * * *
105287183 TCTACTAAAAGTATGATCAATTGAGCTATACCCACTGAA
1 TCTACTGAAAGTATGCTCAATCGAACCATACCCACTGAA
* *
105287222 TCTACTGAAAGTATGCTCAATCGAACCATACCTACTGAT
1 TCTACTGAAAGTATGCTCAATCGAACCATACCCACTGAA
* *
105287261 TCTACTGAAAGTATGCTCAAGCGAGCCATAC
1 TCTACTGAAAGTATGCTCAATCGAACCATAC
105287292 GGATTCTGAC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 61 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.27
Consensus pattern (39 bp):
TCTACTGAAAGTATGCTCAATCGAACCATACCCACTGAA
Found at i:105287389 original size:27 final size:27
Alignment explanation
Indices: 105287351--105287404 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
105287341 TCGATTTCTT
105287351 TGCTGTCCATCAGGCCCTGAATAACAA
1 TGCTGTCCATCAGGCCCTGAATAACAA
105287378 TGCTGTCCATCAGGCCCTGAATAACAA
1 TGCTGTCCATCAGGCCCTGAATAACAA
105287405 CTCTGAACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (27 bp):
TGCTGTCCATCAGGCCCTGAATAACAA
Found at i:105295414 original size:13 final size:13
Alignment explanation
Indices: 105295396--105295433 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
105295386 AAGCCGTGTA
105295396 AAGGACACGGGCC
1 AAGGACACGGGCC
105295409 AAGGACACGGGCC
1 AAGGACACGGGCC
*
105295422 AAGGACATGGGC
1 AAGGACACGGGC
105295434 GTGTGCTCGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.26, G:0.39, T:0.03
Consensus pattern (13 bp):
AAGGACACGGGCC
Found at i:105312234 original size:25 final size:27
Alignment explanation
Indices: 105312197--105312246 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
105312187 TCAAACATGC
105312197 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
105312223 ATTTCGGT-AATTTATCTCCTAGGG
1 ATTTAGGTCAATTTAACTCCTAGGG
105312247 ATAAAACTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:105313771 original size:26 final size:26
Alignment explanation
Indices: 105313735--105313844 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
105313725 CATGAATTTC
*
105313735 TTATCATGAAACATTTACCTAAACCA
1 TTATCATGAAACATTTACCTAACCCA
105313761 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
105313787 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
*
105313813 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
105313839 TTATCA
1 TTATCA
105313845 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:105323156 original size:13 final size:13
Alignment explanation
Indices: 105323140--105323172 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
105323130 TTTGATTAAA
*
105323140 TTAGTTAATTAGT
1 TTAGATAATTAGT
105323153 TTAGATAATTAGT
1 TTAGATAATTAGT
105323166 TTA-ATAA
1 TTAGATAA
105323173 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:105329458 original size:28 final size:28
Alignment explanation
Indices: 105329397--105329494 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
105329387 TCACAAATTG
** * *
105329397 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
105329426 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
105329454 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
105329482 GCACTAAGTGTGC
1 GCACTAAGTGTGC
105329495 GGGCTTATGC
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:105337118 original size:28 final size:28
Alignment explanation
Indices: 105337057--105337154 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
105337047 TCACAAATTG
** * *
105337057 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
105337086 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
105337114 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
105337142 GCACTAAGTGTGC
1 GCACTAAGTGTGC
105337155 GGGCTTATGC
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:105348139 original size:27 final size:28
Alignment explanation
Indices: 105348099--105348233 Score: 170
Period size: 27 Copynumber: 4.9 Consensus size: 28
105348089 AGGAAGCGTC
*
105348099 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAATTATCTGTAT
*
105348126 ATGGTGGCTCTGCCACATATT-TCTGT-T
1 CTGGTGGCTCTGCCACA-ATTATCTGTAT
*
105348153 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTGTAT
* *
105348181 TTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTGTAT
* *
105348209 CTGGTGACTCTGTCAC-ATTATCTGT
1 CTGGTGGCTCTGCCACAATTATCTGT
105348234 TCTAGCAGTC
Statistics
Matches: 96, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.03
27 49 0.51
28 44 0.46
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (28 bp):
CTGGTGGCTCTGCCACAATTATCTGTAT
Found at i:105348229 original size:55 final size:55
Alignment explanation
Indices: 105348099--105348233 Score: 168
Period size: 55 Copynumber: 2.5 Consensus size: 55
105348089 AGGAAGCGTC
* * * *
105348099 CTGGTGGCTATGCCACAATTATCTG-ATATGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGACTCTGCCACGATTATCTGTATATGGTGGCTCTGCCACATATATCTGTT
* *
105348153 CTGGTGGCTCTGCCACGATTATCTGTATTTGGTGGCTCTGCCACGAT-TATCTGTAT
1 CTGGTGACTCTGCCACGATTATCTGTATATGGTGGCTCTGCCAC-ATATATCTGT-T
*
105348209 CTGGTGACTCTGTCAC-ATTATCTGT
1 CTGGTGACTCTGCCACGATTATCTGT
105348234 TCTAGCAGTC
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
54 23 0.32
55 32 0.44
56 17 0.24
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (55 bp):
CTGGTGACTCTGCCACGATTATCTGTATATGGTGGCTCTGCCACATATATCTGTT
Found at i:105355442 original size:45 final size:46
Alignment explanation
Indices: 105355388--105355496 Score: 150
Period size: 47 Copynumber: 2.3 Consensus size: 46
105355378 TGCACACTTT
* *
105355388 TCACAATTGGTCATTCGGCCTTATCACATAT-TCACTTACACATAT-A
1 TCAC-ATTGGCCATTCGGCCTTATCACATATAACACTTACACAT-TCA
*
105355434 TCACATTGGCCATTCGGCCTTATCACATATACACACTTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATA-ACACTTACACATTCA
105355481 TCACATTGGCCATTCG
1 TCACATTGGCCATTCG
105355497 ATCTTAAGCT
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
45 25 0.44
46 5 0.09
47 27 0.47
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33
Consensus pattern (46 bp):
TCACATTGGCCATTCGGCCTTATCACATATAACACTTACACATTCA
Found at i:105358090 original size:22 final size:20
Alignment explanation
Indices: 105358050--105358090 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
105358040 AGTCCTATTA
*
105358050 ACTAAATTCACATGCAATTG
1 ACTAAATTCACATGAAATTG
105358070 ACTAAATTCAAACATGAAATT
1 ACTAAATTC--ACATGAAATT
105358091 TTCACACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.29
Consensus pattern (20 bp):
ACTAAATTCACATGAAATTG
Found at i:105363194 original size:29 final size:29
Alignment explanation
Indices: 105363160--105363349 Score: 89
Period size: 29 Copynumber: 6.6 Consensus size: 29
105363150 TACTCGATTT
* * *
105363160 CGCACACTTAGTGCCATGCGATTTAAGCC
1 CGCACACTTAGTGCCATACCATTCAAGCC
** * * *
105363189 CGCACACACAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATACCATTCAAGCC
* * *
105363218 CGCACACTTAGTGCCATA-TATTTCCAGCA
1 CGCACACTTAGTGCCATACCA-TTCAAGCC
* * *** * *
105363247 TGCACACTCAGTGCCATATTTTTCCAGCA
1 CGCACACTTAGTGCCATACCATTCAAGCC
* * * *
105363276 TGCACACTTAGTGCCATA-TATTTCCAGCA
1 CGCACACTTAGTGCCATACCA-TTCAAGCC
* * * *
105363305 TGCACACTTAGTGCCATA-TATTTCCAGCA
1 CGCACACTTAGTGCCATACCA-TTCAAGCC
*
105363334 TGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
105363350 ATCTCGTCAC
Statistics
Matches: 139, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
28 1 0.01
29 137 0.99
30 1 0.01
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATACCATTCAAGCC
Found at i:105363252 original size:58 final size:58
Alignment explanation
Indices: 105363219--105363349 Score: 244
Period size: 58 Copynumber: 2.3 Consensus size: 58
105363209 CTTCGAGCTC
*
105363219 GCACACTTAGTGCCATATATTTCCAGCATGCACACTCAGTGCCATATTTTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCATGCACACTCAGTGCCATATATTTCCAGCAT
*
105363277 GCACACTTAGTGCCATATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCATGCACACTCAGTGCCATATATTTCCAGCAT
105363335 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
105363350 ATCTCGTCAC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 71 1.00
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.30
Consensus pattern (58 bp):
GCACACTTAGTGCCATATATTTCCAGCATGCACACTCAGTGCCATATATTTCCAGCAT
Found at i:105363281 original size:87 final size:87
Alignment explanation
Indices: 105363190--105363349 Score: 241
Period size: 87 Copynumber: 1.8 Consensus size: 87
105363180 ATTTAAGCCC
* *
105363190 GCACACACAGTGCCATACCCTTCGAGC-TCGCACACTTAGTGCCATATATTTCCAGCATGCACAC
1 GCACACACAGTGCCATACACTTCCAGCAT-GCACACTTAGTGCCATATATTTCCAGCATGCACAC
105363254 TCAGTGCCATATTTTTCCAGCAT
65 TCAGTGCCATATTTTTCCAGCAT
** * *
105363277 GCACACTTAGTGCCATATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCATGCACACT
1 GCACACACAGTGCCATACACTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCATGCACACT
*
105363342 TAGTGCCA
66 CAGTGCCA
105363350 ATCTCGTCAC
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
87 64 0.98
88 1 0.02
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (87 bp):
GCACACACAGTGCCATACACTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCATGCACACT
CAGTGCCATATTTTTCCAGCAT
Found at i:105371054 original size:29 final size:29
Alignment explanation
Indices: 105371020--105371208 Score: 89
Period size: 29 Copynumber: 6.6 Consensus size: 29
105371010 TACTCGATTT
* * *
105371020 CGCACACTTAGTGCCATGCGATTTAAGCC
1 CGCACACTTAGTGCCATACCATTCAAGCC
** * * *
105371049 CGCACACACAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATACCATTCAAGCC
* * *
105371078 CGCACACTTAGTGCCATA-TATTTCCAGCA
1 CGCACACTTAGTGCCATACCA-TTCAAGCC
* * ** * *
105371107 TGCACACTCAGTGCCATA-TTTTCCAGCA
1 CGCACACTTAGTGCCATACCATTCAAGCC
* * * *
105371135 TGCACACTTAGTGCCATA-TATTTCCAGCA
1 CGCACACTTAGTGCCATACCA-TTCAAGCC
* * * *
105371164 TGCACACTTAGTGCCATA-TATTTCCAGCA
1 CGCACACTTAGTGCCATACCA-TTCAAGCC
*
105371193 TGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
105371209 ATCTCGTCAC
Statistics
Matches: 139, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
28 26 0.19
29 113 0.81
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATACCATTCAAGCC
Found at i:105371140 original size:86 final size:86
Alignment explanation
Indices: 105371050--105371208 Score: 239
Period size: 86 Copynumber: 1.8 Consensus size: 86
105371040 ATTTAAGCCC
* *
105371050 GCACACACAGTGCCATACCCTTCGAGC-TCGCACACTTAGTGCCATATATTTCCAGCATGCACAC
1 GCACACACAGTGCCATACACTTCCAGCAT-GCACACTTAGTGCCATATATTTCCAGCATGCACAC
105371114 TCAGTGCCATATTTTCCAGCAT
65 TCAGTGCCATATTTTCCAGCAT
** * *
105371136 GCACACTTAGTGCCATATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCATGCACACT
1 GCACACACAGTGCCATACACTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCATGCACACT
*
105371201 TAGTGCCA
66 CAGTGCCA
105371209 ATCTCGTCAC
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
86 64 0.98
87 1 0.02
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.27
Consensus pattern (86 bp):
GCACACACAGTGCCATACACTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCATGCACACT
CAGTGCCATATTTTCCAGCAT
Found at i:105371152 original size:57 final size:58
Alignment explanation
Indices: 105371079--105371208 Score: 244
Period size: 57 Copynumber: 2.3 Consensus size: 58
105371069 CTTCGAGCTC
105371079 GCACACTTAGTGCCATATATTTCCAGCATGCACACTCAGTGCCATAT-TTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCATGCACACTCAGTGCCATATATTTCCAGCAT
*
105371136 GCACACTTAGTGCCATATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCATGCACACTCAGTGCCATATATTTCCAGCAT
105371194 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
105371209 ATCTCGTCAC
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
57 46 0.65
58 25 0.35
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (58 bp):
GCACACTTAGTGCCATATATTTCCAGCATGCACACTCAGTGCCATATATTTCCAGCAT
Found at i:105373068 original size:28 final size:27
Alignment explanation
Indices: 105373005--105373074 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
105372995 ATAGTGAGTC
105373005 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
105373032 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
105373060 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
105373075 GTACAAGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:105381897 original size:14 final size:15
Alignment explanation
Indices: 105381877--105381933 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
105381867 AGATTACGTA
105381877 TCATATCTAAGATTG
1 TCATATCTAAGATTG
105381892 CATATCATATCTAAGATTG
1 ----TCATATCTAAGATTG
105381911 TATCATATCTAAGATTG
1 --TCATATCTAAGATTG
105381928 -CATATC
1 TCATATC
105381934 CTTAAAGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.16
17 17 0.45
19 15 0.39
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (15 bp):
TCATATCTAAGATTG
Found at i:105381916 original size:17 final size:17
Alignment explanation
Indices: 105381855--105381927 Score: 92
Period size: 19 Copynumber: 3.9 Consensus size: 17
105381845 GGATTACAAG
105381855 ATCATATCTTCAAGATTACGT
1 ATCATATC-T-AAGATT--GT
105381876 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTG--T
105381895 ATCATATCTAAGATTGT
1 ATCATATCTAAGATTGT
105381912 ATCATATCTAAGATTG
1 ATCATATCTAAGATTG
105381928 CATATCCTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
17 18 0.36
19 23 0.46
20 1 0.02
21 8 0.16
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (17 bp):
ATCATATCTAAGATTGT
Found at i:105381918 original size:36 final size:39
Alignment explanation
Indices: 105381855--105381933 Score: 128
Period size: 36 Copynumber: 2.1 Consensus size: 39
105381845 GGATTACAAG
105381855 ATCATATCTTCAAGATTACGTATCATATCTAAGATTGCAT
1 ATCATATCTTCAAGATTA-GTATCATATCTAAGATTGCAT
105381895 ATCATATC-T-AAGATT-GTATCATATCTAAGATTGCAT
1 ATCATATCTTCAAGATTAGTATCATATCTAAGATTGCAT
105381931 ATC
1 ATC
105381934 CTTAAAGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
36 24 0.62
38 6 0.15
39 1 0.03
40 8 0.21
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (39 bp):
ATCATATCTTCAAGATTAGTATCATATCTAAGATTGCAT
Found at i:105382352 original size:45 final size:45
Alignment explanation
Indices: 105382288--105382395 Score: 164
Period size: 45 Copynumber: 2.4 Consensus size: 45
105382278 GGAAAGCGAT
*
105382288 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAA
1 ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* *
105382333 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCGAA
1 ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* *
105382378 ATTTGCT-TCTTCAATCTG
1 ATCTGCTATCTTCGATCTG
105382396 TTCCTTGCAA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 10 0.18
45 47 0.82
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (45 bp):
ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
Found at i:105383210 original size:205 final size:205
Alignment explanation
Indices: 105382473--105383187 Score: 1241
Period size: 205 Copynumber: 3.5 Consensus size: 205
105382463 AAATCTGTTT
* * * *
105382473 CTTCGATTTGTTCCCTGACAATACAAAGATGCAAAATCATCTTAGATTTGCTTTAACGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
*
105382538 GTGAAAGCCAAATCAGCTATATCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCGAACCATCTT
66 GTGAAAGCCAAATCAGCTATATCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* * * *
105382603 GGATCTGCTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTTTTCCTTCCATCGAAGTGG
131 GGATCTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTTCCCTCCGTCGAAGTGG
105382668 AGATGCCAGA
196 AGATGCCAGA
*
105382678 CTTCGATTTGTTCTCTGACAATACAGAGAGGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
*
105382743 GTGAAAGCCAAATCAGCCATATCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATATCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
*
105382808 GGATCTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATATGTCTTCCCTCCGTCGAAGTGG
131 GGATCTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTTCCCTCCGTCGAAGTGG
105382873 AGATGCCAGA
196 AGATGCCAGA
* *
105382883 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGTTTCAACGTAAGTAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
*
105382948 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATATCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
*
105383013 GGATCTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGG
131 GGATCTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTTCCCTCCGTCGAAGTGG
*
105383078 AGATGCTAGA
196 AGATGCCAGA
*
105383088 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
* * *
105383153 GTGAAAGCCAAATCAGCTATGTCTTTGATATGCTC
66 GTGAAAGCCAAATCAGCTATATCTTCGATTTGCTC
105383188 TCCGGCAATA
Statistics
Matches: 485, Mismatches: 25, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
205 485 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (205 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
GTGAAAGCCAAATCAGCTATATCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
GGATCTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTTCCCTCCGTCGAAGTGG
AGATGCCAGA
Found at i:105383241 original size:44 final size:44
Alignment explanation
Indices: 105383174--105383266 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
105383164 ATCAGCTATG
* *
105383174 TCTTTGATATGCTCTCCGGCAATACAGAGATGCCAAATCTAG-TA
1 TCTTCGATATGCTCTCCGACAATACAGAGATGCCAAATCT-GTTA
* *
105383218 TCTTCGATCTGCTCTCTGACAATACAGAGATGCCAAATCTGTTA
1 TCTTCGATATGCTCTCCGACAATACAGAGATGCCAAATCTGTTA
105383262 TCTTC
1 TCTTC
105383267 AACTTGTTCC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 1 0.02
44 43 0.98
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (44 bp):
TCTTCGATATGCTCTCCGACAATACAGAGATGCCAAATCTGTTA
Found at i:105383294 original size:44 final size:43
Alignment explanation
Indices: 105383241--105383428 Score: 166
Period size: 43 Copynumber: 4.3 Consensus size: 43
105383231 CTCTGACAAT
* **
105383241 ACAGAGATGCCAAATCTGTTATCTTCAACTTGTTCCCTATAAAC
1 ACAGGGATGCC-AATCTGAAATCTTCAACTTGTTCCCTATAAAC
105383285 ACAGGGATGCC-ATGCTGAAATCTTCAACTTGTTCCCTATAAAC
1 ACAGGGATGCCAAT-CTGAAATCTTCAACTTGTTCCCTATAAAC
* * ** * * *
105383328 ACAGGGATGGC-ATGCTGAAATCTTCGATCTACTTCGCTGTAAGC
1 ACAGGGATGCCAAT-CTGAAATCTTC-AACTTGTTCCCTATAAAC
* ** * *
105383372 ACA-GGAGTGTCAGATCTGCTATCTTCGATTTGTTCCCTATAAAC
1 ACAGGGA-TGCCA-ATCTGAAATCTTCAACTTGTTCCCTATAAAC
105383416 ACAGGGATGCCAA
1 ACAGGGATGCCAA
105383429 ATCTTGTTTT
Statistics
Matches: 116, Mismatches: 22, Indels: 13
0.77 0.15 0.09
Matches are distributed among these distances:
42 2 0.02
43 55 0.47
44 45 0.39
45 12 0.10
46 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (43 bp):
ACAGGGATGCCAATCTGAAATCTTCAACTTGTTCCCTATAAAC
Found at i:105383310 original size:43 final size:43
Alignment explanation
Indices: 105383261--105383427 Score: 176
Period size: 43 Copynumber: 3.8 Consensus size: 43
105383251 CAAATCTGTT
105383261 ATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTGAA
1 ATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTGAA
*
105383304 ATCTTCAACTTGTTCCCTATAAACACAGGGATGGCATGCTGAA
1 ATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTGAA
* ** * * * * **
105383347 ATCTTCGATCTACTTCGCTGTAAGCACA-GGAGTGTCA-GATCTGCT
1 ATCTTC-AACTTGTTCCCTATAAACACAGGGA-TGCCATG--CTGAA
* *
105383392 ATCTTCGATTTGTTCCCTATAAACACAGGGATGCCA
1 ATCTTCAACTTGTTCCCTATAAACACAGGGATGCCA
105383428 AATCTTGTTT
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
43 52 0.52
44 36 0.36
45 12 0.12
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (43 bp):
ATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTGAA
Found at i:105384316 original size:20 final size:19
Alignment explanation
Indices: 105384284--105384329 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
105384274 TTGGCCTCTC
*
105384284 CATTTTTCTTTTTTCTTTT
1 CATTTTTATTTTTTCTTTT
105384303 CATTTTTATCTTTTTCTTTT
1 CATTTTTAT-TTTTTCTTTT
*
105384323 TATTTTT
1 CATTTTT
105384330 TTTCTCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (19 bp):
CATTTTTATTTTTTCTTTT
Found at i:105384330 original size:14 final size:14
Alignment explanation
Indices: 105384286--105384331 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
105384276 GGCCTCTCCA
105384286 TTTTTC-TTTT-TT
1 TTTTTCTTTTTATT
* *
105384298 CTTTTCATTTTTATC
1 TTTTTC-TTTTTATT
105384313 TTTTTCTTTTTATT
1 TTTTTCTTTTTATT
105384327 TTTTT
1 TTTTT
105384332 TCTCTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 5 0.19
14 16 0.59
15 6 0.22
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTCTTTTTATT
Found at i:105384339 original size:17 final size:16
Alignment explanation
Indices: 105384286--105384360 Score: 66
Period size: 17 Copynumber: 4.5 Consensus size: 16
105384276 GGCCTCTCCA
*
105384286 TTTTTCTTTTTTCT-T
1 TTTTTTTTTTTTCTCT
105384301 TTCATTTTTATCTTTT-TCT
1 TT--TTTTT-T-TTTTCTCT
105384320 TTTTATTTTTTTTCTCT
1 TTTT-TTTTTTTTCTCT
105384337 TTTTTTCTTTTTTC-CT
1 TTTTTT-TTTTTTCTCT
105384353 TTTTTTTT
1 TTTTTTTT
105384361 AAATAAAAGT
Statistics
Matches: 51, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
15 4 0.08
16 14 0.27
17 21 0.41
18 5 0.10
19 7 0.14
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTTTTTTTCTCT
Found at i:105384348 original size:20 final size:21
Alignment explanation
Indices: 105384292--105384349 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 21
105384282 TCCATTTTTC
105384292 TTTTTTCTTTTCATTTTTATCTT
1 TTTTTTCTTTT--TTTTTATCTT
105384315 TTTCTTT-TTATTTTTTT-TCTCT
1 TTT-TTTCTT-TTTTTTTATCT-T
105384337 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
105384350 CCTTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
21 10 0.32
22 11 0.35
23 5 0.16
24 5 0.16
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTTTCTTTTTTTTTATCTT
Found at i:105384349 original size:8 final size:8
Alignment explanation
Indices: 105384286--105384358 Score: 60
Period size: 8 Copynumber: 8.6 Consensus size: 8
105384276 GGCCTCTCCA
105384286 TTTTTC-T
1 TTTTTCTT
105384293 TTTTTCTT
1 TTTTTCTT
*
105384301 TTCATTTTTAT
1 TT--TTTCT-T
105384312 CTTTTTCTT
1 -TTTTTCTT
105384321 TTTATT-TT
1 TTT-TTCTT
105384329 TTTTCTCTT
1 TTTT-TCTT
105384338 TTTTTCTT
1 TTTTTCTT
*
105384346 TTTTCCTT
1 TTTTTCTT
105384354 TTTTT
1 TTTTT
105384359 TTAAATAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
7 7 0.13
8 27 0.50
9 9 0.17
10 8 0.15
11 1 0.02
12 2 0.04
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTCTT
Found at i:105389907 original size:19 final size:19
Alignment explanation
Indices: 105389883--105389968 Score: 151
Period size: 19 Copynumber: 4.7 Consensus size: 19
105389873 ATCATTCTTC
105389883 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCT
105389902 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCT
105389921 AAGATTG--TATCATATCT
1 AAGATTGCATATCATATCT
105389938 AAGATTGCATATCATAT-T
1 AAGATTGCATATCATATCT
105389956 AAGATTGCATATC
1 AAGATTGCATATC
105389969 CTTAAAGATT
Statistics
Matches: 65, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.26
18 14 0.22
19 34 0.52
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (19 bp):
AAGATTGCATATCATATCT
Found at i:105389914 original size:14 final size:15
Alignment explanation
Indices: 105389894--105389950 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
105389884 AGATTGCATA
105389894 TCATATCTAAGATTG
1 TCATATCTAAGATTG
105389909 CATATCATATCTAAGATTG
1 ----TCATATCTAAGATTG
105389928 TATCATATCTAAGATTG
1 --TCATATCTAAGATTG
105389945 -CATATC
1 TCATATC
105389951 ATATTAAGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.16
17 17 0.45
19 15 0.39
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (15 bp):
TCATATCTAAGATTG
Found at i:105389934 original size:36 final size:36
Alignment explanation
Indices: 105389883--105389968 Score: 138
Period size: 36 Copynumber: 2.3 Consensus size: 36
105389873 ATCATTCTTC
105389883 AAGATTGCATATCATATCTAAGATTGCATATCATATCT
1 AAGATTG-ATATCATATCTAAGATTGCATATCATAT-T
105389921 AAGATTG-TATCATATCTAAGATTGCATATCATATT
1 AAGATTGATATCATATCTAAGATTGCATATCATATT
105389956 AAGATTGCATATC
1 AAGATTG-ATATC
105389969 CTTAAAGATT
Statistics
Matches: 46, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
35 8 0.17
36 27 0.59
37 4 0.09
38 7 0.15
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (36 bp):
AAGATTGATATCATATCTAAGATTGCATATCATATT
Found at i:105396104 original size:39 final size:39
Alignment explanation
Indices: 105395998--105396173 Score: 282
Period size: 39 Copynumber: 4.5 Consensus size: 39
105395988 CGGATGATAA
* *
105395998 CCGGACTAAGATCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTATAT
105396038 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAT
105396078 CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAT
*
105396117 CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAT
*
105396156 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGT-CCGAAGG
105396174 TACTTGGGTT
Statistics
Matches: 130, Mismatches: 4, Indels: 5
0.94 0.03 0.04
Matches are distributed among these distances:
38 7 0.05
39 76 0.58
40 47 0.36
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (39 bp):
CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:105404126 original size:40 final size:40
Alignment explanation
Indices: 105404078--105404243 Score: 271
Period size: 40 Copynumber: 4.2 Consensus size: 40
105404068 GGACTAAGAT
105404078 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
* *
105404118 CCTAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTT
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
*
105404158 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTT
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
* * *
105404198 CCGAAGGCATTTGTGCGAGTTGCTATAT-CTGGCTAAATC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
105404237 CCGAAGG
1 CCGAAGG
105404244 TACTTGGGTT
Statistics
Matches: 119, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 15 0.13
40 104 0.87
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
Found at i:105410316 original size:49 final size:47
Alignment explanation
Indices: 105410260--105410389 Score: 170
Period size: 49 Copynumber: 2.7 Consensus size: 47
105410250 GAGTTGTGTT
* *
105410260 AGTGTAAGACCTGTTTGGAACCTAGCATCGACACAAATAAGTGAGAGCC
1 AGTGTAAGACCTGTTTGGAACATGGCATCGACACAAAT--GTGAGAGCC
* * ** *
105410309 AGTGTAAGACCTGTCTGGGACATGGCATCGACTTAGATGTGAGAGCC
1 AGTGTAAGACCTGTTTGGAACATGGCATCGACACAAATGTGAGAGCC
105410356 AGTGTAAGACCATGTTTGGAACATGGCATCGACA
1 AGTGTAAGACC-TGTTTGGAACATGGCATCGACA
105410390 TCATACTCTA
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
47 20 0.29
48 19 0.27
49 31 0.44
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (47 bp):
AGTGTAAGACCTGTTTGGAACATGGCATCGACACAAATGTGAGAGCC
Found at i:105424227 original size:40 final size:39
Alignment explanation
Indices: 105424179--105424349 Score: 229
Period size: 39 Copynumber: 4.3 Consensus size: 39
105424169 ACGACTAGCT
*
105424179 CAAATGCCTTCGGGAC-AAACCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAA-CCCGGATT-TAGTAACTCGCA
* *
105424219 CGAATGCCTTCGGGACTTAACCCGGGTTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAACCCGGATTTAGTAACTCGCA
*
105424259 CAAATGCCTTCGGGCTTAACCCGGATTTATTAACTCGCA
1 CAAATGCCTTCGGGCTTAACCCGGATTTAGTAACTCGCA
*
105424298 CAAATGCCTTCGGGCTTAACCCGGATTTATTAACTCGCA
1 CAAATGCCTTCGGGCTTAACCCGGATTTAGTAACTCGCA
* *
105424337 CGAACGCCTTCGG
1 CAAATGCCTTCGG
105424350 ATCTTAGTCC
Statistics
Matches: 122, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
39 73 0.60
40 45 0.37
41 4 0.03
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAACCCGGATTTAGTAACTCGCA
Found at i:105424293 original size:39 final size:40
Alignment explanation
Indices: 105424179--105424402 Score: 235
Period size: 40 Copynumber: 5.7 Consensus size: 40
105424169 ACGACTAGCT
*
105424179 CAAATGCCTTCGGGAC-AAACCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAA-CCCGGATT-TAGTAACTCGCA
* *
105424219 CGAATGCCTTCGGGACTTAACCCGGGTTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
105424259 CAAATGCCTTCGGG-CTTAACCCGGATTTATTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
105424298 CAAATGCCTTCGGG-CTTAACCCGGATTTATTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * ** * * * **
105424337 CGAACGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAACA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
105424378 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
105424403 CATCATTCAA
Statistics
Matches: 161, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
38 2 0.01
39 71 0.44
40 75 0.47
41 13 0.08
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:105432092 original size:28 final size:28
Alignment explanation
Indices: 105432027--105432127 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
105432017 ATAGTGAATC
*
105432027 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
105432056 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
105432084 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
105432114 CGCACACTTAGTGC
1 CGCACACTTAGTGC
105432128 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:105440045 original size:28 final size:28
Alignment explanation
Indices: 105439980--105440080 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
105439970 ATAGTGAATC
*
105439980 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
105440009 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
105440037 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
105440067 CGCACACTTAGTGC
1 CGCACACTTAGTGC
105440081 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:105441842 original size:28 final size:29
Alignment explanation
Indices: 105441810--105441895 Score: 122
Period size: 28 Copynumber: 3.0 Consensus size: 29
105441800 TCTCTTCCAT
105441810 ATGGCCCATTAGGCCC-AATCACATTTAC
1 ATGGCCCATTAGGCCCAAATCACATTTAC
* * *
105441838 GTGGCTCATTAGGCCCAAATCACATTTAT
1 ATGGCCCATTAGGCCCAAATCACATTTAC
*
105441867 ATGG-CCACTAGGCCCAAATCACATTTAC
1 ATGGCCCATTAGGCCCAAATCACATTTAC
105441895 A
1 A
105441896 GTCATGCTCA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
28 36 0.72
29 14 0.28
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (29 bp):
ATGGCCCATTAGGCCCAAATCACATTTAC
Found at i:105448230 original size:48 final size:49
Alignment explanation
Indices: 105448155--105448523 Score: 182
Period size: 48 Copynumber: 7.7 Consensus size: 49
105448145 TGATATCTGT
* * * *
105448155 GCCAGTGAAAGACCATG-TCTGCGACATGGCGTTAGCCACATTATGAGA
1 GCCAGTGTAAGACCATGTTCTGCGACATGGCATCAGCAACATTATGAGA
* * *
105448203 GCCAGTGTAAGACCATGTTC-G-GAACATGGCATCGGCAATATTGTGAGA
1 GCCAGTGTAAGACCATGTTCTGCG-ACATGGCATCAGCAACATTATGAGA
* * * * ** * *
105448251 GCTAGTGTAAGATCATG-TCTAG-GACACGGCATCGGCATTGA-TATGTGC
1 GCCAGTGTAAGACCATGTTCT-GCGACATGGCATCAGCA-ACATTATGAGA
* * *
105448299 GCTAGTGTAAGACCATG-TCTGGGACATGGCATC-G--ACATTGATATGTGA
1 GCCAGTGTAAGACCATGTTCTGCGACATGGCATCAGCAACA-T--TATGAGA
* * * * *
105448347 GCTAGTGTATGACCATG-TCTAG-GACATGGCATCGGCCACATGATGAGA
1 GCCAGTGTAAGACCATGTTCT-GCGACATGGCATCAGCAACATTATGAGA
* * ** * *
105448395 GCCAGTGTAAAACCATG-TCTAG-GACATGGCATCGGCATTGA-AACGAGA
1 GCCAGTGTAAGACCATGTTCT-GCGACATGGCATCAGCA-ACATTATGAGA
* * * ** *
105448443 GCTAGTGTAAGACCATG-TCTGGGACATGGCATCGGCCTCGA-TATGTGA
1 GCCAGTGTAAGACCATGTTCTGCGACATGGCATCAGCAAC-ATTATGAGA
*
105448491 GCTAGTGTAAGACCATGTT-TG-GAACATGGCATC
1 GCCAGTGTAAGACCATGTTCTGCG-ACATGGCATC
105448524 GGAAATTCAC
Statistics
Matches: 264, Mismatches: 38, Indels: 38
0.78 0.11 0.11
Matches are distributed among these distances:
44 1 0.00
47 8 0.03
48 242 0.92
49 9 0.03
50 1 0.00
51 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24
Consensus pattern (49 bp):
GCCAGTGTAAGACCATGTTCTGCGACATGGCATCAGCAACATTATGAGA
Found at i:105448349 original size:96 final size:96
Alignment explanation
Indices: 105448206--105448525 Score: 375
Period size: 96 Copynumber: 3.3 Consensus size: 96
105448196 TATGAGAGCC
* *
105448206 AGTGTAAGACCATGT-TCGGAACATGGCATCGGCAAT-AT-TGTGAGAGCTAGTGTAAGATCATG
1 AGTGTAAGACCATGTCT-GGAACATGGCATCGGCATTGATATGT--GAGCTAGTGTAAGACCATG
*
105448268 TCTAGGACACGGCATCGGCATTGATATGTGCGCT
63 TCTAGGACATGGCATCGGCATTGATATGTGCGCT
* * *
105448302 AGTGTAAGACCATGTCTGGGACATGGCATCGACATTGATATGTGAGCTAGTGTATGACCATGTCT
1 AGTGTAAGACCATGTCTGGAACATGGCATCGGCATTGATATGTGAGCTAGTGTAAGACCATGTCT
* *
105448367 AGGACATGGCATCGGCCACATGATGA-GAGC-C-
66 AGGACATGGCATCGG-CA-TTGAT-ATGTGCGCT
* * * *
105448398 AGTGTAAAACCATGTCTAGG-ACATGGCATCGGCATTGAAACGAGAGCTAGTGTAAGACCATGTC
1 AGTGTAAGACCATGTCT-GGAACATGGCATCGGCATTGATATGTGAGCTAGTGTAAGACCATGTC
* * * *
105448462 TGGGACATGGCATCGGCCTCGATATGTGAGCT
65 TAGGACATGGCATCGGCATTGATATGTGCGCT
*
105448494 AGTGTAAGACCATGTTTGGAACATGGCATCGG
1 AGTGTAAGACCATGTCTGGAACATGGCATCGG
105448526 AAATTCACCC
Statistics
Matches: 191, Mismatches: 22, Indels: 22
0.81 0.09 0.09
Matches are distributed among these distances:
93 1 0.01
94 5 0.03
95 4 0.02
96 162 0.85
97 8 0.04
98 10 0.05
99 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (96 bp):
AGTGTAAGACCATGTCTGGAACATGGCATCGGCATTGATATGTGAGCTAGTGTAAGACCATGTCT
AGGACATGGCATCGGCATTGATATGTGCGCT
Found at i:105448412 original size:144 final size:144
Alignment explanation
Indices: 105448196--105448525 Score: 466
Period size: 144 Copynumber: 2.3 Consensus size: 144
105448186 TTAGCCACAT
* * * * *
105448196 TATGAGAGCCAGTGTAAGACCATGTTCGGAACATGGCATCGGCAATATTGTGAGAGCTAGTGTAA
1 TATGTGAGCTAGTGTAAGACCATGTTAGGAACATGGCATCGGCAACATTGTGAGAGCCAGTGTAA
* * * * * *
105448261 GATCATGTCTAGGACACGGCATCGGCATTGATATGTGCGCTAGTGTAAGACCATGTCTGGGACAT
66 AACCATGTCTAGGACACGGCATCGGCATTGAAACGAGAGCTAGTGTAAGACCATGTCTGGGACAT
*
105448326 GGCATCGACATTGA
131 GGCATCGACATCGA
* *
105448340 TATGTGAGCTAGTGTATGACCATGTCTAGG-ACATGGCATCGGCCACA-TGATGAGAGCCAGTGT
1 TATGTGAGCTAGTGTAAGACCATGT-TAGGAACATGGCATCGGCAACATTG-TGAGAGCCAGTGT
*
105448403 AAAACCATGTCTAGGACATGGCATCGGCATTGAAACGAGAGCTAGTGTAAGACCATGTCTGGGAC
64 AAAACCATGTCTAGGACACGGCATCGGCATTGAAACGAGAGCTAGTGTAAGACCATGTCTGGGAC
* *
105448468 ATGGCATCGGCCTCGA
129 ATGGCATCGACATCGA
*
105448484 TATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGG
1 TATGTGAGCTAGTGTAAGACCATGTTAGGAACATGGCATCGG
105448526 AAATTCACCC
Statistics
Matches: 164, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
143 5 0.03
144 156 0.95
145 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (144 bp):
TATGTGAGCTAGTGTAAGACCATGTTAGGAACATGGCATCGGCAACATTGTGAGAGCCAGTGTAA
AACCATGTCTAGGACACGGCATCGGCATTGAAACGAGAGCTAGTGTAAGACCATGTCTGGGACAT
GGCATCGACATCGA
Found at i:105448524 original size:48 final size:47
Alignment explanation
Indices: 105448196--105448525 Score: 328
Period size: 48 Copynumber: 6.9 Consensus size: 47
105448186 TTAGCCACAT
* * *
105448196 TATGAGAGCCAGTGTAAGACCATGTTCGGAACATGGCATCGGCA---A
1 TATGTGAGCTAGTGTAAGACCATGTTAGG-ACATGGCATCGGCATCGA
* * *
105448241 TATTGTGAGAGCTAGTGTAAGATCATGTCTAGGACACGGCATCGGCATTGA
1 TA-TGT--GAGCTAGTGTAAGACCATGT-TAGGACATGGCATCGGCATCGA
* * * *
105448292 TATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGA
1 TATGTGAGCTAGTGTAAGACCATGT-TAGGACATGGCATCGGCATCGA
*
105448340 TATGTGAGCTAGTGTATGACCATGTCTAGGACATGGCATCGGCCA-C-A
1 TATGTGAGCTAGTGTAAGACCATGT-TAGGACATGGCATCGG-CATCGA
* * * *
105448387 TGATGAGAGCCAGTGTAAAACCATGTCTAGGACATGGCATCGGCATTGA
1 T-ATGTGAGCTAGTGTAAGACCATGT-TAGGACATGGCATCGGCATCGA
* * * * *
105448436 AACGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGA
1 TATGTGAGCTAGTGTAAGACCATGT-TAGGACATGGCATCGGCATCGA
*
105448484 TATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGG
1 TATGTGAGCTAGTGTAAGACCATGTTAGG-ACATGGCATCGG
105448526 AAATTCACCC
Statistics
Matches: 242, Mismatches: 31, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
45 2 0.01
46 2 0.01
47 7 0.03
48 219 0.90
49 6 0.02
50 3 0.01
51 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (47 bp):
TATGTGAGCTAGTGTAAGACCATGTTAGGACATGGCATCGGCATCGA
Found at i:105459283 original size:40 final size:40
Alignment explanation
Indices: 105459181--105459364 Score: 174
Period size: 40 Copynumber: 4.6 Consensus size: 40
105459171 AAATTGAATG
* * * * *
105459181 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TAGTT
* *
105459221 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
105459261 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
105459301 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
105459341 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
105459365 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 3 0.02
40 115 0.95
41 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:105465720 original size:40 final size:40
Alignment explanation
Indices: 105465675--105465763 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 40
105465665 CGGAATATAA
* **
105465675 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATAACCCGCACAAATGCCTTCGGGTCTTAGC
* *
105465715 CCGGATAGAATAACCCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATAACCCGCACAAATGCCTTCGGGTCTTAGC
105465755 CCGGATATA
1 CCGGATATA
105465764 GCCTGTGAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (40 bp):
CCGGATATAATAACCCGCACAAATGCCTTCGGGTCTTAGC
Found at i:105473456 original size:41 final size:41
Alignment explanation
Indices: 105473411--105473528 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
105473401 TGAAAGATAA
105473411 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
105473452 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
105473482 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
105473523 ATGTAG
1 ATGTAG
105473529 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:105473467 original size:71 final size:71
Alignment explanation
Indices: 105473379--105473542 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
105473369 GAGATGTATC
105473379 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
105473444 AGGACA
66 AGGACA
105473450 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
105473515 AGGACA
66 AGGACA
105473521 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
105473543 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:105481323 original size:40 final size:40
Alignment explanation
Indices: 105481278--105481445 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
105481268 CGGAATATAA
105481278 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
105481318 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
105481358 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
105481398 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
105481438 CCGGATAT
1 CCGGATAT
105481446 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:105485653 original size:22 final size:21
Alignment explanation
Indices: 105485607--105485655 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
105485597 GGCCTCTAGA
*
105485607 ACGGGCGTGTCCCAAGGTCAC
1 ACGGGCGTGTCCCAAGGCCAC
**
105485628 ACGGGCGTGTCCCTTGGACCAC
1 ACGGGCGTGTCCCAAGG-CCAC
105485650 ACGGGC
1 ACGGGC
105485656 ATGTGAGCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.16, C:0.35, G:0.35, T:0.14
Consensus pattern (21 bp):
ACGGGCGTGTCCCAAGGCCAC
Found at i:105485992 original size:18 final size:18
Alignment explanation
Indices: 105485971--105486029 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
105485961 TGCAATATAG
* * *
105485971 GGCTCGCTTACATGCATA
1 GGCTCGCATAAATGAATA
105485989 GGCTCGCATAAATGAATA
1 GGCTCGCATAAATGAATA
* *
105486007 GGCTCACATAAATTAATA
1 GGCTCGCATAAATGAATA
*
105486025 TGCTC
1 GGCTC
105486030 ACATGTATAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (18 bp):
GGCTCGCATAAATGAATA
Found at i:105486030 original size:18 final size:18
Alignment explanation
Indices: 105485986--105486033 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
105485976 GCTTACATGC
*
105485986 ATAGGCTCGCATAAATGA
1 ATAGGCTCACATAAATGA
*
105486004 ATAGGCTCACATAAATTA
1 ATAGGCTCACATAAATGA
*
105486022 ATATGCTCACAT
1 ATAGGCTCACAT
105486034 GTATAGGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (18 bp):
ATAGGCTCACATAAATGA
Found at i:105488817 original size:18 final size:16
Alignment explanation
Indices: 105488786--105488843 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 16
105488776 TTTTTAAACA
*
105488786 ATTTTTAGTTTTTTTGT
1 ATTTTTA-TATTTTTGT
105488803 AATTTTTATAATTTTTGT
1 -ATTTTTAT-ATTTTTGT
105488821 ATTTTGTATATTTTT-T
1 ATTTT-TATATTTTTGT
105488837 ATTTTTA
1 ATTTTTA
105488844 AAAAATTTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
15 2 0.05
16 6 0.16
17 12 0.32
18 17 0.46
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (16 bp):
ATTTTTATATTTTTGT
Found at i:105488996 original size:13 final size:13
Alignment explanation
Indices: 105488978--105489002 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
105488968 AACAATTTGA
105488978 TTTTAAATTAATT
1 TTTTAAATTAATT
105488991 TTTTAAATTAAT
1 TTTTAAATTAAT
105489003 AAATTTTTAT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAAATTAATT
Found at i:105495022 original size:60 final size:60
Alignment explanation
Indices: 105494940--105495057 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 60
105494930 ATATAAAAAA
* * * *
105494940 TCAATAAATTTAGCCTTAAATATTTACAAA-ATTTTTCATTTTAGTTCTAATTCTAAAATT
1 TCAATAAATTTAGCCTTAAATATTTA-AAATATCTGTCAATTTAGTTCTAACTCTAAAATT
* * *
105495000 TCAATAAATTTGGTCC-TCAATATTTAAAATATCTGTCAATTTAGTTTTAACTCTAAAA
1 TCAATAAATTTAG-CCTTAAATATTTAAAATATCTGTCAATTTAGTTCTAACTCTAAAA
105495058 AATTTAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
59 3 0.06
60 44 0.90
61 2 0.04
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (60 bp):
TCAATAAATTTAGCCTTAAATATTTAAAATATCTGTCAATTTAGTTCTAACTCTAAAATT
Found at i:105497933 original size:17 final size:18
Alignment explanation
Indices: 105497891--105497943 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
105497881 AATTAATTTT
105497891 TTAAAATT--TTAAAAATA
1 TTAAAATTAATTAAAAA-A
105497908 TTAAAATTAATTAAAAAA
1 TTAAAATTAATTAAAAAA
*
105497926 TT-ATATTAATTATAAAAA
1 TTAAAATTAATTA-AAAAA
105497944 ACATTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 17 0.53
18 8 0.25
19 7 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAAAATTAATTAAAAAA
Found at i:105508809 original size:3 final size:3
Alignment explanation
Indices: 105508794--105508848 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
105508784 GATAATGTTT
* *
105508794 GAA GAA AAA GAA GAA GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
105508842 GAA GAA G
1 GAA GAA G
105508849 CTTAAGCTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:105511538 original size:40 final size:40
Alignment explanation
Indices: 105511501--105511757 Score: 322
Period size: 40 Copynumber: 6.7 Consensus size: 40
105511491 GCTACTCGTT
* *
105511501 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
105511541 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
105511581 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
105511621 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
105511661 CAAATGCCTTCGGG-CTT-------A-TTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* ** * * *
105511692 CGAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
105511733 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
105511758 CATCATTCGA
Statistics
Matches: 196, Mismatches: 8, Indels: 26
0.85 0.03 0.11
Matches are distributed among these distances:
30 2 0.01
31 23 0.12
32 4 0.02
39 4 0.02
40 151 0.77
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:105511741 original size:71 final size:72
Alignment explanation
Indices: 105511608--105511750 Score: 193
Period size: 71 Copynumber: 2.0 Consensus size: 72
105511598 TAACCCGGAT
* *
105511608 TTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCG
1 TTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAATGCCTTCG
105511673 GG-CTTA
66 GGACTTA
* ** *
105511679 TTAGTAACTCGCACGAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAAA-GCCTT
1 TTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCACAAATGCCTT
105511742 CGGGACTTA
64 CGGGACTTA
105511751 GCCCGGACAT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
70 3 0.05
71 48 0.76
72 12 0.19
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (72 bp):
TTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAATGCCTTCG
GGACTTA
Found at i:105519768 original size:37 final size:38
Alignment explanation
Indices: 105519659--105519832 Score: 221
Period size: 38 Copynumber: 4.5 Consensus size: 38
105519649 GCTACTCGTT
*
105519659 CAAATGCCTTCGGGACTATAGCC-G-TTATAGTAA-TCGCA
1 CAAATGCCTTC-GGACT-TAACCGGATT-TAGTAACTCGCA
105519697 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAA-CCGGATTTAGTAACTCGCA
105519737 CAAATGCCTTC-GACTTAACCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAACCGGATTTAGTAACTCGCA
*
105519774 CAAATGCCTTCGGACTTAACCCGATTTAGTAACTACTTGCA
1 CAAATGCCTTCGGACTTAACCGGATTTAGTAACT-C--GCA
*
105519815 CAAATGCCTTCGGGCTTA
1 CAAATGCCTTCGGACTTA
105519833 GCCCGGANNN
Statistics
Matches: 125, Mismatches: 3, Indels: 13
0.89 0.02 0.09
Matches are distributed among these distances:
37 32 0.26
38 47 0.38
39 8 0.06
40 18 0.14
41 20 0.16
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.27
Consensus pattern (38 bp):
CAAATGCCTTCGGACTTAACCGGATTTAGTAACTCGCA
Found at i:105524916 original size:40 final size:39
Alignment explanation
Indices: 105524751--105524934 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
105524741 AAATTGAATG
* * *
105524751 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
105524791 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
105524831 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
105524871 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
105524910 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
105524935 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:105524959 original size:80 final size:81
Alignment explanation
Indices: 105524791--105524979 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
105524781 GCTGGAAATT
* * * *
105524791 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
105524856 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
105524872 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
105524935 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
105524951 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
105524980 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:105527403 original size:2 final size:2
Alignment explanation
Indices: 105527398--105527428 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
105527388 ATATAGCCGA
105527398 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
105527429 GTTCATCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:105531116 original size:21 final size:20
Alignment explanation
Indices: 105531092--105531131 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
105531082 CACGTATTTT
*
105531092 AATGATTGATTATAGATTATG
1 AATGATTGATGATAG-TTATG
*
105531113 AATGTTTGATGATAGTTAT
1 AATGATTGATGATAGTTAT
105531132 ACAAGTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (20 bp):
AATGATTGATGATAGTTATG
Found at i:105537139 original size:40 final size:40
Alignment explanation
Indices: 105537031--105537140 Score: 148
Period size: 40 Copynumber: 2.8 Consensus size: 40
105537021 ATTGAATGAT
* * * * *
105537031 ATCCGGGCTAAGTCCCGAAGACATTTATGCTGGTAATTAC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
* * *
105537071 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTAC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
105537111 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
105537141 AAATTGTGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
Found at i:105537155 original size:40 final size:39
Alignment explanation
Indices: 105537031--105537180 Score: 133
Period size: 40 Copynumber: 3.8 Consensus size: 39
105537021 ATTGAATGAT
* * * * * * *
105537031 ATCCGGGCTAAGTCCCGAAGACATTTATGCTGGTAATTAC
1 ATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGA-CAC
*
105537071 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTAC
1 ATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGAC-AC
* *
105537111 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATTGTGA-A-
1 ATCCGGGTTAAGACCCGAAGGCATTTGTGC---TAGTGACAC
* *
105537151 ATCCGGGTTAAGTCCCGAAGGCCTTTGTGC
1 ATCCGGGTTAAGACCCGAAGGCATTTGTGC
105537181 GGGTTACCAT
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
40 86 0.93
41 1 0.01
43 5 0.05
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
ATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGACAC
Found at i:105544577 original size:40 final size:40
Alignment explanation
Indices: 105544469--105544578 Score: 148
Period size: 40 Copynumber: 2.8 Consensus size: 40
105544459 ATTGAATGAT
* * * * *
105544469 ATCCGGGCTAAGTCCCGAAGACATTTATGCTGGTAATTAC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
* * *
105544509 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTAC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
105544549 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
105544579 AAATTGTGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
Found at i:105544593 original size:40 final size:39
Alignment explanation
Indices: 105544469--105544618 Score: 133
Period size: 40 Copynumber: 3.8 Consensus size: 39
105544459 ATTGAATGAT
* * * * * * *
105544469 ATCCGGGCTAAGTCCCGAAGACATTTATGCTGGTAATTAC
1 ATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGA-CAC
*
105544509 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTAC
1 ATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGAC-AC
* *
105544549 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATTGTGA-A-
1 ATCCGGGTTAAGACCCGAAGGCATTTGTGC---TAGTGACAC
* *
105544589 ATCCGGGTTAAGTCCCGAAGGCCTTTGTGC
1 ATCCGGGTTAAGACCCGAAGGCATTTGTGC
105544619 GGGTTACCAT
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
40 86 0.93
41 1 0.01
43 5 0.05
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
ATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGACAC
Found at i:105549945 original size:6 final size:6
Alignment explanation
Indices: 105549828--105549944 Score: 227
Period size: 6 Copynumber: 19.7 Consensus size: 6
105549818 ACTAAAACTA
105549828 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
105549876 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
105549924 AAAATC AAAATC AAAAT- AAAA
1 AAAATC AAAATC AAAATC AAAA
105549945 AGAAAATAAA
Statistics
Matches: 111, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 4 0.04
6 107 0.96
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATC
Found at i:105552355 original size:20 final size:20
Alignment explanation
Indices: 105552341--105552396 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
105552331 CATGATTGAG
105552341 ATGATATGCACATGATATGT
1 ATGATATGCACATGATATGT
105552361 ATGATATGCACATGATATGT
1 ATGATATGCACATGATATGT
105552381 ATGATATGCACATGAT
1 ATGATATGCACATGAT
105552397 GTATTCATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34
Consensus pattern (20 bp):
ATGATATGCACATGATATGT
Found at i:105552357 original size:11 final size:11
Alignment explanation
Indices: 105552341--105552396 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
105552331 CATGATTGAG
105552341 ATGATATGCAC
1 ATGATATGCAC
*
105552352 ATGATATG--T
1 ATGATATGCAC
105552361 ATGATATGCAC
1 ATGATATGCAC
*
105552372 ATGATATG--T
1 ATGATATGCAC
105552381 ATGATATGCAC
1 ATGATATGCAC
105552392 ATGAT
1 ATGAT
105552397 GTATTCATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 16 0.43
11 21 0.57
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:105552518 original size:25 final size:26
Alignment explanation
Indices: 105552446--105552542 Score: 137
Period size: 27 Copynumber: 3.8 Consensus size: 26
105552436 GAGGAAGTGC
105552446 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
105552472 AAAAAGGGCTTATGCCTCAGTTTATTG
1 -AAAAGGGCTTATGCCCCAGTTTATTG
**
105552499 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
105552524 AAAAGGGCTT-TG-CCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
105552543 ATTAAAGAGG
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
24 7 0.11
25 24 0.36
26 10 0.15
27 25 0.38
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.29
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:105553138 original size:18 final size:18
Alignment explanation
Indices: 105553115--105553149 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
105553105 ACTTAGGACG
*
105553115 TGTTTTCAAAACGACACT
1 TGTTTTCAAAACAACACT
*
105553133 TGTTTTCCAAACAACAC
1 TGTTTTCAAAACAACAC
105553150 AATGTTACGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (18 bp):
TGTTTTCAAAACAACACT
Found at i:105554597 original size:18 final size:18
Alignment explanation
Indices: 105554557--105554605 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
105554547 TAAATAGAAT
*
105554557 AAAT-AAAATAAAAATAA
1 AAATAAAAATAAAAACAA
105554574 AAATAAAAATAAAAACAA
1 AAATAAAAATAAAAACAA
** *
105554592 GCATAAGAATAAAA
1 AAATAAAAATAAAA
105554606 TAAATAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.14
Consensus pattern (18 bp):
AAATAAAAATAAAAACAA
Found at i:105554603 original size:6 final size:6
Alignment explanation
Indices: 105554557--105554588 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
105554547 TAAATAGAAT
105554557 AAAT-A AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAA
105554589 CAAGCATAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:105575524 original size:40 final size:40
Alignment explanation
Indices: 105575487--105575672 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
105575477 GCTACTCGTT
* *
105575487 CAAATGCTTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
105575527 CAGATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
105575567 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * *
105575607 CGAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
105575648 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
105575673 CATCATTCGA
Statistics
Matches: 127, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.02
40 113 0.89
41 11 0.09
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:105580519 original size:29 final size:29
Alignment explanation
Indices: 105580457--105580559 Score: 102
Period size: 29 Copynumber: 3.6 Consensus size: 29
105580447 GTGACGAGAT
* * *
105580457 TGGCACTGAGTGTGCGAGCTTCTAAT-GTA
1 TGGCACTAAGTGTGCGAGCTT-GAATCATA
* * *
105580486 CGGCACTAAGTGTGCGAGTTTGGA-CTATA
1 TGGCACTAAGTGTGCGAGCTTGAATC-ATA
* *
105580515 TGGCACTATGTGTGCGGGCTTGAATCATA
1 TGGCACTAAGTGTGCGAGCTTGAATCATA
105580544 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
105580560 TGATTGAGTA
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
28 1 0.02
29 57 0.97
30 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.29
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAATCATA
Found at i:105585632 original size:59 final size:59
Alignment explanation
Indices: 105585562--105585680 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
105585552 AAATATTTAC
105585562 GGCTTGATTTATAAAAACGAGGTCTCAATACCTCATTTTCTAAAACCACTTGACTATAG
1 GGCTTGATTTATAAAAACGAGGTCTCAATACCTCATTTTCTAAAACCACTTGACTATAG
* *
105585621 GGCTTGATTTATAAAAACGAGGTCTCGATACCTCATTTTCTAAAACCACTTGACTTTAG
1 GGCTTGATTTATAAAAACGAGGTCTCAATACCTCATTTTCTAAAACCACTTGACTATAG
105585680 G
1 G
105585681 TCATAACACT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (59 bp):
GGCTTGATTTATAAAAACGAGGTCTCAATACCTCATTTTCTAAAACCACTTGACTATAG
Found at i:105592102 original size:42 final size:43
Alignment explanation
Indices: 105592044--105592126 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
105592034 TTATGATTTG
105592044 CGTGTAAGACCATGTCTGGGACA-TCGGCATCG-TATTTGATCT
1 CGTGTAAGACCATGTCTGGGACAGT-GGCATCGATATTTGATCT
* *
105592086 CGTGTAAGACCCTGTCTGGGATAGTGGCATCGATATTTGAT
1 CGTGTAAGACCATGTCTGGGACAGTGGCATCGATATTTGAT
105592127 TACATAGAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 28 0.76
43 9 0.24
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTGGGACAGTGGCATCGATATTTGATCT
Found at i:105592138 original size:43 final size:42
Alignment explanation
Indices: 105592046--105592163 Score: 111
Period size: 43 Copynumber: 2.8 Consensus size: 42
105592036 ATGATTTGCG
* * *
105592046 TGTAAGACCATGTCTGGGACA-TCGGCATCGTATTTGATCTCG
1 TGTAAGACCCTGTCTGGGATAGT-GGCATCGTATTTGATCTCA
105592088 TGTAAGACCCTGTCTGGGATAGTGGCATCGATATTTGAT-TACA
1 TGTAAGACCCTGTCTGGGATAGTGGCATCG-TATTTGATCT-CA
*
105592131 TAG-AAGACCAC-GTCTGGGAT-GTTGGCATTGTAT
1 T-GTAAGACC-CTGTCTGGGATAG-TGGCATCGTAT
105592164 GAGCTTTCCA
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
42 31 0.47
43 33 0.50
44 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (42 bp):
TGTAAGACCCTGTCTGGGATAGTGGCATCGTATTTGATCTCA
Found at i:105598886 original size:27 final size:27
Alignment explanation
Indices: 105598856--105598909 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
105598846 TAGTCTCAAG
105598856 AATGTTTAATTTATAAATCTTTAAAAC
1 AATGTTTAATTTATAAATCTTTAAAAC
105598883 AATGTTTAATTTATAAATCTTTAAAAC
1 AATGTTTAATTTATAAATCTTTAAAAC
105598910 CTGTTACGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (27 bp):
AATGTTTAATTTATAAATCTTTAAAAC
Done.