Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 157 of 444
Found at i:42883081 original size:77 final size:79
Alignment explanation
Indices: 42882961--42883181 Score: 306
Period size: 77 Copynumber: 2.8 Consensus size: 79
42882951 TACTCGTTCA
* * *
42882961 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGG-CTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
42883026 TTAGTAACTCGCAC-
65 TTAGTAACTCGCACG
*
42883040 AATGCCTTCGGGCTTAGCCCGGAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGAT
1 AATGCCTTCGGGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGAT
42883103 TTAGTAACTCGCACG
65 TTAGTAACTCGCACG
* * * *
42883118 AATGCCTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGG-GCTTAGCCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
42883182 CATCATTCGA
Statistics
Matches: 127, Mismatches: 9, Indels: 11
0.86 0.06 0.07
Matches are distributed among these distances:
76 3 0.02
77 47 0.37
78 21 0.17
79 23 0.18
80 22 0.17
81 11 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (79 bp):
AATGCCTTCGGGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT
TAGTAACTCGCACG
Found at i:42883141 original size:117 final size:119
Alignment explanation
Indices: 42882959--42883181 Score: 303
Period size: 117 Copynumber: 1.9 Consensus size: 119
42882949 GCTACTCGTT
42882959 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* * *
42883024 ATTTAGTAAC-TCGCACAATGCCTTCGGG-CTTAGCCCGGATTAGTAACTCGCA
66 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
* * * **
42883076 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGTAACTCGCACGAATGCCTTC-GGATCTTAGTC
1 CAAATGCCTTCGGGA-CATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACC
*
42883138 CGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
63 CGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
42883182 CATCATTCGA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
116 6 0.07
117 57 0.62
118 18 0.20
119 11 0.12
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (119 bp):
CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
Found at i:42883181 original size:40 final size:40
Alignment explanation
Indices: 42882940--42883181 Score: 291
Period size: 40 Copynumber: 6.1 Consensus size: 40
42882930 TCGGATTTAA
** *
42882940 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42882980 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
42883020 CCGGATTTAGTAACTCGCAC-AATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
42883058 CCGGAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
42883097 CCGGATTTAGTAACTCGCACGAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
42883137 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
42883177 CCGGA
1 CCGGA
42883182 CATCATTCGA
Statistics
Matches: 180, Mismatches: 15, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
37 15 0.08
38 20 0.11
39 24 0.13
40 111 0.62
41 10 0.06
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:42891269 original size:77 final size:79
Alignment explanation
Indices: 42891142--42891362 Score: 306
Period size: 77 Copynumber: 2.8 Consensus size: 79
42891132 TACTCGTTCA
* * *
42891142 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGG-CTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
42891207 TTAGTAACTCGCAC-
65 TTAGTAACTCGCACG
*
42891221 AATGCCTTCGGGCTTAGCCCGGAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGAT
1 AATGCCTTCGGGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGAT
42891284 TTAGTAACTCGCACG
65 TTAGTAACTCGCACG
* * * *
42891299 AATGCCTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGG-GCTTAGCCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
42891363 CATCATTCGA
Statistics
Matches: 127, Mismatches: 9, Indels: 11
0.86 0.06 0.07
Matches are distributed among these distances:
76 3 0.02
77 47 0.37
78 21 0.17
79 23 0.18
80 22 0.17
81 11 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (79 bp):
AATGCCTTCGGGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT
TAGTAACTCGCACG
Found at i:42891362 original size:40 final size:40
Alignment explanation
Indices: 42891121--42891362 Score: 291
Period size: 40 Copynumber: 6.1 Consensus size: 40
42891111 CGGAATTTAA
** *
42891121 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42891161 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
42891201 CCGGATTTAGTAACTCGCAC-AATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
42891239 CCGGAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
42891278 CCGGATTTAGTAACTCGCACGAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
42891318 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
42891358 CCGGA
1 CCGGA
42891363 CATCATTCGA
Statistics
Matches: 180, Mismatches: 15, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
37 15 0.08
38 20 0.11
39 24 0.13
40 111 0.62
41 10 0.06
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:42893431 original size:37 final size:37
Alignment explanation
Indices: 42893390--42893464 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
42893380 TGTGAAGAAG
* *
42893390 AAGGATTGGACACTCCAATTGTGCATAGATTATCGTC
1 AAGGATAGAACACTCCAATTGTGCATAGATTATCGTC
42893427 AAGGATAGAACACTCCAATTGTGCATAGATTATCGTC
1 AAGGATAGAACACTCCAATTGTGCATAGATTATCGTC
42893464 A
1 A
42893465 GTTGAATAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (37 bp):
AAGGATAGAACACTCCAATTGTGCATAGATTATCGTC
Found at i:42896470 original size:27 final size:27
Alignment explanation
Indices: 42896432--42896485 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
42896422 ACCATAGATG
*
42896432 TCACATCTAATTCTGGAATCATGCCTT
1 TCACAACTAATTCTGGAATCATGCCTT
*
42896459 TCACAACTAATTTTGGAATCATGCCTT
1 TCACAACTAATTCTGGAATCATGCCTT
42896486 ACCCTCCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (27 bp):
TCACAACTAATTCTGGAATCATGCCTT
Found at i:42901408 original size:39 final size:38
Alignment explanation
Indices: 42901354--42901488 Score: 162
Period size: 40 Copynumber: 3.4 Consensus size: 38
42901344 AAACCAAGTA
* * *
42901354 CCTTCGGAATTTAGCCGGATATAGCTACTTGCTCAAATG
1 CCTTCGGGACTTAGCCGGATATAG-TACTTGCACAAATG
* *
42901393 CCTTCGGGACTTAGCCCGGTTATAGTAATTCGCACAAATG
1 CCTTCGGGACTTAG-CCGGATATAGTACTT-GCACAAATG
* *
42901433 CCTTTGGGACTTAGCCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCC-GGATATAGT-ACTTGCACAAATG
42901473 CCTTCGGGACTTAGCC
1 CCTTCGGGACTTAGCC
42901489 CGATTATCAT
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
39 18 0.22
40 62 0.76
41 2 0.02
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.28
Consensus pattern (38 bp):
CCTTCGGGACTTAGCCGGATATAGTACTTGCACAAATG
Found at i:42901431 original size:40 final size:40
Alignment explanation
Indices: 42901387--42901495 Score: 173
Period size: 40 Copynumber: 2.7 Consensus size: 40
42901377 GCTACTTGCT
*
42901387 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
42901427 CAAATGCCTTTGGGACTTAGCCTGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
42901467 CAAATGCCTTCGGGACTTAGCCCGATTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
42901496 CATCCGAATA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.28
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:42904339 original size:42 final size:42
Alignment explanation
Indices: 42904277--42904429 Score: 171
Period size: 42 Copynumber: 3.6 Consensus size: 42
42904267 TAAGATACCA
* * * ** *
42904277 ATGCCATGTCTTAGACATGGTCTTACATGGGATCTCACATCG
1 ATGCCATATCCTAGACATGGTCTTACACGAAATCTCATATCG
* * *
42904319 ATGCCATATCCTAGATATGGTCTTATACGAAATCTCATTTCG
1 ATGCCATATCCTAGACATGGTCTTACACGAAATCTCATATCG
* * * **
42904361 ATGCCATGTCCCAGACGTGGTCTTACACGAAATCTCATATTA
1 ATGCCATATCCTAGACATGGTCTTACACGAAATCTCATATCG
*
42904403 ATGCCATATCCTAGATATGGTCTTACA
1 ATGCCATATCCTAGACATGGTCTTACA
42904430 AGATGACACA
Statistics
Matches: 90, Mismatches: 21, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 90 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (42 bp):
ATGCCATATCCTAGACATGGTCTTACACGAAATCTCATATCG
Found at i:42904447 original size:84 final size:84
Alignment explanation
Indices: 42904271--42904449 Score: 198
Period size: 84 Copynumber: 2.1 Consensus size: 84
42904261 ACACAATAAG
* ** * ** *
42904271 ATACCAATGCCATGTCTTAGACATGGTCTTACATGGGATCTCACATCGATGCCATATCCTAGATA
1 ATACCGATGCCATGTCCCAGACATGGTCTTACACGAAATCTCACATCAATGCCATATCCTAGATA
* * *
42904336 TGGTCTTATACGAAATCTC
66 TGGTCTTACAAGAAATCAC
** * * *
42904355 ATTTCGATGCCATGTCCCAGACGTGGTCTTACACGAAATCTCATATTAATGCCATATCCTAGATA
1 ATACCGATGCCATGTCCCAGACATGGTCTTACACGAAATCTCACATCAATGCCATATCCTAGATA
*
42904420 TGGTCTTACAAGATGA-CAC
66 TGGTCTTACAAGA-AATCAC
42904439 ATACCGATGCC
1 ATACCGATGCC
42904450 GATGCCATAT
Statistics
Matches: 76, Mismatches: 18, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
84 75 0.99
85 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (84 bp):
ATACCGATGCCATGTCCCAGACATGGTCTTACACGAAATCTCACATCAATGCCATATCCTAGATA
TGGTCTTACAAGAAATCAC
Found at i:42907308 original size:33 final size:33
Alignment explanation
Indices: 42907266--42907332 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
42907256 ACCCAGATGA
42907266 TAGTCAATTACCAACTCATAATCTTTTATCAAC
1 TAGTCAATTACCAACTCATAATCTTTTATCAAC
42907299 TAGTCAATTACCAACTCATAATCTTTTATCAAC
1 TAGTCAATTACCAACTCATAATCTTTTATCAAC
42907332 T
1 T
42907333 CTAGCCACCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (33 bp):
TAGTCAATTACCAACTCATAATCTTTTATCAAC
Found at i:42907333 original size:18 final size:18
Alignment explanation
Indices: 42907277--42907333 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
42907267 AGTCAATTAC
42907277 CAACTCATAATCTTTTAT
1 CAACTCATAATCTTTTAT
* ** *
42907295 CAA--C-TAGTCAATTAC
1 CAACTCATAATCTTTTAT
42907310 CAACTCATAATCTTTTAT
1 CAACTCATAATCTTTTAT
42907328 CAACTC
1 CAACTC
42907334 TAGCCACCTC
Statistics
Matches: 28, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
15 10 0.36
16 1 0.04
17 1 0.04
18 16 0.57
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (18 bp):
CAACTCATAATCTTTTAT
Found at i:42908148 original size:12 final size:13
Alignment explanation
Indices: 42908112--42908149 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
42908102 AAATATTTGA
42908112 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
42908125 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
42908139 CTTG-TCTTAAT
1 CTTGTTCTTAAT
42908150 ATTCCAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:42910013 original size:18 final size:18
Alignment explanation
Indices: 42909987--42910023 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
42909977 AAGTTAAATT
42909987 ACATAGGTAATAATCCTC
1 ACATAGGTAATAATCCTC
*
42910005 ACATGGGTAATAATCCTC
1 ACATAGGTAATAATCCTC
42910023 A
1 A
42910024 ATCTCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.27
Consensus pattern (18 bp):
ACATAGGTAATAATCCTC
Found at i:42917133 original size:39 final size:39
Alignment explanation
Indices: 42917100--42917186 Score: 131
Period size: 39 Copynumber: 2.2 Consensus size: 39
42917090 CCGGCAATTA
*
42917100 GCCTGCTAGGTATAAA-CTTGAACTTATCACCGGCACGAG
1 GCCTGCTAGGTATAAACCTT-AAATTATCACCGGCACGAG
**
42917139 GCCTGCTAGGTATAAACCTTAAATTATCACTAGCACGAG
1 GCCTGCTAGGTATAAACCTTAAATTATCACCGGCACGAG
42917178 GCCTGCTAG
1 GCCTGCTAG
42917187 ACATTAAGTC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 41 0.93
40 3 0.07
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (39 bp):
GCCTGCTAGGTATAAACCTTAAATTATCACCGGCACGAG
Found at i:42920798 original size:28 final size:28
Alignment explanation
Indices: 42920729--42920829 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
42920719 GACAAGATTG
* * * *
42920729 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
42920759 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
42920787 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
42920816 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
42920830 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:42923339 original size:49 final size:50
Alignment explanation
Indices: 42923262--42923493 Score: 254
Period size: 49 Copynumber: 4.7 Consensus size: 50
42923252 TACTAAGTGC
* * * *
42923262 AGTACTAAGTTCAGGCTACTACGTGTACCGGATTATT-GGTCTCATGTGT
1 AGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTCACATGTGT
* * * * * * *
42923311 AGTACTAAGTGTAGGCTACTATGCGTACCCGATAACTTCGATCACGTGTGT
1 AGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TTAGGTCACATGTGT
* ** *
42923362 AGTACTAAGTGCA-GCTACTACGTGTATCAGATGGTTAGGTCACGTGTGT
1 AGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTCACATGTGT
* *
42923411 AGTACTAAGTGCAGGCTATTACGTGTACCAGATAATT-GGTCGCATGTGT
1 AGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTCACATGTGT
* * *
42923460 AGTACTAAGTGCAGACTACTATGCGTACCAGATA
1 AGTACTAAGTGCAGGCTACTACGTGTACCAGATA
42923494 GCTTTGGCTA
Statistics
Matches: 152, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
49 95 0.62
50 36 0.24
51 21 0.14
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (50 bp):
AGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTCACATGTGT
Found at i:42923439 original size:100 final size:97
Alignment explanation
Indices: 42923262--42923492 Score: 264
Period size: 100 Copynumber: 2.3 Consensus size: 97
42923252 TACTAAGTGC
* * * * *
42923262 AGTACTAAGTTCAGGCTACTACGTGTACCGGATTATTGGTCTCATGTGTAGTACTAAGTGTAGGC
1 AGTACTAAGTGCA-GCTACTACGTGTACCAGATGATTGGTCACATGTGTAGTACTAAGTGCAGGC
* * *
42923327 TACTATGCGTACCCGATAACTTCGATCACGTGTGT
65 TACTACGCGTACCAGATAA-TT-GATCACATGTGT
* * *
42923362 AGTACTAAGTGCAGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAAGTGCAGGC
1 AGTACTAAGTGCAGCTACTACGTGTACCAGATGATT-GGTCACATGTGTAGTACTAAGTGCAGGC
* * * *
42923427 TATTACGTGTACCAGATAATTGGTCGCATGTGT
65 TACTACGCGTACCAGATAATTGATCACATGTGT
* *
42923460 AGTACTAAGTGCAGACTACTATGCGTACCAGAT
1 AGTACTAAGTGCAG-CTACTACGTGTACCAGAT
42923493 AGCTTTGGCT
Statistics
Matches: 111, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
98 23 0.21
99 36 0.32
100 52 0.47
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (97 bp):
AGTACTAAGTGCAGCTACTACGTGTACCAGATGATTGGTCACATGTGTAGTACTAAGTGCAGGCT
ACTACGCGTACCAGATAATTGATCACATGTGT
Found at i:42928058 original size:38 final size:38
Alignment explanation
Indices: 42927997--42928109 Score: 127
Period size: 38 Copynumber: 2.9 Consensus size: 38
42927987 ATTTGATGTG
*
42927997 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAAAA
1 TATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAAAA
* **
42928037 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTAGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAA
* * * * *
42928075 TATCGGGGATAAATCCCACAGGCCTAGTGCTGGTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTA
42928110 TTATATTCGG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
38 50 0.79
39 5 0.08
40 8 0.13
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.26
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAA
Found at i:42928111 original size:38 final size:38
Alignment explanation
Indices: 42928025--42928120 Score: 111
Period size: 38 Copynumber: 2.5 Consensus size: 38
42928015 CGCAGGCTTC
** * * * * *
42928025 GTGCTGGTAAAATATCCGGGTTAAATCCCGCAGGCTTC
1 GTGCTGGTATTATATCGGGGATAAATCCCACAGGCCTA
*
42928063 GTGCTAGTATTATATCGGGGATAAATCCCACAGGCCTA
1 GTGCTGGTATTATATCGGGGATAAATCCCACAGGCCTA
42928101 GTGCTGGTATTATATTCGGG
1 GTGCTGGTATTATA-TCGGG
42928121 CCTTCGTGCC
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
38 43 0.90
39 5 0.10
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (38 bp):
GTGCTGGTATTATATCGGGGATAAATCCCACAGGCCTA
Found at i:42928409 original size:43 final size:43
Alignment explanation
Indices: 42928113--42928396 Score: 505
Period size: 43 Copynumber: 6.6 Consensus size: 43
42928103 GCTGGTATTA
42928113 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* *
42928156 TATTCGGGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTA
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
42928199 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* * *
42928242 TATTCAGGCCTTCGTGCCTAGTAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* *
42928285 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCTGGTGATGTA
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
42928328 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
42928371 TATTCGGGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
42928397 GTAATGCCGG
Statistics
Matches: 227, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 227 1.00
ACGTcount: A:0.11, C:0.25, G:0.33, T:0.31
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:42932668 original size:40 final size:40
Alignment explanation
Indices: 42932623--42932790 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
42932613 CGGAATATAA
42932623 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
42932663 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
42932703 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
42932743 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
42932783 CCGGATAT
1 CCGGATAT
42932791 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:42940694 original size:40 final size:40
Alignment explanation
Indices: 42940649--42940816 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
42940639 CGGAATATAA
42940649 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
42940689 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
42940729 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
42940769 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
42940809 CCGGATAT
1 CCGGATAT
42940817 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:42944099 original size:40 final size:39
Alignment explanation
Indices: 42943934--42944117 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
42943924 AAATTGAATG
* * *
42943934 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
42943974 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
42944014 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
42944054 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
42944093 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
42944118 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:42944142 original size:80 final size:81
Alignment explanation
Indices: 42943974--42944162 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
42943964 GCTGGAAATT
* * * *
42943974 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
42944039 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
42944055 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
42944118 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
42944134 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
42944163 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:42952194 original size:40 final size:39
Alignment explanation
Indices: 42952029--42952212 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
42952019 AAATTGAATG
* * *
42952029 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
42952069 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
42952109 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
42952149 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
42952188 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
42952213 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:42952237 original size:80 final size:81
Alignment explanation
Indices: 42952069--42952257 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
42952059 GCTGGAAATT
* * * *
42952069 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
42952134 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
42952150 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
42952213 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
42952229 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
42952258 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:42954305 original size:27 final size:28
Alignment explanation
Indices: 42954270--42954322 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
42954260 TTATTTAGAA
* *
42954270 ATCAGTGTTAA-TTGGGCCTTAGCCCAT
1 ATCAATGTTAATTTGGGCCATAGCCCAT
42954297 ATCAATGTTAATTTGGGCCATAGCCC
1 ATCAATGTTAATTTGGGCCATAGCCC
42954323 CTTACAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.32
Consensus pattern (28 bp):
ATCAATGTTAATTTGGGCCATAGCCCAT
Found at i:42958353 original size:27 final size:28
Alignment explanation
Indices: 42958323--42958375 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
42958313 CTATTTAGAA
* *
42958323 ATCAGTGTTAAT-TGGGCCTTAGCCCAT
1 ATCAATGTTAATCTGGGCCATAGCCCAT
42958350 ATCAATGTTAATCTGGGCCATAGCCC
1 ATCAATGTTAATCTGGGCCATAGCCC
42958376 CTTACAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (28 bp):
ATCAATGTTAATCTGGGCCATAGCCCAT
Found at i:42958518 original size:19 final size:20
Alignment explanation
Indices: 42958476--42958519 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
42958466 CCATATTATC
** *
42958476 ACAGTTGGGCCCATTTCAAT
1 ACAGTTGGGCCCATAACAAA
42958496 ACAGTT-GGCCCATAACAAA
1 ACAGTTGGGCCCATAACAAA
42958515 ACAGT
1 ACAGT
42958520 CTCATATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ACAGTTGGGCCCATAACAAA
Found at i:42971493 original size:33 final size:33
Alignment explanation
Indices: 42971456--42971522 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
42971446 ATGAAAAATG
*
42971456 TGGGTTTTTGTAAGAGGGATTATGAATCGACTA
1 TGGGTTTTTATAAGAGGGATTATGAATCGACTA
42971489 TGGGTTTTTATAAGAGGGATTATGAATCGACTA
1 TGGGTTTTTATAAGAGGGATTATGAATCGACTA
42971522 T
1 T
42971523 ACTTGGGTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.28, C:0.06, G:0.28, T:0.37
Consensus pattern (33 bp):
TGGGTTTTTATAAGAGGGATTATGAATCGACTA
Found at i:42973785 original size:42 final size:42
Alignment explanation
Indices: 42973739--42973860 Score: 145
Period size: 42 Copynumber: 2.9 Consensus size: 42
42973729 CTTACATGGG
* * * *
42973739 ATCTCACATCGATGCCATATCCCTGGTATAGTCTTATACAAA
1 ATCTCATATCGATGCCATATCCCAGATATAGTCTTACACAAA
* * * *
42973781 ATCTCATTTCGATGCCATGTCCCAGATGTAGTCTTACACGAA
1 ATCTCATATCGATGCCATATCCCAGATATAGTCTTACACAAA
** *
42973823 ATCTCATATAAATGCCATATCCCAGATATGGTCTTACA
1 ATCTCATATCGATGCCATATCCCAGATATAGTCTTACA
42973861 TGATAACACA
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.31
Consensus pattern (42 bp):
ATCTCATATCGATGCCATATCCCAGATATAGTCTTACACAAA
Found at i:42975832 original size:11 final size:11
Alignment explanation
Indices: 42975818--42975879 Score: 67
Period size: 11 Copynumber: 5.6 Consensus size: 11
42975808 CCACCCAACA
42975818 ACCACCATATC
1 ACCACCATATC
42975829 ACCACCATA-C
1 ACCACCATATC
42975839 AACCACCATATC
1 -ACCACCATATC
42975851 ACCACCAT-TC
1 ACCACCATATC
*
42975861 AACCATCC-TAGC
1 -ACCA-CCATATC
42975873 ACCACCA
1 ACCACCA
42975880 CACCACCACG
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
10 5 0.11
11 35 0.80
12 4 0.09
ACGTcount: A:0.37, C:0.47, G:0.02, T:0.15
Consensus pattern (11 bp):
ACCACCATATC
Found at i:42975832 original size:22 final size:23
Alignment explanation
Indices: 42975806--42975878 Score: 91
Period size: 22 Copynumber: 3.3 Consensus size: 23
42975796 TAAACTGAAA
42975806 CACCACCCA-ACAACCACCATAT
1 CACCACCCATACAACCACCATAT
42975828 CACCA-CCATACAACCACCATAT
1 CACCACCCATACAACCACCATAT
* *
42975850 CACCA-CCATTCAACCATCC-TAG
1 CACCACCCATACAACCA-CCATAT
42975872 CACCACC
1 CACCACC
42975879 ACACCACCAC
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.07
22 40 0.87
23 3 0.07
ACGTcount: A:0.37, C:0.49, G:0.01, T:0.12
Consensus pattern (23 bp):
CACCACCCATACAACCACCATAT
Found at i:42975879 original size:22 final size:22
Alignment explanation
Indices: 42975806--42975888 Score: 89
Period size: 22 Copynumber: 3.8 Consensus size: 22
42975796 TAAACTGAAA
*
42975806 CACCACCCA-ACAACCACCATAT
1 CACCA-CCATACAACCACCATAG
*
42975828 CACCACCATACAACCACCATAT
1 CACCACCATACAACCACCATAG
*
42975850 CACCACCATTCAACCATCC-TAG
1 CACCACCATACAACCA-CCATAG
* *
42975872 CACCACCACACCACCAC
1 CACCACCATACAACCAC
42975889 GACATCAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.07
22 48 0.89
23 2 0.04
ACGTcount: A:0.37, C:0.51, G:0.01, T:0.11
Consensus pattern (22 bp):
CACCACCATACAACCACCATAG
Found at i:42978642 original size:13 final size:13
Alignment explanation
Indices: 42978624--42978663 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
42978614 AGTTTGGCAA
42978624 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
42978637 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
42978650 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
42978663 T
1 T
42978664 TTGGTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.28, C:0.07, G:0.25, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:42988470 original size:47 final size:47
Alignment explanation
Indices: 42988401--42989174 Score: 1395
Period size: 47 Copynumber: 16.3 Consensus size: 47
42988391 CCCTTCGGGA
* *
42988401 CTTATCACATTTATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
42988448 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
42988495 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
42988542 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
42988591 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTAGGC
42988640 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
42988687 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTAGGC
42988736 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
42988783 CTTATCACATTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACA-TATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
42988831 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
42988878 CTTATCACATATATACACTTTCACATTCATCATATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
42988925 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTAGGC
42988974 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
42989021 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
42989068 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
42989115 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
42989162 CTTATCACATATA
1 CTTATCACATATA
42989175 CATGTATATC
Statistics
Matches: 710, Mismatches: 10, Indels: 14
0.97 0.01 0.02
Matches are distributed among these distances:
47 476 0.67
48 46 0.06
49 188 0.26
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:42988504 original size:22 final size:22
Alignment explanation
Indices: 42988476--42988551 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
42988466 TTTCACATTC
42988476 ATCACATTGGCCATTAGGCCTT
1 ATCACATTGGCCATTAGGCCTT
*** *** *
42988498 ATCACATATATACACTTTCACATT
1 ATCACAT-TGGCCA-TTAGGCCTT
42988522 CATCACATTGGCCATTAGGCCTT
1 -ATCACATTGGCCATTAGGCCTT
42988545 ATCACAT
1 ATCACAT
42988552 ATATATACAC
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
22 14 0.38
23 8 0.22
24 8 0.22
25 7 0.19
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTAGGCCTT
Found at i:42988602 original size:96 final size:94
Alignment explanation
Indices: 42988401--42989174 Score: 1395
Period size: 96 Copynumber: 8.1 Consensus size: 94
42988391 CCCTTCGGGA
*
42988401 CTTATCACATTTATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
42988466 TTTCACATTCATCACATTGGCCATTAGGC
66 TTTCACATTCATCACATTGGCCATTAGGC
*
42988495 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
*
42988560 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATTGGCCATTAGGC
42988591 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
42988656 ACTTTCACATTCATCACATTGGCCATTAGGC
64 ACTTTCACATTCATCACATTGGCCATTAGGC
*
42988687 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
42988752 ACTTTCACATTCATCACATTGGCCATTAGGC
64 ACTTTCACATTCATCACATTGGCCATTAGGC
42988783 CTTATCACATTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
1 CTTATCACA-TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
*
42988848 CTTTCACATTCATCACATCGGCCATTAGGC
65 CTTTCACATTCATCACATTGGCCATTAGGC
* *
42988878 CTTATCACATATATACACTTTCACATTCATCATATTGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
42988943 ACTTTCACATTCATCACATTGGCCATTAGGC
64 ACTTTCACATTCATCACATTGGCCATTAGGC
*
42988974 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
42989039 TTTCACATTCATCACATTGGCCATTAGGC
66 TTTCACATTCATCACATTGGCCATTAGGC
42989068 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
42989133 TTTCACATTCATCACATTGGCCATTAGGC
66 TTTCACATTCATCACATTGGCCATTAGGC
42989162 CTTATCACATATA
1 CTTATCACATATA
42989175 CATGTATATC
Statistics
Matches: 660, Mismatches: 13, Indels: 14
0.96 0.02 0.02
Matches are distributed among these distances:
94 243 0.37
95 92 0.14
96 279 0.42
98 46 0.07
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATTGGCCATTAGGC
Found at i:42988745 original size:22 final size:22
Alignment explanation
Indices: 42988717--42988793 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
42988707 TTTCACATTC
42988717 ATCACATTGGCCATTAGGCCTT
1 ATCACATTGGCCATTAGGCCTT
*** *** *
42988739 ATCACATATATACACTTTCACATT
1 ATCACAT-TGGCCA-TTAGGCCTT
42988763 CATCACATTGGCCATTAGGCCTT
1 -ATCACATTGGCCATTAGGCCTT
42988786 ATCACATT
1 ATCACATT
42988794 ATATACACTT
Statistics
Matches: 38, Mismatches: 14, Indels: 6
0.66 0.24 0.10
Matches are distributed among these distances:
22 15 0.39
23 8 0.21
24 8 0.21
25 7 0.18
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTAGGCCTT
Found at i:42988983 original size:22 final size:22
Alignment explanation
Indices: 42988955--42989077 Score: 66
Period size: 22 Copynumber: 5.3 Consensus size: 22
42988945 TTTCACATTC
42988955 ATCACATTGGCCATTAGGCCTT
1 ATCACATTGGCCATTAGGCCTT
*** *** *
42988977 ATCACATATATACACTTTCACATT
1 ATCACAT-TGGCCA-TTAGGCCTT
42989001 CATCACATTGGCCATTAGGCCTT
1 -ATCACATTGGCCATTAGGCCTT
*** *** *
42989024 ATCACATATATACACTTTCACATT
1 ATCACAT-TGGCCA-TTAGGCCTT
42989048 CATCACATTGGCCATTAGGCCTT
1 -ATCACATTGGCCATTAGGCCTT
42989071 ATCACAT
1 ATCACAT
42989078 ATATACACTT
Statistics
Matches: 67, Mismatches: 28, Indels: 12
0.63 0.26 0.11
Matches are distributed among these distances:
22 21 0.31
23 16 0.24
24 16 0.24
25 14 0.21
ACGTcount: A:0.29, C:0.28, G:0.10, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTAGGCCTT
Found at i:42992056 original size:107 final size:107
Alignment explanation
Indices: 42991865--42992083 Score: 260
Period size: 107 Copynumber: 2.0 Consensus size: 107
42991855 GCTAGACCAT
* **
42991865 GTGGAGCATACTGACTTGATCTCTAATTCAACACCAAGGGACACACGACCATGTAACCAGGCCAT
1 GTGGAGCATACTGACCTGATCTCTAATTCAACACCAAGGGACACACGACCATGTAACCAAACCAT
* *** *
42991930 ATGTCATGTACGGTGGAGACACACGCCCGTGTCTTTGCCCGG
66 ATATCACACACGGTGGAGACACACGCCCGTGTCTCTGCCCGG
* * * * * *
42991972 GTGGAGCATATTGACCTGATCTCTAATTCAATACCAGGGGACACATGGCCGTGTAACCAAACCAT
1 GTGGAGCATACTGACCTGATCTCTAATTCAACACCAAGGGACACACGACCATGTAACCAAACCAT
* * * *
42992037 TTATCACACACGGCT-GAGACACATGCTCGTGTCTCTGCCCGT
66 ATATCACACACGG-TGGAGACACACGCCCGTGTCTCTGCCCGG
42992079 GTGGA
1 GTGGA
42992084 CAAAAATAGG
Statistics
Matches: 93, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
107 92 0.99
108 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (107 bp):
GTGGAGCATACTGACCTGATCTCTAATTCAACACCAAGGGACACACGACCATGTAACCAAACCAT
ATATCACACACGGTGGAGACACACGCCCGTGTCTCTGCCCGG
Found at i:42996127 original size:22 final size:22
Alignment explanation
Indices: 42996092--42996133 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
42996082 GTATGCGAAG
* *
42996092 TAAGGCATTCAACAAAAAAATA
1 TAAGGCAATAAACAAAAAAATA
*
42996114 TAAGGCAATAAACATAAAAA
1 TAAGGCAATAAACAAAAAAA
42996134 GGAAGAAACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.17
Consensus pattern (22 bp):
TAAGGCAATAAACAAAAAAATA
Found at i:43001116 original size:30 final size:29
Alignment explanation
Indices: 43001082--43001145 Score: 101
Period size: 30 Copynumber: 2.2 Consensus size: 29
43001072 ATGGATCGAA
43001082 AGCTTTGGCACTAAGTATACGATTTAAACT
1 AGCTTTGGCACTAAGTATACGATTT-AACT
* *
43001112 AGCTTTGGCACTAAGTGTGCGATTTAACT
1 AGCTTTGGCACTAAGTATACGATTTAACT
43001141 AGCTT
1 AGCTT
43001146 CGGCTACTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 9 0.28
30 23 0.72
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (29 bp):
AGCTTTGGCACTAAGTATACGATTTAACT
Found at i:43009179 original size:27 final size:27
Alignment explanation
Indices: 43009069--43009180 Score: 104
Period size: 27 Copynumber: 4.1 Consensus size: 27
43009059 AGCATGGCTG
* * *
43009069 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGATCAGATAATTGTGGCAGAGCCA
* * *
43009095 TCAGATACAGATAATCGTGGCAGAACCA
1 CCAGAT-CAGATAATTGTGGCAGAGCCA
43009123 CCAGAGT-AGAT-ATATGTGGCAGAGCCA
1 CCAGA-TCAGATAAT-TGTGGCAGAGCCA
* *
43009150 CCAGATCAGATAATTGTGGCATAGCTA
1 CCAGATCAGATAATTGTGGCAGAGCCA
43009177 CCAG
1 CCAG
43009181 GACACTTCCT
Statistics
Matches: 69, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
26 7 0.10
27 46 0.67
28 15 0.22
29 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.19
Consensus pattern (27 bp):
CCAGATCAGATAATTGTGGCAGAGCCA
Found at i:43010610 original size:23 final size:24
Alignment explanation
Indices: 43010567--43010636 Score: 115
Period size: 23 Copynumber: 3.0 Consensus size: 24
43010557 CTAGATTTCC
**
43010567 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
43010591 TCCCTTATCAAC-CCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
43010614 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
43010637 CTCCTGACAG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
23 23 0.53
24 20 0.47
ACGTcount: A:0.26, C:0.39, G:0.01, T:0.34
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:43017392 original size:27 final size:26
Alignment explanation
Indices: 43017357--43017468 Score: 116
Period size: 27 Copynumber: 4.2 Consensus size: 26
43017347 AGCATGGCTG
* *
43017357 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
* *
43017383 CCAGATACAGATAATCGTGGCAAAACCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
43017411 CCAGAATAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
43017438 CCAGATCAGATAATTGTGGCATAGCTA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
43017465 CCAG
1 CCAG
43017469 GACACTTCCT
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
26 6 0.08
27 50 0.70
28 15 0.21
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:43017468 original size:54 final size:54
Alignment explanation
Indices: 43017348--43017468 Score: 145
Period size: 54 Copynumber: 2.2 Consensus size: 54
43017338 GAATTATGCA
* * *
43017348 GCATGGCTGCCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTG
1 GCATAGCTACCAGAACAGATAATGTGACAGAGCCACCAGATACAGATAATCGTG
* * * * * *
43017402 GCAAAACCACCAGAATAGATATATGTGGCAGAGCCACCAGAT-CAGATAATTGTG
1 GCATAGCTACCAGAACAGATA-ATGTGACAGAGCCACCAGATACAGATAATCGTG
43017456 GCATAGCTACCAG
1 GCATAGCTACCAG
43017469 GACACTTCCT
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
54 36 0.67
55 18 0.33
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.18
Consensus pattern (54 bp):
GCATAGCTACCAGAACAGATAATGTGACAGAGCCACCAGATACAGATAATCGTG
Found at i:43018911 original size:24 final size:24
Alignment explanation
Indices: 43018884--43018954 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
43018874 CTAGATTTCC
**
43018884 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
43018908 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
43018932 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
43018955 CTCCTGACAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.25, C:0.38, G:0.01, T:0.35
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:43021003 original size:20 final size:20
Alignment explanation
Indices: 43020978--43021036 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
43020968 CACATACGTG
43020978 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
** **
43020998 CCCCTGGATGTACTTTTGTA
1 CCCCTGTTTGTACTTCGGTA
43021018 -CCCTGTTTAG-ACTTCGGTA
1 CCCCTGTTT-GTACTTCGGTA
43021037 ATTTTGAACT
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.14, C:0.27, G:0.20, T:0.39
Consensus pattern (20 bp):
CCCCTGTTTGTACTTCGGTA
Found at i:43024278 original size:40 final size:40
Alignment explanation
Indices: 43024223--43024447 Score: 294
Period size: 40 Copynumber: 5.6 Consensus size: 40
43024213 TATTCGAATG
43024223 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
* *
43024263 ATATCCGGGCGAAGTCCCGAAGGCATTTGTG-TGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGT-GAT--T
* *
43024306 ATATCCAGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
*
43024346 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
* * * *
43024386 ATATCCGGGCTAAGACCCGAAGGCGTTTGTGCGAGT-AGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGA-TT
*
43024426 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
43024448 TACTTGGGTT
Statistics
Matches: 163, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
39 16 0.10
40 110 0.67
41 2 0.01
42 1 0.01
43 33 0.20
44 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
Found at i:43024362 original size:83 final size:80
Alignment explanation
Indices: 43024223--43024447 Score: 303
Period size: 83 Copynumber: 2.8 Consensus size: 80
43024213 TATTCGAATG
* *
43024223 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTATATCCGGGCGAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCA
*
43024288 TTTGTGTGAGTAGTTG-CT
66 -TT-TGTG-CTA-TTGACT
*
43024306 ATATCCAGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCA
*
43024371 TTTGTGCTATTGATT
66 TTTGTGCTATTGACT
* * * *
43024386 ATATCCGGGCTAAGACCCGAAGGCGTTTGTGCGAGT-AGCTATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGA-CTATATCCGGGCTAAGTCCCGAAGG
43024448 TACTTGGGTT
Statistics
Matches: 130, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
79 19 0.15
80 43 0.33
81 4 0.03
82 2 0.02
83 62 0.48
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCA
TTTGTGCTATTGACT
Found at i:43032261 original size:79 final size:82
Alignment explanation
Indices: 43032146--43032330 Score: 247
Period size: 79 Copynumber: 2.3 Consensus size: 82
43032136 GCTACTCGTT
* * * *
43032146 CAAATGCCTTCGGGACATAGCTCGG-TTATAGTAACTCGCACAAATGCTTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
*
43032209 GGATTTAGTAACTT-GCA
65 GGATATAGTAACTTAGCA
**
43032226 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
*
43032289 GATATAGTCACTTAGCA
66 GATATAGTAACTTAGCA
43032306 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43032331 CATCATTCAA
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 3 0.03
79 57 0.61
80 33 0.35
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:43032330 original size:40 final size:40
Alignment explanation
Indices: 43032127--43032330 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
43032117 CGGAATTTAA
** *
43032127 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * * *
43032167 TCGGTTATAGTAACTCGCACAAATGCTTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
43032207 CCGGATTTAGTAACTTGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
43032246 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
43032286 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
43032326 CCGGA
1 CCGGA
43032331 CATCATTCAA
Statistics
Matches: 138, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 91 0.66
41 12 0.09
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:43033047 original size:2 final size:2
Alignment explanation
Indices: 43033040--43033075 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
43033030 CATCATGTGC
43033040 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
43033076 GCAAGAGCCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43040281 original size:25 final size:25
Alignment explanation
Indices: 43040237--43040284 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
43040227 CTATAATATG
* **
43040237 AAAATGACCATTTTGTCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
43040262 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
43040285 GTTTATACAT
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:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:43040387 original size:20 final size:20
Alignment explanation
Indices: 43040321--43040387 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
43040311 ATTTTGATAA
* *
43040321 ACATGGTATGTATGATACGC
1 ACATGATATGTATGATATGC
*
43040341 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
*
43040361 ACGTGATATGTATGATATGC
1 ACATGATATGTATGATATGC
43040381 ACATGAT
1 ACATGAT
43040388 GTGTTCATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:43040463 original size:24 final size:24
Alignment explanation
Indices: 43040436--43040518 Score: 148
Period size: 24 Copynumber: 3.5 Consensus size: 24
43040426 GGAGGAAGTG
*
43040436 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTACGCCCCAGTTAT
43040460 CAAAAGGGCTTACGCCCCAGTTAT
1 CAAAAGGGCTTACGCCCCAGTTAT
43040484 CAAAAGGGCTTACGCCCCAGTTAT
1 CAAAAGGGCTTACGCCCCAGTTAT
*
43040508 TAAAAGGGCTT
1 CAAAAGGGCTT
43040519 TGACCCAATT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (24 bp):
CAAAAGGGCTTACGCCCCAGTTAT
Found at i:43040552 original size:48 final size:48
Alignment explanation
Indices: 43040436--43040555 Score: 136
Period size: 48 Copynumber: 2.5 Consensus size: 48
43040426 GGAGGAAGTG
* * *
43040436 CAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTACGCCCCAGTTAT
1 CAAAAGGGCTTACGCCCCAGTTATCAAAAGGGCTTACGACCCAATTAT
* * *
43040484 CAAAAGGGCTTACGCCCCAGTTATTAAAAGGGCTT-TGACCCAATTGT
1 CAAAAGGGCTTACGCCCCAGTTATCAAAAGGGCTTACGACCCAATTAT
* *
43040531 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 CAAAAG-GGCTTACGCC-CCAGTTAT
43040556 ATGAAAAGCA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
47 18 0.29
48 44 0.71
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (48 bp):
CAAAAGGGCTTACGCCCCAGTTATCAAAAGGGCTTACGACCCAATTAT
Found at i:43040782 original size:31 final size:31
Alignment explanation
Indices: 43040744--43040807 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
43040734 CCGTTTACAT
43040744 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
43040775 AAAGGCTTCGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
43040806 AA
1 AA
43040808 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:43042046 original size:31 final size:31
Alignment explanation
Indices: 43042003--43042066 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
43041993 CCTTTTCATA
43042003 TTTCATAATTCATAACACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
* **
43042034 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
43042065 TT
1 TT
43042067 ATTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGGCCGAAGCCT
Found at i:43042323 original size:24 final size:24
Alignment explanation
Indices: 43042296--43042426 Score: 226
Period size: 24 Copynumber: 5.5 Consensus size: 24
43042286 AATTGGGTCA
* *
43042296 AAGCCCTTTTAATAACTGGGGCGT
1 AAGCCCTTTTGATAACTGGGGCAT
*
43042320 AAGCCCTTTTGATAACTGGGGCGT
1 AAGCCCTTTTGATAACTGGGGCAT
43042344 AAGCCCTTTTGATAACTGGGGCAT
1 AAGCCCTTTTGATAACTGGGGCAT
43042368 AAGCCCTTTTGATAACTGGGGCAT
1 AAGCCCTTTTGATAACTGGGGCAT
*
43042392 AAGCCCTTTTGATAATTGGGGCAT
1 AAGCCCTTTTGATAACTGGGGCAT
43042416 AAGCCCTTTTG
1 AAGCCCTTTTG
43042427 CACTTCCTCC
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 104 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (24 bp):
AAGCCCTTTTGATAACTGGGGCAT
Found at i:43042496 original size:20 final size:20
Alignment explanation
Indices: 43042475--43042539 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
43042465 CATAATACAT
* *
43042475 CATGTGCATGTCATACATAT
1 CATGTGCATATCATACATAC
*
43042495 CATGTGCATATCATACATGC
1 CATGTGCATATCATACATAC
43042515 CATGTGCATATCATACATAC
1 CATGTGCATATCATACATAC
43042535 CATGT
1 CATGT
43042540 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (20 bp):
CATGTGCATATCATACATAC
Found at i:43050146 original size:31 final size:31
Alignment explanation
Indices: 43050103--43050165 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
43050093 CCTTTTCATA
43050103 TTTCATAATTCATAATACTGGGCCGAAGCCT
1 TTTCATAATTCATAATACTGGGCCGAAGCCT
* * *
43050134 TTTCATATTTCATATTACTGGGTCGAAGCCT
1 TTTCATAATTCATAATACTGGGCCGAAGCCT
43050165 T
1 T
43050166 CATTGTAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATAATTCATAATACTGGGCCGAAGCCT
Found at i:43050450 original size:24 final size:24
Alignment explanation
Indices: 43050358--43050547 Score: 271
Period size: 24 Copynumber: 8.0 Consensus size: 24
43050348 TGCTTTTCAT
* *
43050358 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTG
* *
43050383 ACAACTGGGGCA-AAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTG
*
43050406 ATAACTGGGGCA-AAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTG
*
43050429 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
43050453 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
43050477 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
43050501 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
43050525 ATAA-TTGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
43050548 CACTTCCTCC
Statistics
Matches: 156, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
23 57 0.37
24 92 0.59
25 7 0.04
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:43050621 original size:20 final size:20
Alignment explanation
Indices: 43050598--43050662 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
43050588 ATAAATACAT
* *
43050598 CATGTGCATGTCATACATAT
1 CATGTGCATATCATACATAC
*
43050618 CATGTGCATATCATACATGC
1 CATGTGCATATCATACATAC
43050638 CATGTGCATATCATACATAC
1 CATGTGCATATCATACATAC
43050658 CATGT
1 CATGT
43050663 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (20 bp):
CATGTGCATATCATACATAC
Found at i:43050727 original size:25 final size:25
Alignment explanation
Indices: 43050699--43050746 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
43050689 ATGTATAAAC
* *
43050699 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATGGTCATTTTTA
43050724 CCTAGGGGCAAAATGGTCATTTT
1 CCTAGGGGCAAAATGGTCATTTT
43050747 CATATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATGGTCATTTTTA
Found at i:43055006 original size:31 final size:31
Alignment explanation
Indices: 43054963--43055026 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
43054953 CCTTTTCATA
43054963 TTTCATAATTCATAACACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
* ** *
43054994 TTTCATATTTCATATTACTGGGTCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
43055025 TT
1 TT
43055027 ATTGTAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGGCCGAAGCCT
Found at i:43055385 original size:24 final size:24
Alignment explanation
Indices: 43055219--43055385 Score: 232
Period size: 24 Copynumber: 7.0 Consensus size: 24
43055209 GCTTTTTCAT
* *
43055219 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTG
* *
43055244 ACAACTGGGGCA-AAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTG
*
43055267 ATAACTGGGGCA-AAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTG
*
43055290 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
43055314 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
43055338 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
43055362 ATAATTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
43055386 CACTTCCTCC
Statistics
Matches: 133, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
23 39 0.29
24 87 0.65
25 7 0.05
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:43055459 original size:20 final size:20
Alignment explanation
Indices: 43055436--43055500 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
43055426 ATAAATACAT
* *
43055436 CATGTGCATGTCATACATAT
1 CATGTGCATATCATACATAC
*
43055456 CATGTGCATATCATACATGC
1 CATGTGCATATCATACATAC
43055476 CATGTGCATATCATACATAC
1 CATGTGCATATCATACATAC
43055496 CATGT
1 CATGT
43055501 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (20 bp):
CATGTGCATATCATACATAC
Found at i:43059814 original size:31 final size:30
Alignment explanation
Indices: 43059779--43059837 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
43059769 CACCATTAAA
*
43059779 ATATTTGCACTATT-AGCCCTTCAAATTTTTC
1 ATATTTACACT-TTAAGCCCTT-AAATTTTTC
*
43059810 ATATTTACACTTTAATCCCTTAAATTTT
1 ATATTTACACTTTAAGCCCTTAAATTTT
43059838 GAGTATTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.29, C:0.20, G:0.03, T:0.47
Consensus pattern (30 bp):
ATATTTACACTTTAAGCCCTTAAATTTTTC
Found at i:43060534 original size:12 final size:13
Alignment explanation
Indices: 43060500--43060539 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
43060490 AATTTTTAAG
43060500 TAGTTTATTGATA
1 TAGTTTATTGATA
43060513 TAGTCATTATT-ATA
1 TAGT--TTATTGATA
43060527 TAGTTTATTGATA
1 TAGTTTATTGATA
43060540 AAAATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 5 0.21
13 7 0.29
14 7 0.29
15 5 0.21
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.53
Consensus pattern (13 bp):
TAGTTTATTGATA
Found at i:43063103 original size:14 final size:14
Alignment explanation
Indices: 43063081--43063111 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
43063071 TACAAGATAG
43063081 TTTTCGATATGCCA
1 TTTTCGATATGCCA
*
43063095 TTTTTGATATGCCA
1 TTTTCGATATGCCA
43063109 TTT
1 TTT
43063112 AACTATGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.16, G:0.13, T:0.52
Consensus pattern (14 bp):
TTTTCGATATGCCA
Found at i:43068213 original size:31 final size:30
Alignment explanation
Indices: 43068178--43068236 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
43068168 CACCATTAAA
*
43068178 ATATTTGCACTATT-AGCCCTTCAAATTTTTC
1 ATATTTACACT-TTAAGCCCTT-AAATTTTTC
*
43068209 ATATTTACACTTTAATCCCTTAAATTTT
1 ATATTTACACTTTAAGCCCTTAAATTTT
43068237 GAGTATTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.29, C:0.20, G:0.03, T:0.47
Consensus pattern (30 bp):
ATATTTACACTTTAAGCCCTTAAATTTTTC
Found at i:43071501 original size:14 final size:14
Alignment explanation
Indices: 43071479--43071509 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
43071469 TACAAGATAG
43071479 TTTTCGATATGCCA
1 TTTTCGATATGCCA
*
43071493 TTTTTGATATGCCA
1 TTTTCGATATGCCA
43071507 TTT
1 TTT
43071510 AACTATGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.16, G:0.13, T:0.52
Consensus pattern (14 bp):
TTTTCGATATGCCA
Found at i:43076621 original size:31 final size:30
Alignment explanation
Indices: 43076586--43076644 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
43076576 CACCATTAAA
*
43076586 ATATTTGCACTATT-AGCCCTTCAAATTTTTC
1 ATATTTACACT-TTAAGCCCTT-AAATTTTTC
*
43076617 ATATTTACACTTTAATCCCTTAAATTTT
1 ATATTTACACTTTAAGCCCTTAAATTTT
43076645 GAGTATTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.29, C:0.20, G:0.03, T:0.47
Consensus pattern (30 bp):
ATATTTACACTTTAAGCCCTTAAATTTTTC
Found at i:43079919 original size:14 final size:14
Alignment explanation
Indices: 43079897--43079927 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
43079887 TACAAGATAG
43079897 TTTTCGATATGCCA
1 TTTTCGATATGCCA
*
43079911 TTTTTGATATGCCA
1 TTTTCGATATGCCA
43079925 TTT
1 TTT
43079928 AACTATGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.16, G:0.13, T:0.52
Consensus pattern (14 bp):
TTTTCGATATGCCA
Found at i:43084324 original size:20 final size:20
Alignment explanation
Indices: 43084301--43084411 Score: 71
Period size: 20 Copynumber: 5.5 Consensus size: 20
43084291 AGGAGAACTG
*
43084301 AAGTACAAACAGGGGCACGT
1 AAGTACAAACAAGGGCACGT
* * *
43084321 AAGTGCAAATAAGGGTACCG-
1 AAGTACAAACAAGGGCA-CGT
* * *
43084341 ATGTACAACCAGGGGCACGT
1 AAGTACAAACAAGGGCACGT
* * * *
43084361 ATGTGCAAATAAGGGCACAT
1 AAGTACAAACAAGGGCACGT
* *
43084381 CAGTAGAAACAAGGGCACGT
1 AAGTACAAACAAGGGCACGT
* *
43084401 ATGTGCAAACA
1 AAGTACAAACA
43084412 TTCAATAATT
Statistics
Matches: 64, Mismatches: 25, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
19 2 0.03
20 60 0.94
21 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.14
Consensus pattern (20 bp):
AAGTACAAACAAGGGCACGT
Found at i:43084397 original size:40 final size:39
Alignment explanation
Indices: 43084302--43084409 Score: 137
Period size: 40 Copynumber: 2.7 Consensus size: 39
43084292 GGAGAACTGA
* *
43084302 AGTACAAACAGGGGCACGTAAGTGCAAATAAGGGTACCG
1 AGTACAAACAGGGGCACGTATGTGCAAATAAGGGCACCG
*
43084341 ATGTACAACCAGGGGCACGTATGTGCAAATAAGGGCACATC-
1 A-GTACAAACAGGGGCACGTATGTGCAAATAAGGGCAC--CG
* *
43084382 AGTAGAAACAAGGGCACGTATGTGCAAA
1 AGTACAAACAGGGGCACGTATGTGCAAA
43084410 CATTCAATAA
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
39 1 0.02
40 57 0.95
41 1 0.02
42 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.29, T:0.15
Consensus pattern (39 bp):
AGTACAAACAGGGGCACGTATGTGCAAATAAGGGCACCG
Found at i:43087272 original size:25 final size:25
Alignment explanation
Indices: 43087241--43087289 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
43087231 GTAGGATAAT
43087241 TTATTTTGTGCGACTTTAACTGTAA
1 TTATTTTGTGCGACTTTAACTGTAA
43087266 TTATTTTGTGCGACTTTAACTGTA
1 TTATTTTGTGCGACTTTAACTGTA
43087290 GAGAAACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.49
Consensus pattern (25 bp):
TTATTTTGTGCGACTTTAACTGTAA
Found at i:43092560 original size:36 final size:36
Alignment explanation
Indices: 43092513--43092581 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
43092503 TTGGGATGAT
43092513 TTAGAATGTATCATCCATCAAAATAAGATGTGGTAC
1 TTAGAATGTATCATCCATCAAAATAAGATGTGGTAC
* * *
43092549 TTAGAATGTATCATCCATTAGAATAAGTTGTGG
1 TTAGAATGTATCATCCATCAAAATAAGATGTGG
43092582 CCTTGGTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (36 bp):
TTAGAATGTATCATCCATCAAAATAAGATGTGGTAC
Found at i:43099473 original size:31 final size:33
Alignment explanation
Indices: 43099409--43099475 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
43099399 CACTATCGAT
* *
43099409 GCCACACGGCCTAGGCTATTTCGGGCCATGTAG
1 GCCACACGGCCTAGGCTATCTCAGGCCATGTAG
43099442 GCCACACAGG-CTAGGCTATCT-AGG-CATGTAG
1 GCCACAC-GGCCTAGGCTATCTCAGGCCATGTAG
43099473 GCC
1 GCC
43099476 TAAAATTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 10 0.32
32 2 0.06
33 17 0.55
34 2 0.06
ACGTcount: A:0.21, C:0.30, G:0.30, T:0.19
Consensus pattern (33 bp):
GCCACACGGCCTAGGCTATCTCAGGCCATGTAG
Found at i:43103223 original size:2 final size:2
Alignment explanation
Indices: 43103216--43103258 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
43103206 AGTTCACTTT
43103216 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43103258 T
1 T
43103259 GCTAATATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43106250 original size:2 final size:2
Alignment explanation
Indices: 43106243--43106275 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
43106233 AGACATTCGA
43106243 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43106276 GTTAAATTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43106946 original size:39 final size:39
Alignment explanation
Indices: 43106888--43107140 Score: 373
Period size: 39 Copynumber: 6.5 Consensus size: 39
43106878 ATGATATTTT
*
43106888 GAAATATATCAGGACTTAAGGTCCGCAGGCTATATGCTG
1 GAAATATATCCGGACTTAAGGTCCGCAGGCTATATGCTG
*
43106927 GAATTATATCCGGACTTAAGGTCCGCAGGCTATATGCTG
1 GAAATATATCCGGACTTAAGGTCCGCAGGCTATATGCTG
* *
43106966 GAATTATATCCGGACTTAAGGTCCGCAAGCTATATGCTG
1 GAAATATATCCGGACTTAAGGTCCGCAGGCTATATGCTG
43107005 GAAATATATCCGGACTTAAGGTCCGCAGGCTATATGCTG
1 GAAATATATCCGGACTTAAGGTCCGCAGGCTATATGCTG
43107044 GAAATATATCCGG-CTTAAGGTCCGCAGGCTATATGCTG
1 GAAATATATCCGGACTTAAGGTCCGCAGGCTATATGCTG
* * * * * **
43107082 GAATTATAATCCAGACTTAAGGTTCACAGGTTACGTGCTG
1 GAAATAT-ATCCGGACTTAAGGTCCGCAGGCTATATGCTG
* *
43107122 GAAATATATTCGGGCTTAA
1 GAAATATATCCGGACTTAA
43107141 AGTTCCGAAG
Statistics
Matches: 196, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
38 31 0.16
39 139 0.71
40 26 0.13
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.28
Consensus pattern (39 bp):
GAAATATATCCGGACTTAAGGTCCGCAGGCTATATGCTG
Found at i:43114741 original size:39 final size:39
Alignment explanation
Indices: 43114698--43114949 Score: 359
Period size: 39 Copynumber: 6.5 Consensus size: 39
43114688 GCATGATATT
*
43114698 TGGAAATATATCCGGACTTAAGGTCCGCATGCTATATGC
1 TGGAAATATATCCGGACTTAAGGTCCGCAGGCTATATGC
*
43114737 TGGAATTATAT-CGGACTTAAGGTCCGCAGGCTATATGC
1 TGGAAATATATCCGGACTTAAGGTCCGCAGGCTATATGC
* *
43114775 TGGAATTATATCCGGACTTAAGGTCCGTAGGCTATATGC
1 TGGAAATATATCCGGACTTAAGGTCCGCAGGCTATATGC
*
43114814 TGGAAATATATCTGGACTTAAGGTCCGCAGGCTATATGC
1 TGGAAATATATCCGGACTTAAGGTCCGCAGGCTATATGC
43114853 TGGAAATATATCC-GACTTAAGGTCCGCAGGCTATATGC
1 TGGAAATATATCCGGACTTAAGGTCCGCAGGCTATATGC
* * * * **
43114891 TGGAATTATAATCC-GACTTAAGGTTCACAGGTTACGTG-
1 TGGAAATAT-ATCCGGACTTAAGGTCCGCAGGCTATATGC
*
43114929 TGGAAATATATCCGGGCTTAA
1 TGGAAATATATCCGGACTTAA
43114950 AGTTCCGAAG
Statistics
Matches: 195, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
37 4 0.02
38 84 0.43
39 107 0.55
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (39 bp):
TGGAAATATATCCGGACTTAAGGTCCGCAGGCTATATGC
Found at i:43114825 original size:77 final size:77
Alignment explanation
Indices: 43114698--43114949 Score: 373
Period size: 77 Copynumber: 3.3 Consensus size: 77
43114688 GCATGATATT
*
43114698 TGGAAATATATCCGGACTTAAGGTCCGCATGCTATATGCTGGAATTATATCGGACTTAAGGTCCG
1 TGGAAATATATCCGGACTTAAGGTCCGCAGGCTATATGCTGGAATTATATCGGACTTAAGGTCCG
43114763 CAGGCTATATGC
66 CAGGCTATATGC
* * *
43114775 TGGAATTATATCCGGACTTAAGGTCCGTAGGCTATATGCTGGAAATATATCTGGACTTAAGGTCC
1 TGGAAATATATCCGGACTTAAGGTCCGCAGGCTATATGCTGGAATTATATC-GGACTTAAGGTCC
43114840 GCAGGCTATATGC
65 GCAGGCTATATGC
* *
43114853 TGGAAATATATCC-GACTTAAGGTCCGCAGGCTATATGCTGGAATTATAATCCGACTTAAGGTTC
1 TGGAAATATATCCGGACTTAAGGTCCGCAGGCTATATGCTGGAATTAT-ATCGGACTTAAGGTCC
* * **
43114917 ACAGGTTACGTG-
65 GCAGGCTATATGC
*
43114929 TGGAAATATATCCGGGCTTAA
1 TGGAAATATATCCGGACTTAA
43114950 AGTTCCGAAG
Statistics
Matches: 158, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
76 13 0.08
77 104 0.66
78 41 0.26
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (77 bp):
TGGAAATATATCCGGACTTAAGGTCCGCAGGCTATATGCTGGAATTATATCGGACTTAAGGTCCG
CAGGCTATATGC
Found at i:43114962 original size:116 final size:116
Alignment explanation
Indices: 43114698--43114949 Score: 382
Period size: 116 Copynumber: 2.2 Consensus size: 116
43114688 GCATGATATT
* * *
43114698 TGGAAATATATCCGGACTTAAGGTCCGCATGCTATATGCTGGAATTATATCGGACTTAAGGTCCG
1 TGGAAATATATCCGGACTTAAGGTCCGCAGGCTATATGCTGGAAATATATCCGACTTAAGGTCCG
** *
43114763 CAGGCTATATGCTGGAATTATATCCGGACTTAAGGTCCGTAGGCTATATGC
66 CAGGCTATATGCTGGAATTATATCCGGACTTAAGGTCCACAGGCTACATGC
*
43114814 TGGAAATATATCTGGACTTAAGGTCCGCAGGCTATATGCTGGAAATATATCCGACTTAAGGTCCG
1 TGGAAATATATCCGGACTTAAGGTCCGCAGGCTATATGCTGGAAATATATCCGACTTAAGGTCCG
* * *
43114879 CAGGCTATATGCTGGAATTATAATCC-GACTTAAGGTTCACAGGTTACGTG-
66 CAGGCTATATGCTGGAATTAT-ATCCGGACTTAAGGTCCACAGGCTACATGC
*
43114929 TGGAAATATATCCGGGCTTAA
1 TGGAAATATATCCGGACTTAA
43114950 AGTTCCGAAG
Statistics
Matches: 123, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
115 19 0.15
116 100 0.81
117 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (116 bp):
TGGAAATATATCCGGACTTAAGGTCCGCAGGCTATATGCTGGAAATATATCCGACTTAAGGTCCG
CAGGCTATATGCTGGAATTATATCCGGACTTAAGGTCCACAGGCTACATGC
Found at i:43122172 original size:68 final size:64
Alignment explanation
Indices: 43122055--43122307 Score: 235
Period size: 68 Copynumber: 3.9 Consensus size: 64
43122045 ATACAGATGG
** * * *
43122055 TATGTAGCTAGGTCACATGTATGGTGCTAAGTGCACATCATGTGTACAAGAGAGCTACGAGACAT
1 TATGTAGCTAGGTCACATGGGTGGTACTAAGTGTACACCATGTGTACAAGAGAGCTACGAG--A-
43122120 TA
63 TA
* * *
43122122 TGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGCTAC-AGGA
1 T-ATGTAGCTAGGTCACATGGGTGGTACTAAGTGTACACCATGT-GTACAAGAGAGCTACGA-GA
43122185 TA
63 TA
* * * * * *
43122187 TATGTAGCTAGGTCGCATGCGTGGTTCGAGGTGAAGGACACCATGTAG-ACAAGAGAGCTACGAG
1 TATGTAGCTAGGTCACATGGGTGGTACTAAGT---GTACACCATGT-GTACAAGAGAGCTACGAG
43122251 ATA
62 ATA
** *
43122254 -AACTAGCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGTGTACAAGAGAGC
1 TATGTAGCTAGGTCACATGGGTGGTACTAAGTGTACACCATGTGTACAAGAGAGC
43122308 CGAACTATAT
Statistics
Matches: 155, Mismatches: 23, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
62 1 0.01
63 19 0.12
64 26 0.17
65 3 0.02
66 25 0.16
67 31 0.20
68 49 0.32
69 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (64 bp):
TATGTAGCTAGGTCACATGGGTGGTACTAAGTGTACACCATGTGTACAAGAGAGCTACGAGATA
Found at i:43126063 original size:24 final size:26
Alignment explanation
Indices: 43126036--43126084 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
43126026 AGTTCATGCA
*
43126036 ATATTAAAGC-ATTTAA-ATACAATT
1 ATATGAAAGCTATTTAACATACAATT
43126060 ATATGAAAGCTTATTTAACATACAA
1 ATATGAAAGC-TATTTAACATACAA
43126085 ACTTACCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
26 6 0.29
27 6 0.29
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (26 bp):
ATATGAAAGCTATTTAACATACAATT
Found at i:43127719 original size:26 final size:26
Alignment explanation
Indices: 43127683--43127733 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
43127673 CAAGACTTGG
43127683 GCATTCTGTTAAATTCACATGGCCAT
1 GCATTCTGTTAAATTCACATGGCCAT
*
43127709 GCATTTTGTTAAATTCACATGGCCA
1 GCATTCTGTTAAATTCACATGGCCA
43127734 ACACACACGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (26 bp):
GCATTCTGTTAAATTCACATGGCCAT
Found at i:43130727 original size:28 final size:28
Alignment explanation
Indices: 43130658--43130758 Score: 105
Period size: 28 Copynumber: 3.5 Consensus size: 28
43130648 GACAAGATTG
* * * *
43130658 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
43130688 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
43130716 GCACTAAGTGTGCGAG-CTGAATGTATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
*
43130745 GCACTAAGTATGCG
1 GCACTAAGTGTGCG
43130759 GATTCACTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
27 2 0.03
28 24 0.38
29 19 0.30
30 18 0.29
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:43135738 original size:59 final size:58
Alignment explanation
Indices: 43135665--43135796 Score: 158
Period size: 59 Copynumber: 2.3 Consensus size: 58
43135655 ATTTAAGCCC
* * * * *
43135665 GCACACATAGTGCCATACCCTTCGAGC-TCGCACACCCAGTGCCGTATTTTTTCCAGCAT
1 GCACACTTAGTGCCATACACTTCCAGCAT-GCACACCCAGTGCCATA-TATTTCCAGCAT
* * **
43135724 GCACACTTAGTGCCATATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCAT
43135782 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
43135797 ATCTCGTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
58 26 0.41
59 36 0.57
60 1 0.02
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (58 bp):
GCACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCAT
Found at i:43135754 original size:29 final size:29
Alignment explanation
Indices: 43135714--43135796 Score: 166
Period size: 29 Copynumber: 2.9 Consensus size: 29
43135704 TGCCGTATTT
43135714 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
43135743 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
43135772 TTTCCAGCATGCACACTTAGTGCCA
1 TTTCCAGCATGCACACTTAGTGCCA
43135797 ATCTCGTCAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.30
Consensus pattern (29 bp):
TTTCCAGCATGCACACTTAGTGCCATATA
Found at i:43136997 original size:21 final size:20
Alignment explanation
Indices: 43136955--43137008 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 20
43136945 AATGAACACT
*
43136955 TTTTTTTTC-TTT-TCTTTG
1 TTTTTCTTCATTTCTCTTTG
*
43136973 TTTTTCTTCATATTCTCTTTT
1 TTTTTCTTCAT-TTCTCTTTG
*
43136994 TTTTTTTTCATTTCT
1 TTTTTCTTCATTTCT
43137009 TTATTCTTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 8 0.27
19 1 0.03
20 6 0.20
21 15 0.50
ACGTcount: A:0.06, C:0.15, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTTCTTCATTTCTCTTTG
Found at i:43143647 original size:59 final size:58
Alignment explanation
Indices: 43143574--43143705 Score: 158
Period size: 59 Copynumber: 2.3 Consensus size: 58
43143564 ATTTAAGCCC
* * * * *
43143574 GCACACATAGTGCCATACCCTTCGAGC-TCGCACACCCAGTGCCGTATTTTTTCCAGCAT
1 GCACACTTAGTGCCATACACTTCCAGCAT-GCACACCCAGTGCCATA-TATTTCCAGCAT
* * **
43143633 GCACACTTAGTGCCATATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCAT
43143691 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
43143706 ATCTCGTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
58 26 0.41
59 36 0.57
60 1 0.02
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (58 bp):
GCACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCAT
Found at i:43143663 original size:29 final size:29
Alignment explanation
Indices: 43143623--43143705 Score: 166
Period size: 29 Copynumber: 2.9 Consensus size: 29
43143613 TGCCGTATTT
43143623 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
43143652 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
43143681 TTTCCAGCATGCACACTTAGTGCCA
1 TTTCCAGCATGCACACTTAGTGCCA
43143706 ATCTCGTCAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.30
Consensus pattern (29 bp):
TTTCCAGCATGCACACTTAGTGCCATATA
Found at i:43149579 original size:28 final size:29
Alignment explanation
Indices: 43149537--43149608 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
43149527 AAAATTGTAC
*
43149537 AGCACTAAGTGTGCGAGTTTG-AT-TATAT
1 AGCACTAAGTGTGCGAG-CTGAATGTATAT
*
43149565 AGCACTAAGTCTGCGAGCTGAATGTATAT
1 AGCACTAAGTGTGCGAGCTGAATGTATAT
43149594 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
43149609 GATTCACTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 2 0.05
28 18 0.46
29 19 0.49
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (29 bp):
AGCACTAAGTGTGCGAGCTGAATGTATAT
Found at i:43163806 original size:15 final size:15
Alignment explanation
Indices: 43163782--43163817 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
43163772 GAAGACTTTT
*
43163782 AGCTTTGTCGTTTAG
1 AGCTTCGTCGTTTAG
43163797 AGCTTCGTCGTTTAG
1 AGCTTCGTCGTTTAG
43163812 AGCTTC
1 AGCTTC
43163818 TTGCTCTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.25, T:0.42
Consensus pattern (15 bp):
AGCTTCGTCGTTTAG
Found at i:43173027 original size:15 final size:17
Alignment explanation
Indices: 43173009--43173040 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
43172999 TAGCATAATT
43173009 TACCAAA-TCA-ATTCA
1 TACCAAACTCACATTCA
43173024 TACCAAACTCACATTCA
1 TACCAAACTCACATTCA
43173041 CAAGTATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (17 bp):
TACCAAACTCACATTCA
Found at i:43191531 original size:22 final size:23
Alignment explanation
Indices: 43191478--43191531 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
43191468 GCTGATGAAC
*
43191478 AGTAAGCTCTATTGAACTGAAAT
1 AGTAAGCTCTATCGAACTGAAAT
* *
43191501 GGTATGCTCTATCGAGA-T-AAAT
1 AGTAAGCTCTATCGA-ACTGAAAT
43191523 AGTAAGCTC
1 AGTAAGCTC
43191532 ATACAAGCTG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 11 0.44
23 13 0.52
24 1 0.04
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (23 bp):
AGTAAGCTCTATCGAACTGAAAT
Found at i:43196940 original size:28 final size:27
Alignment explanation
Indices: 43196877--43196946 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
43196867 ATAGTGAGTC
43196877 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
43196904 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
43196932 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43196947 GTACAAATTT
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:43204731 original size:28 final size:27
Alignment explanation
Indices: 43204668--43204737 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
43204658 ATAGTGAGTC
43204668 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
43204695 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
43204723 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43204738 GTACAAATTT
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:43208572 original size:28 final size:29
Alignment explanation
Indices: 43208509--43208609 Score: 125
Period size: 28 Copynumber: 3.6 Consensus size: 29
43208499 TGAATTTGAC
*
43208509 TGGGCCTAATGGGCCATATAAATGTGATT
1 TGGGCCTAATGGGCCATATAAAGGTGATT
**
43208538 TGGGCCTAATGGGCCAT-TTTAGGTGATT
1 TGGGCCTAATGGGCCATATAAAGGTGATT
* **
43208566 TGGGCCTAATGGGCCATATGAATATGA-T
1 TGGGCCTAATGGGCCATATAAAGGTGATT
*
43208594 TGGGCTTAATGGGCCA
1 TGGGCCTAATGGGCCA
43208610 GATACATGTA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
28 41 0.65
29 22 0.35
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.31
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAAGGTGATT
Found at i:43209518 original size:18 final size:18
Alignment explanation
Indices: 43209483--43209524 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
43209473 GGCTTCTTTC
*
43209483 TTATTATTATTTGGATTA
1 TTATTATTATTTGCATTA
*
43209501 TTATTATTATTTTCATTA
1 TTATTATTATTTGCATTA
*
43209519 TAATTA
1 TTATTA
43209525 CGAGAAGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (18 bp):
TTATTATTATTTGCATTA
Found at i:43210973 original size:43 final size:43
Alignment explanation
Indices: 43210876--43210982 Score: 117
Period size: 43 Copynumber: 2.5 Consensus size: 43
43210866 ACATATCGAT
* * * *
43210876 GCCACTGTCCCAGACAGGGTCTTATACGAAATTAATTAACGAG
1 GCCAATGTCCCAGACATGGTCTTATACGAAATTAAATAACAAG
* * * *
43210919 GCCAATATCCCAAACATGGTCTTATACGTAATCTAAAT-ACAAT
1 GCCAATGTCCCAGACATGGTCTTATACGAAAT-TAAATAACAAG
*
43210962 GTCAATGTCCCAGACATGGTC
1 GCCAATGTCCCAGACATGGTC
43210983 ATACTTATAA
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
43 48 0.92
44 4 0.08
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (43 bp):
GCCAATGTCCCAGACATGGTCTTATACGAAATTAAATAACAAG
Found at i:43214099 original size:51 final size:51
Alignment explanation
Indices: 43214015--43214162 Score: 226
Period size: 51 Copynumber: 2.9 Consensus size: 51
43214005 TGGATACACG
* *
43214015 GTGGTCTTCACATAGTACCATC-CTTGTAACCAAAGCTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCA-CACTTGTATCCAAAGCTATTTTATTCACAAA
* *
43214066 GTGGCCTTCACATAGTACCACACTTGTATCCAAAGCTATTATATTCATAAA
1 GTGGCCTTCACATAGTACCACACTTGTATCCAAAGCTATTTTATTCACAAA
* *
43214117 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGTTATTTTATTC
1 GTGGCCTTCACATAGTACCACACTTGTATCCAAAGCTATTTTATTC
43214163 CTAAGGTTCA
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
50 1 0.01
51 88 0.99
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.34
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTATCCAAAGCTATTTTATTCACAAA
Found at i:43225123 original size:15 final size:15
Alignment explanation
Indices: 43225105--43225151 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
43225095 GAAATCTTTG
*
43225105 TTTAGGGTTTTGGGT
1 TTTAGGGTTTAGGGT
*
43225120 TTTAGGGTTTAAGGT
1 TTTAGGGTTTAGGGT
*
43225135 TTTAAGGTTTAGGGT
1 TTTAGGGTTTAGGGT
43225150 TT
1 TT
43225152 AGGATTTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.15, C:0.00, G:0.34, T:0.51
Consensus pattern (15 bp):
TTTAGGGTTTAGGGT
Found at i:43225130 original size:7 final size:7
Alignment explanation
Indices: 43225104--43225154 Score: 57
Period size: 7 Copynumber: 7.0 Consensus size: 7
43225094 GGAAATCTTT
43225104 GTTTAGG
1 GTTTAGG
*
43225111 GTTTTGG
1 GTTTAGG
43225118 GTTTTAGG
1 G-TTTAGG
43225126 GTTTAAGG
1 GTTT-AGG
* *
43225134 TTTTAAG
1 GTTTAGG
43225141 GTTTAGG
1 GTTTAGG
43225148 GTTTAGG
1 GTTTAGG
43225155 ATTTGTGTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 24 0.67
8 12 0.33
ACGTcount: A:0.16, C:0.00, G:0.37, T:0.47
Consensus pattern (7 bp):
GTTTAGG
Found at i:43227961 original size:40 final size:40
Alignment explanation
Indices: 43227906--43228113 Score: 321
Period size: 40 Copynumber: 5.2 Consensus size: 40
43227896 CGGATGATAA
43227906 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
43227946 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
* *
43227986 CCAGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
* **
43228026 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
* * *
43228066 CCGGGCTAAATCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATTT
43228106 CC-GGCTAA
1 CCGGGCTAA
43228114 ACCCTGAAGG
Statistics
Matches: 156, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 8 0.05
40 148 0.95
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
Found at i:43229698 original size:17 final size:18
Alignment explanation
Indices: 43229656--43229704 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
43229646 AGTTGAAAAG
43229656 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
43229675 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
43229692 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
43229705 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:43230593 original size:40 final size:40
Alignment explanation
Indices: 43230527--43230693 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
43230517 AAATTGAATG
* * *
43230527 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
43230566 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
43230606 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
43230646 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
43230686 ATATCCGG
1 ATATCCGG
43230694 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:43235160 original size:60 final size:60
Alignment explanation
Indices: 43235067--43235185 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 60
43235057 TGCCTTTGTT
* * *
43235067 TATGTGTTTTGTAATGGGTTGCTATATGTTTATTATGGTTTAATGCTTTGTTGTGGAATA
1 TATGTGTTTTGTAATAGGTTGCTATATGTTTATTAGGGTTCAATGCTTTGTTGTGGAATA
43235127 TATGTGTTTTGTAATAGGTTGCTATATGTTTATTAGGGTTCAATGCTTTGTTGTGGAAT
1 TATGTGTTTTGTAATAGGTTGCTATATGTTTATTAGGGTTCAATGCTTTGTTGTGGAAT
43235186 GGATAAATTG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.20, C:0.04, G:0.25, T:0.50
Consensus pattern (60 bp):
TATGTGTTTTGTAATAGGTTGCTATATGTTTATTAGGGTTCAATGCTTTGTTGTGGAATA
Found at i:43238746 original size:40 final size:40
Alignment explanation
Indices: 43238642--43238861 Score: 338
Period size: 40 Copynumber: 5.5 Consensus size: 40
43238632 CATTTGAATG
*
43238642 ATATCCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
43238682 ATATCCGGG-TAAGACCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
43238721 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
*
43238761 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
* * * * * *
43238801 ATGTCCGGGTTAAGACCCGAAGGCAATTGGGCGTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
43238841 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGA-CCCGAAG
43238862 AAACTTGGGT
Statistics
Matches: 167, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
38 1 0.01
39 50 0.30
40 116 0.69
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
Found at i:43246751 original size:39 final size:40
Alignment explanation
Indices: 43246692--43246825 Score: 220
Period size: 39 Copynumber: 3.4 Consensus size: 40
43246682 CATTTGAATG
*
43246692 ATATCCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
*
43246732 ATAACCGGG-TAAGACCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
43246771 ATATCC-GGCTAAGA-CCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
*
43246809 ATATCTGGGCTAAGACC
1 ATATCCGGGCTAAGACC
43246826 TGTTATATCC
Statistics
Matches: 87, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
38 31 0.36
39 47 0.54
40 9 0.10
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
Found at i:43246831 original size:21 final size:21
Alignment explanation
Indices: 43246805--43246846 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
43246795 TTGTGCGAGT
*
43246805 TGTTATATCTGGGCTAAGACC
1 TGTTATATCCGGGCTAAGACC
43246826 TGTTATATCCGGGCTAAGACC
1 TGTTATATCCGGGCTAAGACC
43246847 CGAAGGCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (21 bp):
TGTTATATCCGGGCTAAGACC
Found at i:43246860 original size:61 final size:59
Alignment explanation
Indices: 43246767--43246886 Score: 186
Period size: 61 Copynumber: 2.0 Consensus size: 59
43246757 TTGTGCGAGT
* *
43246767 TGTTATATCCGGCTAAGACCGAAGGCATTTGTGCGAGTTGTTATATCTGGGCTAAGACC
1 TGTTATATCCGGCTAAGACCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGACC
* *
43246826 TGTTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATGTCCGGGTTAAGACC
1 TGTTATATCC-GGCTAAGA-CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGACC
43246887 CGAAGGCAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
59 10 0.18
60 8 0.15
61 37 0.67
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (59 bp):
TGTTATATCCGGCTAAGACCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGACC
Found at i:43246917 original size:40 final size:40
Alignment explanation
Indices: 43246827--43246930 Score: 122
Period size: 40 Copynumber: 2.6 Consensus size: 40
43246817 GCTAAGACCT
* * *
43246827 GTTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTT
1 GTTATATCCGGGCTAAGACCCGAAGGCAATTGGGCGAGTG
* * * *
43246867 GCTATGTCCGGGTTAAGACCCGAAGGCAATTGGGCGTGTG
1 GTTATATCCGGGCTAAGACCCGAAGGCAATTGGGCGAGTG
43246907 GTTATATCC-GGCTAA-ATCCCGAAG
1 GTTATATCCGGGCTAAGA-CCCGAAG
43246931 AAACTTGGGT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
38 1 0.02
39 12 0.23
40 40 0.75
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.25
Consensus pattern (40 bp):
GTTATATCCGGGCTAAGACCCGAAGGCAATTGGGCGAGTG
Found at i:43248953 original size:17 final size:17
Alignment explanation
Indices: 43248923--43248956 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43248913 TTATCGTTTG
*
43248923 TTTATTTTTCTTATTTA
1 TTTATTTTACTTATTTA
*
43248940 TTTATTTTAGTTATTTA
1 TTTATTTTACTTATTTA
43248957 ATTTTTCTCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTATTTTACTTATTTA
Done.