Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009132.1 Hibiscus syriacus cultivar Beakdansim tig00112630_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 608087
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:377829 original size:183 final size:182
Alignment explanation
Indices: 377611--377998 Score: 726
Period size: 183 Copynumber: 2.1 Consensus size: 182
377601 TTACAGATGA
*
377611 CCCGAAGGC--TTTGAAAACATCAAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
1 CCCGAAGGCTTTTTGGAAACATC-AAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
377674 GGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACAT
65 GGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACAT
377739 CATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGAT
130 CATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGAT
*
377793 CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
1 CCCGAAGGCTTTTTGGAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
377858 GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATC
66 GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATC
377923 ATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAGAT
131 ATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAGAT
377975 CCCGAAGGCTTTTTGGAAACATCA
1 CCCGAAGGCTTTTTGGAAACATCA
377999 TGCACTGAAG
Statistics
Matches: 202, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
182 40 0.20
183 151 0.75
184 11 0.05
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (182 bp):
CCCGAAGGCTTTTTGGAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATC
ATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAGAT
Found at i:377882 original size:230 final size:229
Alignment explanation
Indices: 377269--377817 Score: 924
Period size: 230 Copynumber: 2.4 Consensus size: 229
377259 GATGGAAATG
* * *
377269 TTTGAAAACATCATGCAC-GAAAGGGCTTATAGATGACCCGAAGGCTTTGAAAACATC-AAAAAG
1 TTTGGAAACATCATGCACTG-AAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAAG
* * * * **
377332 CTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAA
65 ATCCCGAAGGCTTTTTGGAAACATCAAGCACCGAAGGACTTACAGATAACCC-AAGGCACTGAAA
377397 ACATCAAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCG
129 ACATCAAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCG
377462 AAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTT
194 AAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTT
377498 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAAGA
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAAGA
* * * **
377563 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
66 TCCCGAAGGCTTTTTGGAAACATCAAGCACCGAAGGACTTACAGATAACCC-AAGGCACTGAAAA
377628 CATCAAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGA
130 CATCAAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGA
377693 AGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTT
195 AGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTT
377728 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAAGA
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAAGA
377792 TCCCGAAGGCTTTTTGGAAACATCAA
66 TCCCGAAGGCTTTTTGGAAACATCAA
377818 AAAGCTCCCG
Statistics
Matches: 313, Mismatches: 5, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
229 84 0.27
230 229 0.73
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (229 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAAGA
TCCCGAAGGCTTTTTGGAAACATCAAGCACCGAAGGACTTACAGATAACCCAAGGCACTGAAAAC
ATCAAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAA
GGCTTTGAAAACATCAAAAAGATCCCGAAGGCTT
Found at i:377889 original size:76 final size:76
Alignment explanation
Indices: 377793--378476 Score: 1264
Period size: 76 Copynumber: 9.0 Consensus size: 76
377783 TCAAAAAGAT
* *
377793 CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
1 CCCGAAGGC--TTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
377858 GACTTACAGATGA
64 GACTTACAGATGA
377871 CCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
377936 CTTACAGATGA
66 CTTACAGATGA
377947 CCCGAAGGCTTTGAAAACATC-AAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
378011 CTTACAGATGA
66 CTTACAGATGA
378022 CCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
378087 CTTACAGATGA
66 CTTACAGATGA
378098 CCCGAAGGCTTTGAAAACATCAAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGG
1 CCCGAAGGCTTTGAAAACATC-AAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGG
378163 ACTTACAGATGA
65 ACTTACAGATGA
378175 CCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
378240 CTTACAGATGA
66 CTTACAGATGA
378251 CCCGAAGGCTTTGAAAACATC-AAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
378315 CTTACAGATGA
66 CTTACAGATGA
* *
378326 CCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
*
378391 CTTATAGATGA
66 CTTACAGATGA
* *
378402 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGG
1 CCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
378467 CTTACAGATG
66 CTTACAGATG
378477 TGAGAAATAG
Statistics
Matches: 595, Mismatches: 8, Indels: 8
0.97 0.01 0.01
Matches are distributed among these distances:
75 149 0.25
76 361 0.61
77 76 0.13
78 9 0.02
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (76 bp):
CCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
CTTACAGATGA
Found at i:377994 original size:151 final size:152
Alignment explanation
Indices: 377793--378476 Score: 1264
Period size: 151 Copynumber: 4.5 Consensus size: 152
377783 TCAAAAAGAT
* *
377793 CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
1 CCCGAAGGC--TTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
377858 GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATC
64 GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATC
377923 ATGCACTGAAGGACTTACAGATGA
129 ATGCACTGAAGGACTTACAGATGA
377947 CCCGAAGGCTTTGAAAACATC-AAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
378011 CTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCAT
66 CTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCAT
378076 GCACTGAAGGACTTACAGATGA
131 GCACTGAAGGACTTACAGATGA
378098 CCCGAAGGCTTTGAAAACATCAAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGG
1 CCCGAAGGCTTTGAAAACATC-AAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGG
378163 ACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCA
65 ACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCA
378228 TGCACTGAAGGACTTACAGATGA
130 TGCACTGAAGGACTTACAGATGA
378251 CCCGAAGGCTTTGAAAACATC-AAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
* *
378315 CTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
66 CTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCAT
*
378380 GCACTGAAGGACTTATAGATGA
131 GCACTGAAGGACTTACAGATGA
* *
378402 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGG
1 CCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
378467 CTTACAGATG
66 CTTACAGATG
378477 TGAGAAATAG
Statistics
Matches: 520, Mismatches: 7, Indels: 8
0.97 0.01 0.01
Matches are distributed among these distances:
151 298 0.57
152 62 0.12
153 151 0.29
154 9 0.02
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (152 bp):
CCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
CTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCAT
GCACTGAAGGACTTACAGATGA
Found at i:381867 original size:82 final size:82
Alignment explanation
Indices: 381730--382095 Score: 700
Period size: 82 Copynumber: 4.5 Consensus size: 82
381720 CCTACTGAAT
*
381730 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGATAAATTCATCTTCTAAACTAAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGATAAATTCATCTTCTAAACTCAA
381795 TGATTGTTCTGTCCAAC
66 TGATTGTTCTGTCCAAC
381812 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGATAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGATAAATTCATCTTCTAAACTCAA
381877 TGATTGTTCTGTCCAAC
66 TGATTGTTCTGTCCAAC
*
381894 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTTTGATAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGATAAATTCATCTTCTAAACTCAA
381959 TGATTGTTCTGTCCAAC
66 TGATTGTTCTGTCCAAC
381976 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGATAAATTCATCTTCTAAACTC-A
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGATAAATTCATCTTCTAAACTCAA
382040 TGATTGTTCTGTCCAAC
66 TGATTGTTCTGTCCAAC
382057 CAGATCAGATAACTCAAAGAACACTTCCA-AAGATGCTAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
382096 GAGCACATTC
Statistics
Matches: 281, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
80 10 0.04
81 47 0.17
82 224 0.80
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (82 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGATAAATTCATCTTCTAAACTCAA
TGATTGTTCTGTCCAAC
Found at i:388212 original size:11 final size:11
Alignment explanation
Indices: 388196--388224 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
388186 CATACATGGG
388196 AAAATAAAAAA
1 AAAATAAAAAA
388207 AAAAT-AAAAA
1 AAAATAAAAAA
388217 AAAATAAA
1 AAAATAAA
388225 TCCTAACCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (11 bp):
AAAATAAAAAA
Found at i:390792 original size:3 final size:3
Alignment explanation
Indices: 390784--390813 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
390774 ATATATATAT
390784 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
390814 TTTAGTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:390823 original size:28 final size:28
Alignment explanation
Indices: 390791--390845 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
390781 TATATAATAA
*
390791 TAAT-AATAATAATAATAATAATATTTAG
1 TAATAAAT-ATAATAATAATAAAATTTAG
*
390819 TAATAAATTTAATAATAATAAAATTTA
1 TAATAAATATAATAATAATAAAATTTA
390846 AATGAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 21 0.88
29 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (28 bp):
TAATAAATATAATAATAATAAAATTTAG
Found at i:390828 original size:12 final size:13
Alignment explanation
Indices: 390791--390838 Score: 64
Period size: 12 Copynumber: 3.8 Consensus size: 13
390781 TATATAATAA
*
390791 TAATAATAATA-A
1 TAATAATAATATT
390803 TAATAATAATATT
1 TAATAATAATATT
*
390816 TAGTAATAA-ATT
1 TAATAATAATATT
390828 TAATAATAATA
1 TAATAATAATA
390839 AAATTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 22 0.71
13 9 0.29
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (13 bp):
TAATAATAATATT
Found at i:394378 original size:35 final size:36
Alignment explanation
Indices: 394296--394382 Score: 106
Period size: 35 Copynumber: 2.4 Consensus size: 36
394286 TACCAAAATT
* *
394296 TTACCAAACTTTG-AAAAACATTTTTCAAAGAAACAT
1 TTACCAAACTTTGAAAAAACATTTTCCAAAG-AACAG
***
394332 TTACCAAACTTTGAAAAAACATTTTCCAAAG-TTGG
1 TTACCAAACTTTGAAAAAACATTTTCCAAAGAACAG
394367 TTACCAAACTTTGAAA
1 TTACCAAACTTTGAAA
394383 CTTTTAACAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
35 16 0.36
36 13 0.29
37 16 0.36
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (36 bp):
TTACCAAACTTTGAAAAAACATTTTCCAAAGAACAG
Found at i:397027 original size:15 final size:16
Alignment explanation
Indices: 396995--397027 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
396985 AAAATCTTTC
396995 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
397011 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
397026 TT
1 TT
397028 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:397799 original size:16 final size:16
Alignment explanation
Indices: 397775--397808 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
397765 TATCGCCGAC
*
397775 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
397791 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
397807 CG
1 CG
397809 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:398323 original size:35 final size:36
Alignment explanation
Indices: 398241--398327 Score: 106
Period size: 35 Copynumber: 2.4 Consensus size: 36
398231 TACCAAAATT
* *
398241 TTACCAAACTTTG-AAAAACATTTTTCAAAGAAACAT
1 TTACCAAACTTTGAAAAAACATTTTCCAAAG-AACAG
***
398277 TTACCAAACTTTGAAAAAACATTTTCCAAAG-TTGG
1 TTACCAAACTTTGAAAAAACATTTTCCAAAGAACAG
398312 TTACCAAACTTTGAAA
1 TTACCAAACTTTGAAA
398328 CTTTTAACAT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
35 16 0.36
36 13 0.29
37 16 0.36
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (36 bp):
TTACCAAACTTTGAAAAAACATTTTCCAAAGAACAG
Found at i:401475 original size:13 final size:13
Alignment explanation
Indices: 401457--401484 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
401447 TATTAACATC
401457 CAACTCAAATCGT
1 CAACTCAAATCGT
401470 CAACTCAAATCGT
1 CAACTCAAATCGT
401483 CA
1 CA
401485 TTAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.32, G:0.07, T:0.21
Consensus pattern (13 bp):
CAACTCAAATCGT
Found at i:402381 original size:34 final size:32
Alignment explanation
Indices: 402319--402400 Score: 139
Period size: 34 Copynumber: 2.5 Consensus size: 32
402309 ATTATATATA
402319 TATATATATAATA-TTTATATTTTTTATTAAT
1 TATATATATAATATTTTATATTTTTTATTAAT
402350 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATAT-TTTT-TATTAAT
402384 TATATATATAATATTTT
1 TATATATATAATATTTT
402401 TGGGTTTGGG
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
31 13 0.27
32 7 0.15
33 4 0.08
34 24 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
TATATATATAATATTTTATATTTTTTATTAAT
Found at i:405364 original size:2 final size:2
Alignment explanation
Indices: 405357--405381 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
405347 TGAACAGAAC
405357 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 A
405382 GACAATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:406727 original size:19 final size:19
Alignment explanation
Indices: 406703--406741 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
406693 ACCCTAGAAC
406703 CGGTACTCTTCATCATCTA
1 CGGTACTCTTCATCATCTA
406722 CGGTACTCTTCATCATCTA
1 CGGTACTCTTCATCATCTA
406741 C
1 C
406742 ATGTATCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.33, G:0.10, T:0.36
Consensus pattern (19 bp):
CGGTACTCTTCATCATCTA
Found at i:419509 original size:38 final size:38
Alignment explanation
Indices: 419421--419510 Score: 128
Period size: 38 Copynumber: 2.4 Consensus size: 38
419411 TAAAAATATT
419421 ATATATATATATATATAATATTAATAAATTTAATTTAA
1 ATATATATATATATATAATATTAATAAATTTAATTTAA
* * * *
419459 AT-TAAAAAATATATATAATATTTATATATTTAATTTAA
1 ATAT-ATATATATATATAATATTAATAAATTTAATTTAA
419497 ATATATATATATAT
1 ATATATATATATAT
419511 CCGGCCTGAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
37 1 0.02
38 42 0.95
39 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (38 bp):
ATATATATATATATATAATATTAATAAATTTAATTTAA
Found at i:421287 original size:30 final size:31
Alignment explanation
Indices: 421238--421295 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
421228 AAGCAGAGGG
*
421238 AATATTTTTTTAATTTAA-TTATAATTTTGGA
1 AATATTTTTTTAATATAATTTA-AATTTTGGA
*
421269 AATA-TTTTTTGATATAATTTAAATTTT
1 AATATTTTTTTAATATAATTTAAATTTT
421296 AATTTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 17 0.71
31 7 0.29
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (31 bp):
AATATTTTTTTAATATAATTTAAATTTTGGA
Found at i:422858 original size:17 final size:17
Alignment explanation
Indices: 422827--422878 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 17
422817 TAATTTATTT
*
422827 TTTATTAAATTTAAATAA
1 TTTA-TAAATATAAATAA
422845 TTTATAAATATAAATAA
1 TTTATAAATATAAATAA
*
422862 TTTAGAAATATCAAATA
1 TTTATAAATAT-AAATA
422879 TCATCATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 22 0.71
18 9 0.29
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTATAAATATAAATAA
Found at i:429753 original size:15 final size:15
Alignment explanation
Indices: 429733--429765 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
429723 TGAGACATTA
*
429733 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
429748 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
429763 CCC
1 CCC
429766 ACCCAGCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.70, G:0.15, T:0.06
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:430323 original size:34 final size:35
Alignment explanation
Indices: 430285--430365 Score: 87
Period size: 34 Copynumber: 2.3 Consensus size: 35
430275 CTAGTGGGTA
430285 GTGGGTGTGGGGATGGATTTGAAAA-TGTACCCA-C
1 GTGGGTGTGGGG-TGGATTTGAAAATTGTACCCATC
* *
430319 GTGGGCG-GGTGTGGATTTGAAAATTTGTACCCATC
1 GTGGGTGTGGGGTGGATTTGAAAA-TTGTACCCATC
*
430354 ATGGGTGGTGGG
1 GTGGGT-GTGGG
430366 CGGGTGGTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
32 12 0.32
33 3 0.08
34 14 0.38
35 5 0.14
36 1 0.03
37 2 0.05
ACGTcount: A:0.20, C:0.11, G:0.41, T:0.28
Consensus pattern (35 bp):
GTGGGTGTGGGGTGGATTTGAAAATTGTACCCATC
Found at i:443412 original size:37 final size:37
Alignment explanation
Indices: 443362--443435 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
443352 TCATAAAATT
443362 TAAAATAAATTTTAAATAACTACATATTTCTTATTTA
1 TAAAATAAATTTTAAATAACTACATATTTCTTATTTA
*
443399 TAAAATAATTTTTAAATAACTACATATTTCTTATTTA
1 TAAAATAAATTTTAAATAACTACATATTTCTTATTTA
443436 CATGTAGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (37 bp):
TAAAATAAATTTTAAATAACTACATATTTCTTATTTA
Found at i:444584 original size:24 final size:25
Alignment explanation
Indices: 444557--444611 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
444547 AAAACAAACG
444557 TCATTTCATTTTAG-CCGAAAAAAT
1 TCATTTCATTTTAGCCCGAAAAAAT
444581 TCATTTCATTTTAGCCCGAAAAAAT
1 TCATTTCATTTTAGCCCGAAAAAAT
444606 TCATTT
1 TCATTT
444612 AGAGGAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 14 0.47
25 16 0.53
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (25 bp):
TCATTTCATTTTAGCCCGAAAAAAT
Found at i:452934 original size:19 final size:17
Alignment explanation
Indices: 452910--452946 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
452900 AACTCCTTAA
452910 TATTATTTTAATTATAATT
1 TATTATTTT-ATTA-AATT
452929 TATTATTTTATTAAATT
1 TATTATTTTATTAAATT
452946 T
1 T
452947 TCAATTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 4 0.22
19 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTATTTTATTAAATT
Found at i:462596 original size:39 final size:39
Alignment explanation
Indices: 462542--462619 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
462532 TAGAAAATTC
462542 AATAAAGTTGATAATATGAATCTTATTCTCTACAATCAT
1 AATAAAGTTGATAATATGAATCTTATTCTCTACAATCAT
462581 AATAAAGTTGATAATATGAATCTTATTCTCTACAATCAT
1 AATAAAGTTGATAATATGAATCTTATTCTCTACAATCAT
462620 TGGGGTATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (39 bp):
AATAAAGTTGATAATATGAATCTTATTCTCTACAATCAT
Found at i:465085 original size:25 final size:25
Alignment explanation
Indices: 465051--465120 Score: 131
Period size: 25 Copynumber: 2.8 Consensus size: 25
465041 CTAGGGTTTC
*
465051 AACCCTAGATTGCCAAAGTGCTTTT
1 AACCCTAGATTGCCAAAGCGCTTTT
465076 AACCCTAGATTGCCAAAGCGCTTTT
1 AACCCTAGATTGCCAAAGCGCTTTT
465101 AACCCTAGATTGCCAAAGCG
1 AACCCTAGATTGCCAAAGCG
465121 GTTTCGCAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (25 bp):
AACCCTAGATTGCCAAAGCGCTTTT
Found at i:465409 original size:16 final size:16
Alignment explanation
Indices: 465388--465424 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
465378 AAATATTTTC
465388 ATTTAAGTACCAAGTG
1 ATTTAAGTACCAAGTG
465404 ATTTAAGTACCAAGTG
1 ATTTAAGTACCAAGTG
465420 ATTTA
1 ATTTA
465425 TGTGATAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (16 bp):
ATTTAAGTACCAAGTG
Found at i:465679 original size:28 final size:29
Alignment explanation
Indices: 465580--465679 Score: 114
Period size: 29 Copynumber: 3.5 Consensus size: 29
465570 TTAATAAAAA
* * *
465580 ATACCTAGAGTATTTTTTTGTCAAAATAA
1 ATACCTAAAGTATTTTTTGGTCAAAATAG
* *
465609 ATATCTAAATTATTTTTTGGTCAAAATAG
1 ATACCTAAAGTATTTTTTGGTCAAAATAG
**
465638 ACGCCTTAAA-TA-TTTTTGGTCAAAATAG
1 ATACC-TAAAGTATTTTTTGGTCAAAATAG
465666 ATACCTAAAGTATT
1 ATACCTAAAGTATT
465680 CAACTTTTTC
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
27 4 0.07
28 21 0.36
29 29 0.50
30 4 0.07
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (29 bp):
ATACCTAAAGTATTTTTTGGTCAAAATAG
Found at i:465795 original size:28 final size:28
Alignment explanation
Indices: 465759--465883 Score: 133
Period size: 28 Copynumber: 4.4 Consensus size: 28
465749 AAAAAGTTTG
* *
465759 AATAGTTTAAGTACCTATTTTGACATAA
1 AATACTTTAAGTACCTATTTTGACAAAA
* * *
465787 AATACTTTAAATACCTATTTTGATATAA
1 AATACTTTAAGTACCTATTTTGACAAAA
* *
465815 AATACTTTAAGTACCTATTTTAATTAAAA
1 AATACTTTAAGTACCTATTTTGA-CAAAA
* **
465844 AGATAACTTTAATTATTTATTTTGACAAAA
1 A-AT-ACTTTAAGTACCTATTTTGACAAAA
465874 AATACTTTAA
1 AATACTTTAA
465884 CTACTGGAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
28 53 0.64
29 7 0.08
30 7 0.08
31 16 0.19
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.42
Consensus pattern (28 bp):
AATACTTTAAGTACCTATTTTGACAAAA
Found at i:465876 original size:59 final size:56
Alignment explanation
Indices: 465759--465883 Score: 142
Period size: 59 Copynumber: 2.2 Consensus size: 56
465749 AAAAAGTTTG
* * * * *
465759 AATAGTTTAAGTACCTATTTTGACATAAAATACTTTAAATACCTATTTTGATATAA
1 AATACTTTAAGTACCTATTTTAACAAAAAATACTTTAAATACCTATTTTGACAAAA
* * **
465815 AATACTTTAAGTACCTATTTTAATTAAAAAGATAACTTTAATTATTTATTTTGACAAAA
1 AATACTTTAAGTACCTATTTTAA-CAAAAA-AT-ACTTTAAATACCTATTTTGACAAAA
465874 AATACTTTAA
1 AATACTTTAA
465884 CTACTGGAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
56 21 0.37
57 4 0.07
58 2 0.04
59 30 0.53
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.42
Consensus pattern (56 bp):
AATACTTTAAGTACCTATTTTAACAAAAAATACTTTAAATACCTATTTTGACAAAA
Found at i:466231 original size:25 final size:25
Alignment explanation
Indices: 466202--466255 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
466192 TACGGTATTA
*
466202 ATCATTTGTTATTTTATCCTAAAAG
1 ATCATTTGTTATTTTATCCCAAAAG
*
466227 ATCATTTGTTATTTTATCCCGAAAG
1 ATCATTTGTTATTTTATCCCAAAAG
466252 ATCA
1 ATCA
466256 ACGTCTAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.44
Consensus pattern (25 bp):
ATCATTTGTTATTTTATCCCAAAAG
Found at i:466429 original size:35 final size:34
Alignment explanation
Indices: 466371--466454 Score: 107
Period size: 35 Copynumber: 2.4 Consensus size: 34
466361 TAATTATTTA
*
466371 TTTATT-TTGTTTTGTTCGATTATATAATAATAT
1 TTTATTATTATTTTGTTCGATTATATAATAATAT
*
466404 TTTATTATTATTTTAGTTCGGTTATATAATAATAT
1 TTTATTATTATTTT-GTTCGATTATATAATAATAT
466439 TATTATTTATTTATTT
1 T-TTA-TTA-TTATTT
466455 CTCGGATTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
33 6 0.14
34 6 0.14
35 20 0.45
36 3 0.07
37 3 0.07
38 6 0.14
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (34 bp):
TTTATTATTATTTTGTTCGATTATATAATAATAT
Found at i:466448 original size:40 final size:36
Alignment explanation
Indices: 466361--466454 Score: 97
Period size: 35 Copynumber: 2.6 Consensus size: 36
466351 CTCTTTATTT
*
466361 TAATTATTTATTTATTTTGTTTTGTTCGATTATATAA
1 TAATTA-TTATTTATTTTATTTTGTTCGATTATATAA
*
466398 TAA-TA-T-TTTATTATTATTTTAGTTCGGTTATATAA
1 TAATTATTATTTATT-TTATTTT-GTTCGATTATATAA
466433 TAATATTATTATTTA-TTTATTT
1 T-A-ATTATTATTTATTTTATTT
466455 CTCGGATTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
33 6 0.12
34 7 0.15
35 14 0.29
36 3 0.06
37 4 0.08
38 8 0.17
39 2 0.04
40 4 0.08
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (36 bp):
TAATTATTATTTATTTTATTTTGTTCGATTATATAA
Found at i:468830 original size:2 final size:2
Alignment explanation
Indices: 468825--468850 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
468815 TAAAAAAATA
468825 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
468851 TATGTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:478252 original size:18 final size:18
Alignment explanation
Indices: 478229--478274 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
478219 AACATTCATA
*
478229 GTAATCTTATTCCCGCTG
1 GTAATCTTATTCCCACTG
*
478247 GTAATCATATTCCCACTG
1 GTAATCTTATTCCCACTG
* *
478265 ATAATTTTAT
1 GTAATCTTAT
478275 ATTTCGTGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (18 bp):
GTAATCTTATTCCCACTG
Found at i:478762 original size:22 final size:22
Alignment explanation
Indices: 478737--478780 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
478727 AATTTATTAG
478737 TATAGATTGATTTATTTTAAAA
1 TATAGATTGATTTATTTTAAAA
478759 TATAGATTGATTTATTTTAAAA
1 TATAGATTGATTTATTTTAAAA
478781 AATTTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (22 bp):
TATAGATTGATTTATTTTAAAA
Found at i:478943 original size:223 final size:222
Alignment explanation
Indices: 478533--479113 Score: 984
Period size: 223 Copynumber: 2.6 Consensus size: 222
478523 AGAACATTAA
* * *
478533 AAAATATGGATTGATTTA-TTTAAAAAAAATATTATTGAAGTTGTATGGATTACTTAAATTTCAG
1 AAAATATAGATTGATTTATTTTAAAAAAATTATTATTGTAGTTGTATGGATTA-TTAAATTTCAG
* *
478597 TATTGTAAAACTAAAATTATTTAAATTTCAGTATTGTAAAATTCTTTTAAGTTTAAAAAATCAGG
65 TATTGTAAAACTAAAATTATTTAAATTTCAGTATTGCAAAATTCTTTTAAGTTTAAAAAATCAGT
*
478662 TTATTTATATTTCAGTTTATTTTAGCAATTTGCAGACATTAATTTAATAAGGTTATTTATTAAAT
130 TTATTTATATTTCAGTTTATTTTAGCAATTTGCAGACATTAATTTAATAAAGTTATTTATTAAAT
478727 AATTTATTAGTATAGATTGATTTATTTT
195 AATTTATTAGTATAGATTGATTTATTTT
*
478755 AAAATATAGATTGATTTATTTTAAAAAATTTATTATTGTAGTTGTATGGATTATTAAAATTTCAG
1 AAAATATAGATTGATTTATTTTAAAAAAATTATTATTGTAGTTGTATGGATTATT-AAATTTCAG
478820 TATTGTAAAACTAAAATTATTTAAATTTCAGTATTGCAAAATTCTTTTAAGTTTAAAAAATCAGT
65 TATTGTAAAACTAAAATTATTTAAATTTCAGTATTGCAAAATTCTTTTAAGTTTAAAAAATCAGT
* * *
478885 TTATTTATATTTTAGTTTATTTTAGCAGTTTGCAGACATTAATTTAATAAATTTATTTATTAAAT
130 TTATTTATATTTCAGTTTATTTTAGCAATTTGCAGACATTAATTTAATAAAGTTATTTATTAAAT
478950 AATTTATTAGTATAGATTGATTTATTTT
195 AATTTATTAGTATAGATTGATTTATTTT
* * *
478978 AAAATATTGATTGATTTATTTTAAAAAAATTATTATTGTAGTTGTATGGGTCATTTAAATTTCAG
1 AAAATATAGATTGATTTATTTTAAAAAAATTATTATTGTAGTTGTATGGATTA-TTAAATTTCAG
* * *
479043 TATTGTAAAACTAAAATTATTTAAATCTCAGTATTGCAAAACTCTTTTAAGTTTAAAAAACCAGT
65 TATTGTAAAACTAAAATTATTTAAATTTCAGTATTGCAAAATTCTTTTAAGTTTAAAAAATCAGT
479108 TTATTT
130 TTATTT
479114 TAGCAGTCTG
Statistics
Matches: 339, Mismatches: 17, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
222 19 0.06
223 318 0.94
224 2 0.01
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (222 bp):
AAAATATAGATTGATTTATTTTAAAAAAATTATTATTGTAGTTGTATGGATTATTAAATTTCAGT
ATTGTAAAACTAAAATTATTTAAATTTCAGTATTGCAAAATTCTTTTAAGTTTAAAAAATCAGTT
TATTTATATTTCAGTTTATTTTAGCAATTTGCAGACATTAATTTAATAAAGTTATTTATTAAATA
ATTTATTAGTATAGATTGATTTATTTT
Found at i:479118 original size:207 final size:208
Alignment explanation
Indices: 478673--479192 Score: 729
Period size: 223 Copynumber: 2.4 Consensus size: 208
478663 TATTTATATT
* *
478673 TCAGTTTATTTTAGCAATTTGCAGACATTAATTTAATAAGGTTATTTATTAAATAATTTATTAGT
1 TCAGTTTATTTTAGCAGTTTGCAGACATTAATTTAATAA-ATTATTTATTAAATAATTTATTAGT
*
478738 ATAGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAAAATTTATTATTGTAGTTGTATG
65 ATAGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAAAAATTATTATTGTAGTTGTATG
* * *
478803 GATTATTAAAATTTCAGTATTGTAAAACTAAAATTATTTAAATTTCAGTATTGCAAAATTCTTTT
130 GATCATTAAAATTTCAGTATTGTAAAACTAAAATTATTTAAATCTCAGTATTGCAAAACTCTTTT
478868 AAGTTTAAAAAATC
195 AAGTTTAAAAAATC
*
478882 AGTTTATTTATATTTTAGTTTATTTTAGCAGTTTGCAGACATTAATTTAATAAATTTATTTATTA
1 --------------TCAGTTTATTTTAGCAGTTTGCAGACATTAATTTAATAAA-TTATTTATTA
*
478947 AATAATTTATTAGTATAGATTGATTTATTTTAAAATATTGATTGATTTATTTTAAAAAAATTATT
51 AATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAAAAATTATT
* *
479012 ATTGTAGTTGTATGGGTCATTTAAATTTCAGTATTGTAAAACTAAAATTATTTAAATCTCAGTAT
116 ATTGTAGTTGTATGGATCATTAAAATTTCAGTATTGTAAAACTAAAATTATTTAAATCTCAGTAT
479077 TGCAAAACTCTTTTAAGTTTAAAAAA-C
181 TGCAAAACTCTTTTAAGTTTAAAAAATC
* * * *
479104 -CAGTTTATTTTAGCAGTCTGCAGACGTTAATTTAATAAGATTATTTATTAAATAATGTATTCAA
1 TCAGTTTATTTTAGCAGTTTGCAGACATTAATTTAATAA-ATTATTTATTAAATAATTTATT-AG
*
479168 TATGGATTGATTTATTTTAAAATAT
64 TATAGATTGATTTATTTTAAAATAT
479193 GTTGTATGGA
Statistics
Matches: 278, Mismatches: 16, Indels: 21
0.88 0.05 0.07
Matches are distributed among these distances:
207 55 0.20
208 26 0.09
222 1 0.00
223 196 0.71
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (208 bp):
TCAGTTTATTTTAGCAGTTTGCAGACATTAATTTAATAAATTATTTATTAAATAATTTATTAGTA
TAGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAAAAATTATTATTGTAGTTGTATGG
ATCATTAAAATTTCAGTATTGTAAAACTAAAATTATTTAAATCTCAGTATTGCAAAACTCTTTTA
AGTTTAAAAAATC
Found at i:479240 original size:31 final size:31
Alignment explanation
Indices: 479202--479260 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
479192 TGTTGTATGG
*
479202 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATTTCAGTATTGCAAAACTAAA
*
479233 ATTATTTAAATTTCAGTTTTGCAAAACT
1 ATTATTTAAATTTCAGTATTGCAAAACT
479261 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTGCAAAACTAAA
Found at i:499034 original size:18 final size:18
Alignment explanation
Indices: 498994--499043 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
498984 ATGCACGAAC
498994 ATAAACTTTGTTAAAATAAT
1 ATAAA-TTT-TTAAAATAAT
* *
499014 ATAAATTTTTAACATATT
1 ATAAATTTTTAAAATAAT
*
499032 ATAAAATTTTAA
1 ATAAATTTTTAA
499044 TATTACTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 19 0.70
19 3 0.11
20 5 0.19
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (18 bp):
ATAAATTTTTAAAATAAT
Found at i:499048 original size:16 final size:17
Alignment explanation
Indices: 499007--499048 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
498997 AACTTTGTTA
* *
499007 AAATAATATAAATTTTT
1 AAATATTATAAAATTTT
499024 AACATATTATAAAATTTT
1 AA-ATATTATAAAATTTT
499042 -AATATTA
1 AAATATTA
499049 CTAATGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 3 0.14
18 13 0.59
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATATTATAAAATTTT
Found at i:499400 original size:14 final size:15
Alignment explanation
Indices: 499381--499413 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
499371 TTCAAAAAAA
499381 AATATTTTTTATT-T
1 AATATTTTTTATTCT
499395 AATA-TTTTTATTCT
1 AATATTTTTTATTCT
499409 AATAT
1 AATAT
499414 GGTAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (15 bp):
AATATTTTTTATTCT
Found at i:505882 original size:94 final size:95
Alignment explanation
Indices: 505752--505941 Score: 373
Period size: 94 Copynumber: 2.0 Consensus size: 95
505742 AATTTCGAGA
505752 TCATATTTTATCATATCAAATTCAGCAAGTTAACGTTAAGCTAGAATACCGTCAATTGACGAGTT
1 TCATATTTTATCATATCAAATTCAGCAAGTTAACGTTAAGCTAGAATACCGTCAATTGACGAGTT
505817 TGGAACACAATGAATAGTCAGATGACCATT
66 TGGAACACAATGAATAGTCAGATGACCATT
505847 TCATATTTTATCATATC-AATTCAGCAAGTTAACGTTAAGCTAGAATACCGTCAATTGACGAGTT
1 TCATATTTTATCATATCAAATTCAGCAAGTTAACGTTAAGCTAGAATACCGTCAATTGACGAGTT
505911 TGGAACACAATGAATAGTCAGATGACCATT
66 TGGAACACAATGAATAGTCAGATGACCATT
505941 T
1 T
505942 TGTAACTTTT
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
94 78 0.82
95 17 0.18
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (95 bp):
TCATATTTTATCATATCAAATTCAGCAAGTTAACGTTAAGCTAGAATACCGTCAATTGACGAGTT
TGGAACACAATGAATAGTCAGATGACCATT
Found at i:506426 original size:27 final size:27
Alignment explanation
Indices: 506396--506458 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
506386 TAAAAGTACT
506396 TTTTAAAAATT-ATAACTTTATAATTAA
1 TTTT-AAAATTCATAACTTTATAATTAA
**
506423 TTTTTTAATTCATAACTTTATAATTAA
1 TTTTAAAATTCATAACTTTATAATTAA
*
506450 TTTTTAAAT
1 TTTTAAAAT
506459 ATGAATTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 4 0.12
27 28 0.88
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTTAAAATTCATAACTTTATAATTAA
Found at i:507180 original size:19 final size:19
Alignment explanation
Indices: 507140--507181 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
507130 AAAATAACTA
* *
507140 TTTTGATTTTAATCATTAT
1 TTTTAATTTTAATCAATAT
507159 TTTTAATTTTAATCAA-AT
1 TTTTAATTTTAATCAATAT
507177 TTTTA
1 TTTTA
507182 TTAATTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTAATTTTAATCAATAT
Found at i:507917 original size:21 final size:21
Alignment explanation
Indices: 507874--507917 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
507864 TATTTTCATG
* **
507874 TTGATATTGTAGTTCGCGGTA
1 TTGATATTGTAGTTCACAATA
507895 TTGATATTGTAGTTCACAATA
1 TTGATATTGTAGTTCACAATA
507916 TT
1 TT
507918 AATGTAACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.09, G:0.20, T:0.45
Consensus pattern (21 bp):
TTGATATTGTAGTTCACAATA
Found at i:509659 original size:34 final size:34
Alignment explanation
Indices: 509611--509683 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
509601 TGGGCTGAAT
*
509611 ATAAACGAACATACACATACATAAATGAACAAAC
1 ATAAACGAACATACACAGACATAAATGAACAAAC
* * *
509645 ATAAACGAATATACACGGACATAGATGAACAAAC
1 ATAAACGAACATACACAGACATAAATGAACAAAC
509679 ATAAA
1 ATAAA
509684 TAGACATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.58, C:0.18, G:0.10, T:0.15
Consensus pattern (34 bp):
ATAAACGAACATACACAGACATAAATGAACAAAC
Found at i:516574 original size:17 final size:17
Alignment explanation
Indices: 516548--516585 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
516538 GATCGACTCA
516548 ATCTCGAATAACTCACG
1 ATCTCGAATAACTCACG
*
516565 ATCTCTAATAACTCACG
1 ATCTCGAATAACTCACG
516582 ATCT
1 ATCT
516586 GTCTCATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.34, C:0.29, G:0.08, T:0.29
Consensus pattern (17 bp):
ATCTCGAATAACTCACG
Found at i:519846 original size:25 final size:25
Alignment explanation
Indices: 519827--519877 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
519817 AATTAGAGTC
*
519827 ATAAT-AATAAATAAATATTATAAAA
1 ATAATGAA-AAATAAATATTAGAAAA
519852 ATAATGAAAAATAAATATTAGAAAA
1 ATAATGAAAAATAAATATTAGAAAA
519877 A
1 A
519878 GTGAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (25 bp):
ATAATGAAAAATAAATATTAGAAAA
Found at i:522197 original size:58 final size:58
Alignment explanation
Indices: 522104--522229 Score: 198
Period size: 58 Copynumber: 2.2 Consensus size: 58
522094 GGCAAGATTG
*
522104 AAGAAACTTGGATCACACGTAATTGGATTTCGTACCTGCCAGTTAGACTTTATATAGA
1 AAGAAACTTGGATCACAAGTAATTGGATTTCGTACCTGCCAGTTAGACTTTATATAGA
* * * * *
522162 AAGAAACTTGGGTTATAAGTAATTGGATTTTGTACCTGCCAGTTAGAGTTTATATAGA
1 AAGAAACTTGGATCACAAGTAATTGGATTTCGTACCTGCCAGTTAGACTTTATATAGA
522220 AAGAAACTTG
1 AAGAAACTTG
522230 CTTCCAATGT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.33
Consensus pattern (58 bp):
AAGAAACTTGGATCACAAGTAATTGGATTTCGTACCTGCCAGTTAGACTTTATATAGA
Found at i:524036 original size:4 final size:4
Alignment explanation
Indices: 524027--524051 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
524017 ACAAATGAGT
524027 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
524052 CACGAGTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:527192 original size:114 final size:112
Alignment explanation
Indices: 526986--527542 Score: 566
Period size: 114 Copynumber: 5.0 Consensus size: 112
526976 AGAGGGGCTT
* * ** *
526986 CTGCTGCTGAACCAGATGGCCATTCCAGGCAGGAGTTGTGCCTTGAGTGCATAACTGCTCATATC
1 CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCACATGACTGCTCATATC
* ** *
527051 GAGGTGATCCTATGTTTGATATGGTTCCATTTGCTTGAAAATTATGCGG
66 GAGGTGATCCCATGTTTGATACAGTTCCATTTGCATGAAAATT-T-CGG
* * * * *
527100 CTGCTGCTGAACCAGCTGGCCACTCCAGGCAGGACTTGAGCCTTGATCACATGTCTGCTCATAAC
1 CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCACATGACTGCTCATATC
* * * *
527165 GAGGTGATCCCATGCTTGACACAGTTCCATTGGCATGAAAATCCTGT-GA
66 GAGGTGATCCCATGTTTGATACAGTTCCATTTGCATGAAAAT--T-TCGG
* ** * * *
527214 CTGCTGCTGAACCAGTTGGCCGCTCCAGGCAGGACTTGTGCCTTGAGAACATGTCTGCTCATAGC
1 CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCACATGACTGCTCATATC
* * * *
527279 GAGGTGATCCCAAGTTTGATACAGTTCCATTTCCATGGAAA-TTCTG
66 GAGGTGATCCCATGTTTGATACAGTTCCATTTGCATGAAAATTTCGG
* * * * *
527325 CTGCTGCTGAACCATCTGTCCATTCCAGGAAGGAC--CTGCCTTGAGCATATGACTGCTCATATC
1 CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCACATGACTGCTCATATC
* * * * * *
527388 CAGGTGATCCCATGTTTGGTACAGCTCCATTCGCAGGAAAATTT-TG
66 GAGGTGATCCCATGTTTGATACAGTTCCATTTGCATGAAAATTTCGG
** * * * * *
527434 CTGCTGCTGAACCATTTGGCCATTCCAGGCAGGACCTGTACATTGAGCATATGACTGCTCGTATC
1 CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCACATGACTGCTCATATC
** * * * *
527499 GAGGCAATCCCGTGTTTGGTACAGTTCCATTCGTATGAAAATTT
66 GAGGTGATCCCATGTTTGATACAGTTCCATTTGCATGAAAATTT
527543 TGTTGTTGTT
Statistics
Matches: 371, Mismatches: 66, Indels: 15
0.82 0.15 0.03
Matches are distributed among these distances:
109 90 0.24
110 3 0.01
111 91 0.25
114 185 0.50
116 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.29
Consensus pattern (112 bp):
CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCACATGACTGCTCATATC
GAGGTGATCCCATGTTTGATACAGTTCCATTTGCATGAAAATTTCGG
Found at i:532166 original size:11 final size:11
Alignment explanation
Indices: 532152--532176 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
532142 TATTTTTAGA
532152 TTATTTTAATT
1 TTATTTTAATT
532163 TTATTTTAATT
1 TTATTTTAATT
532174 TTA
1 TTA
532177 GTTAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTTTAATT
Found at i:534949 original size:188 final size:188
Alignment explanation
Indices: 534632--534999 Score: 720
Period size: 188 Copynumber: 2.0 Consensus size: 188
534622 CAATTTCGCA
534632 GAGTATGGGGAGAGCTCTAGCTAAAGGTCCCCGTTCGACCGATAGCTCGAAATCTGTAGAGTTTT
1 GAGTATGGGGAGAGCTCTAGCTAAAGGTCCCCGTTCGACCGATAGCTCGAAATCTGTAGAGTTTT
534697 TAACTGCGGTGACGATTGTGATGTCCGGCTGATTTTTGCAGTCTTGGTCGTAGATGAATTTCATA
66 TAACTGCGGTGACGATTGTGATGTCCGGCTGATTTTTGCAGTCTTGGTCGTAGATGAATTTCATA
534762 GCTTGCGTGAATAAATTTACACTCAGGGCCAGGGGGCATTGTCATTTTGTTTTCATTC
131 GCTTGCGTGAATAAATTTACACTCAGGGCCAGGGGGCATTGTCATTTTGTTTTCATTC
534820 GAGTAT-GGGAGAGCTCTAGCTAAAGGTTCCCCGTTCGACCGATAGCTCGAAATCTGTAGAGTTT
1 GAGTATGGGGAGAGCTCTAGCTAAAGG-TCCCCGTTCGACCGATAGCTCGAAATCTGTAGAGTTT
534884 TTAACTGCGGTGACGATTGTGATGTCCGGCTGATTTTTGCAGTCTTGGTCGTAGATGAATTTCAT
65 TTAACTGCGGTGACGATTGTGATGTCCGGCTGATTTTTGCAGTCTTGGTCGTAGATGAATTTCAT
534949 AGCTTGCGTGAATAAATTTACACTCAGGGCCAGGGGGCATTGTCATTTTGT
130 AGCTTGCGTGAATAAATTTACACTCAGGGCCAGGGGGCATTGTCATTTTGT
535000 GTTTTCAGCC
Statistics
Matches: 179, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
187 20 0.11
188 159 0.89
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (188 bp):
GAGTATGGGGAGAGCTCTAGCTAAAGGTCCCCGTTCGACCGATAGCTCGAAATCTGTAGAGTTTT
TAACTGCGGTGACGATTGTGATGTCCGGCTGATTTTTGCAGTCTTGGTCGTAGATGAATTTCATA
GCTTGCGTGAATAAATTTACACTCAGGGCCAGGGGGCATTGTCATTTTGTTTTCATTC
Found at i:539226 original size:15 final size:16
Alignment explanation
Indices: 539206--539235 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
539196 CGTTTTATTA
539206 GAATCA-TTTTCTGAT
1 GAATCATTTTTCTGAT
539221 GAATCATTTTTCTGA
1 GAATCATTTTTCTGA
539236 GCTTCATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (16 bp):
GAATCATTTTTCTGAT
Found at i:545394 original size:29 final size:30
Alignment explanation
Indices: 545360--545454 Score: 122
Period size: 29 Copynumber: 3.2 Consensus size: 30
545350 CTATATATTA
*
545360 TATATAAATTTCCAAAAATATTTTTAAAAAC
1 TATAT-AATTTTCAAAAATATTTTTAAAAAC
* *
545391 TATATAATTTTC-AAAATGTCTTTAAAAAC
1 TATATAATTTTCAAAAATATTTTTAAAAAC
* *
545420 CATATAATTTTCAAAAATA-TTTTAAAAAT
1 TATATAATTTTCAAAAATATTTTTAAAAAC
545449 TATATA
1 TATATA
545455 TTATATATGT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 39 0.71
30 11 0.20
31 5 0.09
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.41
Consensus pattern (30 bp):
TATATAATTTTCAAAAATATTTTTAAAAAC
Found at i:545530 original size:77 final size:73
Alignment explanation
Indices: 545426--545628 Score: 237
Period size: 77 Copynumber: 2.7 Consensus size: 73
545416 AAACCATATA
* * * *
545426 ATTTTCAAAAATATTTTAAAAATTATATATTATATATGTTTTCAAAATGTTTTTCAAAAAATTAT
1 ATTTTCAAAAATGTTTTAAAAACTATATATTATATATGTTTTCAAAATG-TCTT--AAAAACTAT
545491 ATATTCTATATTT
63 ATA-T-TATATTT
* * *
545504 ATTTTC-AAAATGTTTTAAAAACTATATAATATATATTTTTTCAAAAATGTCTTGAAAACTATAT
1 ATTTTCAAAAATGTTTTAAAAACTATATATTATATATGTTTTC-AAAATGTCTTAAAAACTATAT
545568 ATTATATTT
65 ATTATATTT
* *
545577 ATTTTCAAAAACGTTTTAAAAAACTATATAATATATAAATGTTTTCAAAATG
1 ATTTTCAAAAATGTTTT-AAAAACTATAT-AT-TATATATGTTTTCAAAATG
545629 AAAATGTTTT
Statistics
Matches: 109, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
73 13 0.12
74 10 0.09
75 21 0.19
76 7 0.06
77 46 0.42
78 12 0.11
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (73 bp):
ATTTTCAAAAATGTTTTAAAAACTATATATTATATATGTTTTCAAAATGTCTTAAAAACTATATA
TTATATTT
Found at i:546386 original size:165 final size:165
Alignment explanation
Indices: 546215--547163 Score: 1374
Period size: 165 Copynumber: 5.8 Consensus size: 165
546205 AACTCGACAA
*
546215 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGAGCGTAG
1 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* *
546280 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
66 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGT
546345 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
131 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
546380 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
1 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * *
546445 TCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
66 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGT
*
546510 GCCCTTGAAGCTGAGTGTAATCGAACTCGGGGGTC
131 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
546545 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
1 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* ** * *
546610 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATACT-TCAAATGATG
66 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAGTTATGCTGT-AAATGATG
*
546674 TGCCCTCGAAGCTGAGTGTAATCGACCTCGGGGGTC
130 TGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
*
546710 TTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
1 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
** * * *
546775 TCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATG
66 TCGAACTCGAAGGTCTTTTGG-TCACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATG
*
546839 TGCCCTCGAAGCTGAGTGTGATCGAACTCGGGGGTC
130 TGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
* * * * * * * * *
546875 TTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGT
1 TTTGG---CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGC
* ** * * * *
546940 GTAATCGAACTCGGGGGTC-TTTGG---CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATG
62 GTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATG
* * * * *
547001 ATGTG-CCTTGGAGTTGAGCGTGATCGAACTCGGGGGTC
127 ATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
*
547039 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCATA
1 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTA
* * *
547103 GTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAAT
65 GTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAAT
547164 AGTTTGTTTA
Statistics
Matches: 716, Mismatches: 56, Indels: 25
0.90 0.07 0.03
Matches are distributed among these distances:
160 23 0.03
161 42 0.06
164 69 0.10
165 513 0.72
168 37 0.05
169 32 0.04
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.30
Consensus pattern (165 bp):
TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGT
GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
Found at i:546636 original size:249 final size:246
Alignment explanation
Indices: 546215--547163 Score: 1142
Period size: 249 Copynumber: 3.8 Consensus size: 246
546205 AACTCGACAA
* * *
546215 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGAGCGTAG
1 TTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAA
* * * * *
546280 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
66 TCGAACTCGAAGGTCTTTTGG---CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* * ** *
546345 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG---CAGATAGCCCTTCTCGACTTAA
128 GCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCACAGATAACCCTTCTCGACTTAA
* * * * * ***
546407 GCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC
193 GTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
* * * * * *
546460 TTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTTGAAGCTGAG
1 -TTTGG---CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAG
* ** *
546525 TGTAATCGAACTCGGGGGTC-TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAT
61 CGTAATCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGAT
* * * **
546589 GTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACT
126 GTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTCACAGATAACCCTTCTCGACT
* * *
546653 TAAGTTATACTTCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGACCTCGGGGGTC
190 TAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
*
546710 TTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
1 TTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAA
* *
546775 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGT
66 TCGAACTCGAAGGTC-TT--TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* ** * * *
546840 GCCCTCGAAGCTGAGTGT-GATCGAACTCGGGGGTCTTTGGTCACAGATAACCCTTCTAGCCTTG
128 GCCCTCGAAGCTGAGCGTAG-TCGAACTCGAAGGTCTTTGGTCACAGATAACCCTTCTCGACTTA
*
546904 AGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
192 AGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
* * *
546959 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGTTGAGCGTGA
1 TTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAA
** *
547024 TCGAACTCGGGGGTC-TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
66 TCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
* * * * * * *
547088 GTTG-AGCTGAGCATAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGT
131 CTCGAAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTCACAGATAACCCTTCTCGACTTAAGT
*
547152 TATGCTGTAAAT
195 TATGCTGCAAAT
547164 AGTTTGTTTA
Statistics
Matches: 605, Mismatches: 81, Indels: 35
0.84 0.11 0.05
Matches are distributed among these distances:
244 20 0.03
245 147 0.24
246 82 0.14
247 2 0.00
249 275 0.45
250 79 0.13
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.30
Consensus pattern (246 bp):
TTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAA
TCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
CTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCACAGATAACCCTTCTCGACTTAAGTT
ATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
Found at i:550597 original size:18 final size:19
Alignment explanation
Indices: 550554--550599 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
550544 TAGTTAATGT
550554 GAATGCAAAGAAAATAAAA
1 GAATGCAAAGAAAATAAAA
*
550573 GAATGCAAAGAAAATAAGA
1 GAATGCAAAGAAAATAAAA
550592 -AATGCAAA
1 GAATGCAAA
550600 ATGTCTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.65, C:0.07, G:0.17, T:0.11
Consensus pattern (19 bp):
GAATGCAAAGAAAATAAAA
Found at i:553957 original size:3 final size:3
Alignment explanation
Indices: 553927--553968 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
553917 AAAAAAGTAA
*
553927 AAT AA- AAT AAGT AAT AAAT AAT ACT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AA-T AAT -AAT AAT AAT AAT AAT AAT AAT AAT AA
553969 ATATAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 26 0.76
4 6 0.18
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:554074 original size:30 final size:30
Alignment explanation
Indices: 554028--554123 Score: 131
Period size: 30 Copynumber: 3.2 Consensus size: 30
554018 CTATATATTA
*
554028 TATATAAATTTCCAAAAATATTTTTAAAAAC
1 TATAT-AATTTTCAAAAATATTTTTAAAAAC
* *
554059 TATATAATTTTCAAAAATGTCTTTAAAAAC
1 TATATAATTTTCAAAAATATTTTTAAAAAC
* *
554089 CATATAATTTTCAAAAATA-TTTTAAAAAT
1 TATATAATTTTCAAAAATATTTTTAAAAAC
554118 TATATA
1 TATATA
554124 TTATATATGT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 13 0.23
30 39 0.68
31 5 0.09
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.41
Consensus pattern (30 bp):
TATATAATTTTCAAAAATATTTTTAAAAAC
Found at i:554138 original size:37 final size:37
Alignment explanation
Indices: 554090--554282 Score: 203
Period size: 37 Copynumber: 5.1 Consensus size: 37
554080 TTTAAAAACC
* *
554090 ATATA-ATTTTCAAAAATATTTTAAAAATTATATATT
1 ATATATATTTTCAAAAATGTTTTAAAAACTATATATT
* *
554126 ATATATGTTTTC-AAAATGTTTTTCAAAAAATTATATATTCT
1 ATATATATTTTCAAAAATG-TTTT--AAAAACTATATA-T-T
* *
554167 ATATTTATTTTC-AAAATGTTTTAAAAACTATATAAT
1 ATATATATTTTCAAAAATGTTTTAAAAACTATATATT
* * *
554203 ATATATTTTTTCAAAAATGTCTTGAAAACTATATATT
1 ATATATATTTTCAAAAATGTTTTAAAAACTATATATT
* * *
554240 ATATTTATTTTCAAAAACGTTTTAAAAAACTATATAAT
1 ATATATATTTTCAAAAATGTTTT-AAAAACTATATATT
554278 ATATA
1 ATATA
554283 AATGTTTTCA
Statistics
Matches: 131, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
36 21 0.16
37 49 0.37
38 27 0.21
39 12 0.09
40 5 0.04
41 17 0.13
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (37 bp):
ATATATATTTTCAAAAATGTTTTAAAAACTATATATT
Found at i:554189 original size:77 final size:73
Alignment explanation
Indices: 554095--554296 Score: 235
Period size: 77 Copynumber: 2.7 Consensus size: 73
554085 AAACCATATA
* * * *
554095 ATTTTCAAAAATATTTTAAAAATTATATATTATATATGTTTTCAAAATGTTTTTCAAAAAATTAT
1 ATTTTCAAAAATGTTTTAAAAACTATATATTATATATGTTTTCAAAATG-TCTT--AAAAACTAT
554160 ATATTCTATATTT
63 ATA-T-TATATTT
* * *
554173 ATTTTC-AAAATGTTTTAAAAACTATATAATATATATTTTTTCAAAAATGTCTTGAAAACTATAT
1 ATTTTCAAAAATGTTTTAAAAACTATATATTATATATGTTTTC-AAAATGTCTTAAAAACTATAT
554237 ATTATATTT
65 ATTATATTT
* *
554246 ATTTTCAAAAACGTTTTAAAAAACTATATAATATATAAATGTTTTCAAAAT
1 ATTTTCAAAAATGTTTT-AAAAACTATAT-AT-TATATATGTTTTCAAAAT
554297 TAAAATGTTT
Statistics
Matches: 108, Mismatches: 11, Indels: 12
0.82 0.08 0.09
Matches are distributed among these distances:
73 13 0.12
74 10 0.09
75 21 0.19
76 6 0.06
77 46 0.43
78 12 0.11
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.46
Consensus pattern (73 bp):
ATTTTCAAAAATGTTTTAAAAACTATATATTATATATGTTTTCAAAATGTCTTAAAAACTATATA
TTATATTT
Found at i:554696 original size:15 final size:15
Alignment explanation
Indices: 554678--554744 Score: 91
Period size: 15 Copynumber: 4.5 Consensus size: 15
554668 TTTCGGAAAA
*
554678 TGAATTATTGGAATT
1 TGAATTACTGGAATT
554693 TGAATTACTGGAATT
1 TGAATTACTGGAATT
554708 TGAATTACTGGAATT
1 TGAATTACTGGAATT
* **
554723 TAAATT-CTGGAAAA
1 TGAATTACTGGAATT
554737 TGAATTAC
1 TGAATTAC
554745 ATTTCTGGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 11 0.24
15 35 0.76
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.39
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:554712 original size:30 final size:29
Alignment explanation
Indices: 554672--554744 Score: 101
Period size: 30 Copynumber: 2.5 Consensus size: 29
554662 TTGGTTTTTC
* *
554672 GGAAAATGAATTATTGGAATTTGAATTACT
1 GGAAAATGAATTACTGGAATTTAAATT-CT
**
554702 GGAATTTGAATTACTGGAATTTAAATTCT
1 GGAAAATGAATTACTGGAATTTAAATTCT
554731 GGAAAATGAATTAC
1 GGAAAATGAATTAC
554745 ATTTCTGGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 14 0.38
30 23 0.62
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (29 bp):
GGAAAATGAATTACTGGAATTTAAATTCT
Found at i:555259 original size:22 final size:22
Alignment explanation
Indices: 555232--555286 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
555222 TTGATTATTT
555232 TATATAATATTAAAAATA-TAA
1 TATATAATATTAAAAATATTAA
* *
555253 TATTATATTATTATAAATATTAA
1 TA-TATAATATTAAAAATATTAA
*
555276 TAAATAATATT
1 TATATAATATT
555287 TTGATGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.07
22 21 0.75
23 5 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TATATAATATTAAAAATATTAA
Found at i:555259 original size:52 final size:51
Alignment explanation
Indices: 555139--555268 Score: 145
Period size: 54 Copynumber: 2.4 Consensus size: 51
555129 TTAAATATAT
* * *
555139 AAATAATATTATTCATTATTAAATATATAATTTTTTTATTATATATTATTAAAA
1 AAATAATATTA-T-ATTATTATA-ATATAATTTTATTATTATATAATATTAAAA
*
555193 AAAAAATATCTTATATTATTATAATATAATTGATTATT-TTATATAATATTAAAA
1 AAATAATA--TTATATTATTATAATATAATT--TTATTATTATATAATATTAAAA
*
555247 ATATAATATTATATTATTATAA
1 AAATAATATTATATTATTATAA
555269 ATATTAATAA
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
52 14 0.21
53 8 0.12
54 36 0.55
55 5 0.08
56 3 0.05
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (51 bp):
AAATAATATTATATTATTATAATATAATTTTATTATTATATAATATTAAAA
Found at i:555498 original size:42 final size:42
Alignment explanation
Indices: 555450--555562 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 42
555440 ATTACGTTCA
*
555450 GAAAAATCAATTACGTGAAACAAACACTGGAAAACAT-TTTTC
1 GAAAAATCAATTACGTGAAACAAACACTAGAAAA-ATATTTTC
*
555492 GAAAAATGAATTACGTGAAACAAACAC-AGAAAAATATTTTC
1 GAAAAATCAATTACGTGAAACAAACACTAGAAAAATATTTTC
* * **
555533 TAAAAACCGAATTATATGAAACAAACACTA
1 GAAAAATC-AATTACGTGAAACAAACACTA
555563 AAATTCAGAG
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
40 2 0.03
41 15 0.25
42 43 0.70
43 1 0.02
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (42 bp):
GAAAAATCAATTACGTGAAACAAACACTAGAAAAATATTTTC
Found at i:560088 original size:32 final size:32
Alignment explanation
Indices: 560052--560158 Score: 97
Period size: 32 Copynumber: 3.3 Consensus size: 32
560042 CAATTTTATA
*
560052 TAAAATTATTTAAAATAAAATAAACATCAATT
1 TAAAACTATTTAAAATAAAATAAACATCAATT
* ** * ** ** *
560084 TAAAACTATTTAGAATATTTATCAATTTTTATA
1 TAAAACTATTTAAAATA-AAATAAACATCAATT
*
560117 TAAAACTATTTAAAATAAAATAAACATCACTT
1 TAAAACTATTTAAAATAAAATAAACATCAATT
*
560149 TAAAAATATT
1 TAAAACTATT
560159 AATATTATAG
Statistics
Matches: 53, Mismatches: 21, Indels: 2
0.70 0.28 0.03
Matches are distributed among these distances:
32 30 0.57
33 23 0.43
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.38
Consensus pattern (32 bp):
TAAAACTATTTAAAATAAAATAAACATCAATT
Found at i:560114 original size:65 final size:64
Alignment explanation
Indices: 560037--560158 Score: 208
Period size: 65 Copynumber: 1.9 Consensus size: 64
560027 ATTCTTCAAT
* *
560037 TTTATCAATTTTATATAAAATTATTTAAAATAAAATAAACATCAATTTAAAACTATTTAGAATA
1 TTTATCAATTTTATATAAAACTATTTAAAATAAAATAAACATCAATTTAAAAATATTTAGAATA
*
560101 TTTATCAATTTTTATATAAAACTATTTAAAATAAAATAAACATCACTTTAAAAATATT
1 TTTATCAA-TTTTATATAAAACTATTTAAAATAAAATAAACATCAATTTAAAAATATT
560159 AATATTATAG
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
64 8 0.15
65 46 0.85
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (64 bp):
TTTATCAATTTTATATAAAACTATTTAAAATAAAATAAACATCAATTTAAAAATATTTAGAATA
Found at i:561918 original size:15 final size:15
Alignment explanation
Indices: 561898--561927 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
561888 AGTTACCTAA
561898 TATAAACTTTTAGAT
1 TATAAACTTTTAGAT
561913 TATAAACTTTTAGAT
1 TATAAACTTTTAGAT
561928 AGTTACCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (15 bp):
TATAAACTTTTAGAT
Found at i:562716 original size:66 final size:65
Alignment explanation
Indices: 562671--562974 Score: 408
Period size: 66 Copynumber: 4.8 Consensus size: 65
562661 TGGAGTACAT
*
562671 GTGAACACCGGGAAAGGAAAACCAGGTGGTGGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGG
1 GTGAACACCGGGAAAGGAAAACCAGG-GGCGGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGG
562736 G
65 G
* *
562737 GTGAACACCGGGAAA-G-------GGGGAGGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGGA
1 GTGAACACCGGGAAAGGAAAACCAGGGGCGGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGGG
* * * * * *
562794 GTGAGCACCGGGAAAGGAAAACCAGGGGTGGTACTCACGTGAGCGTCGGTAAGGGCGGAGTTGGC
1 GTGAACACCGGGAAAGGAAAACCAGGGGCGGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGGG
* * *
562859 GTGAACACCGGGAAAGGAAAGCCAGGGGGCGGCACTCATGTGAGCGTCGGAAAGGGCGGAGTTGG
1 GTGAACACCGGGAAAGGAAAACCA-GGGGCGGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGG
562924 G
65 G
*
562925 GTGAACACCGGGAAAGGAAAACCAGGCGGCGGCACTCACGTGAGCGTCGG
1 GTGAACACCGGGAAAGGAAAACCAGG-GGCGGCACTCACGTGAACGTCGG
562975 CGGCAAAGGC
Statistics
Matches: 211, Mismatches: 17, Indels: 20
0.85 0.07 0.08
Matches are distributed among these distances:
57 51 0.24
58 3 0.01
65 61 0.29
66 96 0.45
ACGTcount: A:0.27, C:0.19, G:0.42, T:0.11
Consensus pattern (65 bp):
GTGAACACCGGGAAAGGAAAACCAGGGGCGGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGGG
Found at i:562789 original size:57 final size:57
Alignment explanation
Indices: 562701--562941 Score: 239
Period size: 57 Copynumber: 3.9 Consensus size: 57
562691 ACCAGGTGGT
562701 GGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGGGGTGAACACCGGGAAAGGGGGA
1 GGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGGGGTGAACACCGGGAAAGGGGGA
* * *
562758 GGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGGAGTGAGCACCGGGAAAGGAAAACCAGGGGT
1 GGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGGGGTGAACACCGGGAAA-G-------GGGGA
* * * *
562823 GGTACTCACGTGAGCGTCGGTAAGGGCGGAGTTGGCGTGAACACCGGGAAAGGAAAGCCAGGGGG
1 GGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGGGGTGAACACC--G---GG-AA---AGGGGG
*
562888 C
57 A
* *
562889 GGCACTCATGTGAGCGTCGGAAAGGGCGGAGTTGGGGTGAACACCGGGAAAGG
1 GGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGGGGTGAACACCGGGAAAGG
562942 AAAACCAGGC
Statistics
Matches: 154, Mismatches: 13, Indels: 34
0.77 0.06 0.17
Matches are distributed among these distances:
57 52 0.34
58 1 0.01
60 2 0.01
61 2 0.01
64 1 0.01
65 44 0.29
66 45 0.29
67 1 0.01
70 2 0.01
71 2 0.01
73 1 0.01
74 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.44, T:0.12
Consensus pattern (57 bp):
GGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGGGGTGAACACCGGGAAAGGGGGA
Found at i:571154 original size:19 final size:19
Alignment explanation
Indices: 571118--571156 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
571108 TCTCAACTTC
* **
571118 AAATGGTTGAATGTATGCA
1 AAATGCTTGAATAAATGCA
571137 AAATGCTTGAATAAATGCA
1 AAATGCTTGAATAAATGCA
571156 A
1 A
571157 TGTTAATGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.28
Consensus pattern (19 bp):
AAATGCTTGAATAAATGCA
Found at i:573412 original size:60 final size:60
Alignment explanation
Indices: 573348--573503 Score: 167
Period size: 60 Copynumber: 2.6 Consensus size: 60
573338 TCTCATTTCG
* * *
573348 AATTAGT-CTTAAACTTTTTTAATATTTTAATTTCATCCTTAAACTACGAC-TCTTATT-TTA
1 AATTAGTCCTTAAAC-TTTTTAATATTTTAATTTCATCATTAAAATACGACAT-TT-TTCCTA
* * *
573408 AATTAGTCCTTAAAC-TTTTAAGCATTTTAATTTCATTATTAAAATATGACATTTTTCCTA
1 AATTAGTCCTTAAACTTTTTAA-TATTTTAATTTCATCATTAAAATACGACATTTTTCCTA
* * *
573468 AATTGGTCCCTAAACTTTTTAATATTTCAATTTCAT
1 AATTAGTCCTTAAACTTTTTAATATTTTAATTTCAT
573504 TCCCAAATTC
Statistics
Matches: 81, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
59 8 0.10
60 59 0.73
61 14 0.17
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.48
Consensus pattern (60 bp):
AATTAGTCCTTAAACTTTTTAATATTTTAATTTCATCATTAAAATACGACATTTTTCCTA
Found at i:574181 original size:20 final size:20
Alignment explanation
Indices: 574087--574455 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
574077 GATTTTCCAT
* ** *
574087 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
574107 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
574127 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
574147 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
574167 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
574187 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
574207 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
574227 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
574247 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
574267 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
574287 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
574307 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
574327 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
574347 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
574367 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
574387 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
574407 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
574427 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
574447 AATCACAAC
1 AATCGCAAC
574456 ACTTAAATTT
Statistics
Matches: 303, Mismatches: 38, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
19 3 0.01
20 297 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:575177 original size:24 final size:24
Alignment explanation
Indices: 575138--575184 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
575128 AAATTTGGTC
575138 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
575162 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
575185 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:575376 original size:12 final size:12
Alignment explanation
Indices: 575359--575383 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
575349 ATATAATCCT
575359 GAAGAAGAAAAA
1 GAAGAAGAAAAA
575371 GAAGAAGAAAAA
1 GAAGAAGAAAAA
575383 G
1 G
575384 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:577752 original size:19 final size:19
Alignment explanation
Indices: 577689--577953 Score: 380
Period size: 19 Copynumber: 14.7 Consensus size: 19
577679 AAATCCCAAC
577689 ATGAAAATCGCAATGCGGAA
1 ATGAAAATCGCAATGC-GAA
577709 ATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAA
*
577724 A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
577742 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
*
577761 ATGAAAATCGCAA--CGAC
1 ATGAAAATCGCAATGCGAA
577778 A-G--AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
*
577794 ATTAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
577813 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
577832 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
577851 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
577870 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
*
577889 ATAAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAA
577906 A-G--AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
577922 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
577941 ATGAAAATCGCAA
1 ATGAAAATCGCAA
577954 CGAGATAATC
Statistics
Matches: 222, Mismatches: 8, Indels: 31
0.85 0.03 0.12
Matches are distributed among these distances:
14 26 0.12
15 1 0.00
16 12 0.05
17 11 0.05
18 2 0.01
19 157 0.71
20 13 0.06
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
ATGAAAATCGCAATGCGAA
Found at i:577880 original size:128 final size:128
Alignment explanation
Indices: 577689--577975 Score: 450
Period size: 128 Copynumber: 2.3 Consensus size: 128
577679 AAATCCCAAC
*
577689 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAA
* * *
577749 TCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGAA
65 TCGCAATGCGAAATAAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAA
577813 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAAT
577878 CGCAATGCGAAATAAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAA
66 CGCAATGCGAAATAAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAA
*
577941 ATGAAAATCGCAA--CG--A-GATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAAT
577976 TATAAACGCA
Statistics
Matches: 153, Mismatches: 5, Indels: 11
0.91 0.03 0.07
Matches are distributed among these distances:
123 34 0.22
124 17 0.11
125 2 0.01
126 2 0.01
127 1 0.01
128 97 0.63
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (128 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAAT
CGCAATGCGAAATAAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAA
Found at i:577991 original size:52 final size:52
Alignment explanation
Indices: 577662--577975 Score: 312
Period size: 52 Copynumber: 5.9 Consensus size: 52
577652 CGGAAAATAC
* *
577662 AATCGCAACGCGAAATG-AAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAAAATCGCAATGC-GAAATGAA
*
577714 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAA
* *
577766 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAA
577818 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAA
*
577875 AATCGCAATGCGAAATAAAAATCGCAACGA-AAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA-AATCGCAATGCGAAATGAA
*
577927 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAAT
577976 TATAAACGCA
Statistics
Matches: 239, Mismatches: 8, Indels: 30
0.86 0.03 0.11
Matches are distributed among these distances:
47 1 0.00
48 8 0.03
50 3 0.01
51 2 0.01
52 135 0.56
53 18 0.08
54 6 0.03
55 3 0.01
57 63 0.26
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:578026 original size:19 final size:19
Alignment explanation
Indices: 577982--578083 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
577972 AAATTATAAA
577982 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
578001 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
578021 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
578037 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
578054 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
578073 CGCATTGCGAT
1 CGCATTGCGAT
578084 AGTAATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:578091 original size:19 final size:19
Alignment explanation
Indices: 578050--578091 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
578040 TGCGATTTTC
** *
578050 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATAGTA
578069 ATTTCGCATTGCGATAGTA
1 ATTTCGCATTGCGATAGTA
578088 ATTT
1 ATTT
578092 TTGCCTTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (19 bp):
ATTTCGCATTGCGATAGTA
Found at i:578206 original size:13 final size:14
Alignment explanation
Indices: 578190--578225 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
578180 CATCAATTAC
578190 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
*
578203 ACAAATCATCTTTT
1 ACAAATCAACTTTT
578217 ACAAATCAA
1 ACAAATCAA
578226 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:580150 original size:20 final size:19
Alignment explanation
Indices: 580125--580189 Score: 80
Period size: 18 Copynumber: 3.4 Consensus size: 19
580115 TAGTTTACTT
*
580125 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
*
580145 TCGCAACGCGAAAC-CAAA
1 TCGCAACGCGAAACTAAAA
580163 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
580182 TCGCAACG
1 TCGCAACG
580190 ACAGAATCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
18 16 0.40
19 11 0.28
20 13 0.32
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:580184 original size:19 final size:19
Alignment explanation
Indices: 580125--580258 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
580115 TAGTTTACTT
* *
580125 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
580145 TCGCAACGCGAAA-CCAAA
1 TCGCAACGCGAAATGAAAA
580163 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
580182 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
580196 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
580215 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
580229 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
580248 TCGCAATGCGA
1 TCGCAACGCGA
580259 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 8, Indels: 23
0.75 0.06 0.18
Matches are distributed among these distances:
14 16 0.17
16 11 0.12
17 11 0.12
18 16 0.17
19 29 0.31
20 12 0.13
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:580199 original size:14 final size:14
Alignment explanation
Indices: 580180--580236 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
580170 GCGAAATGAA
*
580180 AATCGCAACGACAG
1 AATCGCAACGAAAG
580194 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
580211 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
580227 AATCGCAACG
1 AATCGCAACG
580237 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:580207 original size:33 final size:33
Alignment explanation
Indices: 580125--580253 Score: 168
Period size: 33 Copynumber: 3.8 Consensus size: 33
580115 TAGTTTACTT
* * *
580125 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAA
1 TCGCAACGCGAAA-TGAAAATCGCAA--CGAAA--GAA
*
580163 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAATGAAAATCGCAACGAAAGAA
*
580196 TCGCAATGCGAAATGAAAATCGCAACGAAAGAA
1 TCGCAACGCGAAATGAAAATCGCAACGAAAGAA
580229 TCGCAACGCGAAATGAAAATCGCAA
1 TCGCAACGCGAAATGAAAATCGCAA
580254 TGCGATTTTG
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
33 57 0.68
35 4 0.05
37 11 0.13
38 12 0.14
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (33 bp):
TCGCAACGCGAAATGAAAATCGCAACGAAAGAA
Found at i:580276 original size:19 final size:19
Alignment explanation
Indices: 580254--580382 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
580244 AAAATCGCAA
580254 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
580273 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
580287 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
580306 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
580320 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
580339 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
580358 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
580378 TGCGA
1 TGCGA
580383 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:580296 original size:33 final size:33
Alignment explanation
Indices: 580254--580345 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
580244 AAAATCGCAA
580254 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
580287 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
580320 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
580346 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:580719 original size:93 final size:93
Alignment explanation
Indices: 580426--580896 Score: 903
Period size: 93 Copynumber: 5.1 Consensus size: 93
580416 TTGAATGGAT
580426 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
580491 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
580519 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
580582 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
580610 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
580675 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
580703 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
580767 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
580795 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
580860 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
580888 AAATTTACT
1 AAATTTACT
580897 AAGCAATCTA
Statistics
Matches: 372, Mismatches: 3, Indels: 6
0.98 0.01 0.02
Matches are distributed among these distances:
91 89 0.24
92 95 0.26
93 188 0.51
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:580735 original size:184 final size:185
Alignment explanation
Indices: 580426--580896 Score: 917
Period size: 185 Copynumber: 2.6 Consensus size: 185
580416 TTGAATGGAT
580426 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
580491 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
580556 TATA-TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
580610 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
580675 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
580740 TATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
580795 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
580860 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
580897 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
184 134 0.47
185 150 0.53
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:582617 original size:14 final size:14
Alignment explanation
Indices: 582598--582687 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
582588 TTGAAATGAA
582598 AATCGCAACGAGAG
1 AATCGCAACGAGAG
582612 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
582629 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
582645 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
582664 AATCGCAACGAGAG
1 AATCGCAACGAGAG
582678 AATCGCAACG
1 AATCGCAACG
582688 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:582635 original size:33 final size:33
Alignment explanation
Indices: 582590--582704 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
582580 TCTTTTGGTT
582590 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
582623 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
582656 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
582689 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
582705 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:582636 original size:19 final size:18
Alignment explanation
Indices: 582597--582709 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
582587 GTTGAAATGA
582597 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
582612 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
582629 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
582645 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
582662 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
582678 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
582695 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
582710 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:582740 original size:14 final size:14
Alignment explanation
Indices: 582721--582775 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
582711 TTTGGTTTCG
582721 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
582735 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
582754 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
582768 CGTTGCGA
1 CGTTGCGA
582776 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:582753 original size:33 final size:33
Alignment explanation
Indices: 582705--582775 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
582695 AAAATCGCAA
**
582705 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
582738 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
582771 TGCGA
1 TGCGA
582776 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:582783 original size:33 final size:33
Alignment explanation
Indices: 582716--582797 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
582706 GCGATTTTGG
***
582716 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
582749 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
582782 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
582798 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:582802 original size:20 final size:20
Alignment explanation
Indices: 582728--582816 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
582718 TCGCGTTGCG
582728 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
582748 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
582761 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
582781 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
582801 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
582817 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:582938 original size:33 final size:33
Alignment explanation
Indices: 582896--582966 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
582886 AATACTAACT
*
582896 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
582929 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
582962 TGAAA
1 TGAAA
582967 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:583200 original size:22 final size:22
Alignment explanation
Indices: 583148--583202 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
583138 TGGTTGTGAG
**
583148 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
583170 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
583192 GGATTTCTTCG
1 GGATTTCTTCG
583203 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:583373 original size:20 final size:20
Alignment explanation
Indices: 583348--583540 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
583338 CTTTAAATAT
583348 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
583368 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
583390 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
583409 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
583429 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
583449 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
583469 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
583489 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
583509 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
583529 CGCGTTGCGATT
1 CGCGTTGCGATT
583541 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:583535 original size:60 final size:60
Alignment explanation
Indices: 583348--583540 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
583338 CTTTAAATAT
**
583348 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
583409 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
583469 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
583529 CGCGTTGCGATT
1 CGCGTTGCGATT
583541 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:583621 original size:20 final size:20
Alignment explanation
Indices: 583596--583647 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
583586 AAGAATCGCG
*
583596 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
583616 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
583636 TTGCGATTCTGG
1 TTGCGATTCTGG
583648 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:604412 original size:23 final size:23
Alignment explanation
Indices: 604382--604426 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
604372 TTCCATTAGT
604382 GGGTAATGGTTTAGTCATATGGC
1 GGGTAATGGTTTAGTCATATGGC
604405 GGGTAATGGTTTAGTCATATGG
1 GGGTAATGGTTTAGTCATATGG
604427 TCGGCAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.07, G:0.36, T:0.36
Consensus pattern (23 bp):
GGGTAATGGTTTAGTCATATGGC
Found at i:604569 original size:78 final size:78
Alignment explanation
Indices: 604451--604602 Score: 268
Period size: 78 Copynumber: 1.9 Consensus size: 78
604441 GAACTCGCGG
* * *
604451 TGTCTGAAGTGTATCGAGATAGCCCACTGCTTGCATAAATAGAATATGATCCTTCTGATAAGCAT
1 TGTCTGAAGTGTATCGAGATAGCCCACTGCTTGCACAAATAAAATATAATCCTTCTGATAAGCAT
604516 ATTAGACTCGCAT
66 ATTAGACTCGCAT
604529 TGTCTGAAGTGTATCGAGATAGCCCACTGCTTGCACAAATAAAATATAATCCTTCTGATAAGCAT
1 TGTCTGAAGTGTATCGAGATAGCCCACTGCTTGCACAAATAAAATATAATCCTTCTGATAAGCAT
*
604594 ATTGGACTC
66 ATTAGACTC
604603 AGGGTCGTGG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (78 bp):
TGTCTGAAGTGTATCGAGATAGCCCACTGCTTGCACAAATAAAATATAATCCTTCTGATAAGCAT
ATTAGACTCGCAT
Done.