Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 91 of 175
Found at i:28911845 original size:22 final size:21
Alignment explanation
Indices: 28911799--28911846 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
28911789 ATTTGTTGGT
28911799 AAAAACTCATTTCTAAGTTTTA
1 AAAAACTCATTTCTAAG-TTTA
* *
28911821 AAAACCTC-TTTTTAATGTTTA
1 AAAAACTCATTTCTAA-GTTTA
28911842 AAAAA
1 AAAAA
28911847 ACACCCAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (21 bp):
AAAAACTCATTTCTAAGTTTA
Found at i:28912330 original size:28 final size:27
Alignment explanation
Indices: 28912285--28912398 Score: 183
Period size: 28 Copynumber: 4.1 Consensus size: 27
28912275 CTATTCAGTG
*
28912285 ACAGTATAGTATGGGCCTTAGCCCAAT
1 ACAGTATAGTGTGGGCCTTAGCCCAAT
28912312 ACAGTATCAGTGTGGGCCTTAGCCCAAT
1 ACAGTAT-AGTGTGGGCCTTAGCCCAAT
28912340 ACAGTATCAGTGTGGGCCTTAGCCCAAT
1 ACAGTAT-AGTGTGGGCCTTAGCCCAAT
*
28912368 ACAGTAATAGTGTGGGGCTTAGCCCAAT
1 ACAGT-ATAGTGTGGGCCTTAGCCCAAT
28912396 ACA
1 ACA
28912399 ATAACAATGC
Statistics
Matches: 83, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
27 7 0.08
28 74 0.89
29 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (27 bp):
ACAGTATAGTGTGGGCCTTAGCCCAAT
Found at i:28912790 original size:27 final size:26
Alignment explanation
Indices: 28912771--28913054 Score: 282
Period size: 27 Copynumber: 10.6 Consensus size: 26
28912761 GGGTATAATA
*
28912771 GTCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTA-TTTC
* *
28912798 GTCATTTTACCCTATAGAGGTATTTC
1 GTCATTTTACCCTATGGGGGTATTTC
* *
28912824 GATCATTTTACCCTATAGGGGTATTCTG
1 G-TCATTTTACCCTATGGGGGTATT-TC
* *
28912852 GTCATTTTACCCTATAGGGGTATTCTG
1 GTCATTTTACCCTATGGGGGTATT-TC
*
28912879 GTCATTTTACCCTATGGGGGTAATTC
1 GTCATTTTACCCTATGGGGGTATTTC
* *
28912905 GGTTATTCTACCCTATGGGGGTATTTC
1 -GTCATTTTACCCTATGGGGGTATTTC
* * *
28912932 GATTATCTTACCCTATGAGGGTATTTC
1 G-TCATTTTACCCTATGGGGGTATTTC
* * *
28912959 GATCATTTTATCCTATGAGCGTATTTC
1 G-TCATTTTACCCTATGGGGGTATTTC
**
28912986 AGTCATTTTACCCTACAGGGGTATTTC
1 -GTCATTTTACCCTATGGGGGTATTTC
**
28913013 GATCATTTTACCCTAT-GGTATATTTC
1 G-TCATTTTACCCTATGGGGGTATTTC
*
28913039 GGTCATTTAACCCTAT
1 -GTCATTTTACCCTAT
28913055 TTTGGGGTCT
Statistics
Matches: 223, Mismatches: 27, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
26 28 0.13
27 192 0.86
28 3 0.01
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.41
Consensus pattern (26 bp):
GTCATTTTACCCTATGGGGGTATTTC
Found at i:28912881 original size:81 final size:79
Alignment explanation
Indices: 28912772--28913054 Score: 320
Period size: 81 Copynumber: 3.5 Consensus size: 79
28912762 GGTATAATAG
*
28912772 TCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATAGAGGTATTTCGATCATTTTACCC
1 TCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTAT-GAGGTATTTCGATCATTTTACCC
*
28912837 TATAGGGGTA-TTCTGG
64 TATAGGGGTATTTC-GA
* * * * *
28912853 TCATTTTACCCTATAGGGGTA-TTCTGGTCATTTTACCCTATGGGGGTAATTCGGTTATTCTACC
1 TCATTTTACCCTAT-GGGGTATTTC-GGTCATTTTACCCTAT-GAGGTATTTCGATCATTTTACC
*
28912917 CTATGGGGGTATTTCGA
63 CTATAGGGGTATTTCGA
* * * *
28912934 TTATCTTACCCTATGAGGGTATTTCGATCATTTTATCCTATGAGCGTATTTC-AGTCATTTTACC
1 TCATTTTACCCTATG-GGGTATTTCGGTCATTTTACCCTATGAG-GTATTTCGA-TCATTTTACC
*
28912998 CTACAGGGGTATTTCGA
63 CTATAGGGGTATTTCGA
** *
28913015 TCATTTTACCCTATGGTATATTTCGGTCATTTAACCCTAT
1 TCATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTAT
28913055 TTTGGGGTCT
Statistics
Matches: 168, Mismatches: 28, Indels: 13
0.80 0.13 0.06
Matches are distributed among these distances:
80 25 0.15
81 137 0.82
82 6 0.04
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.41
Consensus pattern (79 bp):
TCATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATGAGGTATTTCGATCATTTTACCCTA
TAGGGGTATTTCGA
Found at i:28918515 original size:21 final size:21
Alignment explanation
Indices: 28918476--28918516 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28918466 TAAAGTAGAC
*
28918476 TATATATTATTTTTATAGTAT
1 TATATATTATATTTATAGTAT
28918497 TATATATTATGATTT-TAGTA
1 TATATATTAT-ATTTATAGTA
28918517 AATTCATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (21 bp):
TATATATTATATTTATAGTAT
Found at i:28918804 original size:48 final size:49
Alignment explanation
Indices: 28918743--28918839 Score: 137
Period size: 48 Copynumber: 2.0 Consensus size: 49
28918733 ATTATAATAT
*
28918743 CATTCCATTCAACCAAACACA-AGAA-TAC-TATTACAGTTCTATTTCATC
1 CATTCCATTCAACCAAACA-ATA-AATTACTTATTACAGCTCTATTTCATC
28918791 CATTCCATTCAACCAAACAATTAAATTACTTATTACAGCTCTATTTCAT
1 CATTCCATTCAACCAAACAA-TAAATTACTTATTACAGCTCTATTTCAT
28918840 TATAGGTCTA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
47 1 0.02
48 21 0.48
49 4 0.09
50 18 0.41
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (49 bp):
CATTCCATTCAACCAAACAATAAATTACTTATTACAGCTCTATTTCATC
Found at i:28918890 original size:16 final size:16
Alignment explanation
Indices: 28918822--28918892 Score: 81
Period size: 16 Copynumber: 4.4 Consensus size: 16
28918812 TAAATTACTT
28918822 ATTACAGCTCTATTTC-
1 ATTACAGCTCTA-TTCA
* *
28918838 ATTATAGGTCTATTCA
1 ATTACAGCTCTATTCA
* *
28918854 ATTATAGCGCTATTCA
1 ATTACAGCTCTATTCA
*
28918870 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCA
28918886 ATTACAG
1 ATTACAG
28918893 TGAACCAAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
15 3 0.06
16 44 0.94
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:28930865 original size:48 final size:48
Alignment explanation
Indices: 28930787--28931062 Score: 278
Period size: 48 Copynumber: 5.8 Consensus size: 48
28930777 AACCCGTATA
*
28930787 TATATGTGTGATAAGGCCGAATGGCTAATGTGAAATATATGTGTGATATG
1 TATATGTG-G-TAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATG
* * * *
28930837 TATATGTGGTAAAGCCGAATGGCGAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATG
*
28930885 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTTTGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATG
* * * *
28930933 TATATGTGGTAAAGCCGAATGGCCAATGTG--ATAAATGTGAG-CATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATG
* * * * * *
28930978 CATATATGTGATAAGGCCGAATGGCCAATGTG--GTGA-ATATG-GAAATG
1 --TATATGTGGTAAAGCCGAATGGCTAATGTGAAAT-ATATGTGTGATATG
* *
28931025 CATATATGCGGTAAAGCCGAATGGCTAGTGTGAAATAT
1 --TATATGTGGTAAAGCCGAATGGCTAATGTGAAATAT
28931063 GTAGGCGATG
Statistics
Matches: 193, Mismatches: 26, Indels: 15
0.82 0.11 0.06
Matches are distributed among these distances:
45 3 0.02
46 9 0.05
47 63 0.33
48 108 0.56
49 2 0.01
50 8 0.04
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.30
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATG
Found at i:28930911 original size:96 final size:96
Alignment explanation
Indices: 28930786--28931065 Score: 324
Period size: 96 Copynumber: 2.9 Consensus size: 96
28930776 GAACCCGTAT
28930786 ATATATGTGTGATAAGGCCGAATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAG
1 ATATATGTG-G-TAAGGCCGAATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAG
* *
28930851 CCGAATGGCGAATGTGAAATATGTATGAGATATG
64 CCGAATGGCCAATGTGAAATATGTATGAG-CATG
* *
28930885 -TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTTTGATATGTATATGTGGTAAAGCC
1 ATATATGTGGTAAGGCCGAATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCC
28930949 GAATGGCCAATGTGATAA-ATG--TGAGCATG
66 GAATGGCCAATGTGA-AATATGTATGAGCATG
* * * * * *
28930978 CATATATGTGATAAGGCCGAATGGCCAATGTG--GTGA-ATATG-GAAATGCATATATGCGGTAA
1 -ATATATGTGGTAAGGCCGAATGGCTAATGTGAAAT-ATATGTGTGATATG--TATATGTGGTAA
* *
28931039 AGCCGAATGGCTAGTGTGAAATATGTA
62 AGCCGAATGGCCAATGTGAAATATGTA
28931066 GGCGATGTGC
Statistics
Matches: 158, Mismatches: 14, Indels: 21
0.82 0.07 0.11
Matches are distributed among these distances:
92 5 0.03
93 9 0.06
94 36 0.23
95 27 0.17
96 70 0.44
97 3 0.02
98 8 0.05
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.30
Consensus pattern (96 bp):
ATATATGTGGTAAGGCCGAATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCC
GAATGGCCAATGTGAAATATGTATGAGCATG
Found at i:28931262 original size:37 final size:37
Alignment explanation
Indices: 28931212--28931363 Score: 232
Period size: 37 Copynumber: 4.1 Consensus size: 37
28931202 GGAAATATAT
*
28931212 TCCGGGTGAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
28931249 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
28931286 TCCGGGTAAGACCCGATGACTACTTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* * * * *
28931323 TTCGGGTAAGATCCGATAACTTCGTGTGGAGATTACG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
28931360 TCCG
1 TCCG
28931364 AGCTAAAGGT
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 104 1.00
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:28932531 original size:12 final size:13
Alignment explanation
Indices: 28932506--28932534 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28932496 TAGGTTTCCA
28932506 AAAATGGAAAATG
1 AAAATGGAAAATG
28932519 AAAATGG-AAATG
1 AAAATGGAAAATG
28932531 AAAA
1 AAAA
28932535 CTTGCAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.14
Consensus pattern (13 bp):
AAAATGGAAAATG
Found at i:28942283 original size:18 final size:19
Alignment explanation
Indices: 28942250--28942285 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
28942240 CTTGAAAAGG
28942250 TATTTGATATAGCGATTTT
1 TATTTGATATAGCGATTTT
*
28942269 TATTTTATA-AGCGATTT
1 TATTTGATATAGCGATTT
28942286 ATTAAGTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.53
Consensus pattern (19 bp):
TATTTGATATAGCGATTTT
Found at i:28956947 original size:23 final size:23
Alignment explanation
Indices: 28956905--28956950 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
28956895 CTGTCTTATT
*
28956905 GTAGTAAATTTCGGGGTATTACA
1 GTAGTAAATTTCGGGATATTACA
* *
28956928 GTAGTAATTTTTGGGATATTACA
1 GTAGTAAATTTCGGGATATTACA
28956951 TACACGACCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.07, G:0.24, T:0.39
Consensus pattern (23 bp):
GTAGTAAATTTCGGGATATTACA
Found at i:28960071 original size:11 final size:11
Alignment explanation
Indices: 28960055--28960088 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
28960045 AGGCATAAAG
28960055 ATGTTCACACC
1 ATGTTCACACC
*
28960066 ATGTTCA-GCC
1 ATGTTCACACC
28960076 ATGTTCACACC
1 ATGTTCACACC
28960087 AT
1 AT
28960089 ATGGCTCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.26, C:0.32, G:0.12, T:0.29
Consensus pattern (11 bp):
ATGTTCACACC
Found at i:28960901 original size:13 final size:12
Alignment explanation
Indices: 28960868--28960918 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 12
28960858 AAATTGTAGT
28960868 TTCGAGAAAAAAA
1 TTCGA-AAAAAAA
28960881 TT-GAAAAAACAAA
1 TTCG-AAAAA-AAA
28960894 TTCGAAAAAAATA
1 TTCGAAAAAAA-A
28960907 TTCGAAAAAAAA
1 TTCGAAAAAAAA
28960919 GAAGAGAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 8 0.24
13 25 0.74
14 1 0.03
ACGTcount: A:0.65, C:0.08, G:0.10, T:0.18
Consensus pattern (12 bp):
TTCGAAAAAAAA
Found at i:28974333 original size:11 final size:11
Alignment explanation
Indices: 28974317--28974350 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
28974307 AGGCATAAAG
28974317 ATGTTCACACC
1 ATGTTCACACC
*
28974328 ATGTTCA-GCC
1 ATGTTCACACC
28974338 ATGTTCACACC
1 ATGTTCACACC
28974349 AT
1 AT
28974351 ATGGCTCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.26, C:0.32, G:0.12, T:0.29
Consensus pattern (11 bp):
ATGTTCACACC
Found at i:28990037 original size:27 final size:27
Alignment explanation
Indices: 28990007--28990184 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28989997 ATATCGAGTC
* * * *
28990007 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
28990034 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
28990061 TGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28990089 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28990116 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28990143 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28990170 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28990185 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 107 0.82
28 23 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28990148 original size:82 final size:81
Alignment explanation
Indices: 28990028--28990183 Score: 235
Period size: 82 Copynumber: 1.9 Consensus size: 81
28990018 TGCTATATAA
*
28990028 TCAACTCGCACACTTAGTGCTACATAATCAAATTGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATTGCACACTTAGTGCAACATAGTCAAA-TCGCA
28990093 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * *
28990110 TCAATTCGCACACTTAGTGC-ATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAATCGC
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATT-GCACACTTAGTGCAACATAGTCAAATCGC
28990173 ACACTTAGTGC
64 ACACTTAGTGC
28990184 TGTACAATTT
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
81 19 0.28
82 49 0.72
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATTGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28998073 original size:27 final size:27
Alignment explanation
Indices: 28998043--28998219 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
28998033 ATATCGAGTC
* * * *
28998043 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
28998070 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28998097 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** *
28998125 CGCACACTTAGTGCCGCAT-GTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28998151 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28998178 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28998205 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28998220 GTACATTTAT
Statistics
Matches: 132, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
26 18 0.14
27 95 0.72
28 19 0.14
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28998157 original size:81 final size:80
Alignment explanation
Indices: 28998064--28998218 Score: 240
Period size: 81 Copynumber: 1.9 Consensus size: 80
28998054 TGCTATATAA
*
28998064 TCAACTCGCACACTTAGTGC-TACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGC
1 TCAACTCGCACACTTAGTGCAT-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGC
28998128 ACACTTAGTGCCGCATG
64 ACACTTAGTGCCGCATG
* * **
28998145 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCAC
1 TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
28998210 ACTTAGTGC
66 ACTTAGTGC
28998219 TGTACATTTA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
80 15 0.22
81 52 0.76
82 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.27
Consensus pattern (80 bp):
TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATG
Found at i:28998240 original size:54 final size:53
Alignment explanation
Indices: 28998043--28998242 Score: 190
Period size: 54 Copynumber: 3.7 Consensus size: 53
28998033 ATATCGAGTC
* * * * * *
28998043 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACAT-ATTATCTCGCACACTTAGTGCAACATAGTCAAAT
* * ** *
28998097 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCAT-GTCAATT
1 CGCACACTTAGTGCTACATA-T-TATCTCGCACACTTAGTGCAACATAGTCAAAT
*
28998151 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATATT-ATCTCGCACACTTAGTGCAACATAGTCAAAT
* *
28998205 CGCACACTTAGTGCTGTACAT-TTATCCCGCGCACTTAG
1 CGCACACTTAGTGC--TACATATTATCTCGCACACTTAG
28998243 CGCCAATCTC
Statistics
Matches: 122, Mismatches: 16, Indels: 16
0.79 0.10 0.10
Matches are distributed among these distances:
53 22 0.18
54 73 0.60
55 23 0.19
56 3 0.02
57 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.28
Consensus pattern (53 bp):
CGCACACTTAGTGCTACATATTATCTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:29004918 original size:16 final size:16
Alignment explanation
Indices: 29004897--29004928 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29004887 AATTGGGTTG
*
29004897 AGAAAATTATTTAATT
1 AGAAAATTAATTAATT
29004913 AGAAAATTAATTAATT
1 AGAAAATTAATTAATT
29004929 TCATTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (16 bp):
AGAAAATTAATTAATT
Found at i:29007662 original size:53 final size:54
Alignment explanation
Indices: 29007534--29007669 Score: 168
Period size: 53 Copynumber: 2.5 Consensus size: 54
29007524 TTTAATTTTG
* * * * **
29007534 TAAATGTTTATTTTAAGTTGTTTGAATATGGAGAATGGTTGTTGTCTTAATGTCT
1 TAAATGTGTATTTTTAGTTGTCTG-ATGTGGAGAATGGTTGTCATCTTAATGTCT
*
29007589 TAAATGTGTATTTTTAGTTGTCTGATGTGGAGAATGGTTG-CATCTTAATGTTT
1 TAAATGTGTATTTTTAGTTGTCTGATGTGGAGAATGGTTGTCATCTTAATGTCT
*
29007642 TAAATG-GTATTTTTATGTTGTCTCATGT
1 TAAATGTGTATTTTTA-GTTGTCTGATGT
29007670 TGAATAATGG
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
52 9 0.12
53 27 0.38
54 15 0.21
55 21 0.29
ACGTcount: A:0.24, C:0.05, G:0.22, T:0.49
Consensus pattern (54 bp):
TAAATGTGTATTTTTAGTTGTCTGATGTGGAGAATGGTTGTCATCTTAATGTCT
Found at i:29025866 original size:21 final size:22
Alignment explanation
Indices: 29025821--29025866 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
29025811 AGAGAAAAAT
*
29025821 AAAAGTGAAAAAGAAGAAAATG
1 AAAAGTGAAAAAGAAGAAAAGG
**
29025843 AAAA-TGAAAAAGGCGAAAAGG
1 AAAAGTGAAAAAGAAGAAAAGG
29025864 AAA
1 AAA
29025867 GCGAGAGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.07
Consensus pattern (22 bp):
AAAAGTGAAAAAGAAGAAAAGG
Found at i:29032800 original size:10 final size:11
Alignment explanation
Indices: 29032777--29032810 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
29032767 AGGCATAAAG
29032777 ATGTTCACACC
1 ATGTTCACACC
29032788 ATGTTCA-ACC
1 ATGTTCACACC
29032798 ATGTTCACACC
1 ATGTTCACACC
29032809 AT
1 AT
29032811 ATGGCTCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.29, C:0.32, G:0.09, T:0.29
Consensus pattern (11 bp):
ATGTTCACACC
Found at i:29034469 original size:15 final size:16
Alignment explanation
Indices: 29034442--29034474 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
29034432 CTCACATTGT
29034442 AATAAAAATGAAAAAG
1 AATAAAAATGAAAAAG
29034458 AATAAAAA-GAAAAAG
1 AATAAAAATGAAAAAG
29034473 AA
1 AA
29034475 AGTGAAGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (16 bp):
AATAAAAATGAAAAAG
Found at i:29034524 original size:5 final size:6
Alignment explanation
Indices: 29034461--29034580 Score: 60
Period size: 6 Copynumber: 19.5 Consensus size: 6
29034451 GAAAAAGAAT
** * * * *
29034461 AAAAAG AAAAAG AAAGTG AAGAAG AAAATG AAAATG AAAAAT AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
** * ** ** * * *
29034509 AAATTG CAAAAG AAAAAG AAATTG AAAAAG TGAGAG AAAAAT AAAACG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
*
29034557 AAGAAAC AAAAATTG AAAAAG AAA
1 AA-AAAG AAAAA--G AAAAAG AAA
29034581 TTGAGATTGA
Statistics
Matches: 79, Mismatches: 32, Indels: 6
0.68 0.27 0.05
Matches are distributed among these distances:
6 70 0.89
7 4 0.05
8 5 0.06
ACGTcount: A:0.70, C:0.03, G:0.17, T:0.10
Consensus pattern (6 bp):
AAAAAG
Found at i:29034537 original size:18 final size:18
Alignment explanation
Indices: 29034445--29034538 Score: 104
Period size: 18 Copynumber: 5.3 Consensus size: 18
29034435 ACATTGTAAT
29034445 AAAAATGAAAAAG-AA-T-
1 AAAAA-GAAAAAGAAATTG
*
29034461 AAAAAGAAAAAGAAAGTG
1 AAAAAGAAAAAGAAATTG
* * *
29034479 AAGAAGAAAATGAAAATG
1 AAAAAGAAAAAGAAATTG
*
29034497 AAAAATAAAAAGAAATTG
1 AAAAAGAAAAAGAAATTG
*
29034515 CAAAAGAAAAAGAAATTG
1 AAAAAGAAAAAGAAATTG
29034533 AAAAAG
1 AAAAAG
29034539 TGAGAGAAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
15 7 0.11
16 7 0.11
17 1 0.02
18 50 0.77
ACGTcount: A:0.71, C:0.01, G:0.17, T:0.11
Consensus pattern (18 bp):
AAAAAGAAAAAGAAATTG
Found at i:29034538 original size:12 final size:12
Alignment explanation
Indices: 29034446--29034529 Score: 62
Period size: 12 Copynumber: 6.8 Consensus size: 12
29034436 CATTGTAATA
29034446 AAAATGAAAAAG
1 AAAATGAAAAAG
*
29034458 AATAAAAAGAAAAAG
1 ---AAAATGAAAAAG
* *
29034473 AAAGTGAAGAAG
1 AAAATGAAAAAG
*
29034485 AAAATGAAAATG
1 AAAATGAAAAAG
29034497 AAAAAT-AAAAAG
1 -AAAATGAAAAAG
* *
29034509 AAATTGCAAAAG
1 AAAATGAAAAAG
*
29034521 AAAAAGAAA
1 AAAATGAAA
29034530 TTGAAAAAGT
Statistics
Matches: 54, Mismatches: 13, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
11 4 0.07
12 34 0.63
13 5 0.09
15 11 0.20
ACGTcount: A:0.73, C:0.01, G:0.17, T:0.10
Consensus pattern (12 bp):
AAAATGAAAAAG
Found at i:29034612 original size:17 final size:18
Alignment explanation
Indices: 29034592--29034629 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
29034582 TGAGATTGAG
29034592 AAAAAAT-TTGAAAAAGA
1 AAAAAATGTTGAAAAAGA
* *
29034609 AAAAGATGTTGAAAAATA
1 AAAAAATGTTGAAAAAGA
29034627 AAA
1 AAA
29034630 GAGAGAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.18
Consensus pattern (18 bp):
AAAAAATGTTGAAAAAGA
Found at i:29037129 original size:16 final size:15
Alignment explanation
Indices: 29037108--29037137 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
29037098 GTTTGGTTAA
29037108 GGATAGAAACAAGGTG
1 GGATAGAAA-AAGGTG
29037124 GGATAGAAAAAGGT
1 GGATAGAAAAAGGT
29037138 AATTGATGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.03, G:0.37, T:0.13
Consensus pattern (15 bp):
GGATAGAAAAAGGTG
Found at i:29052631 original size:20 final size:19
Alignment explanation
Indices: 29052601--29052650 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
29052591 TCACTCTCAA
29052601 TCTCTTTTTTCTCTTTTTCAT
1 TCTC-TTTTTCT-TTTTTCAT
*
29052622 TCTCTTTTTCTTTTTTGAT
1 TCTCTTTTTCTTTTTTCAT
29052641 T-TCTTTTTCT
1 TCTCTTTTTCT
29052651 GTCTTCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 8 0.29
20 7 0.25
21 4 0.14
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.74
Consensus pattern (19 bp):
TCTCTTTTTCTTTTTTCAT
Found at i:29052635 original size:18 final size:17
Alignment explanation
Indices: 29052607--29052650 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
29052597 TCAATCTCTT
29052607 TTTTCTCTTTTTCATTCTC
1 TTTT-TCTTTTTCATT-TC
*
29052626 TTTTTCTTTTTTGATTTC
1 TTTTTC-TTTTTCATTTC
29052644 TTTTTCT
1 TTTTTCT
29052651 GTCTTCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 1 0.04
18 10 0.43
19 12 0.52
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTTCTTTTTCATTTC
Found at i:29059199 original size:20 final size:20
Alignment explanation
Indices: 29059176--29059220 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
29059166 TAGCTCCAAC
*
29059176 CAGCTCATTTGAGCTCAATT
1 CAGCTCATTTAAGCTCAATT
29059196 CAGCTCATTTAAGCTCAATT
1 CAGCTCATTTAAGCTCAATT
*
29059216 TAGCT
1 CAGCT
29059221 TTTTATCAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (20 bp):
CAGCTCATTTAAGCTCAATT
Found at i:29072427 original size:12 final size:12
Alignment explanation
Indices: 29072410--29072440 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
29072400 CCACCCTTAA
29072410 ACACATTGAATT
1 ACACATTGAATT
29072422 ACACATTGAATT
1 ACACATTGAATT
29072434 ACACATT
1 ACACATT
29072441 AAATCAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (12 bp):
ACACATTGAATT
Found at i:29072660 original size:20 final size:20
Alignment explanation
Indices: 29072637--29072691 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
29072627 AGTTCAATTC
29072637 AGCTTAATTTTAGCTCAATG
1 AGCTTAATTTTAGCTCAATG
**
29072657 AGC-TCGTTCTTAGCTCAATG
1 AGCTTAATT-TTAGCTCAATG
*
29072677 AGCTTATTTTTAGCT
1 AGCTTAATTTTAGCT
29072692 TACTTTAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.10
20 23 0.79
21 3 0.10
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (20 bp):
AGCTTAATTTTAGCTCAATG
Found at i:29077141 original size:20 final size:20
Alignment explanation
Indices: 29077118--29077163 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
29077108 TCAGCTAATT
*
29077118 TTAGCTCAATGAGCTCGTTC
1 TTAGCTCAATGAGCTCATTC
*
29077138 TTAGCTCAATGAGCTCATTT
1 TTAGCTCAATGAGCTCATTC
29077158 TTAGCT
1 TTAGCT
29077164 TCCTTTAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCAATGAGCTCATTC
Found at i:29079316 original size:28 final size:27
Alignment explanation
Indices: 29079284--29079337 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
29079274 ATAAATCAGC
* *
29079284 ACAACCAGAAATTAATAAAGATGAAAGA
1 ACAACAAGAAAATAATAAAGAT-AAAGA
*
29079312 ACAACAAGAAAATAGTAAAGATAAAG
1 ACAACAAGAAAATAATAAAGATAAAG
29079338 TCCTAAGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.63, C:0.09, G:0.15, T:0.13
Consensus pattern (27 bp):
ACAACAAGAAAATAATAAAGATAAAGA
Found at i:29083698 original size:21 final size:22
Alignment explanation
Indices: 29083669--29083719 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
29083659 TCTCTCTCGC
*
29083669 TTTCCTTTTCGCCTTTTTCA-T
1 TTTCATTTTCGCCTTTTTCACT
**
29083690 TTTCATTTTCTTCTTTTTCACT
1 TTTCATTTTCGCCTTTTTCACT
29083712 TTT-ATTTT
1 TTTCATTTT
29083720 TCTCTTCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.08, C:0.22, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCATTTTCGCCTTTTTCACT
Found at i:29085723 original size:29 final size:27
Alignment explanation
Indices: 29085685--29085739 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
29085675 GTGATTAAAT
29085685 AAAATCGACA-CAAGCAGAATTTAAAAGAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAA
*
29085714 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
29085740 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 2 0.08
29 10 0.42
30 4 0.17
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.15
Consensus pattern (27 bp):
AAAATCGACAGCAAGAAATTAAAAGAA
Found at i:29102508 original size:14 final size:14
Alignment explanation
Indices: 29102489--29102515 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29102479 TTCGAGAGAT
29102489 TTGTGAGGTTTTTG
1 TTGTGAGGTTTTTG
29102503 TTGTGAGGTTTTT
1 TTGTGAGGTTTTT
29102516 ATTTTTTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.00, G:0.33, T:0.59
Consensus pattern (14 bp):
TTGTGAGGTTTTTG
Found at i:29104248 original size:24 final size:23
Alignment explanation
Indices: 29104216--29104266 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
29104206 AAATGAGAGA
* *
29104216 AAAAGAAAA-GAGTGAAAATAAAG
1 AAAAGAAAATGAG-AAAAAGAAAG
29104239 AAAAGAAAAATGAGAAAAAGAAAG
1 AAAAG-AAAATGAGAAAAAGAAAG
29104263 AAAA
1 AAAA
29104267 TCTGAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.21
24 16 0.67
25 3 0.12
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.06
Consensus pattern (23 bp):
AAAAGAAAATGAGAAAAAGAAAG
Found at i:29104276 original size:20 final size:20
Alignment explanation
Indices: 29104216--29104276 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 20
29104206 AAATGAGAGA
29104216 AAAAGAAAAGAGTGAAAATAAAG
1 AAAAGAAAA-A-TGAAAA-AAAG
*
29104239 AAAAGAAAAATGAGAAAAAG
1 AAAAGAAAAATGAAAAAAAG
*
29104259 -AAAGAAAATCTGAAAAAA
1 AAAAGAAAA-ATGAAAAAA
29104277 GAGAGTGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 8 0.24
20 11 0.32
21 5 0.15
22 1 0.03
23 9 0.26
ACGTcount: A:0.72, C:0.02, G:0.18, T:0.08
Consensus pattern (20 bp):
AAAAGAAAAATGAAAAAAAG
Found at i:29104305 original size:15 final size:15
Alignment explanation
Indices: 29104287--29104326 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
29104277 GAGAGTGAAA
29104287 AGAAAGTGAGAAAAG
1 AGAAAGTGAGAAAAG
29104302 AGAAAGATGA-AAAAG
1 AGAAAG-TGAGAAAAG
*
29104317 AAAAAGTGAG
1 AGAAAGTGAG
29104327 TGAAAAACTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 3 0.14
15 16 0.73
16 3 0.14
ACGTcount: A:0.62, C:0.00, G:0.30, T:0.07
Consensus pattern (15 bp):
AGAAAGTGAGAAAAG
Found at i:29114188 original size:19 final size:20
Alignment explanation
Indices: 29114164--29114201 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
29114154 TGAGCTGATT
29114164 GGAGCTGAAA-TGAGCTAAG
1 GGAGCTGAAATTGAGCTAAG
29114183 GGAGCTGAAATTGAGCTAA
1 GGAGCTGAAATTGAGCTAA
29114202 AATCAGCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.37, C:0.11, G:0.34, T:0.18
Consensus pattern (20 bp):
GGAGCTGAAATTGAGCTAAG
Found at i:29127263 original size:20 final size:20
Alignment explanation
Indices: 29127208--29127265 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
29127198 GTGCTAATAA
*
29127208 TGAGCTC-AATGAGCTAAAT
1 TGAGCTCGAATGAGCTGAAT
*
29127227 TGAGCTCGAACGAGCTGAAT
1 TGAGCTCGAATGAGCTGAAT
29127247 TGAGCTCGAATGAGCTGAA
1 TGAGCTCGAATGAGCTGAA
29127266 CCGCATGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
19 7 0.20
20 28 0.80
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (20 bp):
TGAGCTCGAATGAGCTGAAT
Found at i:29127289 original size:40 final size:40
Alignment explanation
Indices: 29127245--29127332 Score: 167
Period size: 40 Copynumber: 2.2 Consensus size: 40
29127235 AACGAGCTGA
*
29127245 ATTGAGCTCGAATGAGCTGAACCGCATGGAAAGAAGTTTG
1 ATTGAGCTCGAATGAGCTGAACCGCATGAAAAGAAGTTTG
29127285 ATTGAGCTCGAATGAGCTGAACCGCATGAAAAGAAGTTTG
1 ATTGAGCTCGAATGAGCTGAACCGCATGAAAAGAAGTTTG
29127325 ATTGAGCT
1 ATTGAGCT
29127333 GAAAATGAGC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (40 bp):
ATTGAGCTCGAATGAGCTGAACCGCATGAAAAGAAGTTTG
Found at i:29134005 original size:17 final size:18
Alignment explanation
Indices: 29133983--29134022 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
29133973 ATGAGATTTC
29133983 AAAAAC-AAAAGAGAGTG
1 AAAAACAAAAAGAGAGTG
*
29134000 AAAAACAAAAAGAGATTG
1 AAAAACAAAAAGAGAGTG
29134018 AAAAA
1 AAAAA
29134023 GAAATCGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.70, C:0.05, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAACAAAAAGAGAGTG
Found at i:29134021 original size:12 final size:12
Alignment explanation
Indices: 29134006--29134045 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
29133996 AGTGAAAAAC
29134006 AAAAAGAGATTG
1 AAAAAGAGATTG
* *
29134018 AAAAAGAAATCG
1 AAAAAGAGATTG
*
29134030 AAAAAGAGCTTG
1 AAAAAGAGATTG
29134042 AAAA
1 AAAA
29134046 GAAATCGAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.62, C:0.05, G:0.20, T:0.12
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:29134026 original size:24 final size:24
Alignment explanation
Indices: 29133999--29134049 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
29133989 AAAAGAGAGT
29133999 GAAAAAC-AAAAAGAGATTGAAAA
1 GAAAAACGAAAAAGAGATTGAAAA
* *
29134022 -AGAAATCGAAAAAGAGCTTGAAAA
1 GA-AAAACGAAAAAGAGATTGAAAA
29134046 GAAA
1 GAAA
29134050 TCGAGTGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
22 1 0.04
23 4 0.17
24 17 0.74
25 1 0.04
ACGTcount: A:0.65, C:0.06, G:0.20, T:0.10
Consensus pattern (24 bp):
GAAAAACGAAAAAGAGATTGAAAA
Found at i:29134045 original size:23 final size:24
Alignment explanation
Indices: 29134006--29134053 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
29133996 AGTGAAAAAC
29134006 AAAAAGAGATTGAAAAAGAAATCG
1 AAAAAGAGATTGAAAAAGAAATCG
*
29134030 AAAAAGAGCTTG-AAAAGAAATCG
1 AAAAAGAGATTGAAAAAGAAATCG
29134053 A
1 A
29134054 GTGGAAAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.60, C:0.06, G:0.21, T:0.12
Consensus pattern (24 bp):
AAAAAGAGATTGAAAAAGAAATCG
Found at i:29137502 original size:12 final size:12
Alignment explanation
Indices: 29137485--29137519 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
29137475 CGATTAACTA
29137485 CTTCAGTTTGGC
1 CTTCAGTTTGGC
29137497 CTTCAGTTTGGC
1 CTTCAGTTTGGC
*
29137509 CATCAGTTTGG
1 CTTCAGTTTGG
29137520 AGGTGACATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.11, C:0.23, G:0.26, T:0.40
Consensus pattern (12 bp):
CTTCAGTTTGGC
Found at i:29145811 original size:79 final size:78
Alignment explanation
Indices: 29145709--29145931 Score: 265
Period size: 79 Copynumber: 2.8 Consensus size: 78
29145699 GCTCCTCGTT
* *
29145709 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
29145774 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
*
29145789 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
*
29145852 AATTAGTATCTCGCA
64 AATTAGTAACTCGCA
* * * * *
29145867 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
29145930 GA
63 GA
29145932 CATCATCCAA
Statistics
Matches: 125, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
78 47 0.38
79 57 0.46
80 20 0.16
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:29145826 original size:39 final size:40
Alignment explanation
Indices: 29145709--29145931 Score: 266
Period size: 39 Copynumber: 5.7 Consensus size: 40
29145699 GCTCCTCGTT
* *
29145709 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
29145749 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
29145789 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
29145828 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
29145867 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
29145908 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29145932 CATCATCCAA
Statistics
Matches: 166, Mismatches: 9, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
38 2 0.01
39 89 0.54
40 64 0.39
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:29147027 original size:13 final size:13
Alignment explanation
Indices: 29147009--29147033 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29146999 AGGATGAGCA
29147009 TTTTTTTTCTTTG
1 TTTTTTTTCTTTG
29147022 TTTTTTTTCTTT
1 TTTTTTTTCTTT
29147034 CTAGTTTCGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTTTTCTTTG
Found at i:29153785 original size:79 final size:78
Alignment explanation
Indices: 29153685--29153907 Score: 238
Period size: 79 Copynumber: 2.8 Consensus size: 78
29153675 GCTCCTCGTT
* * *
29153685 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATACCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
29153750 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
* * *
29153765 CAAATACCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGA
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
*
29153828 AATTAGTATCTCGCA
64 AATTAGTAACTCGCA
* * * * *
29153843 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
29153906 GA
63 GA
29153908 CATCATTCAA
Statistics
Matches: 120, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
78 45 0.38
79 55 0.46
80 19 0.16
81 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:29153802 original size:39 final size:40
Alignment explanation
Indices: 29153685--29153907 Score: 239
Period size: 39 Copynumber: 5.7 Consensus size: 40
29153675 GCTCCTCGTT
* *
29153685 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * * *
29153725 CAAATACCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
29153765 CAAATACCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
29153804 CAAATGCCTTCGGG-CTTAGCCCGAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
29153843 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
29153884 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29153908 CATCATTCAA
Statistics
Matches: 162, Mismatches: 13, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
38 2 0.01
39 87 0.54
40 62 0.38
41 11 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:29164967 original size:29 final size:29
Alignment explanation
Indices: 29164904--29164971 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
29164894 TAATCAACCG
29164904 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
29164933 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
29164962 CGCACACTTA
1 CGCACACTTA
29164972 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:29165084 original size:174 final size:174
Alignment explanation
Indices: 29164793--29165293 Score: 941
Period size: 174 Copynumber: 2.9 Consensus size: 174
29164783 AACTCAAGGT
* * *
29164793 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
*
29164858 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
29164923 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
29164967 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
29165032 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
29165097 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
29165141 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
*
29165206 G-AAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
*
29165270 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
29165294 TGTACAATTT
Statistics
Matches: 321, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
173 85 0.26
174 236 0.74
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:29165141 original size:29 final size:29
Alignment explanation
Indices: 29165078--29165145 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
29165068 TAATCAACCA
29165078 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
29165107 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
29165136 CGCACACTTA
1 CGCACACTTA
29165146 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:29165285 original size:29 final size:30
Alignment explanation
Indices: 29165246--29165324 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
29165236 CTTAATAATC
29165246 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
29165276 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
29165305 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
29165325 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:29181643 original size:18 final size:17
Alignment explanation
Indices: 29181620--29181658 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
29181610 CTCCTTTGGC
29181620 TCTTTTTCATTCTCTTTT
1 TCTTTTTCATT-TCTTTT
*
29181638 TCTTTTTTGATTTCTTTT
1 TC-TTTTTCATTTCTTTT
29181656 TCT
1 TCT
29181659 GTCTTCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 1 0.05
18 10 0.53
19 8 0.42
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (17 bp):
TCTTTTTCATTTCTTTT
Found at i:29184494 original size:17 final size:18
Alignment explanation
Indices: 29184461--29184496 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
29184451 GATTTTTTTA
*
29184461 TTTCACTTTTCTTTTCTT
1 TTTCACTTTTCTCTTCTT
29184479 TTTCA-TTTTCTCTTCTT
1 TTTCACTTTTCTCTTCTT
29184496 T
1 T
29184497 GTTTTTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTCACTTTTCTCTTCTT
Found at i:29184522 original size:19 final size:18
Alignment explanation
Indices: 29184470--29184524 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
29184460 ATTTCACTTT
29184470 TCTTTTCTTTTTCATTT--
1 TCTTTTCTTTTTC-TTTCA
*
29184487 TCTCTTCTTTGTT-TTTCAA
1 TCTTTTCTTT-TTCTTTC-A
29184506 TCTTTTCTTTTTCTTTCA
1 TCTTTTCTTTTTCTTTCA
29184524 T
1 T
29184525 TTGGGTTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 3 0.10
17 9 0.29
18 6 0.19
19 13 0.42
ACGTcount: A:0.07, C:0.20, G:0.02, T:0.71
Consensus pattern (18 bp):
TCTTTTCTTTTTCTTTCA
Found at i:29187992 original size:20 final size:19
Alignment explanation
Indices: 29187956--29188006 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
29187946 ACATGTATTA
29187956 AATTAAGACAAACTTAATT
1 AATTAAGACAAACTTAATT
* *
29187975 AATTCAAGACATATTTAATTT
1 AATT-AAGACAAACTTAA-TT
*
29187996 AACTAAGACAA
1 AATTAAGACAA
29188007 GACAAATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 4 0.15
20 17 0.65
21 5 0.19
ACGTcount: A:0.51, C:0.12, G:0.06, T:0.31
Consensus pattern (19 bp):
AATTAAGACAAACTTAATT
Found at i:29190381 original size:19 final size:20
Alignment explanation
Indices: 29190348--29190386 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
29190338 GCAAGCTGAT
29190348 TTTAGCTCGGTTTTAGCTCC
1 TTTAGCTCGGTTTTAGCTCC
29190368 TTTAGCTC-GTTTTAGCTCC
1 TTTAGCTCGGTTTTAGCTCC
29190387 AACCAGCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.10, C:0.26, G:0.18, T:0.46
Consensus pattern (20 bp):
TTTAGCTCGGTTTTAGCTCC
Found at i:29190413 original size:20 final size:20
Alignment explanation
Indices: 29190390--29190429 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29190380 TAGCTCCAAC
**
29190390 CAGCTCATTTGAGCTCAATT
1 CAGCTCATTCAAGCTCAATT
29190410 CAGCTCATTCAAGCTCAATT
1 CAGCTCATTCAAGCTCAATT
29190430 TAGTTTCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.33
Consensus pattern (20 bp):
CAGCTCATTCAAGCTCAATT
Found at i:29192761 original size:28 final size:28
Alignment explanation
Indices: 29192698--29192879 Score: 321
Period size: 28 Copynumber: 6.5 Consensus size: 28
29192688 ATATTAAGTC
* *
29192698 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
29192725 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
29192753 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
29192781 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
29192809 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
29192837 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
29192865 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29192880 GTACAATTTA
Statistics
Matches: 151, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
27 22 0.15
28 129 0.85
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:29200627 original size:28 final size:28
Alignment explanation
Indices: 29200564--29200717 Score: 265
Period size: 28 Copynumber: 5.5 Consensus size: 28
29200554 ATATTAAGTC
* *
29200564 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
29200591 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
29200619 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
29200647 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
29200675 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
29200703 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29200718 GTACAATTTA
Statistics
Matches: 123, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
27 22 0.18
28 101 0.82
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:29203118 original size:12 final size:12
Alignment explanation
Indices: 29203101--29203125 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29203091 CCTTATACAC
29203101 ATTACACATTGA
1 ATTACACATTGA
29203113 ATTACACATTGA
1 ATTACACATTGA
29203125 A
1 A
29203126 ATCAGATTTT
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:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
ATTACACATTGA
Found at i:29226702 original size:12 final size:12
Alignment explanation
Indices: 29226685--29226709 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29226675 CAGAGGCTAT
29226685 TAACAATATTTA
1 TAACAATATTTA
29226697 TAACAATATTTA
1 TAACAATATTTA
29226709 T
1 T
29226710 GTTATAAAAT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAACAATATTTA
Found at i:29229259 original size:21 final size:20
Alignment explanation
Indices: 29229230--29229268 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
29229220 ACGCCTACGA
29229230 AAAGATCGCTTGGATTTAAG
1 AAAGATCGCTTGGATTTAAG
29229250 AAAGAGTCGCTTGGATTTA
1 AAAGA-TCGCTTGGATTTA
29229269 TCCATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (20 bp):
AAAGATCGCTTGGATTTAAG
Found at i:29229461 original size:15 final size:15
Alignment explanation
Indices: 29229441--29229479 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
29229431 TATCATTTCA
29229441 ATATATAATTTAAAT
1 ATATATAATTTAAAT
29229456 ATATATAAATTTAAAT
1 ATATAT-AATTTAAAT
29229472 ATAT-TAAT
1 ATATATAAT
29229480 AATATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.13
15 7 0.30
16 13 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATATATAATTTAAAT
Found at i:29231243 original size:13 final size:13
Alignment explanation
Indices: 29231225--29231258 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
29231215 ACCTCCTTGG
29231225 ATTAAATTATTAA
1 ATTAAATTATTAA
29231238 ATTAAAATTATTAA
1 ATT-AAATTATTAA
29231252 A-TAAATT
1 ATTAAATT
29231259 GAAATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 4 0.20
14 11 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTAAATTATTAA
Found at i:29236912 original size:8 final size:8
Alignment explanation
Indices: 29236899--29236924 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
29236889 AATCCACTTG
29236899 TTTAGTTC
1 TTTAGTTC
29236907 TTTAGTTC
1 TTTAGTTC
29236915 TTTAGTTC
1 TTTAGTTC
29236923 TT
1 TT
29236925 AAGGAGCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.65
Consensus pattern (8 bp):
TTTAGTTC
Found at i:29238525 original size:17 final size:17
Alignment explanation
Indices: 29238505--29238538 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
29238495 TTCGTATATT
*
29238505 ATACTAATTATATCTAA
1 ATACTAAGTATATCTAA
29238522 ATACTAAGTATATCTAA
1 ATACTAAGTATATCTAA
29238539 GCGAATCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (17 bp):
ATACTAAGTATATCTAA
Found at i:29241408 original size:18 final size:18
Alignment explanation
Indices: 29241385--29241421 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29241375 ATGAAGCTGG
* *
29241385 TTTATCTCATTTTTCCAC
1 TTTATCTAATTTATCCAC
29241403 TTTATCTAATTTATCCAC
1 TTTATCTAATTTATCCAC
29241421 T
1 T
29241422 GCGTCGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTATCTAATTTATCCAC
Found at i:29243196 original size:20 final size:19
Alignment explanation
Indices: 29243126--29243209 Score: 70
Period size: 20 Copynumber: 4.4 Consensus size: 19
29243116 ATAGATAAGA
29243126 AATAGATAAATAATATAA-A-
1 AATA-ATAAAT-ATATAATAG
*
29243145 AATAATACTAATATATATTAG
1 AATAATA--AATATATAATAG
29243166 AAT-AT--ATATATAATAG
1 AATAATAAATATATAATAG
29243182 AATAGATAAATATATAATAG
1 AATA-ATAAATATATAATAG
29243202 AATTAATA
1 AA-TAATA
29243210 TTCTAACATC
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
16 13 0.24
18 5 0.09
19 9 0.17
20 22 0.41
21 5 0.09
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (19 bp):
AATAATAAATATATAATAG
Found at i:29254463 original size:19 final size:19
Alignment explanation
Indices: 29254410--29254452 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
29254400 GTATTTGTTA
29254410 TGTTAGGGTTATAATAATT
1 TGTTAGGGTTATAATAATT
29254429 TGTTAGGGTTATAATAATT
1 TGTTAGGGTTATAATAATT
29254448 TGTTA
1 TGTTA
29254453 TTTTTATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.49
Consensus pattern (19 bp):
TGTTAGGGTTATAATAATT
Found at i:29255241 original size:21 final size:21
Alignment explanation
Indices: 29255217--29255260 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
29255207 ACGACCTAAT
*
29255217 TAAATAGAAAGGATA-ATTAAA
1 TAAATA-AAAGGATACAATAAA
*
29255238 TAAATAAAATGATACAATAAA
1 TAAATAAAAGGATACAATAAA
29255259 TA
1 TA
29255261 CTAAAGACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (21 bp):
TAAATAAAAGGATACAATAAA
Found at i:29257341 original size:8 final size:8
Alignment explanation
Indices: 29257328--29257354 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
29257318 TTTTAAATGA
29257328 TATTTTAT
1 TATTTTAT
29257336 TATTTTAT
1 TATTTTAT
29257344 TATTTTAT
1 TATTTTAT
29257352 TAT
1 TAT
29257355 ATATAAGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TATTTTAT
Found at i:29261371 original size:539 final size:539
Alignment explanation
Indices: 29260348--29261427 Score: 1914
Period size: 539 Copynumber: 2.0 Consensus size: 539
29260338 GCAATTTATT
* * * *
29260348 AAGTTTAAGTGGTATGAACTTAGGTCAAGTGGTTTTAGAAATTTAGGTATTGGGACCTCATTTTT
1 AAGTTCAAGTGGTATGAACTAAGGTCAAGTGGTTTTAGAAATTCAGGTATCGGGACCTCATTTTT
* * * * *
29260413 ATAAATGGAGCTGTAAATATTTTTTAAAATATTTGTGAAGTGTCATTAAGGTGGTATTAATGTTT
66 AGAAATGGAGCCGTAAATATTTTTTAAAATATTTATGAAGTGTCATTAAGGTGGTACTAAAGTTT
*
29260478 CGTTGAATAATTTTAACATTTCGATAGTAAATTAATTAAAAAGGACTAAAATGTAAAAGATGTAA
131 CGTTGAAAAATTTTAACATTTCGATAGTAAATTAATTAAAAAGGACTAAAATGTAAAAGATGTAA
29260543 AATTTAATCACTATTTGATATGAGTGATTAAATGGTTAATTGAATAAAGGAAAAGGGGCTTAAAT
196 AATTTAATCACTATTTGATATGAGTGATTAAATGGTTAATTGAATAAAGGAAAAGGGGCTTAAAT
* *
29260608 GGTAATTAGACCATTTAAGAATATAGTGGACGGCTTTGGGCAACTAAAAGCATGAAATTTTGGAT
261 GGTAATTAGACCATTTAAAAATATAGTGGACGGCTTTGGGCAACGAAAAGCATGAAATTTTGGAT
** *
29260673 GTTTATAAAAGGGACAAAATAGTAATTTTGATTAATAAAAGTATGAGGATTTAATGTGAAATTTT
326 GTTTATAAAAGGGACAAAATAGTAATTTTGATTAATAAAAGTACAAGGATTTAATGTGAAATTGT
*
29260738 TGCATAAATGGGATGTTTTGAATACTATGAACATTCGGCTAGCTTGGGTTTGTATGAAAAATGGT
391 TGCATAAATGGGATGTTTTGAATACTATGAACATTCGGCTAGCTTGGATTTGTATGAAAAATGGT
29260803 TAATTTGCATGTTTTGGGCTTAGAGACTAAATTGAATAAAAGTAAAACTTTAGGGAAAATTTTGT
456 TAATTTGCATGTTTTGGGCTTAGAGACTAAATTGAATAAAAGTAAAACTTTAGGGAAAATTTTGT
29260868 AAAAATGAT-AAAAATGACC
521 AAAAATG-TCAAAAATGACC
29260887 AAGTTCAAGTGGTATGAACCTAAGGTCAAGTGGTTTTAGAAATTCAGGTATCGGGACCTCATTTT
1 AAGTTCAAGTGGTATGAA-CTAAGGTCAAGTGGTTTTAGAAATTCAGGTATCGGGACCTCATTTT
29260952 TAGAAATGGAGCCGTAAATATTTTTGT-AAATATTTATGAAGTGTCATTAAGGTGGTACTAAAGT
65 TAGAAATGGAGCCGTAAATATTTTT-TAAAATATTTATGAAGTGTCATTAAGGTGGTACTAAAGT
*
29261016 TTCGTTGAAAAATTTTAACGTTTCGATAGTAAATTAATT-AAAAGGACTAAAATGTAAAAGATGT
129 TTCGTTGAAAAATTTTAACATTTCGATAGTAAATTAATTAAAAAGGACTAAAATGTAAAAGATGT
29261080 AAAATTTAATCACTATTTGATATGAGTGATTAAATGGTTAATTGAATAAAGGAAAAGGGGCTTAA
194 AAAATTTAATCACTATTTGATATGAGTGATTAAATGGTTAATTGAATAAAGGAAAAGGGGCTTAA
29261145 ATGGTAATTAGACCATTTAAAAATATAGTGGACGGCTTTGGGCAACGAAAAGCATGAAATTTTGG
259 ATGGTAATTAGACCATTTAAAAATATAGTGGACGGCTTTGGGCAACGAAAAGCATGAAATTTTGG
* *
29261210 ATGTTTATAAATGGGACAAAATATTAATTTTGATTAATAAAAGTACAAGGATTTAATGTGAAATT
324 ATGTTTATAAAAGGGACAAAATAGTAATTTTGATTAATAAAAGTACAAGGATTTAATGTGAAATT
*
29261275 GTTGCATAAATGTGATGTTTTGAATACTATGAACATTCGGCTAGCTTGGATTTGTATGAAAAATG
389 GTTGCATAAATGGGATGTTTTGAATACTATGAACATTCGGCTAGCTTGGATTTGTATGAAAAATG
* *
29261340 GTTAATTTGCATGTTTTGGGCTTGGAGACTAAATTGAATAAAAGTAAAACTTTAGGGACAATTTT
454 GTTAATTTGCATGTTTTGGGCTTAGAGACTAAATTGAATAAAAGTAAAACTTTAGGGAAAATTTT
29261405 GTAAAAATGTCAAAAATGACC
519 GTAAAAATGTCAAAAATGACC
29261426 AA
1 AA
29261428 ATTTCATGGA
Statistics
Matches: 516, Mismatches: 22, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
538 1 0.00
539 377 0.73
540 137 0.27
541 1 0.00
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (539 bp):
AAGTTCAAGTGGTATGAACTAAGGTCAAGTGGTTTTAGAAATTCAGGTATCGGGACCTCATTTTT
AGAAATGGAGCCGTAAATATTTTTTAAAATATTTATGAAGTGTCATTAAGGTGGTACTAAAGTTT
CGTTGAAAAATTTTAACATTTCGATAGTAAATTAATTAAAAAGGACTAAAATGTAAAAGATGTAA
AATTTAATCACTATTTGATATGAGTGATTAAATGGTTAATTGAATAAAGGAAAAGGGGCTTAAAT
GGTAATTAGACCATTTAAAAATATAGTGGACGGCTTTGGGCAACGAAAAGCATGAAATTTTGGAT
GTTTATAAAAGGGACAAAATAGTAATTTTGATTAATAAAAGTACAAGGATTTAATGTGAAATTGT
TGCATAAATGGGATGTTTTGAATACTATGAACATTCGGCTAGCTTGGATTTGTATGAAAAATGGT
TAATTTGCATGTTTTGGGCTTAGAGACTAAATTGAATAAAAGTAAAACTTTAGGGAAAATTTTGT
AAAAATGTCAAAAATGACC
Found at i:29269524 original size:24 final size:24
Alignment explanation
Indices: 29269473--29269530 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
29269463 TTTGTAATTA
*
29269473 ATTTTGGGATAATTTTTATTTGTC
1 ATTTTAGGATAATTTTTATTTGTC
*
29269497 ATTTTTGGATAATTTTTCTATTT-T-
1 ATTTTAGGATAA-TTTT-TATTTGTC
29269521 ATTTTAGGAT
1 ATTTTAGGAT
29269531 TTTCTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 20 0.67
25 5 0.17
26 5 0.17
ACGTcount: A:0.22, C:0.03, G:0.14, T:0.60
Consensus pattern (24 bp):
ATTTTAGGATAATTTTTATTTGTC
Found at i:29275073 original size:40 final size:40
Alignment explanation
Indices: 29274976--29275159 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
29274966 TTGAATGCTG
* * * *
29274976 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
**
29275015 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * * *
29275056 TCCAGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
29275096 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
29275136 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
29275160 GTATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:29275116 original size:80 final size:81
Alignment explanation
Indices: 29274983--29275156 Score: 216
Period size: 80 Copynumber: 2.2 Consensus size: 81
29274973 CTGTCCGGGC
* *
29274983 TAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTTGTGCGA
1 TAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATTCGTGCGA
*
29275047 GTTATT-AATTCCAGGT
66 GTT-TTAAAATCCAGGT
**
29275063 TAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGCATTCGTG
1 TAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGCATTCGTG
*
29275124 CGAGTTTTAAAATCCGGGT
63 CGAGTTTTAAAATCCAGGT
29275143 TAAGTCCCGAAGGC
1 TAAGTCCCGAAGGC
29275157 ATTGTATGAG
Statistics
Matches: 83, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
79 4 0.05
80 70 0.84
81 9 0.11
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (81 bp):
TAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATTCGTGCGA
GTTTTAAAATCCAGGT
Found at i:29283023 original size:40 final size:40
Alignment explanation
Indices: 29282939--29283122 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
29282929 TTGAATGCTG
* * * *
29282939 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
**
29282978 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
29283019 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
29283059 TCCGGGTTAAGTCCCAAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
29283099 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
29283123 GTATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:29283079 original size:80 final size:81
Alignment explanation
Indices: 29282939--29283119 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
29282929 TTGAATGCTG
* * *
29282939 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCAAAGGCATT
* *
29283003 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
29283019 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCAAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCAAAGGC
29283080 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
29283099 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
29283120 ATTGTATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCAAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:29289754 original size:27 final size:27
Alignment explanation
Indices: 29289724--29289933 Score: 262
Period size: 27 Copynumber: 7.8 Consensus size: 27
29289714 TCATAATCTG
** *
29289724 CCACAAAGGCGTTTCTTTCATGGTTCA
1 CCACAAAGGCAATTCTTTCATGATTCA
*
29289751 CCACAAAGGAAATTCTTTCATGATATGC-
1 CCACAAAGGCAATTCTTTCATGAT-T-CA
**
29289779 CC-CAAAGGCAATTCTTTCATGATTTG
1 CCACAAAGGCAATTCTTTCATGATTCA
* *
29289805 CCACAAAGACATTTCTTTCATGATTCA
1 CCACAAAGGCAATTCTTTCATGATTCA
29289832 CCACAAAGGCAATTCTTTCATGATTCA
1 CCACAAAGGCAATTCTTTCATGATTCA
*
29289859 CCACAAAGGCATTTCTTTCATGATTCA
1 CCACAAAGGCAATTCTTTCATGATTCA
* * *
29289886 CTACAAATGCATTTCTTTCATGATTCA
1 CCACAAAGGCAATTCTTTCATGATTCA
* *
29289913 CCATAGAGGCAATTCTTTCAT
1 CCACAAAGGCAATTCTTTCAT
29289934 CACGTGTTTA
Statistics
Matches: 159, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
26 3 0.02
27 152 0.96
28 3 0.02
29 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (27 bp):
CCACAAAGGCAATTCTTTCATGATTCA
Found at i:29302492 original size:73 final size:73
Alignment explanation
Indices: 29302401--29302546 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
29302391 TAACAGCCAA
*
29302401 CTCCACATACAAATGGGATCCCAAATTGCTTACCAATTGCATAACATCAAAGCAGGTCCAAGCAA
1 CTCCACATACAAATGGGATCCCAAATTGCTTACAAATTGCATAACATCAAAGCAGGTCCAAGCAA
29302466 GCTAAGAG
66 GCTAAGAG
29302474 CTCCACATACAAATGGGATCCCAAATTGCTTACAAATTGCATAACATCAAAGCAGGTCCAAGCAA
1 CTCCACATACAAATGGGATCCCAAATTGCTTACAAATTGCATAACATCAAAGCAGGTCCAAGCAA
29302539 GCTAAGAG
66 GCTAAGAG
29302547 GATTAGAACT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.19
Consensus pattern (73 bp):
CTCCACATACAAATGGGATCCCAAATTGCTTACAAATTGCATAACATCAAAGCAGGTCCAAGCAA
GCTAAGAG
Found at i:29309784 original size:66 final size:66
Alignment explanation
Indices: 29309673--29309804 Score: 228
Period size: 66 Copynumber: 2.0 Consensus size: 66
29309663 GCAGACTTGA
*
29309673 TTGATTTAAATTTAAGACAGTGGAAGGAGGAAGTAATTACTAGACTCTTTAGAAACAAAGAGGCA
1 TTGATTTAAATTTAAGACAGTGGAAGGAGGAAGTAATTACCAGACTCTTTAGAAACAAAGAGGCA
29309738 G
66 G
* * *
29309739 TTGATTTAAATTTAAGACAGTGGAATGAGGAAGTAATTACCAGACTCTTTAGTAATAAAGAGGCA
1 TTGATTTAAATTTAAGACAGTGGAAGGAGGAAGTAATTACCAGACTCTTTAGAAACAAAGAGGCA
29309804 G
66 G
29309805 AGGTGATCCT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.27
Consensus pattern (66 bp):
TTGATTTAAATTTAAGACAGTGGAAGGAGGAAGTAATTACCAGACTCTTTAGAAACAAAGAGGCA
G
Found at i:29312043 original size:16 final size:16
Alignment explanation
Indices: 29311977--29312043 Score: 62
Period size: 16 Copynumber: 4.2 Consensus size: 16
29311967 GGTTCACTGG
*
29311977 AATGAAATAGAGTTAT
1 AATGAAATAGAGCTAT
* * *
29311993 AATGGAATAGATCTGT
1 AATGAAATAGAGCTAT
* *
29312009 AATGAAATAAAACTAT
1 AATGAAATAGAGCTAT
* *
29312025 AATGGAATAGAGCTGT
1 AATGAAATAGAGCTAT
29312041 AAT
1 AAT
29312044 CAGTAATTCA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.48, C:0.04, G:0.19, T:0.28
Consensus pattern (16 bp):
AATGAAATAGAGCTAT
Found at i:29312080 original size:46 final size:44
Alignment explanation
Indices: 29312024--29312113 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 44
29312014 AATAAAACTA
* *
29312024 TAATGGAATAGAGCTGTAATCAGTAATTCAATT-T-TTTGGTTGAATG
1 TAATGAAATAGAACTGTAAT-AGT-ATTC--TTGTGTTTGGTTGAATG
29312070 TAATGAAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATG
1 TAATGAAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATG
29312114 GAATAGATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
42 2 0.05
43 1 0.03
44 16 0.40
45 3 0.08
46 18 0.45
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.40
Consensus pattern (44 bp):
TAATGAAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATG
Found at i:29312298 original size:61 final size:58
Alignment explanation
Indices: 29312203--29312339 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 58
29312193 TTGTTATTAA
* *
29312203 ATTTTAATA-ACATTATTATTAAATATAAGTTAATAAAAATAAAAATAAATAATTTAATCAT
1 ATTTTAATATA-ATTATTATTAAATATAAGTTAATAAAAAT---AATAAATAATTTAATAAC
* *
29312264 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATATAAGTTAATAAAAATAATAAATAATTTAATAAC
29312322 ATTCTTAATATAATTATT
1 ATT-TTAATATAATTATT
29312340 TTTATATTAA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
58 18 0.26
59 14 0.20
61 37 0.53
62 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (58 bp):
ATTTTAATATAATTATTATTAAATATAAGTTAATAAAAATAATAAATAATTTAATAAC
Found at i:29312362 original size:59 final size:58
Alignment explanation
Indices: 29312203--29312377 Score: 183
Period size: 61 Copynumber: 2.9 Consensus size: 58
29312193 TTGTTATTAA
* * *
29312203 ATTTTAATA-ACATTATTATTAAATATAAGTTAATAAAAATAAAAATAAATAATTTAATCAT
1 ATTTTAATATA-ATTATTATTAAATATAAATTAATAAAAAT---AATAAATAATTTAATAAC
* *
29312264 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATATAAATTAATAAAAATAATAAATAATTTAATAAC
* * * *
29312322 ATTCTTAATATAATTATTTTTATAT-TAAATTATATTAAAATATTTAAAATAATTTA
1 ATT-TTAATATAATTATTATTAAATATAAATTA-ATAAAAATA-AT-AAATAATTTA
29312378 TTTACTACCT
Statistics
Matches: 99, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
58 24 0.24
59 27 0.27
60 1 0.01
61 46 0.46
62 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (58 bp):
ATTTTAATATAATTATTATTAAATATAAATTAATAAAAATAATAAATAATTTAATAAC
Found at i:29318875 original size:15 final size:16
Alignment explanation
Indices: 29318846--29318875 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29318836 CAAACATGCT
29318846 TTAACACATTATCAAA
1 TTAACACATTATCAAA
29318862 TTAACACA-TATCAA
1 TTAACACATTATCAA
29318876 CAAGGCACCA
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:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:29319075 original size:17 final size:17
Alignment explanation
Indices: 29319053--29319092 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
29319043 ATCTTCAACG
29319053 AGCTTCCAACCCAATCA
1 AGCTTCCAACCCAATCA
* *
29319070 AGCTTCCAACCTAATCG
1 AGCTTCCAACCCAATCA
29319087 AGCTTC
1 AGCTTC
29319093 TGATAATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.30, C:0.38, G:0.10, T:0.23
Consensus pattern (17 bp):
AGCTTCCAACCCAATCA
Found at i:29322509 original size:14 final size:14
Alignment explanation
Indices: 29322490--29322517 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29322480 TAAAGTTATA
29322490 TTTAATAATTCATT
1 TTTAATAATTCATT
29322504 TTTAATAATTCATT
1 TTTAATAATTCATT
29322518 AGTAAATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATAATTCATT
Found at i:29322989 original size:19 final size:19
Alignment explanation
Indices: 29322967--29323004 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
29322957 TTAATCATCC
29322967 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
29322986 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
29323005 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:29326651 original size:25 final size:25
Alignment explanation
Indices: 29326604--29326654 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
29326594 AAATCACATC
* *
29326604 AACGTGCTACAAAGAGTAGACTATA
1 AACGTGCTACAAAAAGCAGACTATA
* *
29326629 AACGTTCTACAAAAAGCATACTATA
1 AACGTGCTACAAAAAGCAGACTATA
29326654 A
1 A
29326655 TTTTTTGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.22
Consensus pattern (25 bp):
AACGTGCTACAAAAAGCAGACTATA
Found at i:29330489 original size:3 final size:3
Alignment explanation
Indices: 29330481--29330519 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
29330471 TATGGAAATG
*
29330481 GAT GAT GAT GAT GAT GAT GGT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
29330520 AGCTAGCTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:29334579 original size:23 final size:23
Alignment explanation
Indices: 29334551--29334598 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
29334541 ATCTCTTCCC
* *
29334551 TTTATTCTATTCTTTATGTCTCT
1 TTTATTCTATTATTTATATCTCT
29334574 TTTATTCTATTATTTATATCTCT
1 TTTATTCTATTATTTATATCTCT
29334597 TT
1 TT
29334599 CTTTAACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.15, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTATTCTATTATTTATATCTCT
Found at i:29345662 original size:25 final size:25
Alignment explanation
Indices: 29345626--29345675 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
29345616 CATGTGATTT
* *
29345626 TGTATGATGCCTTCGTGGTGTATTC
1 TGTATGACGCCTTCGTGGCGTATTC
*
29345651 TGTATGACGCCTTTGTGGCGTATTC
1 TGTATGACGCCTTCGTGGCGTATTC
29345676 GATTTGGCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.12, C:0.18, G:0.28, T:0.42
Consensus pattern (25 bp):
TGTATGACGCCTTCGTGGCGTATTC
Found at i:29347162 original size:46 final size:46
Alignment explanation
Indices: 29347105--29347298 Score: 205
Period size: 46 Copynumber: 4.2 Consensus size: 46
29347095 TACTCATCAA
* * *
29347105 GGTTAAACCTACACGAATCAGATAATAGTGCCTTATAACCCGTTAG
1 GGTTGAACCTACACGAATCGGATAATAGTGCCTTATCACCCGTTAG
* * *
29347151 GGTTGAGCCTACACGAATTGAATAATAGTGCC-TAGTCACCCGTTAG
1 GGTTGAACCTACACGAATCGGATAATAGTGCCTTA-TCACCCGTTAG
* * *
29347197 GTTTGAACCTACA-GAAATCGGATAATAATG-CTTGCTCACCCGTTAG
1 GGTTGAACCTACACG-AATCGGATAATAGTGCCTT-ATCACCCGTTAG
* ** ** *
29347243 GGTTGAACCTACATGAATCGGATAATAGTGCCTGGTCACCTATTAA
1 GGTTGAACCTACACGAATCGGATAATAGTGCCTTATCACCCGTTAG
29347289 GGTTGAACCT
1 GGTTGAACCT
29347299 TCATAACAAA
Statistics
Matches: 123, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
45 4 0.03
46 116 0.94
47 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (46 bp):
GGTTGAACCTACACGAATCGGATAATAGTGCCTTATCACCCGTTAG
Found at i:29347295 original size:92 final size:92
Alignment explanation
Indices: 29347033--29347298 Score: 247
Period size: 92 Copynumber: 2.9 Consensus size: 92
29347023 CAGGTGAAAG
* * * * * *
29347033 TAATAATGCC-TAGTTACCCATTTGGGTTAAACCTACACGAGTAAT-GAATCATAGTGCCTGGTT
1 TAATAATGCCTTA-TAACCCGTTAGGGTTGAACCTACAC--G-AATCGAATAATAGTGCCTGGTC
* *
29347096 A-CTCATCAAGGTTAAACCTACACGAATCAGA
62 ACCT-ATTAAGGTTGAACCTACACGAATCAGA
* * * * *
29347127 TAATAGTGCCTTATAACCCGTTAGGGTTGAGCCTACACGAATTGAATAATAGTGCCTAGTCACCC
1 TAATAATGCCTTATAACCCGTTAGGGTTGAACCTACACGAATCGAATAATAGTGCCTGGTCACCT
* *
29347192 GTT-AGGTTTGAACCTACA-GAAATCGGA
66 ATTAAGG-TTGAACCTACACG-AATCAGA
* * * *
29347219 TAATAATG-CTTGCTCACCCGTTAGGGTTGAACCTACATGAATCGGATAATAGTGCCTGGTCACC
1 TAATAATGCCTT-ATAACCCGTTAGGGTTGAACCTACACGAATCGAATAATAGTGCCTGGTCACC
29347283 TATTAAGGTTGAACCT
65 TATTAAGGTTGAACCT
29347299 TCATAACAAA
Statistics
Matches: 141, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
91 10 0.07
92 96 0.68
93 4 0.03
94 29 0.21
95 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (92 bp):
TAATAATGCCTTATAACCCGTTAGGGTTGAACCTACACGAATCGAATAATAGTGCCTGGTCACCT
ATTAAGGTTGAACCTACACGAATCAGA
Found at i:29350334 original size:27 final size:27
Alignment explanation
Indices: 29350304--29350481 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
29350294 ATATTGAGCC
* *
29350304 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
29350331 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
29350358 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
* ** ** *
29350386 CGCACTCTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
29350413 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
29350440 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
29350467 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
29350482 GTACAATTTA
Statistics
Matches: 124, Mismatches: 24, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
27 101 0.81
28 23 0.19
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:29350443 original size:82 final size:81
Alignment explanation
Indices: 29350325--29350480 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
29350315 TGCTATATAA
* * *
29350325 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCA-AATCGCA
*
29350390 CTCTTAGTGCCGCATGG
65 CCCTTAGTGCCGCATGG
* * **
29350407 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
29350471 CCCTTAGTGC
65 CCCTTAGTGC
29350481 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 17 0.26
82 48 0.74
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
CCTTAGTGCCGCATGG
Found at i:29354285 original size:21 final size:22
Alignment explanation
Indices: 29354261--29354311 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
29354251 CGATGTTGCA
** *
29354261 ACATAGTAAGTTG-GTGTCGCG
1 ACATAGTAAGGGGCGTGTCACG
29354282 ACATAGT-AGGGGCGTGTCACG
1 ACATAGTAAGGGGCGTGTCACG
29354303 ACATAGTAA
1 ACATAGTAA
29354312 ATAGTTTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 21 0.84
22 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (22 bp):
ACATAGTAAGGGGCGTGTCACG
Found at i:29356454 original size:21 final size:20
Alignment explanation
Indices: 29356419--29356471 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 20
29356409 TAAAACACTG
29356419 AAATAAG-AAATATAAAATAT
1 AAATAAGAAAATA-AAAATAT
29356439 AATATAAAGAAAATAAAAATAT
1 AA-AT-AAGAAAATAAAAATAT
29356461 AAATAAGAAAA
1 AAATAAGAAAA
29356472 CAAATAAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 9 0.30
21 4 0.13
22 12 0.40
23 5 0.17
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (20 bp):
AAATAAGAAAATAAAAATAT
Found at i:29357856 original size:6 final size:6
Alignment explanation
Indices: 29357847--29357890 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
29357837 ATAACAATTT
29357847 TCACCA TCACCA TCACCA TCACCA TCACCA TCACCA TCACCA TC
1 TCACCA TCACCA TCACCA TCACCA TCACCA TCACCA TCACCA TC
29357891 CCCAACAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (6 bp):
TCACCA
Found at i:29385318 original size:25 final size:25
Alignment explanation
Indices: 29385290--29385344 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
29385280 GTCACGCGGT
29385290 CGTGTCACAC-TCCTGTGTGCAAAGC
1 CGTGTCACACGTCC-GTGTGCAAAGC
*
29385315 CGTGTCACACGTCCGTGTGCCAAGC
1 CGTGTCACACGTCCGTGTGCAAAGC
29385340 CGTGT
1 CGTGT
29385345 AACTCACTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 25 0.89
26 3 0.11
ACGTcount: A:0.16, C:0.33, G:0.27, T:0.24
Consensus pattern (25 bp):
CGTGTCACACGTCCGTGTGCAAAGC
Found at i:29386668 original size:74 final size:74
Alignment explanation
Indices: 29386411--29386662 Score: 310
Period size: 74 Copynumber: 3.4 Consensus size: 74
29386401 GAAAGTTGTG
* *
29386411 CCCAACGCTAGTCGAATAAACCGACAAATAATTAGGGAGCCCAACTCTAGTTGGATATACCAACA
1 CCCAGCGCTAGTCGAATAAACCGACAAATAATTAGTGAGCCCAACTCTAGTTGGATATACCAACA
*
29386476 GTATTTGCG
66 GTATTTGCA
* * * * *
29386485 TCCAGCGCTAGTCAAATAAATCGACAAATAATTAGTGAGCCTAGCTCTAGTTGGATATACCAACA
1 CCCAGCGCTAGTCGAATAAACCGACAAATAATTAGTGAGCCCAACTCTAGTTGGATATACCAACA
29386550 GTATTTGCA
66 GTATTTGCA
* ** * * *
29386559 CCCAGCGCTAGTCCG-TTAAACCGACGTATAAATAGTGAGCCCAACTCTAGTTGGATTTAACAA-
1 CCCAGCGCTAGT-CGAATAAACCGACAAATAATTAGTGAGCCCAACTCTAGTTGGATATACCAAC
* * *
29386622 TGAAAATTGCA
65 AG-TATTTGCA
*
29386633 CCCAGCACTAGTCGAATAAACCGACAAATA
1 CCCAGCGCTAGTCGAATAAACCGACAAATA
29386663 GATAGTTATT
Statistics
Matches: 149, Mismatches: 26, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
73 3 0.02
74 145 0.97
75 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (74 bp):
CCCAGCGCTAGTCGAATAAACCGACAAATAATTAGTGAGCCCAACTCTAGTTGGATATACCAACA
GTATTTGCA
Found at i:29395161 original size:24 final size:24
Alignment explanation
Indices: 29395129--29395174 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
29395119 CTTTAATTCC
29395129 TCAAAAGCTACCAAGCAATGTTCA
1 TCAAAAGCTACCAAGCAATGTTCA
29395153 TCAAAAGCTACCAAGCAATGTT
1 TCAAAAGCTACCAAGCAATGTT
29395175 GATTTGGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.13, T:0.22
Consensus pattern (24 bp):
TCAAAAGCTACCAAGCAATGTTCA
Found at i:29397099 original size:22 final size:20
Alignment explanation
Indices: 29397052--29397104 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
29397042 GAGAAGAAAT
29397052 AACAAAGAAAACAAACTAAC
1 AACAAAGAAAACAAACTAAC
*
29397072 ACACAAAGAAAAGCAAACTTACC
1 A-ACAAAGAAAA-CAAAC-TAAC
29397095 AACAAA-AAAA
1 AACAAAGAAAA
29397105 TAAGGTTTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 1 0.03
21 14 0.48
22 10 0.34
23 4 0.14
ACGTcount: A:0.68, C:0.21, G:0.06, T:0.06
Consensus pattern (20 bp):
AACAAAGAAAACAAACTAAC
Found at i:29402681 original size:73 final size:74
Alignment explanation
Indices: 29402604--29402741 Score: 242
Period size: 73 Copynumber: 1.9 Consensus size: 74
29402594 TCTTTTAATA
* *
29402604 TATTATATTTTTCATTTGTTAAAATTAATCCTTATAC-TTTTTTTAAACAATTTAAATTTTTTTC
1 TATTATATTTTCCATTTGTTAAAACTAATCCTTATACTTTTTTTTAAACAATTTAAATTTTTTTC
29402668 TTTTTAACG
66 TTTTTAACG
*
29402677 TATTATATTTTCCATTTGTTAAAACTAATCCTTATACTTTTTTTTGAACAATTTAAATTTTTTTC
1 TATTATATTTTCCATTTGTTAAAACTAATCCTTATACTTTTTTTTAAACAATTTAAATTTTTTTC
29402742 CTTATACTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
73 35 0.57
74 26 0.43
ACGTcount: A:0.30, C:0.11, G:0.03, T:0.57
Consensus pattern (74 bp):
TATTATATTTTCCATTTGTTAAAACTAATCCTTATACTTTTTTTTAAACAATTTAAATTTTTTTC
TTTTTAACG
Found at i:29412629 original size:16 final size:16
Alignment explanation
Indices: 29412608--29412677 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
29412598 TTTGGTTCGC
* *
29412608 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
29412624 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
29412640 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
29412656 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
29412672 TGTAAT
1 TGTAAT
29412678 AGCAAATCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:29412710 original size:45 final size:44
Alignment explanation
Indices: 29412656--29412750 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 44
29412646 GGAATAGAGG
*
29412656 TGTAATGGAATAGAGGTGTAATAGCAAATCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATC-ATGTGTTTGGTTGAA
* *
29412701 TGTAATGGAATAGAGGCGTAATAGTAATCCTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAA
29412745 TGTAAT
1 TGTAAT
29412751 AGAGGTGTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.48
45 23 0.50
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAA
Found at i:29412931 original size:18 final size:17
Alignment explanation
Indices: 29412910--29412944 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29412900 TTATTATTAA
*
29412910 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
29412928 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
29412945 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:29418988 original size:21 final size:21
Alignment explanation
Indices: 29418947--29418989 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
29418937 AATAAAGTAG
*
29418947 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
29418968 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
29418989 A
1 A
29418990 AATTCATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:29419279 original size:45 final size:44
Alignment explanation
Indices: 29419198--29419286 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 44
29419188 ACCTCTATTC
*
29419198 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
*** *
29419242 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTATTCCATTA
29419287 TGCCTCTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 16 0.41
45 23 0.59
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.33
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
Found at i:29429428 original size:41 final size:38
Alignment explanation
Indices: 29429383--29429487 Score: 129
Period size: 41 Copynumber: 2.7 Consensus size: 38
29429373 CGAATATTAT
* * *
29429383 AATTATAATTACCATAATTATAATAATGTTTGACCGAAAAA
1 AATTATAATTACAATAATTATAATAATATTCGACCG---AA
* * *
29429424 AATTACAATTACAATAATTATAATAATATTCGATCGTA
1 AATTATAATTACAATAATTATAATAATATTCGACCGAA
29429462 AATTATAATTACAATAATTATAATAA
1 AATTATAATTACAATAATTATAATAA
29429488 GGATTTTGGT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
38 26 0.46
41 31 0.54
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (38 bp):
AATTATAATTACAATAATTATAATAATATTCGACCGAA
Done.