Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 102 of 190
Found at i:31022002 original size:30 final size:31
Alignment explanation
Indices: 31021966--31022029 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
31021956 TTTTAGTTTT
31021966 ATTGGGTTGGGTAATTAGGTTAGGTTGG-TA
1 ATTGGGTTGGGTAATTAGGTTAGGTTGGATA
* * *
31021996 ATTGGGTTGGGTCATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTAATTAGGTTAGGTTGGATA
31022027 ATT
1 ATT
31022030 TTATTTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.17, C:0.02, G:0.41, T:0.41
Consensus pattern (31 bp):
ATTGGGTTGGGTAATTAGGTTAGGTTGGATA
Found at i:31022014 original size:13 final size:13
Alignment explanation
Indices: 31021996--31022020 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31021986 TAGGTTGGTA
31021996 ATTGGGTTGGGTC
1 ATTGGGTTGGGTC
31022009 ATTGGGTTGGGT
1 ATTGGGTTGGGT
31022021 TGGATAATTT
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:0.08, C:0.04, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTC
Found at i:31023569 original size:25 final size:25
Alignment explanation
Indices: 31023541--31023595 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
31023531 TACTGATTTT
*
31023541 AGCTCGTATGAGCTTACCGATACTC
1 AGCTCGCATGAGCTTACCGATACTC
* *
31023566 AGCTCGCATGAGCTTACCGTTATTC
1 AGCTCGCATGAGCTTACCGATACTC
31023591 AGCTC
1 AGCTC
31023596 AAAGGAGCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (25 bp):
AGCTCGCATGAGCTTACCGATACTC
Found at i:31023603 original size:25 final size:25
Alignment explanation
Indices: 31023550--31023611 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
31023540 TAGCTCGTAT
** *
31023550 GAGCTTACCGATACTCAGCTCGCAT
1 GAGCTTACCGATACTCAGCTCAAAG
* *
31023575 GAGCTTACCGTTATTCAGCTCAAAG
1 GAGCTTACCGATACTCAGCTCAAAG
*
31023600 GAGCATACCGAT
1 GAGCTTACCGAT
31023612 TCAAAGCTCG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (25 bp):
GAGCTTACCGATACTCAGCTCAAAG
Found at i:31027285 original size:30 final size:31
Alignment explanation
Indices: 31027246--31027305 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
31027236 GGAGGTGGGA
*
31027246 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
31027277 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
31027306 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:31032798 original size:25 final size:25
Alignment explanation
Indices: 31032770--31032833 Score: 101
Period size: 25 Copynumber: 2.6 Consensus size: 25
31032760 ATAGTGCTAA
* *
31032770 ACATAACATTCTTTAAACATAACAT
1 ACATAACATACATTAAACATAACAT
31032795 ACATAACATACATTAAACATAACAT
1 ACATAACATACATTAAACATAACAT
*
31032820 ACATAATATACATT
1 ACATAACATACATT
31032834 CATAAACATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.30
Consensus pattern (25 bp):
ACATAACATACATTAAACATAACAT
Found at i:31032800 original size:9 final size:9
Alignment explanation
Indices: 31032786--31032832 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
31032776 CATTCTTTAA
31032786 ACATAACAT
1 ACATAACAT
31032795 ACATAACAT
1 ACATAACAT
*
31032804 ACATTA-A-
1 ACATAACAT
31032811 ACATAACAT
1 ACATAACAT
*
31032820 ACATAATAT
1 ACATAACAT
31032829 ACAT
1 ACAT
31032833 TCATAAACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
7 5 0.15
8 2 0.06
9 26 0.79
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.26
Consensus pattern (9 bp):
ACATAACAT
Found at i:31033028 original size:79 final size:79
Alignment explanation
Indices: 31032852--31033030 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 79
31032842 TTAAAATGCT
* * * *
31032852 ACGTAATATACATACATAACAGACATGTTTATAATAGTAATATACCACATAACAGTCACATACAT
1 ACGTAACATACATACATAACAGACATATTCATAACAGTAATATACCACATAACAGTCACATACAT
* ** *
31032917 AATAGTAAAATACT
66 AACAACAAAATACC
* * *
31032931 ACAG-AACATACA-AGCATAACAGACATATTCATAACAGTAATATACCACATAACTGTTACGTAC
1 AC-GTAACATACATA-CATAACAGACATATTCATAACAGTAATATACCACATAACAGTCACATAC
*
31032994 ATAACAACAATATACC
64 ATAACAACAAAATACC
*
31033010 ACGTAACAAACATACATAACA
1 ACGTAACATACATACATAACA
31033031 ATAATATACA
Statistics
Matches: 83, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
78 2 0.02
79 79 0.95
80 2 0.02
ACGTcount: A:0.49, C:0.20, G:0.07, T:0.23
Consensus pattern (79 bp):
ACGTAACATACATACATAACAGACATATTCATAACAGTAATATACCACATAACAGTCACATACAT
AACAACAAAATACC
Found at i:31033029 original size:31 final size:28
Alignment explanation
Indices: 31032991--31033094 Score: 105
Period size: 28 Copynumber: 3.9 Consensus size: 28
31032981 AACTGTTACG
*
31032991 TACATAACAACAATATACCACGTAACAAACA
1 TACATAACAATAATATA-CA--TAACAAACA
*
31033022 TACATAACAATAATATACATAACATACA
1 TACATAACAATAATATACATAACAAACA
31033050 TACATAAC----A-ATA-ATAAC-AACA
1 TACATAACAATAATATACATAACAAACA
*
31033071 TACATAACAGTAATATACATAACA
1 TACATAACAATAATATACATAACA
31033095 TACTTTGGTA
Statistics
Matches: 63, Mismatches: 3, Indels: 17
0.76 0.04 0.20
Matches are distributed among these distances:
21 11 0.17
22 5 0.08
23 3 0.05
24 1 0.02
25 1 0.02
26 3 0.05
27 5 0.08
28 16 0.25
30 2 0.03
31 16 0.25
ACGTcount: A:0.57, C:0.20, G:0.02, T:0.21
Consensus pattern (28 bp):
TACATAACAATAATATACATAACAAACA
Found at i:31033073 original size:21 final size:22
Alignment explanation
Indices: 31033018--31033097 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 22
31033008 CCACGTAACA
*
31033018 AACATACATAACAATAA-TATACAT
1 AACATACAT-AC-ATAACAATA-AT
31033042 AACATACATACATAACAATAAT
1 AACATACATACATAACAATAAT
*
31033064 AACA-ACATACATAACAGTAAT
1 AACATACATACATAACAATAAT
31033085 ATACATAACATAC
1 A-ACAT-ACATAC
31033098 TTTGGTAAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
21 17 0.34
22 13 0.26
23 5 0.10
24 15 0.30
ACGTcount: A:0.57, C:0.19, G:0.01, T:0.23
Consensus pattern (22 bp):
AACATACATACATAACAATAAT
Found at i:31033202 original size:6 final size:6
Alignment explanation
Indices: 31033191--31033221 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
31033181 CACGAATGCC
31033191 AACAAA AACAAA AACAAA AACAAA AACAAA A
1 AACAAA AACAAA AACAAA AACAAA AACAAA A
31033222 TTTGAAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:31047065 original size:9 final size:9
Alignment explanation
Indices: 31047053--31047119 Score: 64
Period size: 9 Copynumber: 7.2 Consensus size: 9
31047043 AATTTAAAAC
*
31047053 GAGAAAGTT
1 GAGAGAGTT
*
31047062 GAGAGACTT
1 GAGAGAGTT
*
31047071 GAGAGGGTTT
1 GAGAGAG-TT
*
31047081 GACAGAGTT
1 GAGAGAGTT
31047090 GAGAGAGTTT
1 GAGAGAG-TT
31047100 GAGAGAGTT
1 GAGAGAGTT
31047109 G-GAAGAGTT
1 GAG-AGAGTT
31047118 GA
1 GA
31047120 AAGAAGGATG
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
8 1 0.02
9 30 0.64
10 16 0.34
ACGTcount: A:0.33, C:0.03, G:0.40, T:0.24
Consensus pattern (9 bp):
GAGAGAGTT
Found at i:31047115 original size:28 final size:28
Alignment explanation
Indices: 31047058--31047119 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
31047048 AAAACGAGAA
* *
31047058 AGTTGAGAGACTTGAGAGGGTTTGACAG
1 AGTTGAGAGACTTGAGAGAGTTGGACAG
*
31047086 AGTTGAGAGAGTTTGAGAGAGTTGGA-AG
1 AGTTGAGAGA-CTTGAGAGAGTTGGACAG
31047114 AGTTGA
1 AGTTGA
31047120 AAGAAGGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.31, C:0.03, G:0.40, T:0.26
Consensus pattern (28 bp):
AGTTGAGAGACTTGAGAGAGTTGGACAG
Found at i:31047117 original size:19 final size:19
Alignment explanation
Indices: 31047069--31047109 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
31047059 GTTGAGAGAC
*
31047069 TTGAGAGGGTTTGACAGAG
1 TTGAGAGAGTTTGACAGAG
*
31047088 TTGAGAGAGTTTGAGAGAG
1 TTGAGAGAGTTTGACAGAG
31047107 TTG
1 TTG
31047110 GAAGAGTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.27, C:0.02, G:0.41, T:0.29
Consensus pattern (19 bp):
TTGAGAGAGTTTGACAGAG
Found at i:31052929 original size:27 final size:27
Alignment explanation
Indices: 31052899--31053109 Score: 214
Period size: 27 Copynumber: 7.9 Consensus size: 27
31052889 TCATCTTCTA
**
31052899 GGGGTATAACAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
31052926 GGGGTATTTCGGTCATTTTACCCCAT-
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
31052952 GGGGTATTTC-GCTCATTCTACCTTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
*
31052979 GGGGTATTCCTA-TCATTTTACCCTATG
1 GGGGTATTTC-AGTCATTTTACCCTATG
* *
31053006 GGGATATTTCAGTCATTTTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
31053033 AGGGTATTTCGGTCATTTTATCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
** * *
31053060 GGGGTATTTTGGTCATTTTATCTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
31053087 GGGGTATTTC-GATTATTTTACCC
1 GGGGTATTTCAG-TCATTTTACCC
31053110 ATTTTAGGGT
Statistics
Matches: 153, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
25 1 0.01
26 23 0.15
27 129 0.84
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTATG
Found at i:31053087 original size:81 final size:79
Alignment explanation
Indices: 31052910--31053109 Score: 242
Period size: 81 Copynumber: 2.5 Consensus size: 79
31052900 GGGTATAACA
*
31052910 GTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCCATGGGGTATTTCGCTCATTCTACCT
1 GTCATTTTACCCTATGGGGGTATTTC-GTCATTTTACCCCATAGGGTATTTCGCTCATTCTACCT
31052975 TATGGGGGTATTCCT
65 TATGGGGGTATTCCT
* * * * *
31052990 ATCATTTTACCCTATGGGGATATTTCAGTCATTTTACCCTATAAGGGTATTTCGGTCATTTTATC
1 GTCATTTTACCCTATGGGGGTATTTC-GTCATTTTACCCCAT-AGGGTATTTCGCTCATTCTA-C
*
31053055 C-TATGGGGGTATT-TT
63 CTTATGGGGGTATTCCT
* * *
31053070 GGTCATTTTATCTTATGGGGGTATTTCGATTATTTTACCC
1 -GTCATTTTACCCTATGGGGGTATTTCG-TCATTTTACCC
31053110 ATTTTAGGGT
Statistics
Matches: 103, Mismatches: 13, Indels: 7
0.84 0.11 0.06
Matches are distributed among these distances:
80 40 0.39
81 61 0.59
82 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.43
Consensus pattern (79 bp):
GTCATTTTACCCTATGGGGGTATTTCGTCATTTTACCCCATAGGGTATTTCGCTCATTCTACCTT
ATGGGGGTATTCCT
Found at i:31053378 original size:19 final size:19
Alignment explanation
Indices: 31053343--31053380 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
31053333 GTGTAGGGCC
*
31053343 CACGAGCCCATTGAGCCCA
1 CACGAGCCCATTCAGCCCA
31053362 CACG-GCCCATTTCAGCCCA
1 CACGAGCCCA-TTCAGCCCA
31053381 ACGTGGCCCA
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:0.24, C:0.45, G:0.18, T:0.13
Consensus pattern (19 bp):
CACGAGCCCATTCAGCCCA
Found at i:31053747 original size:20 final size:22
Alignment explanation
Indices: 31053718--31053775 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 22
31053708 ACAACAACAA
*
31053718 TCTCCCCAAATC-CC-AATATC
1 TCTCCTCAAATCTCCAAATATC
31053738 TCTCCTCAAATTTCTCCAAATATC
1 TCTCCTCAAA--TCTCCAAATATC
*
31053762 CCTCCTCAAATCTC
1 TCTCCTCAAATCTC
31053776 TTTATGACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 9 0.28
22 6 0.19
23 2 0.06
24 15 0.47
ACGTcount: A:0.28, C:0.41, G:0.00, T:0.31
Consensus pattern (22 bp):
TCTCCTCAAATCTCCAAATATC
Found at i:31058062 original size:19 final size:20
Alignment explanation
Indices: 31058024--31058065 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
31058014 GACCCCAAGG
*
31058024 CGGCGCCGGCGACCGGTGGC
1 CGGCGCCGGCGACCGATGGC
*
31058044 CGGCG-CGGCGGCCGATGGC
1 CGGCGCCGGCGACCGATGGC
31058063 CGG
1 CGG
31058066 AGCCTTCGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.05, C:0.38, G:0.52, T:0.05
Consensus pattern (20 bp):
CGGCGCCGGCGACCGATGGC
Found at i:31058542 original size:18 final size:18
Alignment explanation
Indices: 31058499--31058570 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 18
31058489 GTCCCCTTTT
*
31058499 TTATTTTATTTTTATTTTTA
1 TTATTTTA--TTTATTTTCA
*
31058519 TAATTTTATTTATTTTCA
1 TTATTTTATTTATTTTCA
*
31058537 TTATTTT-TATTATTGTC-
1 TTATTTTAT-TTATTTTCA
31058554 TTATTTGATATTTATTT
1 TTATTT--TATTTATTT
31058571 CTTTATGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
17 7 0.16
18 22 0.51
19 6 0.14
20 8 0.19
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (18 bp):
TTATTTTATTTATTTTCA
Found at i:31058548 original size:9 final size:9
Alignment explanation
Indices: 31058496--31058550 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
31058486 ATAGTCCCCT
31058496 TTTTTATT-
1 TTTTTATTA
31058504 TTATTT-TTA
1 TT-TTTATTA
31058513 TTTTTA-TA
1 TTTTTATTA
*
31058521 ATTTTATTTA
1 TTTTTA-TTA
*
31058531 TTTTCATTA
1 TTTTTATTA
31058540 TTTTTATTA
1 TTTTTATTA
31058549 TT
1 TT
31058551 GTCTTATTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
8 14 0.37
9 18 0.47
10 6 0.16
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTATTA
Found at i:31061264 original size:12 final size:12
Alignment explanation
Indices: 31061247--31061280 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
31061237 TTAGAGCAAT
31061247 TGCAAGAACAGA
1 TGCAAGAACAGA
**
31061259 TGCAAGCCCAGA
1 TGCAAGAACAGA
31061271 TGCAAGAACA
1 TGCAAGAACA
31061281 ACTAGAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.24, G:0.24, T:0.09
Consensus pattern (12 bp):
TGCAAGAACAGA
Found at i:31063544 original size:17 final size:17
Alignment explanation
Indices: 31063524--31063567 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
31063514 AAGAATGTTC
31063524 AAAAAAAAAAAGAAAAG
1 AAAAAAAAAAAGAAAAG
*
31063541 AAAAATAAAAAGAAAAG
1 AAAAAAAAAAAGAAAAG
31063558 AAAAGAAAAA
1 AAAA-AAAAA
31063568 GGAGAGGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.02
Consensus pattern (17 bp):
AAAAAAAAAAAGAAAAG
Found at i:31063556 original size:22 final size:22
Alignment explanation
Indices: 31063525--31063567 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
31063515 AGAATGTTCA
31063525 AAAAAAAAAAGAAAAGAAAAAT
1 AAAAAAAAAAGAAAAGAAAAAT
*
31063547 AAAAAGAAAAGAAAAGAAAAA
1 AAAAAAAAAAGAAAAGAAAAA
31063568 GGAGAGGCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAAGAAAAGAAAAAT
Found at i:31065280 original size:219 final size:219
Alignment explanation
Indices: 31064894--31065873 Score: 1532
Period size: 219 Copynumber: 4.5 Consensus size: 219
31064884 CATCATATCA
* * *
31064894 AGTCCTATCTCTCTGAGCAGCAACGGAGTAGGTCAAAGATTGTAGATCTTGTCTTCCTGTACTGG
1 AGTCCTATCTCCCTGAGCAGCAGCGGAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTGG
* * * *
31064959 TAGTGAAGTAGATTGACAGCACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTG
66 CAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTG
* * *
31065024 TAGATCTTATCTCCCTAAGAAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAAAT
131 TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCAAGAT
31065089 AGTAGGAAGCAGATTTAAGCCACC
196 AGTAGGAAGCAGATTTAAGCCACC
* * * *
31065113 AGTCCTATGTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTATAGATCTTGTCTTCCTGTATTGG
1 AGTCCTATCTCCCTGAGCAGCAGCGGAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTGG
* *
31065178 CAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCTCTCAGCAGCAGTGGAGTAGGTTGAAGATTG
66 CAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTG
* * *
31065243 TAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATGGCGAATCTTATCTTCCCAAGAT
131 TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCAAGAT
31065308 AGTAGGAAGCAGATTTAAGCCACC
196 AGTAGGAAGCAGATTTAAGCCACC
* * * *
31065332 AGTCCTATCTCCCTGAGCAACAGTGGAGTAGGTCGAAGATTGTAGATCTTGTCTTTCTTTACTGG
1 AGTCCTATCTCCCTGAGCAGCAGCGGAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTGG
*
31065397 CAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGGAGCAGTGGAGTAGGTTGAAGATTG
66 CAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTG
*
31065462 TAGATCTTATCTCCCTAAGCAGTACTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCAAGAT
131 TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCAAGAT
**
31065527 AGTAGGAAATAGATTTAAGCCACC
196 AGTAGGAAGCAGATTTAAGCCACC
*
31065551 AGTCCTATCTCCCTGAGCAGCAGCGAAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTGG
1 AGTCCTATCTCCCTGAGCAGCAGCGGAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTGG
*
31065616 CAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGGAGCAGTGGAGTAGGTTGAAGATTG
66 CAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTG
* * ** *
31065681 TAGATCTTATCTCCCTAGGCAATAGTGGAGCAGATTAAAGACGACGAATCTTATCTTCCCAAGGT
131 TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCAAGAT
* **
31065746 AGTAGGGAAGTAGATTTAAGCCATT
196 AGTA-GGAAGCAGATTTAAGCCACC
* * * * *
31065771 AG-CCTTATCTCCCTAAGTAGCAGTGGAGTAGGTCGATGATTGTAGATCTTGTCTTCTTGTACTG
1 AGTCC-TATCTCCCTGAGCAGCAGCGGAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTG
* *
31065835 GCAGTGAAGCAGATTGAAAGCACCAGGCTTATC-CCCTGA
65 GCAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCCCTGA
31065874 AGTTGCAGTG
Statistics
Matches: 703, Mismatches: 56, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
219 600 0.85
220 103 0.15
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (219 bp):
AGTCCTATCTCCCTGAGCAGCAGCGGAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTGG
CAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTG
TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCAAGAT
AGTAGGAAGCAGATTTAAGCCACC
Found at i:31065294 original size:44 final size:44
Alignment explanation
Indices: 31065204--31065298 Score: 111
Period size: 44 Copynumber: 2.2 Consensus size: 44
31065194 AAGCACCAGC
* * * * * *
31065204 CTTATCTCTCTCAGCAGCAGTGGAGTAGGTTGAAGATTGTAGAT
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGATCGAAGATGGGAGAT
*
31065248 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATGGCGA-AT
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGATCGAAGATGG-GAGAT
31065292 CTTATCT
1 CTTATCT
31065299 TCCCAAGATA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 42 0.98
45 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (44 bp):
CTTATCTCCCTAAGCAGCAGTGGAGTAGATCGAAGATGGGAGAT
Found at i:31065381 original size:87 final size:87
Alignment explanation
Indices: 31065248--31065473 Score: 226
Period size: 88 Copynumber: 2.6 Consensus size: 87
31065238 GATTGTAGAT
* * * ** *
31065248 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGA-TGGCGAATCTTATCTTCCCAAGATAGTA
1 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATTGTAG-ATCTTATCTTCCCAA-ATAGCA
**
31065312 G-GAAGCAGAT-TTAAGCCACCAGTC
64 GTGAAGCAGATCGAAAG-CACCAG-C
* * *** * *
31065336 C-TATCTCCCTGAGCAACAGTGGAGTAGGTCGAAGATTGTAGATCTTGTCTTTCTTTACTGGCAG
1 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATTGTAGATCTTATC-TTCCCAAATAGCAG
31065400 TGAAGCAGATCGAAAGCACCAGC
65 TGAAGCAGATCGAAAGCACCAGC
* *
31065423 CTTATCTCCCTGAGGAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCT
1 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATTGTAGATCTTATCT
31065474 CCCTAAGCAG
Statistics
Matches: 114, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
87 44 0.39
88 67 0.59
89 3 0.03
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (87 bp):
CTTATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATTGTAGATCTTATCTTCCCAAATAGCAGT
GAAGCAGATCGAAAGCACCAGC
Found at i:31071181 original size:21 final size:21
Alignment explanation
Indices: 31071152--31071226 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 21
31071142 GTATATATAT
*
31071152 ATTTTAAAATTTAAATAAAAA
1 ATTTAAAAATTTAAATAAAAA
* *
31071173 ATTTCAAAATTCAGAA-AAAATA
1 ATTTAAAAATTTA-AATAAAA-A
*
31071195 ATTTAAAAGCATATAAATAAAAA
1 ATTTAAAA--ATTTAAATAAAAA
*
31071218 ATATAAAAA
1 ATTTAAAAA
31071227 ATATTTTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
21 16 0.37
22 10 0.23
23 10 0.23
24 7 0.16
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (21 bp):
ATTTAAAAATTTAAATAAAAA
Found at i:31072959 original size:27 final size:27
Alignment explanation
Indices: 31072929--31072987 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
31072919 GAGTTGATAA
*
31072929 AATTCTCTTTTAAGT-TTTCTTTTA-AAG
1 AATT-TCTCTTAAGTGTTT-TTTTAGAAG
*
31072956 AATTTCTCTTGAGTGTTTTTTTAGAAG
1 AATTTCTCTTAAGTGTTTTTTTAGAAG
31072983 AATTT
1 AATTT
31072988 TAACAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.25, C:0.08, G:0.12, T:0.54
Consensus pattern (27 bp):
AATTTCTCTTAAGTGTTTTTTTAGAAG
Found at i:31077486 original size:41 final size:43
Alignment explanation
Indices: 31077439--31077544 Score: 146
Period size: 41 Copynumber: 2.5 Consensus size: 43
31077429 CTGTTACTCT
* *
31077439 GTGGAATCAGCACTTAGCAACCACCTT-ATATTC-AGTGATACG
1 GTGGAATCAGCACTTAGCAACCACCTTCACAATCAAG-GATACG
* *
31077481 G-GGAATCAGCACATAGCAACCACTTTCACAATCAAGGATACG
1 GTGGAATCAGCACTTAGCAACCACCTTCACAATCAAGGATACG
31077523 GTGGAATCAGCACTTAGCAACC
1 GTGGAATCAGCACTTAGCAACC
31077545 CCTCAGGGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
41 23 0.41
42 12 0.21
43 21 0.38
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (43 bp):
GTGGAATCAGCACTTAGCAACCACCTTCACAATCAAGGATACG
Found at i:31084370 original size:30 final size:30
Alignment explanation
Indices: 31084266--31084378 Score: 106
Period size: 30 Copynumber: 3.8 Consensus size: 30
31084256 ATAGCTTCAA
* *
31084266 CTATC-AATTATGAAAAGGGATGG-TGATGA
1 CTATCAAATTATGAAAAGGGATGGCT-TTGG
* * *
31084295 TTATCAACTTATGAAAAGGGATGGCTTCGG
1 CTATCAAATTATGAAAAGGGATGGCTTTGG
** *
31084325 CTAT-TGATATCTGAAAAGGGATGGCTTTGG
1 CTATCAAAT-TATGAAAAGGGATGGCTTTGG
*
31084355 CTATCAAATTATGAAAAGGAATGG
1 CTATCAAATTATGAAAAGGGATGG
31084379 TGATGACCAT
Statistics
Matches: 65, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
29 5 0.08
30 57 0.88
31 3 0.05
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.29
Consensus pattern (30 bp):
CTATCAAATTATGAAAAGGGATGGCTTTGG
Found at i:31084431 original size:120 final size:120
Alignment explanation
Indices: 31084279--31084496 Score: 285
Period size: 120 Copynumber: 1.8 Consensus size: 120
31084269 TCAATTATGA
* * ** * * * * *
31084279 AAAGGGATGGTGATGATTATCAACTTATGAAAAGGGATGGCTTCGGCTATTGATA-TCTGAAAAG
1 AAAGGAATGGTGAAGACCATCAAATTATGAAAAGGGATAGCTTCAGCTATCGA-ACTATGAAAAG
** * *
31084343 GGATGGCTTTGGCTATCAAATTATGAAAAGGAATGGTGATGACCATCGAAAAATAG
65 GGATAACTTCGGCTATCAAATTACGAAAAGGAATGGTGATGACCATCGAAAAATAG
31084399 AAAGGAATGGTGAAGACCATCAAATTATGAAAAGGGATAGCTTCAGCTATCGAACTATGAAAAGG
1 AAAGGAATGGTGAAGACCATCAAATTATGAAAAGGGATAGCTTCAGCTATCGAACTATGAAAAGG
* *
31084464 GATAACTTCGGTTATCGAATTACGAAAAGGAAT
66 GATAACTTCGGCTATCAAATTACGAAAAGGAAT
31084497 ATGTCAACCA
Statistics
Matches: 82, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
119 1 0.01
120 81 0.99
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.25
Consensus pattern (120 bp):
AAAGGAATGGTGAAGACCATCAAATTATGAAAAGGGATAGCTTCAGCTATCGAACTATGAAAAGG
GATAACTTCGGCTATCAAATTACGAAAAGGAATGGTGATGACCATCGAAAAATAG
Found at i:31084433 original size:30 final size:30
Alignment explanation
Indices: 31084357--31084433 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
31084347 GGCTTTGGCT
*
31084357 ATCAAATTATGAAAAGGAATGGTGATGACC
1 ATCAAATTATGAAAAGGAATGGTGAAGACC
*
31084387 ATCGAAA-AAT-AGAAAGGAATGGTGAAGACC
1 ATC-AAATTATGA-AAAGGAATGGTGAAGACC
31084417 ATCAAATTATGAAAAGG
1 ATCAAATTATGAAAAGG
31084434 GATAGCTTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
29 4 0.10
30 32 0.80
31 4 0.10
ACGTcount: A:0.48, C:0.09, G:0.23, T:0.19
Consensus pattern (30 bp):
ATCAAATTATGAAAAGGAATGGTGAAGACC
Found at i:31084458 original size:30 final size:30
Alignment explanation
Indices: 31084424--31084493 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
31084414 ACCATCAAAT
*
31084424 TATGAAAAGGGATAGCTTCAGCTATCGAAC
1 TATGAAAAGGGATAACTTCAGCTATCGAAC
* * *
31084454 TATGAAAAGGGATAACTTCGGTTATCGAAT
1 TATGAAAAGGGATAACTTCAGCTATCGAAC
*
31084484 TACGAAAAGG
1 TATGAAAAGG
31084494 AATATGTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (30 bp):
TATGAAAAGGGATAACTTCAGCTATCGAAC
Found at i:31084463 original size:60 final size:59
Alignment explanation
Indices: 31084246--31084466 Score: 173
Period size: 60 Copynumber: 3.7 Consensus size: 59
31084236 TCATCAACGA
* * * *
31084246 ATGAAAATGGATAGCTTCAACTATC-AATTATGAAAAGGGATGGTGATGATTATCAACTT
1 ATGAAAAGGGATAGCTTCAGCTATCGAA-TATGAAAAGGGATGGTGATGACTATCAAATT
* * * * * *
31084305 ATGAAAAGGGATGGCTTCGGCTATTGATATCTGAAAAGGGATGGCT-TTGGCTATCAAATT
1 ATGAAAAGGGATAGCTTCAGCTATCGA-ATATGAAAAGGGATGG-TGATGACTATCAAATT
* * * * * * * *
31084365 ATGAAAAGGAAT-G-GTGATGACCATCGAAAAAT-AGAAAGGAATGGTGAAGACCATCAAATT
1 ATGAAAAGGGATAGCTTCA-G-CTATCG-AATATGA-AAAGGGATGGTGATGACTATCAAATT
31084425 ATGAAAAGGGATAGCTTCAGCTATCGAACTATGAAAAGGGAT
1 ATGAAAAGGGATAGCTTCAGCTATCGAA-TATGAAAAGGGAT
31084467 AACTTCGGTT
Statistics
Matches: 121, Mismatches: 29, Indels: 23
0.70 0.17 0.13
Matches are distributed among these distances:
58 1 0.01
59 26 0.21
60 86 0.71
61 6 0.05
62 2 0.02
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (59 bp):
ATGAAAAGGGATAGCTTCAGCTATCGAATATGAAAAGGGATGGTGATGACTATCAAATT
Found at i:31087348 original size:50 final size:49
Alignment explanation
Indices: 31087166--31087362 Score: 175
Period size: 50 Copynumber: 4.0 Consensus size: 49
31087156 TTAACTATTA
* * *
31087166 TCATT-CGATACACGTAGTAGCCTTCACATAGTAATACACACGTGA-TT
1 TCATTCCGGTACACGTAGTAGCCTACACATAGTACTACACACGTGACTT
* * * * *
31087213 AAACTTTCCAGTTCACGTAGTAGCCTACACATAGTACTACACACGTGA-TC
1 --TCATTCCGGTACACGTAGTAGCCTACACATAGTACTACACACGTGACTT
** * * * * *
31087263 GAAGCTATCTGGTACGCATAGTAGCCTACACATAGTACTACACATGCGACCTT
1 TCA--T-TCCGGTACACGTAGTAGCCTACACATAGTACTACACACGTGA-CTT
*
31087316 TCATTCCGGTACACGTAGTAGCCTACACATAGTACTACACACTTGAC
1 TCATTCCGGTACACGTAGTAGCCTACACATAGTACTACACACGTGAC
31087363 CATCACTTTC
Statistics
Matches: 115, Mismatches: 27, Indels: 12
0.75 0.18 0.08
Matches are distributed among these distances:
49 4 0.03
50 73 0.63
51 36 0.31
53 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (49 bp):
TCATTCCGGTACACGTAGTAGCCTACACATAGTACTACACACGTGACTT
Found at i:31096435 original size:43 final size:43
Alignment explanation
Indices: 31096388--31096471 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
31096378 TATGTGATTT
31096388 ATATTGAAATGGAAAAA-ATGAAAAATGAATATGAGATGAGAAA
1 ATATTGAAAT-GAAAAATATGAAAAATGAATATGAGATGAGAAA
* *
31096431 ATATTGAAATGAAAAATATGATAAATGATTATGAGATGAGA
1 ATATTGAAATGAAAAATATGAAAAATGAATATGAGATGAGA
31096472 TATGAGATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 6 0.16
43 32 0.84
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (43 bp):
ATATTGAAATGAAAAATATGAAAAATGAATATGAGATGAGAAA
Found at i:31096446 original size:15 final size:16
Alignment explanation
Indices: 31096403--31096458 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
31096393 GAAATGGAAA
31096403 AAATGAAAAATGAATATG
1 AAATGAAAAAT--ATATG
*
31096421 AGATGAGAAAATAT-TG
1 AAATGA-AAAATATATG
31096437 AAATGAAAAATATGAT-
1 AAATGAAAAATAT-ATG
31096453 AAATGA
1 AAATGA
31096459 TTATGAGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
15 7 0.21
16 13 0.39
17 3 0.09
18 5 0.15
19 5 0.15
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.23
Consensus pattern (16 bp):
AAATGAAAAATATATG
Found at i:31113208 original size:18 final size:19
Alignment explanation
Indices: 31113177--31113213 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
31113167 AAGGAGAAGA
31113177 TGAGGAGAATGATG-GGAG
1 TGAGGAGAATGATGAGGAG
31113195 TGAGGAG-ATGGATGAGGAG
1 TGAGGAGAAT-GATGAGGAG
31113214 GACGATTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.12
18 11 0.65
19 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.51, T:0.16
Consensus pattern (19 bp):
TGAGGAGAATGATGAGGAG
Found at i:31117417 original size:20 final size:19
Alignment explanation
Indices: 31117392--31117436 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
31117382 AAGGATCAAA
31117392 TTGGAACAAA-ATAGAAAATT
1 TTGGAA-AAACATA-AAAATT
*
31117412 TTGGAAAAACTTAAAAATT
1 TTGGAAAAACATAAAAATT
31117431 TTGGAA
1 TTGGAA
31117437 GTAGGGATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.51, C:0.04, G:0.16, T:0.29
Consensus pattern (19 bp):
TTGGAAAAACATAAAAATT
Found at i:31132839 original size:39 final size:39
Alignment explanation
Indices: 31132781--31132918 Score: 215
Period size: 39 Copynumber: 3.5 Consensus size: 39
31132771 AACATGTTTT
* * *
31132781 TGAGTATTGTGATAGATGCTTGAATGTTATATGATTACA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
31132820 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
*
31132859 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
*
31132898 T-ATGTAATGTGATATATGCTT
1 TGA-GTATTGTGATATATGCTT
31132919 AAAAGTGCAT
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
38 1 0.01
39 92 0.99
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.45
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
Found at i:31132852 original size:22 final size:22
Alignment explanation
Indices: 31132827--31132898 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
31132817 ACATGAGTAT
31132827 TGTGATATATGCTTGAATGTTA
1 TGTGATATATGCTTGAATGTTA
*
31132849 TGTGAT-TAT--ATG-A-G-TA
1 TGTGATATATGCTTGAATGTTA
*
31132865 TTGTGATATATGCTTAAATGTTA
1 -TGTGATATATGCTTGAATGTTA
31132888 TGTGATTATAT
1 TGTGA-TATAT
31132899 ATGTAATGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 15
0.68 0.05 0.26
Matches are distributed among these distances:
16 2 0.05
17 7 0.18
18 4 0.10
19 2 0.05
20 1 0.03
21 4 0.10
22 12 0.31
23 7 0.18
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (22 bp):
TGTGATATATGCTTGAATGTTA
Found at i:31132919 original size:39 final size:39
Alignment explanation
Indices: 31132781--31132935 Score: 213
Period size: 39 Copynumber: 3.9 Consensus size: 39
31132771 AACATGTTTT
* * * *
31132781 TGAGTATTGTGATAGATGCTTGAATGTTATATGATTACA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
*
31132820 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
31132859 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * *
31132898 T-ATGTAATGTGATATATGCTTAAAAGTGCATGTGATTA
1 TGA-GTATTGTGATATATGCTTAAATGT-TATGTGATTA
31132936 CCATGTAAAT
Statistics
Matches: 107, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
38 1 0.01
39 97 0.91
40 9 0.08
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.43
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:31135876 original size:20 final size:20
Alignment explanation
Indices: 31135853--31135928 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
31135843 GTGCTCCTAT
31135853 TTGTACTTCGATACCCCTGA
1 TTGTACTTCGATACCCCTGA
* *
31135873 TTGTACTTCAATACCCCTTA
1 TTGTACTTCGATACCCCTGA
* * * *
31135893 TTGCAGTTAC-ATGCCCCTGT
1 TTGTACTT-CGATACCCCTGA
*
31135913 TTGTACTTCGGTACCC
1 TTGTACTTCGATACCC
31135929 TTGAATGCAC
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.18, C:0.30, G:0.14, T:0.37
Consensus pattern (20 bp):
TTGTACTTCGATACCCCTGA
Found at i:31140895 original size:18 final size:18
Alignment explanation
Indices: 31140869--31140909 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
31140859 TTTGAAGCGT
31140869 GATGCTGGTTTTGATGAA
1 GATGCTGGTTTTGATGAA
*
31140887 GATGTTGGTTTTGATGAA
1 GATGCTGGTTTTGATGAA
31140905 GATGC
1 GATGC
31140910 AATCTTATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.22, C:0.05, G:0.34, T:0.39
Consensus pattern (18 bp):
GATGCTGGTTTTGATGAA
Found at i:31148397 original size:18 final size:18
Alignment explanation
Indices: 31148374--31148411 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
31148364 AATTTGAAAT
31148374 AAAACAAAAAATTTTGGA
1 AAAACAAAAAATTTTGGA
**
31148392 AAAACATGAAATTTTGGA
1 AAAACAAAAAATTTTGGA
31148410 AA
1 AA
31148412 CAGAGGTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.58, C:0.05, G:0.13, T:0.24
Consensus pattern (18 bp):
AAAACAAAAAATTTTGGA
Found at i:31151034 original size:41 final size:41
Alignment explanation
Indices: 31150974--31151055 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
31150964 CTCACTTATC
31150974 GAAATCATGGTCCCAAAACCATTATTTCTGACACCACCGAA
1 GAAATCATGGTCCCAAAACCATTATTTCTGACACCACCGAA
* * *
31151015 GAAATCATGGTCCCGAAACCATTATTTTTGGCACCACCGAA
1 GAAATCATGGTCCCAAAACCATTATTTCTGACACCACCGAA
31151056 AATGAATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (41 bp):
GAAATCATGGTCCCAAAACCATTATTTCTGACACCACCGAA
Found at i:31151700 original size:2 final size:2
Alignment explanation
Indices: 31151693--31151722 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31151683 CTACTAGTAA
31151693 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
31151723 TACTAATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:31155917 original size:20 final size:19
Alignment explanation
Indices: 31155893--31155940 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
31155883 TTTTTAACCC
* *
31155893 AAATTAATTATTTTCTCTA
1 AAATTAATTAATTACTCTA
* *
31155912 ATAATTATTTAATTACTTTA
1 A-AATTAATTAATTACTCTA
31155932 AAATTAATT
1 AAATTAATT
31155941 TTCCCAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (19 bp):
AAATTAATTAATTACTCTA
Found at i:31157141 original size:6 final size:6
Alignment explanation
Indices: 31157123--31157158 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
31157113 GCAAATATAT
31157123 CATTTC TCATTTC CATTTC CATTTC CATTTC CATTT
1 CATTTC -CATTTC CATTTC CATTTC CATTTC CATTT
31157159 TGAGAAACCT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.17, C:0.31, G:0.00, T:0.53
Consensus pattern (6 bp):
CATTTC
Found at i:31164660 original size:6 final size:6
Alignment explanation
Indices: 31164644--31164702 Score: 73
Period size: 6 Copynumber: 9.7 Consensus size: 6
31164634 TAAATGTATC
* * *
31164644 ATTTCT AATTTCT ATTTCT ATTTCT ATTTCT ATTTCC ATTTCC ATTTCC
1 ATTTCT -ATTTCT ATTTCT ATTTCT ATTTCT ATTTCT ATTTCT ATTTCT
*
31164693 ATTTCC ATTT
1 ATTTCT ATTT
31164703 TAAGAAACCT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
6 45 0.88
7 6 0.12
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (6 bp):
ATTTCT
Found at i:31164674 original size:18 final size:18
Alignment explanation
Indices: 31164643--31164702 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
31164633 GTAAATGTAT
31164643 CATTTCTAATTTCTATTTC
1 CATTTCT-ATTTCTATTTC
*
31164662 TATTTCTATTTCTATTTC
1 CATTTCTATTTCTATTTC
* *
31164680 CATTTCCATTTCCATTTC
1 CATTTCTATTTCTATTTC
31164698 CATTT
1 CATTT
31164703 TAAGAAACCT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
18 31 0.84
19 6 0.16
ACGTcount: A:0.18, C:0.23, G:0.00, T:0.58
Consensus pattern (18 bp):
CATTTCTATTTCTATTTC
Found at i:31178859 original size:16 final size:17
Alignment explanation
Indices: 31178838--31178877 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
31178828 TTTTTAGCAT
*
31178838 TTTTTAATATTGTAT-A
1 TTTTTAATATTCTATCA
31178854 TTTTT-AT-TTCTATCA
1 TTTTTAATATTCTATCA
31178869 TTTTTAATA
1 TTTTTAATA
31178878 ATTTTTGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
14 5 0.25
15 8 0.40
16 7 0.35
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTTTAATATTCTATCA
Found at i:31182388 original size:24 final size:25
Alignment explanation
Indices: 31182348--31182412 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 25
31182338 AACAGTAGAA
31182348 GAAGAGAAGAAGAAGAA-GAATAAG
1 GAAGAGAAGAAGAAGAAGGAATAAG
* *
31182372 GAAGAGGAGAATG-AGAAGGAATAGAA
1 GAAGAGAAGAA-GAAGAAGGAATA-AG
*
31182398 GAAGTAGAATAAGAA
1 GAAG-AGAAGAAGAA
31182413 TTGGCGAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
24 14 0.44
25 6 0.19
26 6 0.19
27 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.34, T:0.08
Consensus pattern (25 bp):
GAAGAGAAGAAGAAGAAGGAATAAG
Found at i:31183350 original size:20 final size:20
Alignment explanation
Indices: 31183325--31183374 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
31183315 TATCGATCCA
*
31183325 GTATCGATACT-TTTCTTAAG
1 GTATCGATA-TATTTCCTAAG
31183345 GTATCGATATATTTCCTAAG
1 GTATCGATATATTTCCTAAG
31183365 GTATCGATAT
1 GTATCGATAT
31183375 TCCTGCTCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (20 bp):
GTATCGATATATTTCCTAAG
Found at i:31184155 original size:19 final size:19
Alignment explanation
Indices: 31184131--31184168 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
31184121 AATAGAATGG
*
31184131 CCTTTCATATTAGGAAATT
1 CCTTTCATATCAGGAAATT
31184150 CCTTTCATATCAGGAAATT
1 CCTTTCATATCAGGAAATT
31184169 GGCTTATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (19 bp):
CCTTTCATATCAGGAAATT
Found at i:31184183 original size:3 final size:3
Alignment explanation
Indices: 31184175--31184255 Score: 153
Period size: 3 Copynumber: 27.0 Consensus size: 3
31184165 AATTGGCTTA
*
31184175 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TTT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
31184223 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
31184256 CCTCACTACA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:31184303 original size:22 final size:22
Alignment explanation
Indices: 31184273--31184314 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
31184263 ACACCAAAAC
* *
31184273 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGACGCTTTTTT
31184295 AGGCCTTTAGCGACGCTTTT
1 AGGCCTTTAGCGACGCTTTT
31184315 AGCGCCGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.40
Consensus pattern (22 bp):
AGGCCTTTAGCGACGCTTTTTT
Found at i:31184423 original size:43 final size:43
Alignment explanation
Indices: 31184375--31184469 Score: 138
Period size: 43 Copynumber: 2.2 Consensus size: 43
31184365 TTATTTCTAA
* *
31184375 AAACGCCGCT-AAGGGTCATGGTCTTTAGTGGCACTTACAAAAC
1 AAACGCCGCTGAA-GGTCATGGACTTTAGCGGCACTTACAAAAC
* *
31184418 AAACGCCGCTGAAGGTCATGGACTTTAGCGGCGCTTACCAAAC
1 AAACGCCGCTGAAGGTCATGGACTTTAGCGGCACTTACAAAAC
31184461 AAACGCCGC
1 AAACGCCGC
31184470 AAAAGACAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
43 45 0.96
44 2 0.04
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.19
Consensus pattern (43 bp):
AAACGCCGCTGAAGGTCATGGACTTTAGCGGCACTTACAAAAC
Found at i:31184487 original size:43 final size:43
Alignment explanation
Indices: 31184397--31184665 Score: 192
Period size: 43 Copynumber: 6.3 Consensus size: 43
31184387 GGGTCATGGT
* * * * **
31184397 CTTTAGTGGCACTTACAAAACAAACGCCGCTGAAGGTCATGGA-
1 CTTTAGCGGCGCTTACCAAACAAACGCCGCTAAAGACCAT-GAC
* *
31184440 CTTTAGCGGCGCTTACCAAACAAACGCCGCAAAAGACAATGAC
1 CTTTAGCGGCGCTTACCAAACAAACGCCGCTAAAGACCATGAC
* * ** * * *
31184483 CTTTAGCAGCGCTTCCCTTACAAACGCCGCTAAATACCCTGAT
1 CTTTAGCGGCGCTTACCAAACAAACGCCGCTAAAGACCATGAC
* * * *
31184526 CTTTAGCGGCGCTT-CTGCATA-AAACGCCGCTAAAGACCCTAAT
1 CTTTAGCGGCGCTTAC--CAAACAAACGCCGCTAAAGACCATGAC
* * * * *
31184569 CTTTAGCGGCGTTTTTCTC-CA-AAACGCCGCTGAAGACCATGAA
1 CTTTAGCGGCG-CTTAC-CAAACAAACGCCGCTAAAGACCATGAC
*
31184612 CTTTAGCGGCGCTTTTACC--ACAAACGCCGCTAAAGACCATTAC
1 CTTTAGCGGCGC--TTACCAAACAAACGCCGCTAAAGACCATGAC
*
31184655 CTTTAGTGGCG
1 CTTTAGCGGCG
31184666 TTTTTTTAAA
Statistics
Matches: 184, Mismatches: 34, Indels: 16
0.79 0.15 0.07
Matches are distributed among these distances:
42 4 0.02
43 170 0.92
44 9 0.05
45 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (43 bp):
CTTTAGCGGCGCTTACCAAACAAACGCCGCTAAAGACCATGAC
Found at i:31184666 original size:86 final size:86
Alignment explanation
Indices: 31184416--31184670 Score: 248
Period size: 86 Copynumber: 3.0 Consensus size: 86
31184406 CACTTACAAA
** * * *
31184416 ACAAACGCCGCTGAAGGTCATGGACTTTAGCGGCGC--TTACCAAACAAACGCCGCAAAAGACAA
1 ACAAACGCCGCTGAAGACCATGAACTTTAGCGGCGCTTTTACC--ACAAACGCCGCTAAAGACCA
* * * ** *
31184479 TGACCTTTAGCAGCGCTTCCCTT
64 TAACCTTTAGCGGCGTTTTTCTC
* * * * * * * *
31184502 ACAAACGCCGCTAAATACCCTGATCTTTAGCGGCGCTTCT-GCATAAAACGCCGCTAAAGACCCT
1 ACAAACGCCGCTGAAGACCATGAACTTTAGCGGCGCTTTTACCA-CAAACGCCGCTAAAGACCAT
*
31184566 AATCTTTAGCGGCGTTTTTCTC
65 AACCTTTAGCGGCGTTTTTCTC
31184588 -CAAAACGCCGCTGAAGACCATGAACTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCAT
1 AC-AAACGCCGCTGAAGACCATGAACTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCAT
* *
31184652 TACCTTTAGTGGCGTTTTT
65 AACCTTTAGCGGCGTTTTT
31184671 TTAAAAATGC
Statistics
Matches: 133, Mismatches: 31, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
85 2 0.02
86 127 0.95
87 3 0.02
88 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (86 bp):
ACAAACGCCGCTGAAGACCATGAACTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCATA
ACCTTTAGCGGCGTTTTTCTC
Found at i:31184811 original size:10 final size:10
Alignment explanation
Indices: 31184792--31184823 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
31184782 AATCTGTAAT
31184792 ATAT-AATAA
1 ATATCAATAA
31184801 ATATCAATAA
1 ATATCAATAA
31184811 ATATCAATAA
1 ATATCAATAA
31184821 ATA
1 ATA
31184824 AAATGAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (10 bp):
ATATCAATAA
Found at i:31185022 original size:21 final size:21
Alignment explanation
Indices: 31184996--31185043 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
31184986 TTACGCTACG
*
31184996 CTGCTTCCCTCACTGCAGCCT
1 CTGCTTCCCTCACTGCAGCAT
* * *
31185017 CTGCTTCTCTCGCTGCCGCAT
1 CTGCTTCCCTCACTGCAGCAT
31185038 CTGCTT
1 CTGCTT
31185044 TAAGCTACTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.06, C:0.44, G:0.17, T:0.33
Consensus pattern (21 bp):
CTGCTTCCCTCACTGCAGCAT
Found at i:31192389 original size:15 final size:16
Alignment explanation
Indices: 31192346--31192395 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
31192336 TTATTATGTC
*
31192346 GTATTATGTAAGTTAT
1 GTATTATATAAGTTAT
31192362 GTATTATATAAGTTAT
1 GTATTATATAAGTTAT
31192378 GTATTA-ATAAGTTAT
1 GTATTATATAAGTTAT
31192393 GTA
1 GTA
31192396 AGTTATGTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 12 0.36
16 21 0.64
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (16 bp):
GTATTATATAAGTTAT
Found at i:31192402 original size:9 final size:9
Alignment explanation
Indices: 31192349--31192404 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 9
31192339 TTATGTCGTA
31192349 TTATGTAAG
1 TTATGTAAG
31192358 TTATGT-A-
1 TTATGTAAG
*
31192365 TTATATAAG
1 TTATGTAAG
31192374 TTATGT-A-
1 TTATGTAAG
*
31192381 TTA-ATAAG
1 TTATGTAAG
31192389 TTATGTAAG
1 TTATGTAAG
31192398 TTATGTA
1 TTATGTA
31192405 TCATTTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
6 1 0.03
7 9 0.24
8 6 0.16
9 22 0.58
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:31192438 original size:43 final size:40
Alignment explanation
Indices: 31192349--31192455 Score: 121
Period size: 43 Copynumber: 2.6 Consensus size: 40
31192339 TTATGTCGTA
* * *
31192349 TTATGTAAGTTATGTATTATATAAGTTATGTATTAATAAG
1 TTATGTAAGTTATGTATCATATAAATTATATATTAATAAG
*
31192389 TTATGTAAGTTATGTATCATTTTAAAATATATATATTAATAAG
1 TTATGTAAGTTATGTATCA-TAT-AAAT-TATATATTAATAAG
31192432 TTATGTAA-TGTATGTAT--TATAAAT
1 TTATGTAAGT-TATGTATCATATAAAT
31192456 GGGTAATTCA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
39 4 0.07
40 20 0.34
41 2 0.03
42 4 0.07
43 28 0.48
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.48
Consensus pattern (40 bp):
TTATGTAAGTTATGTATCATATAAATTATATATTAATAAG
Found at i:31193074 original size:15 final size:14
Alignment explanation
Indices: 31193051--31193084 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
31193041 TAAATAAAAG
*
31193051 GAAAAAGTATAAAT
1 GAAAAAGTACAAAT
31193065 GAAAATAGTACAAAT
1 GAAAA-AGTACAAAT
31193080 GAAAA
1 GAAAA
31193085 CAAATTGGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.65, C:0.03, G:0.15, T:0.18
Consensus pattern (14 bp):
GAAAAAGTACAAAT
Found at i:31196413 original size:17 final size:17
Alignment explanation
Indices: 31196388--31196421 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
31196378 AATATGTTTC
*
31196388 ATAATATATATATATAT
1 ATAACATATATATATAT
31196405 ATAACATATATATATAT
1 ATAACATATATATATAT
31196422 CGTGGCATAT
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:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAACATATATATATAT
Found at i:31197460 original size:41 final size:41
Alignment explanation
Indices: 31197412--31197505 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
31197402 CCTAGCTACA
* * *
31197412 AAACGCCGCTAATGCTCCGGTCTTTAGCTGCG-TTTTCTAAG
1 AAACGCCGCTAATGCTCAGGTATTTAGCGGCGCTTTT-TAAG
**
31197453 ATGCGCCGCTAATGCTCAGGTATTTAGCGGCGCTTTTTAAG
1 AAACGCCGCTAATGCTCAGGTATTTAGCGGCGCTTTTTAAG
31197494 AAACGCCGCTAA
1 AAACGCCGCTAA
31197506 AGACCGGAGC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 41 0.91
42 4 0.09
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (41 bp):
AAACGCCGCTAATGCTCAGGTATTTAGCGGCGCTTTTTAAG
Found at i:31197521 original size:41 final size:40
Alignment explanation
Indices: 31197476--31197705 Score: 211
Period size: 41 Copynumber: 5.7 Consensus size: 40
31197466 GCTCAGGTAT
31197476 TTAGCGGCGCTTTTTAAGAAACGCCGCTAAAGACCGGAGCA
1 TTAGCGGCGCTTTTTAA-AAACGCCGCTAAAGACCGGAGCA
* * *
31197517 TTAGCAGCGCTTTCTGAGAAACGCCGCTAAAGACC---G--
1 TTAGCGGCGCTTT-TTAAAAACGCCGCTAAAGACCGGAGCA
* * **
31197553 TTAGCGGCACTTTGTAAAAAACGCCGCTAAAGACTTGAGCA
1 TTAGCGGCGCTTT-TTAAAAACGCCGCTAAAGACCGGAGCA
* * * *
31197594 TTAGCGGCGCCTCTTACAAAGCGCCGCTAAAGACCTGAGCA
1 TTAGCGGCGCTTTTTA-AAAACGCCGCTAAAGACCGGAGCA
* * **
31197635 TTAGCGGCGATTATTCAAAAACGCCGCTAAAGATAGGAGCA
1 TTAGCGGCGCTT-TTTAAAAACGCCGCTAAAGACCGGAGCA
*
31197676 TTAGCGGCG-TGTTTTGAAAAGCGCCGCTAA
1 TTAGCGGCGCT-TTTT-AAAAACGCCGCTAA
31197706 GGGCCCAAAA
Statistics
Matches: 154, Mismatches: 25, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
36 29 0.19
38 1 0.01
39 1 0.01
40 5 0.03
41 114 0.74
42 4 0.03
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.20
Consensus pattern (40 bp):
TTAGCGGCGCTTTTTAAAAACGCCGCTAAAGACCGGAGCA
Found at i:31197593 original size:77 final size:77
Alignment explanation
Indices: 31197476--31197680 Score: 209
Period size: 77 Copynumber: 2.6 Consensus size: 77
31197466 GCTCAGGTAT
* * * * *
31197476 TTAGCGGCGCTTTTTAAGAAACGCCGCTAAAGACCGGAGCATTAGCAGCGCTTTCTGAGAAA-CG
1 TTAGCGGCACTTTGTAAAAAACGCCGCTAAAGACCGGAGCATTAGCAGCGC-CTCTGACAAAGCG
31197540 CCGCTAAAGACCG
65 CCGCTAAAGACCG
** * *
31197553 TTAGCGGCACTTTGTAAAAAACGCCGCTAAAGACTTGAGCATTAGCGGCGCCTCTTACAAAGCGC
1 TTAGCGGCACTTTGTAAAAAACGCCGCTAAAGACCGGAGCATTAGCAGCGCCTCTGACAAAGCGC
31197618 CGCTAAAGACCTGAG
66 CGCTAAAGACC---G
* **
31197633 CATTAGCGGCGA-TTAT-TCAAAAACGCCGCTAAAGATAGGAGCATTAGC
1 --TTAGCGGC-ACTT-TGTAAAAAACGCCGCTAAAGACCGGAGCATTAGC
31197681 GGCGTGTTTT
Statistics
Matches: 107, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
76 7 0.07
77 59 0.55
80 1 0.01
82 38 0.36
83 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.20
Consensus pattern (77 bp):
TTAGCGGCACTTTGTAAAAAACGCCGCTAAAGACCGGAGCATTAGCAGCGCCTCTGACAAAGCGC
CGCTAAAGACCG
Found at i:31197816 original size:39 final size:41
Alignment explanation
Indices: 31197773--31197863 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 41
31197763 TGTAAACGCT
*
31197773 GCTAATGCTTGT-T-TTTAGCGGCGTTTTAC-AAATAGCGCC
1 GCTAATGCTCGTATCTTTAGCGGCGTTTTACGAAA-AGCGCC
* * *
31197812 GCTAATGCTCGTATCTTTGGCGGCGTTTTGCGTAAAGCGCC
1 GCTAATGCTCGTATCTTTAGCGGCGTTTTACGAAAAGCGCC
31197853 GCTAATGCTCG
1 GCTAATGCTCG
31197864 ATTTTTTGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
39 11 0.24
40 1 0.02
41 31 0.69
42 2 0.04
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (41 bp):
GCTAATGCTCGTATCTTTAGCGGCGTTTTACGAAAAGCGCC
Found at i:31197928 original size:3 final size:3
Alignment explanation
Indices: 31197920--31197954 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
31197910 GGTGTAGTGC
31197920 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
31197955 ACTACTACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:31197959 original size:3 final size:3
Alignment explanation
Indices: 31197953--31197986 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
31197943 TCTTCTTCTT
31197953 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA C
1 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA C
31197987 CCATCTAGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (3 bp):
CTA
Found at i:31198423 original size:58 final size:58
Alignment explanation
Indices: 31198349--31198460 Score: 176
Period size: 58 Copynumber: 1.9 Consensus size: 58
31198339 ATAACATTAG
31198349 TGATCAAAACATAATAAATTAAAGTTCAATA-ACCAAAAC-ATAATAAATTAAAGTCCAA
1 TGATCAAAACATAATAAATTAAAGTTCAA-AGACCAAAACGA-AATAAATTAAAGTCCAA
31198407 TGATCAAAACGA-AATAAATTAAAGTTCAAAGACCAAAACGAAATAAATTAAAGT
1 TGATCAAAAC-ATAATAAATTAAAGTTCAAAGACCAAAACGAAATAAATTAAAGT
31198461 TTAGTGACCT
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
57 1 0.02
58 48 0.94
59 2 0.04
ACGTcount: A:0.57, C:0.12, G:0.08, T:0.22
Consensus pattern (58 bp):
TGATCAAAACATAATAAATTAAAGTTCAAAGACCAAAACGAAATAAATTAAAGTCCAA
Found at i:31198469 original size:29 final size:29
Alignment explanation
Indices: 31198353--31198461 Score: 150
Period size: 29 Copynumber: 3.8 Consensus size: 29
31198343 CATTAGTGAT
*
31198353 CAAAACATAATAAATTAAAGTTCAATAAC
1 CAAAACATAATAAATTAAAGTTCAATGAC
* *
31198382 CAAAACATAATAAATTAAAGTCCAATGAT
1 CAAAACATAATAAATTAAAGTTCAATGAC
*
31198411 CAAAACGA-AATAAATTAAAGTTCAAAGAC
1 CAAAAC-ATAATAAATTAAAGTTCAATGAC
31198440 CAAAACGA-AATAAATTAAAGTT
1 CAAAAC-ATAATAAATTAAAGTT
31198462 TAGTGACCTA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
29 72 0.99
30 1 0.01
ACGTcount: A:0.58, C:0.13, G:0.07, T:0.22
Consensus pattern (29 bp):
CAAAACATAATAAATTAAAGTTCAATGAC
Found at i:31200374 original size:12 final size:13
Alignment explanation
Indices: 31200349--31200378 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
31200339 TGAGCTATAA
31200349 TTATTGCATTTAT
1 TTATTGCATTTAT
31200362 TTATTGC-TTTAT
1 TTATTGCATTTAT
31200374 TTATT
1 TTATT
31200379 CATGTATGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (13 bp):
TTATTGCATTTAT
Found at i:31214795 original size:68 final size:68
Alignment explanation
Indices: 31214686--31214821 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
31214676 GGTTTCAAGT
31214686 AATCTTTTAACTTCTCGAGCCGTATTGCATTTATAAACTTTCAAGTGTGTCTTGTTGGCAATTCT
1 AATCTTTTAACTTCTCGAGCCGTATTGCATTTATAAACTTTCAAGTGTGTCTTGTTGGCAATTCT
31214751 GCC
66 GCC
31214754 AATCTTTTAACTTCTCGAGCCGTATTGCATTTATAAACTTTCAAGTGTGTCTTGTTGGCAATTCT
1 AATCTTTTAACTTCTCGAGCCGTATTGCATTTATAAACTTTCAAGTGTGTCTTGTTGGCAATTCT
31214819 GCC
66 GCC
31214822 CATGGTATTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (68 bp):
AATCTTTTAACTTCTCGAGCCGTATTGCATTTATAAACTTTCAAGTGTGTCTTGTTGGCAATTCT
GCC
Found at i:31218444 original size:80 final size:80
Alignment explanation
Indices: 31218348--31218507 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
31218338 CCAAAGTTAC
31218348 ATGCCTGATCCAGTCCTTACGGGTCCACCTCAGGACAATTTTTCTTAAATTGGAATAAATTTATG
1 ATGCCTGATCCAGTCCTTACGGGTCCACCTCAGGACAATTTTTCTTAAATTGGAATAAATTTATG
31218413 GGTAAATTATTTTGT
66 GGTAAATTATTTTGT
31218428 ATGCCTGATCCAGTCCTTACGGGTCCACCTCAGGACAATTTTTCTTAAATTGGAATAAATTTATG
1 ATGCCTGATCCAGTCCTTACGGGTCCACCTCAGGACAATTTTTCTTAAATTGGAATAAATTTATG
31218493 GGTAAATTATTTTGT
66 GGTAAATTATTTTGT
31218508 TAGTAAATTA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (80 bp):
ATGCCTGATCCAGTCCTTACGGGTCCACCTCAGGACAATTTTTCTTAAATTGGAATAAATTTATG
GGTAAATTATTTTGT
Found at i:31227773 original size:6 final size:6
Alignment explanation
Indices: 31227732--31227789 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
31227722 AGTATAAAAT
* * * *
31227732 AATAAT AATAACA AATAAA AGTAACA AGAAAAA AATAAA AATAAA AATAAC
1 AATAAA AATAA-A AATAAA AATAA-A A-ATAAA AATAAA AATAAA AATAAA
31227783 AATAAA A
1 AATAAA A
31227790 GAGTAATATA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
6 31 0.74
7 9 0.21
8 2 0.05
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:31227900 original size:12 final size:12
Alignment explanation
Indices: 31227885--31227932 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
31227875 AAACCGATAG
31227885 ATAAATACATAA
1 ATAAATACATAA
* *
31227897 ATAAATACGTGA
1 ATAAATACATAA
* *
31227909 ATGAATAAATAA
1 ATAAATACATAA
*
31227921 ATAAATATATAA
1 ATAAATACATAA
31227933 TACTAGATTT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.27
Consensus pattern (12 bp):
ATAAATACATAA
Found at i:31229336 original size:23 final size:23
Alignment explanation
Indices: 31229305--31229402 Score: 124
Period size: 23 Copynumber: 4.3 Consensus size: 23
31229295 GTGTTATTGA
*
31229305 TCAGTGGTAGCTTCGGTTACATT
1 TCAGTGGTAGCTTCGGCTACATT
** *
31229328 TCAACGGTAGCTACGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
* *
31229351 ACAGTGGTAGCTTCGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
* *
31229374 TCAGTGGTAGCTTTGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
31229397 TCAGTG
1 TCAGTG
31229403 TGACGCTTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:31229652 original size:23 final size:25
Alignment explanation
Indices: 31229606--31229653 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
31229596 GAAAATGCTA
* *
31229606 AGAAATGTTTGATTAGTTATATGAG
1 AGAAATGTTTAATTAGTTAAATGAG
31229631 AGAAATG-TTAATT-GTTAAATGAG
1 AGAAATGTTTAATTAGTTAAATGAG
31229654 TATTTATAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 5 0.24
25 7 0.33
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.38
Consensus pattern (25 bp):
AGAAATGTTTAATTAGTTAAATGAG
Found at i:31231607 original size:16 final size:16
Alignment explanation
Indices: 31231586--31231617 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31231576 AAGATGTTAG
*
31231586 ACGACACGTAGAGGCT
1 ACGACACGAAGAGGCT
31231602 ACGACACGAAGAGGCT
1 ACGACACGAAGAGGCT
31231618 GGTGTATCTG
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:0.34, C:0.25, G:0.31, T:0.09
Consensus pattern (16 bp):
ACGACACGAAGAGGCT
Found at i:31237045 original size:25 final size:25
Alignment explanation
Indices: 31236978--31237154 Score: 102
Period size: 25 Copynumber: 7.2 Consensus size: 25
31236968 AGGCTCATAG
*
31236978 GAGCCA-TAATCAGGAAGCTCATG-A
1 GAGCCATTAATCGGGAAGCTC-TGAA
** *
31237002 GAGCCAAGAA-CGGGTAGCTCTGAA
1 GAGCCATTAATCGGGAAGCTCTGAA
*
31237026 GAGCCATTAATCGGGAAGCTCCGAA
1 GAGCCATTAATCGGGAAGCTCTGAA
* * * *
31237051 TAGTCA-TATATAGGGAAG-T-TCAA
1 GAGCCATTA-ATCGGGAAGCTCTGAA
*
31237074 GCGAGCC-TT-ATCGGGAAGCTC-CAGA
1 --GAGCCATTAATCGGGAAGCTCTGA-A
* *
31237099 GAGCCATTAATCAGGAAGCTCATAAA
1 GAGCCATTAATCGGGAAGCTC-TGAA
* * *
31237125 GAGCCTTTAATCGAGAAGCTCCGAA
1 GAGCCATTAATCGGGAAGCTCTGAA
31237150 GAGCC
1 GAGCC
31237155 GTATATCGAG
Statistics
Matches: 117, Mismatches: 22, Indels: 27
0.70 0.13 0.16
Matches are distributed among these distances:
23 17 0.15
24 31 0.26
25 49 0.42
26 19 0.16
27 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.27, T:0.18
Consensus pattern (25 bp):
GAGCCATTAATCGGGAAGCTCTGAA
Found at i:31237176 original size:25 final size:25
Alignment explanation
Indices: 31237113--31237178 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
31237103 CATTAATCAG
*
31237113 GAAGCTCATAAAGAGCCTTTAATCGA
1 GAAGCTCAT-AAGAGCCTATAATCGA
**
31237139 GAAGCTCCGAAGAGCCGTAT-ATCGA
1 GAAGCTCATAAGAGCC-TATAATCGA
*
31237164 GACGCTCATAAGAGC
1 GAAGCTCATAAGAGC
31237179 TGCGGTGTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 24 0.73
26 9 0.27
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (25 bp):
GAAGCTCATAAGAGCCTATAATCGA
Found at i:31242808 original size:25 final size:25
Alignment explanation
Indices: 31242721--31242850 Score: 99
Period size: 25 Copynumber: 5.2 Consensus size: 25
31242711 ATCTCTGAAA
** * *
31242721 AGCCATTAATCGGGAAGCTCCGAAT
1 AGCCATTAATTAGGAAGCTCCAAAG
* * *
31242746 AGCCA-TATATTGGGAAG-TTCAAGCG
1 AGCCATTA-ATTAGGAAGCTCCAA-AG
31242771 AGCCA-T-ATTAGGAAGCTCCAAAG
1 AGCCATTAATTAGGAAGCTCCAAAG
31242794 AGCCATTAATTAGGAAGCTCACATAA-
1 AGCCATTAATTAGGAAGCTC-CA-AAG
* * *
31242820 AGCCTTTAATCAGGAAGCTCCGAAG
1 AGCCATTAATTAGGAAGCTCCAAAG
31242845 AGCCAT
1 AGCCAT
31242851 ATATCGGGAT
Statistics
Matches: 85, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
23 14 0.16
24 12 0.14
25 37 0.44
26 20 0.24
27 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (25 bp):
AGCCATTAATTAGGAAGCTCCAAAG
Found at i:31244280 original size:5 final size:5
Alignment explanation
Indices: 31244270--31244307 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
31244260 ATCAGCACAG
31244270 ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT A-CAT ATCA
1 ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCA
31244308 AAAGCCGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (5 bp):
ATCAT
Found at i:31260986 original size:22 final size:21
Alignment explanation
Indices: 31260952--31261003 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
31260942 TAATATTTCA
*
31260952 AAAGAAAAAAAAATTAG-TAAT
1 AAAGAAAATAAAA-TAGATAAT
*
31260973 CAAGCAAAATAAAATAGATAAT
1 AAAG-AAAATAAAATAGATAAT
31260995 AAAGAAAAT
1 AAAGAAAAT
31261004 GTTACTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.69, C:0.04, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAGAAAATAAAATAGATAAT
Found at i:31262762 original size:20 final size:20
Alignment explanation
Indices: 31262737--31262780 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
31262727 TAATTTGGAT
31262737 AATTCCATAATTTTATTCTC
1 AATTCCATAATTTTATTCTC
31262757 AATTCCATAATTTTATTCTC
1 AATTCCATAATTTTATTCTC
31262777 AATT
1 AATT
31262781 TGACGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTCCATAATTTTATTCTC
Found at i:31263521 original size:54 final size:54
Alignment explanation
Indices: 31263463--31263673 Score: 255
Period size: 54 Copynumber: 3.9 Consensus size: 54
31263453 GTGTCTCAAG
* * * * * *
31263463 CCATGCAACAATCGAAATAGGGACACACGGCCATGTCCTAGCCCGTGTC-CTTGC
1 CCATGTAACATTCGAACTAGAGACACACGGCCGTGTCCCAGCCCGTGTCTC-TGC
* ** *
31263517 CCATGTAACATTCGAACTAGAGACACATGGCCGTGTCCCAGGTCGTGTCTCTGA
1 CCATGTAACATTCGAACTAGAGACACACGGCCGTGTCCCAGCCCGTGTCTCTGC
* * **
31263571 CCGTGTAACATTCTAACTAGAGACACACGGTTGTGTCCCAGCCCGTGTCTCTGC
1 CCATGTAACATTCGAACTAGAGACACACGGCCGTGTCCCAGCCCGTGTCTCTGC
* *
31263625 CCATGTAACATTTGAACTAAAGACACACGGCCGTGT-CCAGCCCGTGTCT
1 CCATGTAACATTCGAACTAGAGACACACGGCCGTGTCCCAGCCCGTGTCT
31263674 ATACCCGTCT
Statistics
Matches: 132, Mismatches: 24, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
53 13 0.10
54 118 0.89
55 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.23
Consensus pattern (54 bp):
CCATGTAACATTCGAACTAGAGACACACGGCCGTGTCCCAGCCCGTGTCTCTGC
Found at i:31263723 original size:108 final size:108
Alignment explanation
Indices: 31263502--31263726 Score: 251
Period size: 108 Copynumber: 2.1 Consensus size: 108
31263492 GCCATGTCCT
* * **
31263502 AGCCCGTGTCCTTGCCCATGTAACATTCGAACTAGAGACACATGGCCGTGTCCCAGGTCGTGTCT
1 AGCCCGTGTCCTTGCCCATGTAACATTCGAACTAAAGACACACGGCCGTGTCCCAGCCCGTGTCT
* * * ** *
31263567 CTGACCGTGTAACATTCTAACTAGAGACACACGGTTGTGTCCC
66 ATGACCGTCTAACATACTAACTAGAGACACACGACTGTGTCAC
*
31263610 AGCCCGTGT-CTCTGCCCATGTAACATTTGAACTAAAGACACACGGCCGTGT-CCAGCCCGTGTC
1 AGCCCGTGTCCT-TGCCCATGTAACATTCGAACTAAAGACACACGGCCGTGTCCCAGCCCGTGTC
* * * *
31263673 TAT-ACCCGTCTAAC-TCACTAAGTAGGGTCACATGACTGTGTCAC
65 TATGA-CCGTCTAACAT-ACTAACTAGAGACACACGACTGTGTCAC
31263717 ACGCCCGTGT
1 A-GCCCGTGT
31263727 ACCAAGCCGT
Statistics
Matches: 98, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
106 2 0.02
107 43 0.44
108 53 0.54
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (108 bp):
AGCCCGTGTCCTTGCCCATGTAACATTCGAACTAAAGACACACGGCCGTGTCCCAGCCCGTGTCT
ATGACCGTCTAACATACTAACTAGAGACACACGACTGTGTCAC
Found at i:31265967 original size:50 final size:49
Alignment explanation
Indices: 31265845--31265978 Score: 162
Period size: 49 Copynumber: 2.7 Consensus size: 49
31265835 TAATAACATT
* *
31265845 CCAAAGCCATGTCTCAGACATGGTCTTACATGGGATGTTTCCTGTACTG
1 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTATACTG
* * * * * *
31265894 CCAATGCTATATCCCAGATATGGTCTTACATGGGA-GTTCTCGTATCAGTG
1 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCCTAT-ACTG
*
31265944 CCAACGCCATGTCCCAGACATGGTCTTACATGGGA
1 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGA
31265979 CCTCTCATAA
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
48 3 0.04
49 34 0.48
50 34 0.48
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.28
Consensus pattern (49 bp):
CCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTATACTG
Found at i:31270632 original size:21 final size:21
Alignment explanation
Indices: 31270606--31270650 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
31270596 CCGAAACACG
*
31270606 TGAACAGAAGCTCATAAGAGC
1 TGAACAGAAGATCATAAGAGC
31270627 TGAACAGAAGATCATAAGAGC
1 TGAACAGAAGATCATAAGAGC
31270648 TGA
1 TGA
31270651 TCCACCCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (21 bp):
TGAACAGAAGATCATAAGAGC
Found at i:31272318 original size:20 final size:19
Alignment explanation
Indices: 31272278--31272320 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
31272268 CATTCCACTT
*
31272278 TTATTTTATTTATTTTCTA
1 TTATTTTATTTATTTTATA
31272297 TTATTATTATTT-TGTTTATA
1 TTATT-TTATTTAT-TTTATA
31272317 TTAT
1 TTAT
31272321 AATATGACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (19 bp):
TTATTTTATTTATTTTATA
Found at i:31285455 original size:13 final size:13
Alignment explanation
Indices: 31285439--31285463 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31285429 AAAATCTGAT
31285439 TTCAAGTGTATTC
1 TTCAAGTGTATTC
31285452 TTCAAGTGTATT
1 TTCAAGTGTATT
31285464 GTGTATAAGA
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:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (13 bp):
TTCAAGTGTATTC
Found at i:31287434 original size:27 final size:27
Alignment explanation
Indices: 31287396--31287452 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
31287386 TGCCCTTTCA
31287396 CTTGAGTTAAGTTATCCTCGTTGGGCT
1 CTTGAGTTAAGTTATCCTCGTTGGGCT
31287423 CTTGAGTTAAGTTATCCTCGTTGGGCT
1 CTTGAGTTAAGTTATCCTCGTTGGGCT
31287450 CTT
1 CTT
31287453 TTCTCCACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.14, C:0.19, G:0.25, T:0.42
Consensus pattern (27 bp):
CTTGAGTTAAGTTATCCTCGTTGGGCT
Found at i:31292590 original size:19 final size:19
Alignment explanation
Indices: 31292566--31292628 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
31292556 ATATATATAT
31292566 TAATAAATGATGAATTTAA
1 TAATAAATGATGAATTTAA
* *
31292585 TAATAATATG-TCAAGTTAAA
1 TAATAA-ATGATGAA-TTTAA
31292605 TTTAAT-AAT-ATGAATTTAA
1 --TAATAAATGATGAATTTAA
31292624 TAATA
1 TAATA
31292629 GTAATATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 13
0.67 0.08 0.25
Matches are distributed among these distances:
17 4 0.12
19 13 0.38
20 12 0.35
21 1 0.03
22 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.40
Consensus pattern (19 bp):
TAATAAATGATGAATTTAA
Found at i:31292819 original size:4 final size:4
Alignment explanation
Indices: 31292810--31292839 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
31292800 GGCTGCAAAC
31292810 ATAA ATAA ATAA ATAA ATAA ATAAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA AT-AA ATAA A
31292840 AGGATTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:31294394 original size:45 final size:44
Alignment explanation
Indices: 31294345--31294429 Score: 107
Period size: 45 Copynumber: 1.9 Consensus size: 44
31294335 ATTTGCTATT
*
31294345 CTCAGTCTACCCCACTGCAACTTCAAGGGGGATAAGACCTGCTTA
1 CTCAGTCTACCCCACTGCAACTTC-AGGGAGATAAGACCTGCTTA
* * ** *
31294390 CTCAGTCTGCTCCGTTGCAACTTCATGGAGATAAGACCTG
1 CTCAGTCTACCCCACTGCAACTTCAGGGAGATAAGACCTG
31294430 ATGTGATCCA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 14 0.41
45 20 0.59
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (44 bp):
CTCAGTCTACCCCACTGCAACTTCAGGGAGATAAGACCTGCTTA
Found at i:31294500 original size:44 final size:44
Alignment explanation
Indices: 31294445--31294986 Score: 367
Period size: 44 Copynumber: 12.4 Consensus size: 44
31294435 ATCCACTCTG
* * *
31294445 CTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCTGCGCCA
1 CTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCTGCTCCA
* * *
31294489 CTACAACTTCAGGGAGATAGGAT-TATCGACTTCAATCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCTAT-TACTTCAATCTGCTCCA
* *** * *
31294533 CTGCAACTTCAGGGAGATAAGATTTGCCATCTTCGATCTGCCCCA
1 CTGCAACTTCAGGGAGATAAGATCTATTA-CTTCAATCTGCTCCA
* * *
31294578 CTGCAACTTCAGAGAGATAAGATTTATTACTTTAAT-TCGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCT-GCTCCA
* * * * **
31294622 CTACAATTTTAGGGAGATAGGAT-TATCGGCTTCAATCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCTAT-TACTTCAATCTGCTCCA
* * * *
31294666 CTGTAACTTCAGGGAGATAAGAT-T-TTCCATCTTCGATCTACCCCA
1 CTGCAACTTCAGGGAGATAAGATCTATT--A-CTTCAATCTGCTCCA
* * * * * *
31294711 CTGCAACCTCAAGGG-GATAAGA-C--TTGCTACGATCTACTCTA
1 CTGCAACTTC-AGGGAGATAAGATCTATTACTTCAATCTGCTCCA
* * *
31294752 CTGCAACTTTAGAGAGATAAGATCTATTACTTTAATCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCTGCTCCA
* * * * **
31294796 CTACAACTTTAGGGAAATAGGAT-TATCGGCTTCAATCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCTAT-TACTTCAATCTGCTCCA
* ** ** *
31294840 CTACTGCTT-AGGGAGATAAGATCTACTT-CTTCGGTCTGCTCTA
1 CTGCAACTTCAGGGAGATAAGATCTA-TTACTTCAATCTGCTCCA
* * * * * *
31294883 CTGCAACCTCAGGGAGATAAGATC--TGA-TGCGATCTACTCTA
1 CTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCTGCTCCA
** * *
31294924 CTGCAACTTCAGATAGATAAGATCTATTACTTTAATCCGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCTGCTCCA
* *
31294968 CTACATCTTCAGGGAGATA
1 CTGCAACTTCAGGGAGATA
31294987 GGATTTGCGG
Statistics
Matches: 385, Mismatches: 90, Indels: 46
0.74 0.17 0.09
Matches are distributed among these distances:
40 3 0.01
41 60 0.16
42 1 0.00
43 41 0.11
44 208 0.54
45 68 0.18
46 4 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
CTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCTGCTCCA
Found at i:31294606 original size:133 final size:133
Alignment explanation
Indices: 31294445--31294717 Score: 458
Period size: 133 Copynumber: 2.1 Consensus size: 133
31294435 ATCCACTCTG
31294445 CTGCAACTTCAGAGAGATAAGATCTATTACTTTAA-TCTGCGCCACTACAACTTCAGGGAGATAG
1 CTGCAACTTCAGAGAGATAAGATCTATTACTTTAATTC-GCGCCACTACAACTTCAGGGAGATAG
*
31294509 GATTATCGACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCGATCTGC
65 GATTATCGACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCGATCTAC
31294574 CCCA
130 CCCA
* * * *
31294578 CTGCAACTTCAGAGAGATAAGATTTATTACTTTAATTCGCTCCACTACAATTTTAGGGAGATAGG
1 CTGCAACTTCAGAGAGATAAGATCTATTACTTTAATTCGCGCCACTACAACTTCAGGGAGATAGG
* * *
31294643 ATTATCGGCTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTTCCATCTTCGATCTACC
66 ATTATCGACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCGATCTACC
31294708 CCA
131 CCA
31294711 CTGCAAC
1 CTGCAAC
31294718 CTCAAGGGGA
Statistics
Matches: 131, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
133 129 0.98
134 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (133 bp):
CTGCAACTTCAGAGAGATAAGATCTATTACTTTAATTCGCGCCACTACAACTTCAGGGAGATAGG
ATTATCGACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCGATCTACC
CCA
Found at i:31294959 original size:172 final size:174
Alignment explanation
Indices: 31294478--31295008 Score: 623
Period size: 172 Copynumber: 3.0 Consensus size: 174
31294468 CTATTACTTT
* * * *
31294478 AATCTGCGCCACTAC-AACTTCAGGGAGATAGGATTAT-CGA-CTTCAATCTGCTCCACTGCAAC
1 AATCTGCTCCACT-CTAACTTCAGGGAGATAAGATTCTAC-ATCTTCGATCTGCTCCACTGCAAC
* * * * * * *
31294540 TTCAGGGAGATAAGATTTGCCATCTTCGATCTGCCCCACTGCAACTTCAGAGAGATAAGATTTAT
64 CTCAGGGAGATAAGATCTG--A--TACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTAT
*
31294605 TACTTTAAT-TCGCTCCACTACAATTTTAGGGAGATAGGATTATCGGCTTC
125 TACTTTAATCT-GCTCCACTACAACTTTAGGGAGATAGGATTATCGGCTTC
* * * * *
31294655 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTTCCATCTTCGATCTACCCCACTGCAACCT
1 AATCTGCTCCACTCTAACTTCAGGGAGATAAGATTCTACATCTTCGATCTGCTCCACTGCAACCT
* *
31294720 CAAGGG-GATAAGA-CTTGCTACGATCTACTCTACTGCAACTTTAGAGAGATAAGATCTATTACT
66 C-AGGGAGATAAGATC-TGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTACT
*
31294783 TTAATCTGCTCCACTACAACTTTAGGGAAATAGGATTATCGGCTTC
129 TTAATCTGCTCCACTACAACTTTAGGGAGATAGGATTATCGGCTTC
* * * *
31294829 AATCTGCTCCACTACT-GCTT-AGGGAGATAAGA-TCTACTTCTTCGGTCTGCTCTACTGCAACC
1 AATCTGCTCCACT-CTAACTTCAGGGAGATAAGATTCTACATCTTCGATCTGCTCCACTGCAACC
* *
31294891 TCAGGGAGATAAGATCTGATGCGATCTACTCTACTGCAACTTCAGATAGATAAGATCTATTACTT
65 TCAGGGAGATAAGATCTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTT
* * * *
31294956 TAATCCGCTCCACTACATCTTCAGGGAGATAGGATT-TGCGGCTTA
130 TAATCTGCTCCACTACAACTTTAGGGAGATAGGATTAT-CGGCTTC
31295001 AATCTGCT
1 AATCTGCT
31295009 TCCTTACTCT
Statistics
Matches: 308, Mismatches: 36, Indels: 25
0.83 0.10 0.07
Matches are distributed among these distances:
171 5 0.02
172 123 0.40
173 13 0.04
174 97 0.31
175 2 0.01
177 33 0.11
178 31 0.10
179 4 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (174 bp):
AATCTGCTCCACTCTAACTTCAGGGAGATAAGATTCTACATCTTCGATCTGCTCCACTGCAACCT
CAGGGAGATAAGATCTGATACGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTT
AATCTGCTCCACTACAACTTTAGGGAGATAGGATTATCGGCTTC
Found at i:31295130 original size:129 final size:129
Alignment explanation
Indices: 31294977--31295252 Score: 444
Period size: 129 Copynumber: 2.1 Consensus size: 129
31294967 ACTACATCTT
* * * * * *
31294977 CAGGGAGATAGGATTTGCGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTATCGTCTTC
1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTC
* * * *
31295042 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
66 AATCTGCTCCGCTATTACTTAGGAAGACAAGATCTGTAATTTCCCAACATATTCCACTGCTGAC
31295106 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTC
1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTC
* *
31295171 AATCTGCTCCGCTATTACTTAGGAAGACAAGATCTGTACTTTTCCAACATATTCCACTGCTGAC
66 AATCTGCTCCGCTATTACTTAGGAAGACAAGATCTGTAATTTCCCAACATATTCCACTGCTGAC
31295235 CAGGGATATAGGACTTGT
1 CAGGGATATAGGACTTGT
31295253 AATCTTCAAC
Statistics
Matches: 135, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
129 135 1.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.32
Consensus pattern (129 bp):
CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTC
AATCTGCTCCGCTATTACTTAGGAAGACAAGATCTGTAATTTCCCAACATATTCCACTGCTGAC
Found at i:31295283 original size:44 final size:44
Alignment explanation
Indices: 31295215--31295548 Score: 431
Period size: 44 Copynumber: 7.6 Consensus size: 44
31295205 TGTACTTTTC
* ** *
31295215 CAACATATTCCACTGCTGACCAGGGATATAGGACTTGTAATCTT
1 CAACCTATTCCACTGCTGGTCAGGGATATAGGACTTGCAATCTT
31295259 CAACCTATTCCACTGCTGGTCAGGGAGT-TAGGACTTGCAATCTT
1 CAACCTATTCCACTGCTGGTCAGGGA-TATAGGACTTGCAATCTT
* *
31295303 CTACCTATTCCACTACTGGTCAGGGAGT-TAGGACTTGCAATCTT
1 CAACCTATTCCACTGCTGGTCAGGGA-TATAGGACTTGCAATCTT
31295347 CAACCTATTCCACTGCTGGTCAGGGAGT-TAGGACTTGCAATCTT
1 CAACCTATTCCACTGCTGGTCAGGGA-TATAGGACTTGCAATCTT
* * * *
31295391 CTACCTATTCCTCTACTGGTCAGGGAGATAGGACTTGCAATCTT
1 CAACCTATTCCACTGCTGGTCAGGGATATAGGACTTGCAATCTT
* * * * **
31295435 CTACCTATTCCTCTGCTGGTCAAGGAGATAGGACTTATAATCTT
1 CAACCTATTCCACTGCTGGTCAGGGATATAGGACTTGCAATCTT
* * ** *
31295479 CAACCCATTCCATTGCTGACCAGGGATATAGGACTTACAATCTT
1 CAACCTATTCCACTGCTGGTCAGGGATATAGGACTTGCAATCTT
31295523 CAACCTATTCCACTGCTGGTCAGGGA
1 CAACCTATTCCACTGCTGGTCAGGGA
31295549 GCTAGGTTTT
Statistics
Matches: 259, Mismatches: 29, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
44 258 1.00
45 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (44 bp):
CAACCTATTCCACTGCTGGTCAGGGATATAGGACTTGCAATCTT
Found at i:31295467 original size:132 final size:132
Alignment explanation
Indices: 31295215--31295554 Score: 502
Period size: 132 Copynumber: 2.6 Consensus size: 132
31295205 TGTACTTTTC
* *
31295215 CAACATATTCCACTGCTGACCAGGGATATAGGACTTGTAATCTTCAACCTATTCCACTGCTGGTC
1 CAACCTATTCCACTGCTGACCAGGGATATAGGACTTGCAATCTTCAACCTATTCCACTGCTGGTC
* * * *
31295280 AGGGAGTTAGGACTTGCAATCTTCTACCTATTCCACTACTGGTCAGGGAGTTAGGACTTGCAATC
66 AGGGAGATAGGACTTGCAATCTTCTACCTATTCCACTACTGGTCAAGGAGATAGGACTTACAATC
31295345 TT
131 TT
** * * *
31295347 CAACCTATTCCACTGCTGGTCAGGGAGT-TAGGACTTGCAATCTTCTACCTATTCCTCTACTGGT
1 CAACCTATTCCACTGCTGACCAGGGA-TATAGGACTTGCAATCTTCAACCTATTCCACTGCTGGT
* * *
31295411 CAGGGAGATAGGACTTGCAATCTTCTACCTATTCCTCTGCTGGTCAAGGAGATAGGACTTATAAT
65 CAGGGAGATAGGACTTGCAATCTTCTACCTATTCCACTACTGGTCAAGGAGATAGGACTTACAAT
31295476 CTT
130 CTT
* * *
31295479 CAACCCATTCCATTGCTGACCAGGGATATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
1 CAACCTATTCCACTGCTGACCAGGGATATAGGACTTGCAATCTTCAACCTATTCCACTGCTGGTC
*
31295544 AGGGAGCTAGG
66 AGGGAGATAGG
31295555 TTTTGTGATT
Statistics
Matches: 183, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
131 1 0.01
132 181 0.99
133 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (132 bp):
CAACCTATTCCACTGCTGACCAGGGATATAGGACTTGCAATCTTCAACCTATTCCACTGCTGGTC
AGGGAGATAGGACTTGCAATCTTCTACCTATTCCACTACTGGTCAAGGAGATAGGACTTACAATC
TT
Found at i:31296786 original size:8 final size:7
Alignment explanation
Indices: 31296766--31296823 Score: 66
Period size: 7 Copynumber: 8.0 Consensus size: 7
31296756 TTAGCCTCTC
31296766 CATTTTT
1 CATTTTT
31296773 -ACTTTTT
1 CA-TTTTT
31296780 CATTTTTT
1 CA-TTTTT
31296788 CATTTTT
1 CATTTTT
31296795 CA-TTTT
1 CATTTTT
31296801 CATTTTTT
1 CA-TTTTT
31296809 CATTTTT
1 CATTTTT
31296816 CATATTTT
1 CAT-TTTT
31296824 TTCTGACTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
6 7 0.16
7 20 0.44
8 18 0.40
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.71
Consensus pattern (7 bp):
CATTTTT
Found at i:31296800 original size:21 final size:21
Alignment explanation
Indices: 31296766--31296818 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
31296756 TTAGCCTCTC
*
31296766 CATTTTTACTTTTTCATTTTTT
1 CATTTTT-CATTTTCATTTTTT
31296788 CATTTTTCATTTTCATTTTTT
1 CATTTTTCATTTTCATTTTTT
31296809 CATTTTTCAT
1 CATTTTTCAT
31296819 ATTTTTTCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 23 0.77
22 7 0.23
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (21 bp):
CATTTTTCATTTTCATTTTTT
Found at i:31297712 original size:20 final size:18
Alignment explanation
Indices: 31297674--31297772 Score: 80
Period size: 18 Copynumber: 5.6 Consensus size: 18
31297664 TTGGCCTCTC
*
31297674 CTTTTTCTTTTTCTTTTT
1 CTTTTTATTTTTCTTTTT
31297692 CTTTTTATTTTTCATTTTTT
1 CTTTTTATTTTTC--TTTTT
31297712 CTTTTTA--TTT-TTTTT
1 CTTTTTATTTTTCTTTTT
* * **
31297727 CTTTTGACTTTGATTTTT
1 CTTTTTATTTTTCTTTTT
* *
31297745 ATTTTTATTTTTCTTATT
1 CTTTTTATTTTTCTTTTT
*
31297763 -TTTTGATTTT
1 CTTTTTATTTT
31297773 GATTTTGATT
Statistics
Matches: 66, Mismatches: 10, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
15 11 0.17
17 11 0.17
18 32 0.48
20 12 0.18
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (18 bp):
CTTTTTATTTTTCTTTTT
Found at i:31297743 original size:41 final size:41
Alignment explanation
Indices: 31297681--31297790 Score: 109
Period size: 41 Copynumber: 2.7 Consensus size: 41
31297671 CTCCTTTTTC
* *
31297681 TTTTTCTTTT-TCTTTTTATTTTTCATTTTT-TCTTT-TTATTT
1 TTTTTCTTTTGAC-TTTGATTTTT-ATTTTTATCTTTCTTA-TT
*
31297722 TTTTTCTTTTGACTTTGATTTTTATTTTTATTTTTCTTATT
1 TTTTTCTTTTGACTTTGATTTTTATTTTTATCTTTCTTATT
** * *
31297763 TTTTGATTTTGATTTTGATTTTGATTTT
1 TTTTTCTTTTGACTTTGATTTTTATTTT
31297791 GATTTTGATT
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
40 6 0.10
41 49 0.83
42 4 0.07
ACGTcount: A:0.11, C:0.06, G:0.05, T:0.77
Consensus pattern (41 bp):
TTTTTCTTTTGACTTTGATTTTTATTTTTATCTTTCTTATT
Found at i:31297744 original size:33 final size:35
Alignment explanation
Indices: 31297707--31297790 Score: 109
Period size: 35 Copynumber: 2.5 Consensus size: 35
31297697 TATTTTTCAT
*
31297707 TTTTTCTTTTTATTTTT-TT-TCTTTTGACTTTGA
1 TTTTTATTTTTATTTTTCTTATCTTTTGACTTTGA
* *
31297740 TTTTTATTTTTATTTTTCTTATTTTTTGATTTTGA
1 TTTTTATTTTTATTTTTCTTATCTTTTGACTTTGA
* *
31297775 TTTTGATTTTGATTTT
1 TTTTTATTTTTATTTT
31297791 GATTTTGATT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
33 16 0.36
34 2 0.05
35 26 0.59
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.76
Consensus pattern (35 bp):
TTTTTATTTTTATTTTTCTTATCTTTTGACTTTGA
Found at i:31297748 original size:6 final size:6
Alignment explanation
Indices: 31297675--31297803 Score: 71
Period size: 6 Copynumber: 20.8 Consensus size: 6
31297665 TGGCCTCTCC
* * * * *
31297675 TTTTTC TTTTTC TTTTTC TTTTTA TTTTTCA TTTTTTC TTTTTA TTTTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT-A -TTTTTA TTTTTA -TTTTTA
* * * * * *
31297726 TCTTTTGA CTTTGA TTTTTA TTTTTA TTTTTC TTATT- TTTTGA TTTTGA
1 T-TTTT-A TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* * * *
31297775 TTTTGA TTTTGA TTTTGA TTTTGA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
31297804 GATTGAATCT
Statistics
Matches: 103, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
5 3 0.03
6 82 0.80
7 13 0.13
8 5 0.05
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:31297749 original size:18 final size:18
Alignment explanation
Indices: 31297722--31297807 Score: 84
Period size: 18 Copynumber: 4.8 Consensus size: 18
31297712 CTTTTTATTT
* *
31297722 TTTTTCTTTTGACTTTGA
1 TTTTTATTTTGATTTTGA
* **
31297740 TTTTTATTTTTATTTTTC
1 TTTTTATTTTGATTTTGA
*
31297758 TTATT-TTTTGATTTTGA
1 TTTTTATTTTGATTTTGA
*
31297775 TTTTGATTTTGATTTTGA
1 TTTTTATTTTGATTTTGA
*
31297793 TTTTGATTTTTGATT
1 TTTTTA-TTTTGATT
31297808 GAATCTGAGC
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
17 12 0.22
18 35 0.64
19 8 0.15
ACGTcount: A:0.14, C:0.03, G:0.10, T:0.72
Consensus pattern (18 bp):
TTTTTATTTTGATTTTGA
Found at i:31297779 original size:47 final size:45
Alignment explanation
Indices: 31297693--31297803 Score: 125
Period size: 47 Copynumber: 2.4 Consensus size: 45
31297683 TTTCTTTTTC
**
31297693 TTTTTATTTTTCATTTTTTCTTTTTATTTTTTTTCTTTTGACTTTGA
1 TTTTTATTTTT-A-TTTTTCTTTTTATTTTTTTGATTTTGACTTTGA
*
31297740 TTTTTATTTTTATTTTTCTTATTT-TTTGATTTTGATTTTGATTTTGA
1 TTTTTATTTTTATTTTTCTT-TTTATTT--TTTTGATTTTGACTTTGA
* *
31297787 TTTTGATTTTGATTTTT
1 TTTTTATTTTTATTTTT
31297804 GATTGAATCT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
45 11 0.20
46 4 0.07
47 41 0.73
ACGTcount: A:0.13, C:0.05, G:0.07, T:0.76
Consensus pattern (45 bp):
TTTTTATTTTTATTTTTCTTTTTATTTTTTTGATTTTGACTTTGA
Found at i:31298962 original size:9 final size:9
Alignment explanation
Indices: 31298948--31298984 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
31298938 TATAGTTTGA
31298948 TATTCGAAT
1 TATTCGAAT
31298957 TATTCGAAT
1 TATTCGAAT
* *
31298966 TATTTGAGT
1 TATTCGAAT
31298975 TATTCGAAT
1 TATTCGAAT
31298984 T
1 T
31298985 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:31299056 original size:9 final size:9
Alignment explanation
Indices: 31299039--31299069 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
31299029 TCGAGTTGAT
31299039 TCGAATAAC
1 TCGAATAAC
*
31299048 TCGATTAAC
1 TCGAATAAC
31299057 TCGAATAAC
1 TCGAATAAC
31299066 TCGA
1 TCGA
31299070 TTCGTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:31304740 original size:18 final size:19
Alignment explanation
Indices: 31304704--31304741 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
31304694 CGATTTCTGC
*
31304704 TCCTCTTTTCGTTTGTTTG
1 TCCTCTGTTCGTTTGTTTG
*
31304723 TCCTCTGTT-GTTTTTTTG
1 TCCTCTGTTCGTTTGTTTG
31304741 T
1 T
31304742 GACATTGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.00, C:0.18, G:0.16, T:0.66
Consensus pattern (19 bp):
TCCTCTGTTCGTTTGTTTG
Found at i:31309504 original size:17 final size:17
Alignment explanation
Indices: 31309448--31309507 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
31309438 TTCCTCAAAT
* *
31309448 TTTAGTAAAATTAATAAA
1 TTTAATAAAATT-TTAAA
* *
31309466 TTTTAATTAAAATATT-AC
1 -TTTAA-TAAAATTTTAAA
31309484 TTTAATAAAATTTTAAA
1 TTTAATAAAATTTTAAA
31309501 TTTAATA
1 TTTAATA
31309508 TAAAAATACA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
16 8 0.24
17 13 0.39
18 1 0.03
19 5 0.15
20 6 0.18
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
TTTAATAAAATTTTAAA
Found at i:31312075 original size:14 final size:14
Alignment explanation
Indices: 31312058--31312087 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31312048 AAAATATTTG
31312058 TATTATTTTAATAT
1 TATTATTTTAATAT
*
31312072 TATTTTTTTAATAT
1 TATTATTTTAATAT
31312086 TA
1 TA
31312088 AAAAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTATTTTAATAT
Found at i:31314086 original size:34 final size:34
Alignment explanation
Indices: 31314048--31314161 Score: 131
Period size: 34 Copynumber: 3.4 Consensus size: 34
31314038 TTGATTTATG
*
31314048 ATAAGCATATTAATTGCAATTGTATTGACCTGTT
1 ATAAGCATATTAATTGCAACTGTATTGACCTGTT
* * * *
31314082 ATAAGCATATTAAGTACTACTGTATTGATCTGTT
1 ATAAGCATATTAATTGCAACTGTATTGACCTGTT
* ** *
31314116 ATAAGCATATTAATTGCTAC-CAATTGATCTGTT
1 ATAAGCATATTAATTGCAACTGTATTGACCTGTT
*
31314149 ATAAGCACATTAA
1 ATAAGCATATTAA
31314162 ATGCTATCAC
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
33 23 0.33
34 47 0.67
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (34 bp):
ATAAGCATATTAATTGCAACTGTATTGACCTGTT
Done.