Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 104 of 230
Found at i:29646966 original size:23 final size:26
Alignment explanation
Indices: 29646912--29646972 Score: 85
Period size: 23 Copynumber: 2.5 Consensus size: 26
29646902 GAGCCATGAT
29646912 CGGTAAGCTCATTCCGAGCTGAAGAA
1 CGGTAAGCTCATTCCGAGCTGAAGAA
29646938 CGGTAAGCTC-TAT-CGAGCTG-A-AA
1 CGGTAAGCTCAT-TCCGAGCTGAAGAA
29646961 CGGTAAGCTCAT
1 CGGTAAGCTCAT
29646973 AAGAGCTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
23 12 0.36
24 2 0.06
25 8 0.24
26 11 0.33
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (26 bp):
CGGTAAGCTCATTCCGAGCTGAAGAA
Found at i:29646978 original size:23 final size:24
Alignment explanation
Indices: 29646912--29647006 Score: 86
Period size: 26 Copynumber: 3.8 Consensus size: 24
29646902 GAGCCATGAT
*
29646912 CGGTAAGCTCATTCCGAGCTGAAGAA
1 CGGTAAGCTCA-TACGAGCTG-AGAA
29646938 CGGTAAGCTC-TATCGAGCTGA-AA
1 CGGTAAGCTCATA-CGAGCTGAGAA
* *
29646961 CGGTAAGCTCATAAGAGCTGATATA
1 CGGTAAGCTCATACGAGCTGAGA-A
* *
29646986 TCGATAAGCTCATACAAGCTG
1 -CGGTAAGCTCATACGAGCTG
29647007 TGGTGAGTCC
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
23 19 0.32
24 5 0.08
25 8 0.14
26 27 0.46
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (24 bp):
CGGTAAGCTCATACGAGCTGAGAA
Found at i:29656706 original size:9 final size:9
Alignment explanation
Indices: 29656692--29656716 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
29656682 CCGATGTACT
29656692 GTCAGTCCA
1 GTCAGTCCA
29656701 GTCAGTCCA
1 GTCAGTCCA
29656710 GTCAGTC
1 GTCAGTC
29656717 ACATCTATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.32, G:0.24, T:0.24
Consensus pattern (9 bp):
GTCAGTCCA
Found at i:29658662 original size:15 final size:16
Alignment explanation
Indices: 29658632--29658663 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29658622 TAAGTGTGTT
29658632 AATGTAATATTCTTTA
1 AATGTAATATTCTTTA
29658648 AATGTAATATT-TTTA
1 AATGTAATATTCTTTA
29658663 A
1 A
29658664 TAAATAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (16 bp):
AATGTAATATTCTTTA
Found at i:29658814 original size:22 final size:24
Alignment explanation
Indices: 29658783--29658837 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
29658773 TGAACTATTT
*
29658783 TTTATGTTTTT-CATAAGTT-AAA
1 TTTATATTTTTACATAAGTTAAAA
* *
29658805 TTTATATTTTTACATTATTTAAAA
1 TTTATATTTTTACATAAGTTAAAA
29658829 TTTA-ATTTT
1 TTTATATTTT
29658838 GTTCCAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.36
23 11 0.39
24 7 0.25
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTATATTTTTACATAAGTTAAAA
Found at i:29659284 original size:31 final size:31
Alignment explanation
Indices: 29659246--29659318 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
29659236 ACTACAAAAA
*
29659246 TAGTCACTTTTGTTTG-CTTCAAATTACATTT
1 TAGTCACTTATGTTTGAC-TCAAATTACATTT
**
29659277 TAGTCACTTATGTTTGACTCAGGTTACATTT
1 TAGTCACTTATGTTTGACTCAAATTACATTT
29659308 TAGTCACTTAT
1 TAGTCACTTAT
29659319 ATTACCATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 37 0.97
32 1 0.03
ACGTcount: A:0.23, C:0.16, G:0.12, T:0.48
Consensus pattern (31 bp):
TAGTCACTTATGTTTGACTCAAATTACATTT
Found at i:29662322 original size:12 final size:12
Alignment explanation
Indices: 29662305--29662329 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29662295 GAAATGATGG
29662305 AAAAAAAACAAA
1 AAAAAAAACAAA
29662317 AAAAAAAACAAA
1 AAAAAAAACAAA
29662329 A
1 A
29662330 TGATAATTTT
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:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAA
Found at i:29663236 original size:16 final size:16
Alignment explanation
Indices: 29663215--29663245 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
29663205 TTCACTATTA
29663215 TGTCTTTTATATTTTC
1 TGTCTTTTATATTTTC
29663231 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
29663246 GCATGCATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.10, G:0.06, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:29663940 original size:62 final size:62
Alignment explanation
Indices: 29663874--29664071 Score: 161
Period size: 62 Copynumber: 3.1 Consensus size: 62
29663864 TAATATTATT
* * *
29663874 TTAAAAGTTTAATATTAAATTTAATTTAATACTTATCTTAAT-AGTATTTTATTAATTTAATA
1 TTAAAA-TTTAATATTAAATTTAATTTAATATTTATCTTAATAAATATTATATTAATTTAATA
* * *
29663936 TTAAAGTGATTATCTTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAACATTCTATT-A
1 TT-AA---A--AT-TTAATATTAAATTTAATTTAATATTTATC-T-TA-ATAAATATTATATTAA
29664000 TTT--TA
56 TTTAATA
* * * * * *
29664005 ATAAGATTTAATATTATATTTAATATAATATTTATCTTGATAAATATTATATTAATATAATA
1 TTAAAATTTAATATTAAATTTAATTTAATATTTATCTTAATAAATATTATATTAATTTAATA
29664067 TTAAA
1 TTAAA
29664072 GTAATTAAGT
Statistics
Matches: 106, Mismatches: 16, Indels: 28
0.71 0.11 0.19
Matches are distributed among these distances:
59 12 0.11
60 4 0.04
61 1 0.01
62 33 0.31
63 4 0.04
66 1 0.01
67 1 0.01
68 30 0.28
69 4 0.04
70 2 0.02
71 6 0.06
72 8 0.08
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.50
Consensus pattern (62 bp):
TTAAAATTTAATATTAAATTTAATTTAATATTTATCTTAATAAATATTATATTAATTTAATA
Found at i:29664027 original size:12 final size:12
Alignment explanation
Indices: 29664005--29664038 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
29663995 TATTATTTTA
*
29664005 ATAAGATTTAAT
1 ATAATATTTAAT
*
29664017 ATTATATTTAAT
1 ATAATATTTAAT
29664029 ATAATATTTA
1 ATAATATTTA
29664039 TCTTGATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (12 bp):
ATAATATTTAAT
Found at i:29666406 original size:20 final size:21
Alignment explanation
Indices: 29666381--29666433 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
29666371 GATAACATTT
*
29666381 TATTTTGAATTTTTTG-TTTA
1 TATTTTGAATTTTTAGTTTTA
*
29666401 TATTTT-TATTTTTAGTTTTA
1 TATTTTGAATTTTTAGTTTTA
*
29666421 TTTTTTGAATTTT
1 TATTTTGAATTTT
29666434 AAAGTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.74
Consensus pattern (21 bp):
TATTTTGAATTTTTAGTTTTA
Found at i:29666413 original size:19 final size:18
Alignment explanation
Indices: 29666378--29666425 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
29666368 TTAGATAACA
* *
29666378 TTTTATTTTGAATTTTTTG
1 TTTTATTTT-TATTTTTAG
29666397 TTTATATTTTTATTTTTAG
1 TTT-TATTTTTATTTTTAG
29666416 TTTTATTTTT
1 TTTTATTTTT
29666426 TGAATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 7 0.27
19 13 0.50
20 6 0.23
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (18 bp):
TTTTATTTTTATTTTTAG
Found at i:29667103 original size:29 final size:29
Alignment explanation
Indices: 29667072--29667127 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
29667062 AAAAACCATT
*
29667072 TTTTTTAA-AATTTATCGAAATGGGCCAC
1 TTTTTTAATAATTTACCGAAATGGGCCAC
* *
29667100 TTTTTTAATTATTTACCGGAATGGGCCA
1 TTTTTTAATAATTTACCGAAATGGGCCA
29667128 ATTCCGCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (29 bp):
TTTTTTAATAATTTACCGAAATGGGCCAC
Found at i:29667454 original size:22 final size:22
Alignment explanation
Indices: 29667429--29667481 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
29667419 TTCTCTTAAA
29667429 CTCTCAAATTCCTTC-CAAAAT
1 CTCTCAAATTCCTTCACAAAAT
*
29667450 CCTCTCAATTTCCTTCACAAAAT
1 -CTCTCAAATTCCTTCACAAAAT
29667473 CTCTCAAAT
1 CTCTCAAAT
29667482 CCATATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (22 bp):
CTCTCAAATTCCTTCACAAAAT
Found at i:29667549 original size:30 final size:28
Alignment explanation
Indices: 29667513--29667571 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 28
29667503 ATTCAATTTC
29667513 ATTTTTTTAAAGAAAATTTTAAATATTTTT
1 ATTTTTTTAAA-AAAATTTTAAA-ATTTTT
*
29667543 ATTTTTTTAAAATAATTTTAAAATTTTT
1 ATTTTTTTAAAAAAATTTTAAAATTTTT
29667571 A
1 A
29667572 ATACTTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 7 0.25
29 10 0.36
30 11 0.39
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
ATTTTTTTAAAAAAATTTTAAAATTTTT
Found at i:29668672 original size:7 final size:7
Alignment explanation
Indices: 29668660--29668684 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29668650 AGTGGATTGA
29668660 TATTTAG
1 TATTTAG
29668667 TATTTAG
1 TATTTAG
29668674 TATTTAG
1 TATTTAG
29668681 TATT
1 TATT
29668685 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:29669926 original size:29 final size:29
Alignment explanation
Indices: 29669847--29670520 Score: 894
Period size: 29 Copynumber: 23.4 Consensus size: 29
29669837 TTTTGATATT
* *
29669847 ATTTGATTCAAAACCCTAA-CCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
*
29669875 ATTTAATTAAAAACCC-AAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
*
29669903 ATTTAATTAAAAACCCCAACCCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
* * *
29669932 ATTTAATTAAAACCCCCAACCCTAATTTG
1 ATTTAATTAAAAACCCTAACCCTAATTTA
29669961 ATTTAATTAAAAACCCTAACCCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
*
29669990 ATTTAATTAAAAACCCCAACCCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
* *
29670019 ATTTAATTAAAAACCCCAACCCTAATTTG
1 ATTTAATTAAAAACCCTAACCCTAATTTA
29670048 ATTTAATTAAAAACCCTAACCCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
* **
29670077 ATTTAATTAAAAACCCCAACCCTAATCCA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
* *
29670106 TTTTAATTAAAAACCCTAACCCTAGTTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
*
29670135 ATTTAATTAAAAACCCTAACCTTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
***
29670164 ATTTAATTAAAAACCCTAACCCTAACCCA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
* **
29670193 TTTTAATTAAAAACCCTAACCCTGGTTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
29670222 ATTTAATTAAAAACCCTAACCCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
* ***
29670251 ATTTAATTAAAAACTCTAACCCTAACCCA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
* *
29670280 TTTTAATTAAAAACCCTAACCCTAGTTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
*
29670309 ATTTAATTAAAAACCCTAACCCTAGTTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
**
29670338 ATTTAATT--AAA-CCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
**
29670364 ATTTAATT-AAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
* *
29670392 ATTTGATTAAAAACCCTAACCCTAGTTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
* **
29670421 ATTTAATT-AAAACCCTAAACTCTAACCTA
1 ATTTAATTAAAAACCCT-AACCCTAATTTA
***
29670450 ATTTAATTAAAAACCCTAACCCTAACCCA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
* **
29670479 TTTTAATTAAAAACCCTAACCCTAAACTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
29670508 ATTTAATTAAAAA
1 ATTTAATTAAAAA
29670521 ACCATTTTAA
Statistics
Matches: 574, Mismatches: 65, Indels: 13
0.88 0.10 0.02
Matches are distributed among these distances:
26 20 0.03
27 8 0.01
28 69 0.12
29 469 0.82
30 8 0.01
ACGTcount: A:0.43, C:0.23, G:0.01, T:0.32
Consensus pattern (29 bp):
ATTTAATTAAAAACCCTAACCCTAATTTA
Found at i:29673928 original size:125 final size:123
Alignment explanation
Indices: 29673723--29674001 Score: 373
Period size: 125 Copynumber: 2.3 Consensus size: 123
29673713 CACGAGGGCG
* * * *
29673723 CGATTTGACACTATTTGCTCAGAAACGTCAAAAAAATTATTTCCTACATGACCAACTGTAGCGAA
1 CGATTTTATACTATTTGCTCAAAAACGTCAAAAAAATTATTTCCTACATGACCAACTGTACCGAA
** * * **
29673788 ATTGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAT-ATAGCATCCTGGTATCAC
66 AGCGCGTCCACGAGGGCACGATTTCACAATTTCTTCT-ATGATAGCATACTGGTAGAAC
*
29673846 CGATTTTATACTATTTGCTCAAAAAACGTCAAAAAAAATTATTTCTTACATGACCAACTGTACCG
1 CGATTTTATACTATTTGCTC-AAAAACGTC-AAAAAAATTATTTCCTACATGACCAACTGTACCG
* * *
29673911 AAAGCGCGTCCACGAGGGCACGATTTCATAATTTCTTCTTTGATAGCATACTGGTAGAAG
64 AAAGCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTATGATAGCATACTGGTAGAAC
*
29673971 CGATTTTATACTATTTGAC-CAGAAACGTCAA
1 CGATTTTATACTATTTG-CTCAAAAACGTCAA
29674002 CTCGAAATAA
Statistics
Matches: 137, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
123 20 0.15
124 17 0.12
125 99 0.72
126 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (123 bp):
CGATTTTATACTATTTGCTCAAAAACGTCAAAAAAATTATTTCCTACATGACCAACTGTACCGAA
AGCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTATGATAGCATACTGGTAGAAC
Found at i:29677055 original size:26 final size:27
Alignment explanation
Indices: 29677008--29677063 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
29676998 CATATTTTTA
* * *
29677008 TTTTTAAACAAATTATAATTTTTATTT
1 TTTTTAAAAAAAATATAATTTTTAATT
*
29677035 TTTTTAAAAAAAATAT-TTTTTTAATT
1 TTTTTAAAAAAAATATAATTTTTAATT
29677061 TTT
1 TTT
29677064 ATGTTTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTTTAAAAAAAATATAATTTTTAATT
Found at i:29678636 original size:20 final size:21
Alignment explanation
Indices: 29678613--29678658 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
29678603 AAATATATAA
*
29678613 ATTTTGAAATATTTATAAA-T
1 ATTTTGAAATATTTAAAAATT
*
29678633 ATTTT-AAATTTTTAAAAATT
1 ATTTTGAAATATTTAAAAATT
29678653 ATTTTG
1 ATTTTG
29678659 TAATTTTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (21 bp):
ATTTTGAAATATTTAAAAATT
Found at i:29690003 original size:116 final size:116
Alignment explanation
Indices: 29689839--29690089 Score: 421
Period size: 116 Copynumber: 2.2 Consensus size: 116
29689829 AGCCTAAACA
* * *
29689839 CCTCAAGCCCTAAGGCTTCTTGTCGTGTATTCTTGAAAGGCAATACTTCATATTTAAAGGGAGTT
1 CCTCAAGCCCCAAGGCTCCTTGTCGTGTATTCTTGAAAGCCAATACTTCATATTTAAAGGGAGTT
*
29689904 CAATTAGTTAAGGAAAACTATAAGCCTCCAAAGTAACTTCGAGTGTAGGCT
66 CAAGTAGTTAAGGAAAACTATAAGCCTCCAAAGTAACTTCGAGTGTAGGCT
* * *
29689955 TCTCAAGCCCCAAGGCTCCTTGTCGTGTATTCTTGAAAGCCAGTACTTCATATTTAAGGGGAGTT
1 CCTCAAGCCCCAAGGCTCCTTGTCGTGTATTCTTGAAAGCCAATACTTCATATTTAAAGGGAGTT
*
29690020 CAAGTAGTTAAGGAAAACTGTAAGCCTCCAAAGTAACTTCGAGTGTAGGCT
66 CAAGTAGTTAAGGAAAACTATAAGCCTCCAAAGTAACTTCGAGTGTAGGCT
29690071 CCTCAAGCCCTCAAGGCTC
1 CCTCAAGCCC-CAAGGCTC
29690090 TTCATCAACA
Statistics
Matches: 125, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
116 117 0.94
117 8 0.06
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (116 bp):
CCTCAAGCCCCAAGGCTCCTTGTCGTGTATTCTTGAAAGCCAATACTTCATATTTAAAGGGAGTT
CAAGTAGTTAAGGAAAACTATAAGCCTCCAAAGTAACTTCGAGTGTAGGCT
Found at i:29690454 original size:36 final size:36
Alignment explanation
Indices: 29690413--29690484 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
29690403 CGAAAGTAAT
*
29690413 CAAATTGATTGAAAGGCTAATATGCCATCTATCAAG
1 CAAATTGATTGAAAGGCTAATATACCATCTATCAAG
*
29690449 CAAATTGATTGAAAGGCTAATATACCGTCTATCAAG
1 CAAATTGATTGAAAGGCTAATATACCATCTATCAAG
29690485 TCTAGAGGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (36 bp):
CAAATTGATTGAAAGGCTAATATACCATCTATCAAG
Found at i:29694974 original size:17 final size:17
Alignment explanation
Indices: 29694954--29694991 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
29694944 AAAAGAGTCT
29694954 GCCAAGCCCTAGAGTTC
1 GCCAAGCCCTAGAGTTC
* *
29694971 GCC-AGCCTTAGAGTTT
1 GCCAAGCCCTAGAGTTC
29694987 GCCAA
1 GCCAA
29694992 ATGGTGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.21
Consensus pattern (17 bp):
GCCAAGCCCTAGAGTTC
Found at i:29706620 original size:6 final size:6
Alignment explanation
Indices: 29706611--29706662 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
29706601 TATTTATATT
29706611 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA
29706659 TTAA
1 TTAA
29706663 TATTGATTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TTAAAA
Found at i:29708054 original size:18 final size:20
Alignment explanation
Indices: 29708003--29708058 Score: 71
Period size: 18 Copynumber: 2.9 Consensus size: 20
29707993 TTACACCACT
29708003 TTGTGGATAAACCACTTATCG
1 TTGTGGATAAACCAC-TATCG
**
29708024 TTGTGGACGAACCACT-T-G
1 TTGTGGATAAACCACTATCG
29708042 TTGTGGATAAACCACTA
1 TTGTGGATAAACCACTA
29708059 GCAATAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 15 0.50
19 1 0.03
20 1 0.03
21 13 0.43
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (20 bp):
TTGTGGATAAACCACTATCG
Found at i:29720536 original size:25 final size:24
Alignment explanation
Indices: 29720464--29720539 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 24
29720454 ATTGAATAAC
29720464 TATTATCATTA-TTATTTGTTATTGT
1 TATT-TCATTATTTATTTGTTATT-T
*
29720489 TATATTCATTATATTATAT-TTATTT
1 TAT-TTCATTAT-TTATTTGTTATTT
29720514 TATTTCATTATTTATGTTGTTATTT
1 TATTTCATTATTTAT-TTGTTATTT
29720539 T
1 T
29720540 GTTAATGTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
23 4 0.09
24 9 0.20
25 20 0.45
26 6 0.14
27 5 0.11
ACGTcount: A:0.25, C:0.04, G:0.05, T:0.66
Consensus pattern (24 bp):
TATTTCATTATTTATTTGTTATTT
Found at i:29724170 original size:51 final size:50
Alignment explanation
Indices: 29724091--29724225 Score: 207
Period size: 50 Copynumber: 2.7 Consensus size: 50
29724081 GATAATAACA
* **
29724091 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATATCGG
* * *
29724142 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
29724192 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
29724226 TGGCCAACGC
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
50 42 0.55
51 34 0.45
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:29724241 original size:35 final size:35
Alignment explanation
Indices: 29724193--29724260 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
29724183 TCATCTCGGT
* *
29724193 GCCAATGCCATGTCCCAGACATGGTCTTACATGTG
1 GCCAACGCCATGTCCCAAACATGGTCTTACATGTG
*
29724228 GCCAACGCTATGTCCCAAACATGGTCTTACATG
1 GCCAACGCCATGTCCCAAACATGGTCTTACATG
29724261 GGACCTCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (35 bp):
GCCAACGCCATGTCCCAAACATGGTCTTACATGTG
Found at i:29724636 original size:30 final size:30
Alignment explanation
Indices: 29724602--29724659 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
29724592 CCTCAACTCT
29724602 AACTTTGGA-AAAATTACAATTTTGCCCCTA
1 AACTTT-GACAAAATTACAATTTTGCCCCTA
* * *
29724632 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTGACAAAATTACAATTTTGCCCC
29724660 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (30 bp):
AACTTTGACAAAATTACAATTTTGCCCCTA
Found at i:29731851 original size:94 final size:94
Alignment explanation
Indices: 29731740--29732373 Score: 640
Period size: 94 Copynumber: 6.8 Consensus size: 94
29731730 AATTCCAATC
* * ** *
29731740 CCCCTAAAGTTGTAGTGGGTCAGAATAAAGCTACCATAGCGAATCTTATCTCCCTAAAGTTGCAG
1 CCCCTGAAGTTGCAGTGGGTTGGAATAAAGCTACCATAGCGAATCTTATCTCCCTGAAGTTGCAG
* *
29731805 TGGAGCAAGATAAAACTACAAATCCTATA
66 TGGAGCAAGATGAAGCTACAAATCCTATA
* * * *
29731834 CCCCTGAAGTTACAGTGGGTTGGAATGAAA-CTA-CATTGGTGAATCTTATCTCCCTTAAGTTGC
1 CCCCTGAAGTTGCAGTGGGTTGGAAT-AAAGCTACCA-TAGCGAATCTTATCTCCCTGAAGTTGC
29731897 AGTGGAGCAAGATGAAGCTACAAATCCTATA
64 AGTGGAGCAAGATGAAGCTACAAATCCTATA
* * * * * *
29731928 CCCTTGAAGTTGCAATAGGTTGGAATAAAACTA-CA-A-CGAAAAATCTTATCTCCCTGAAGATA
1 CCCCTGAAGTTGCAGTGGGTTGGAATAAAGCTACCATAGCG---AATCTTATCTCCCTGAAGTTG
* *
29731990 CAGTGGAGCAATATGAAGTTACAAA--C--T-
63 CAGTGGAGCAAGATGAAGCTACAAATCCTATA
* * * *
29732017 --CCTGAAGTTACAGTGGGTCGGAATAAAGCTACCATAGCGAATCTTCTCT-CCTAGAAGTTGTA
1 CCCCTGAAGTTGCAGTGGGTTGGAATAAAGCTACCATAGCGAATCTTATCTCCCT-GAAGTTGCA
*
29732079 GTGGAGCAATATGAAGCTACAAATCCTATA
65 GTGGAGCAAGATGAAGCTACAAATCCTATA
* * * * * * * * *
29732109 CCCCTAAAGTTGTAGTAGGTTGAAATGAAGCTACCATAGCGAATCTTATATCTCTGAAGTTGTAA
1 CCCCTGAAGTTGCAGTGGGTTGGAATAAAGCTACCATAGCGAATCTTATCTCCCTGAAGTTGCAG
*
29732174 TGGAGCAAGATGAAGCTACAAATCTTATA
66 TGGAGCAAGATGAAGCTACAAATCCTATA
* * * * *
29732203 CCCCTGGAA-TTGTAGTGGGTTGGGATGAAA-CTACAATGGCGAATCTTATCTCCTTGAAGTTGC
1 CCCCT-GAAGTTGCAGTGGGTTGGAAT-AAAGCTACCATAGCGAATCTTATCTCCCTGAAGTTGC
29732266 AGTGGAGCAAGATGAAGCTACAAATCCTATA
64 AGTGGAGCAAGATGAAGCTACAAATCCTATA
* * * * *
29732297 CTCCTGAAGTTGCAGTGGGTTGGAATGAAAG-TACAATAGCAAATATTATCT-CCTAGAAATTGC
1 CCCCTGAAGTTGCAGTGGGTTGGAAT-AAAGCTACCATAGCGAATCTTATCTCCCT-GAAGTTGC
*
29732360 A--AGAGCAAGATGAA
64 AGTGGAGCAAGATGAA
29732374 ACTATGACAT
Statistics
Matches: 450, Mismatches: 67, Indels: 48
0.80 0.12 0.08
Matches are distributed among these distances:
86 3 0.01
87 62 0.14
88 2 0.00
89 2 0.00
90 3 0.01
91 2 0.00
92 13 0.03
93 10 0.02
94 344 0.76
95 9 0.02
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (94 bp):
CCCCTGAAGTTGCAGTGGGTTGGAATAAAGCTACCATAGCGAATCTTATCTCCCTGAAGTTGCAG
TGGAGCAAGATGAAGCTACAAATCCTATA
Found at i:29731918 original size:50 final size:45
Alignment explanation
Indices: 29731780--29731922 Score: 114
Period size: 44 Copynumber: 3.1 Consensus size: 45
29731770 CTACCATAGC
*
29731780 GAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAGATAAAACTACA
1 GAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAGATGAAACTACA
* * * ***
29731825 -AATCCTATAC-CCCTGAAGTTACAGTGG-GTTGGAATGAAACTACA
1 GAATCTTAT-CTCCCTAAAGTTGCAGTGGAGCAAG-ATGAAACTACA
* *
29731869 TTGGTGAATCTTATCTCCCTTAAGTTGCAGTGGAGCAAGATGAAGCTACA
1 -----GAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAGATGAAACTACA
29731919 -AATC
1 GAATC
29731923 CTATACCCTT
Statistics
Matches: 74, Mismatches: 14, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
43 2 0.03
44 36 0.49
45 1 0.01
49 1 0.01
50 32 0.43
51 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (45 bp):
GAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAGATGAAACTACA
Found at i:29732096 original size:50 final size:49
Alignment explanation
Indices: 29732042--29732286 Score: 137
Period size: 50 Copynumber: 5.1 Consensus size: 49
29732032 GGTCGGAATA
*
29732042 AAGCTACCATAGCGAATCTTCTCTCCTAGAAGTTGTAGTGGAGCAATATG
1 AAGCTACCATAGCGAATCTTATCTCCTAGAAGTTGTAGTGGAGCAA-ATG
* * *
29732092 AAGCTA-C--A---AATCCTATACCCCTA-AAGTTGTAGTAGGTTG-AAATG
1 AAGCTACCATAGCGAATCTTAT-CTCCTAGAAGTTGTAGT-GG-AGCAAATG
* *
29732136 AAGCTACCATAGCGAATCTTATATCTCT-GAAGTTGTAATGGAGCAAGATG
1 AAGCTACCATAGCGAATCTTATCTC-CTAGAAGTTGTAGTGGAGCAA-ATG
* * ***
29732186 AAGCTA-C--A---AATCTTATACCCCTGGAA-TTGTAGTGG-GTTGGGATG
1 AAGCTACCATAGCGAATCTTAT-CTCCTAGAAGTTGTAGTGGAG--CAAATG
* * * * *
29732230 AAACTACAATGGCGAATCTTATCTCCTTGAAGTTGCAGTGGAGCAAGATG
1 AAGCTACCATAGCGAATCTTATCTCCTAGAAGTTGTAGTGGAGCAA-ATG
29732280 AAGCTAC
1 AAGCTAC
29732287 AAATCCTATA
Statistics
Matches: 144, Mismatches: 25, Indels: 52
0.65 0.11 0.24
Matches are distributed among these distances:
43 1 0.01
44 51 0.35
45 14 0.10
46 1 0.01
47 3 0.02
48 1 0.01
49 14 0.10
50 58 0.40
51 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27
Consensus pattern (49 bp):
AAGCTACCATAGCGAATCTTATCTCCTAGAAGTTGTAGTGGAGCAAATG
Found at i:29732250 original size:275 final size:274
Alignment explanation
Indices: 29731753--29732293 Score: 710
Period size: 275 Copynumber: 2.0 Consensus size: 274
29731743 CTAAAGTTGT
29731753 AGTGGGTCAGAATAAAGCTACCATAGCGAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAGATAA
1 AGTGGGTCAGAATAAAGCTACCATAGCGAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAGATAA
* * * * *
29731818 AACTACAAATCCTATACCCCTGAAGTTACAGTGGGTTGGAATGAAACTACATTGGTGAATCTTAT
66 AACTACAAATCCTATACCCCTAAAGTTACAGTAGGTTGAAATGAAACTACATTAGCGAATCTTAT
* * * *
29731883 CTCCCTTAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCCTATACCCTTGAAGTTGCAATAGGT
131 ATCCCTGAAGTTGCAATGGAGCAAGATGAAGCTACAAATCCTATACCCTGGAAGTTGCAATAGGT
* *
29731948 TGGAATAAAACTACAACGAAAAATCTTATCTCCCTGAAGATACAGTGGAGCAATATGAAGTTACA
196 TGGAATAAAACTACAACGAAAAATCTTATCTCCCTGAAGATACAGTGGAGCAAGATGAAGCTACA
29732013 AACTCCTGAAGTTAC
261 AA-TCCTGAAGTTAC
* * * * *
29732028 AGTGGGTCGGAATAAAGCTACCATAGCGAATCTTCTCT-CCTAGAAGTTGTAGTGGAGCAATATG
1 AGTGGGTCAGAATAAAGCTACCATAGCGAATCTTATCTCCCTA-AAGTTGCAGTGGAGCAAGATA
* ** *
29732092 AAGCTACAAATCCTATACCCCTAAAGTTGTAGTAGGTTGAAATGAAGCTACCA-TAGCGAATCTT
65 AAACTACAAATCCTATACCCCTAAAGTTACAGTAGGTTGAAATGAAACTA-CATTAGCGAATCTT
* * * * * *
29732156 ATATCTCTGAAGTTGTAATGGAGCAAGATGAAGCTACAAATCTTATACCCCTGGAA-TTGTAGTG
129 ATATCCCTGAAGTTGCAATGGAGCAAGATGAAGCTACAAATCCTATA-CCCTGGAAGTTGCAATA
* * * *** * * *
29732220 GGTTGGGATGAAACTACAATGGCGAATCTTATCTCCTTGAAGTTGCAGTGGAGCAAGATGAAGCT
193 GGTTGGAATAAAACTACAACGAAAAATCTTATCTCCCTGAAGATACAGTGGAGCAAGATGAAGCT
29732285 ACAAATCCT
258 ACAAATCCT
29732294 ATACTCCTGA
Statistics
Matches: 228, Mismatches: 35, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
274 8 0.04
275 211 0.93
276 9 0.04
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (274 bp):
AGTGGGTCAGAATAAAGCTACCATAGCGAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAGATAA
AACTACAAATCCTATACCCCTAAAGTTACAGTAGGTTGAAATGAAACTACATTAGCGAATCTTAT
ATCCCTGAAGTTGCAATGGAGCAAGATGAAGCTACAAATCCTATACCCTGGAAGTTGCAATAGGT
TGGAATAAAACTACAACGAAAAATCTTATCTCCCTGAAGATACAGTGGAGCAAGATGAAGCTACA
AATCCTGAAGTTAC
Found at i:29732325 original size:44 final size:43
Alignment explanation
Indices: 29732089--29732325 Score: 120
Period size: 44 Copynumber: 5.1 Consensus size: 43
29732079 GTGGAGCAAT
* * * * *
29732089 ATGAAGCTACAAATCCTATACCCCTAAAGTTGTAGTAGGTTGAA
1 ATGAAGCTACAAATCTTATACTCCTGAAGTTGTAGTGGGTTG-G
* ***
29732133 ATGAAGCTACCATAGCGAATCTTATA-TCTCTGAAGTTGTAATGGAGCAAG
1 ATGAAGCTA-C--A---AATCTTATACTC-CTGAAGTTGTAGTGG-GTTGG
*
29732183 ATGAAGCTACAAATCTTATACCCCTGGAA-TTGTAGTGGGTTGGG
1 ATGAAGCTACAAATCTTATACTCCT-GAAGTTGTAGTGGGTT-GG
* * ***
29732227 ATGAAACTACAATGGCGAATCTTAT-CTCCTTGAAGTTGCAGTGGAGCAAG
1 ATGAAGCTAC-A-----AATCTTATACTCC-TGAAGTTGTAGTGG-GTTGG
* *
29732277 ATGAAGCTACAAATCCTATACTCCTGAAGTTGCAGTGGGTTGG
1 ATGAAGCTACAAATCTTATACTCCTGAAGTTGTAGTGGGTTGG
29732320 AATGAA
1 -ATGAA
29732326 AGTACAATAG
Statistics
Matches: 146, Mismatches: 25, Indels: 44
0.68 0.12 0.20
Matches are distributed among these distances:
43 3 0.02
44 64 0.44
45 10 0.07
47 2 0.01
49 9 0.06
50 56 0.38
51 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27
Consensus pattern (43 bp):
ATGAAGCTACAAATCTTATACTCCTGAAGTTGTAGTGGGTTGG
Found at i:29734046 original size:9 final size:9
Alignment explanation
Indices: 29734032--29734066 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
29734022 TTAAATGTTG
29734032 ATACTATTA
1 ATACTATTA
29734041 ATACTATTA
1 ATACTATTA
29734050 ATACTATTA
1 ATACTATTA
*
29734059 GTACTATT
1 ATACTATT
29734067 TTATTTTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.46
Consensus pattern (9 bp):
ATACTATTA
Found at i:29734211 original size:23 final size:26
Alignment explanation
Indices: 29734155--29734211 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 26
29734145 TAATTGAATT
*
29734155 ATTA-TTATTTCTTATTGTTATATTC
1 ATTATTTATTTCTCATTGTTATATTC
29734180 A-TATATTATTT-TCATT-TTAT-TTC
1 ATTAT-TTATTTCTCATTGTTATATTC
29734203 ATTATTTAT
1 ATTATTTAT
29734212 GTTGTTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
23 8 0.29
24 9 0.32
25 5 0.18
26 6 0.21
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (26 bp):
ATTATTTATTTCTCATTGTTATATTC
Found at i:29756283 original size:25 final size:25
Alignment explanation
Indices: 29756255--29756302 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
29756245 ACACGGCTTG
29756255 GCACA-GGAGCATGTGACACAACCTA
1 GCACATGG-GCATGTGACACAACCTA
*
29756280 GCACATGGGCGTGTGACACAACC
1 GCACATGGGCATGTGACACAACC
29756303 ATGAGACCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.31, C:0.29, G:0.27, T:0.12
Consensus pattern (25 bp):
GCACATGGGCATGTGACACAACCTA
Found at i:29764776 original size:12 final size:12
Alignment explanation
Indices: 29764761--29764786 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29764751 ATATTTTCCC
29764761 AACTCTTTTTAA
1 AACTCTTTTTAA
29764773 AACTCTTTTTAA
1 AACTCTTTTTAA
29764785 AA
1 AA
29764787 AGTCGGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (12 bp):
AACTCTTTTTAA
Found at i:29767561 original size:5 final size:5
Alignment explanation
Indices: 29767551--29767578 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
29767541 TTATTTTGCA
29767551 AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA
29767579 AGGTAATGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:29767831 original size:35 final size:35
Alignment explanation
Indices: 29767785--29767855 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
29767775 TATAGAATCT
29767785 GGAAACTCGGGAAGAACATCAAGAGATTTAACTAA
1 GGAAACTCGGGAAGAACATCAAGAGATTTAACTAA
29767820 GGAAACTCGGGAAGAACATCAAGAGATTTAACTAA
1 GGAAACTCGGGAAGAACATCAAGAGATTTAACTAA
29767855 G
1 G
29767856 TTCTAAAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.45, C:0.14, G:0.24, T:0.17
Consensus pattern (35 bp):
GGAAACTCGGGAAGAACATCAAGAGATTTAACTAA
Found at i:29768153 original size:62 final size:62
Alignment explanation
Indices: 29768079--29768267 Score: 378
Period size: 62 Copynumber: 3.0 Consensus size: 62
29768069 GTATTATCTG
29768079 TGTTTTTCTAGTGATGTCACCTTCTACCCTAGAGATATCATAGGCAGTAATCATACCTCTAT
1 TGTTTTTCTAGTGATGTCACCTTCTACCCTAGAGATATCATAGGCAGTAATCATACCTCTAT
29768141 TGTTTTTCTAGTGATGTCACCTTCTACCCTAGAGATATCATAGGCAGTAATCATACCTCTAT
1 TGTTTTTCTAGTGATGTCACCTTCTACCCTAGAGATATCATAGGCAGTAATCATACCTCTAT
29768203 TGTTTTTCTAGTGATGTCACCTTCTACCCTAGAGATATCATAGGCAGTAATCATACCTCTAT
1 TGTTTTTCTAGTGATGTCACCTTCTACCCTAGAGATATCATAGGCAGTAATCATACCTCTAT
29768265 TGT
1 TGT
29768268 AAGGTTCCTC
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 127 1.00
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (62 bp):
TGTTTTTCTAGTGATGTCACCTTCTACCCTAGAGATATCATAGGCAGTAATCATACCTCTAT
Found at i:29770648 original size:25 final size:25
Alignment explanation
Indices: 29770614--29770832 Score: 183
Period size: 25 Copynumber: 8.8 Consensus size: 25
29770604 GTTCAGACCC
* *
29770614 ACAGCTCGTGTGAGCATACTGATTT
1 ACAGCTCGTGTGAGCATACCGATCT
*
29770639 ACAGCTCGTGAGAGCATACC-AGTCT
1 ACAGCTCGTGTGAGCATACCGA-TCT
** *
29770664 ACAGCTCGTGTGAGCATACTAATTT
1 ACAGCTCGTGTGAGCATACCGATCT
* **
29770689 ACAGCTCAT-TAGATTATACCGATCT
1 ACAGCTCGTGT-GAGCATACCGATCT
* *
29770714 ACAGCTTGTGAGAGCATACCGATCT
1 ACAGCTCGTGTGAGCATACCGATCT
* * *
29770739 ACAACTCATGTGAGCATACCGATTT
1 ACAGCTCGTGTGAGCATACCGATCT
* * * *
29770764 ACAGCTCTTGAGATCATATCGATCT
1 ACAGCTCGTGTGAGCATACCGATCT
* * **
29770789 AAAACTCGAATGAGCATACCGAT-T
1 ACAGCTCGTGTGAGCATACCGATCT
*
29770813 CACAGCTCGTATGAGCATAC
1 -ACAGCTCGTGTGAGCATAC
29770833 ATGTACAGGA
Statistics
Matches: 150, Mismatches: 39, Indels: 10
0.75 0.20 0.05
Matches are distributed among these distances:
24 3 0.02
25 146 0.97
26 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (25 bp):
ACAGCTCGTGTGAGCATACCGATCT
Found at i:29770740 original size:75 final size:75
Alignment explanation
Indices: 29770614--29770832 Score: 230
Period size: 75 Copynumber: 2.9 Consensus size: 75
29770604 GTTCAGACCC
* * * * *
29770614 ACAGCTCGTGTGAGCATACTGATTTACAGCTCGTGAGAGCATACC-AGTCTACAGCTCGTGTGAG
1 ACAGCTCTTGAGATCATACCGATCTACAGCTCGTGAGAGCATACCGA-TCTACAGCTCGTGTGAG
*
29770678 CATACTAATTT
65 CATACCAATTT
* * * *
29770689 ACAGCTCATT-AGATTATACCGATCTACAGCTTGTGAGAGCATACCGATCTACAACTCATGTGAG
1 ACAGCTC-TTGAGATCATACCGATCTACAGCTCGTGAGAGCATACCGATCTACAGCTCGTGTGAG
*
29770753 CATACCGATTT
65 CATACCAATTT
* * * * *
29770764 ACAGCTCTTGAGATCATATCGATCTAAAACTCG-AATGAGCATACCGAT-TCACAGCTCGTATGA
1 ACAGCTCTTGAGATCATACCGATCTACAGCTCGTGA-GAGCATACCGATCT-ACAGCTCGTGTGA
29770827 GCATAC
64 GCATAC
29770833 ATGTACAGGA
Statistics
Matches: 119, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
74 4 0.03
75 113 0.95
76 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (75 bp):
ACAGCTCTTGAGATCATACCGATCTACAGCTCGTGAGAGCATACCGATCTACAGCTCGTGTGAGC
ATACCAATTT
Found at i:29771969 original size:20 final size:20
Alignment explanation
Indices: 29771936--29771974 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
29771926 GCCATATGGT
29771936 TTGGCTTGTGTTATGGTATC
1 TTGGCTTGTGTTATGGTATC
29771956 TTGG-TTGTGATTATGGTAT
1 TTGGCTTGTG-TTATGGTAT
29771975 TTTGAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.13, C:0.05, G:0.31, T:0.51
Consensus pattern (20 bp):
TTGGCTTGTGTTATGGTATC
Found at i:29776717 original size:25 final size:25
Alignment explanation
Indices: 29776653--29776798 Score: 100
Period size: 25 Copynumber: 5.8 Consensus size: 25
29776643 ATTTTGACCC
* * *
29776653 ACAGCTCGTGTGAGCATACTGATTT
1 ACAGCTCATGTGAGCATACCGATCT
* * **
29776678 ATAGCTCGTAAGAGCATACCGATCT
1 ACAGCTCATGTGAGCATACCGATCT
* ** *
29776703 ACAACTCATGTGAGCATATTGATTT
1 ACAGCTCATGTGAGCATACCGATCT
* * *
29776728 ACAGCT--TGCGATAGCATATCAATCT
1 ACAGCTCATGTG--AGCATACCGATCT
* *
29776753 ACAGCTCATGTGAGCATACCAATTT
1 ACAGCTCATGTGAGCATACCGATCT
29776778 ACAGCTCGA-GTGAGCATACCG
1 ACAGCTC-ATGTGAGCATACCG
29776799 GTTCACAGCT
Statistics
Matches: 94, Mismatches: 22, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
23 3 0.03
25 87 0.93
26 1 0.01
27 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (25 bp):
ACAGCTCATGTGAGCATACCGATCT
Found at i:29776806 original size:25 final size:26
Alignment explanation
Indices: 29776740--29776810 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
29776730 AGCTTGCGAT
*
29776740 AGCATATCAA-TCTACAGCTC-ATGTG
1 AGCATACCAATTC-ACAGCTCGATGTG
*
29776765 AGCATACCAATTTACAGCTCGA-GTG
1 AGCATACCAATTCACAGCTCGATGTG
**
29776790 AGCATACCGGTTCACAGCTCG
1 AGCATACCAATTCACAGCTCG
29776811 TATGATCATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
25 37 0.95
26 2 0.05
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.24
Consensus pattern (26 bp):
AGCATACCAATTCACAGCTCGATGTG
Found at i:29776809 original size:50 final size:49
Alignment explanation
Indices: 29776653--29776798 Score: 168
Period size: 50 Copynumber: 2.9 Consensus size: 49
29776643 ATTTTGACCC
* * *
29776653 ACAGCTCGTGTGAGCATACTGATTTATAGCTCGTAAGAGCATACCGATCT
1 ACAGCTCATGTGAGCATACTGATTTACAGCTCG-ATGAGCATACCGATCT
* * * *
29776703 ACAACTCATGTGAGCATATTGATTTACAGCTTGCGAT-AGCATATCAATCT
1 ACAGCTCATGTGAGCATACTGATTTACAGC-T-CGATGAGCATACCGATCT
**
29776753 ACAGCTCATGTGAGCATACCAATTTACAGCTCGAGTGAGCATACCG
1 ACAGCTCATGTGAGCATACTGATTTACAGCTCGA-TGAGCATACCG
29776799 GTTCACAGCT
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
48 3 0.04
49 2 0.03
50 70 0.89
51 2 0.03
52 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (49 bp):
ACAGCTCATGTGAGCATACTGATTTACAGCTCGATGAGCATACCGATCT
Found at i:29777942 original size:20 final size:20
Alignment explanation
Indices: 29777917--29777955 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
29777907 GCCATATGGT
29777917 TTGGTTTGTG-TTATGGTATC
1 TTGG-TTGTGATTATGGTATC
29777937 TTGGTTGTGATTATGGTAT
1 TTGGTTGTGATTATGGTAT
29777956 TTTGAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.13, C:0.03, G:0.31, T:0.54
Consensus pattern (20 bp):
TTGGTTGTGATTATGGTATC
Found at i:29781315 original size:16 final size:17
Alignment explanation
Indices: 29781278--29781320 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
29781268 TATCTACAAC
*
29781278 TAAAAATAAAATGAAAT
1 TAAAAATTAAATGAAAT
29781295 T-AAAATTAAA-GAAAT
1 TAAAAATTAAATGAAAT
29781310 TAAAAATTAAA
1 TAAAAATTAAA
29781321 AATAAGGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 6 0.25
16 17 0.71
17 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (17 bp):
TAAAAATTAAATGAAAT
Found at i:29788063 original size:15 final size:15
Alignment explanation
Indices: 29788043--29788073 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29788033 CGCGTAGCAG
29788043 TTACTAAATTAATTA
1 TTACTAAATTAATTA
29788058 TTACTAAATTAATTA
1 TTACTAAATTAATTA
29788073 T
1 T
29788074 AAAATGAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (15 bp):
TTACTAAATTAATTA
Found at i:29791021 original size:39 final size:41
Alignment explanation
Indices: 29790926--29791109 Score: 208
Period size: 40 Copynumber: 4.6 Consensus size: 41
29790916 TTGAATGATG
*
29790926 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATA
*
29790965 TCCGGACTAAGAT-CCGAAGGCATTTGTGCG-AGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAG-TACTAATA
29791005 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATA
* *
29791044 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
* *
29791084 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
29791110 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
39 54 0.43
40 61 0.48
41 11 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
Found at i:29791061 original size:79 final size:81
Alignment explanation
Indices: 29790926--29791109 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 81
29790916 TTGAATGATG
29790926 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
29790989 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * **
29791004 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCGGGTTAAG-TCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
29791065 ATTTGTGCGAATTACTATA
63 ATTTGTGCGAATTACTATA
* *
29791084 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
29791110 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
78 11 0.12
79 58 0.63
80 23 0.25
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:29791131 original size:79 final size:79
Alignment explanation
Indices: 29790978--29791132 Score: 192
Period size: 79 Copynumber: 2.0 Consensus size: 79
29790968 GGACTAAGAT
* ** *
29790978 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
29791043 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
*
29791057 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
*
29791119 CTATATCC-GGTTAA
62 CTAAATCCGGGTTAA
29791133 ATTTCGAAGG
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
78 3 0.05
79 38 0.58
80 25 0.38
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAGTC
Found at i:29792582 original size:50 final size:50
Alignment explanation
Indices: 29792484--29792616 Score: 223
Period size: 50 Copynumber: 2.7 Consensus size: 50
29792474 GTGCCCATGT
* * *
29792484 CATGTCCCAGACATGGTCTTAC-GGGGACTTCTCATCTCGGTGCCAACGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACGC
29792533 CATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACGC
*
29792583 CATGTCCCAGACATGATCTTACATGGGACCTCTT
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTT
29792617 TACCCAAATG
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
49 22 0.28
50 57 0.72
ACGTcount: A:0.20, C:0.32, G:0.22, T:0.26
Consensus pattern (50 bp):
CATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACGC
Found at i:29794692 original size:40 final size:40
Alignment explanation
Indices: 29794647--29794755 Score: 130
Period size: 40 Copynumber: 2.7 Consensus size: 40
29794637 GCAAACTCAA
29794647 GCTTAACATGCTTATGGTAACATATTCAATTC-AATGGCAT
1 GCTTAACATGCTTATGGTAACATATTCAATTCAAAT-GCAT
* * * * *
29794687 GCTTAACATGATTATGGTAACATAATCATTTCAAAATTCGT
1 GCTTAACATGCTTATGGTAACATATTCAATTC-AAATGCAT
**
29794728 GCTTAACATGCTTACCGTAACATATTCA
1 GCTTAACATGCTTATGGTAACATATTCA
29794756 GTACATGGAT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
40 29 0.50
41 26 0.45
42 3 0.05
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (40 bp):
GCTTAACATGCTTATGGTAACATATTCAATTCAAATGCAT
Found at i:29799238 original size:26 final size:26
Alignment explanation
Indices: 29799209--29799258 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
29799199 GTTATGCGTG
*
29799209 GGAATAAAGAGAGGAAATGAGAGAAT
1 GGAAGAAAGAGAGGAAATGAGAGAAT
* * *
29799235 GGAAGAATGATATGAAATGAGAGA
1 GGAAGAAAGAGAGGAAATGAGAGA
29799259 TGCGAGATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.34, T:0.14
Consensus pattern (26 bp):
GGAAGAAAGAGAGGAAATGAGAGAAT
Found at i:29802014 original size:16 final size:16
Alignment explanation
Indices: 29801995--29802047 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
29801985 ATAACAGTCC
29801995 TTAAATTTTAAAGTAA
1 TTAAATTTTAAAGTAA
*
29802011 TTAAATAATTAAA-TAA
1 TTAAAT-TTTAAAGTAA
29802027 TT-AATTTTAAAGTAA
1 TTAAATTTTAAAGTAA
29802042 TTAAAT
1 TTAAAT
29802048 AATTATTAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
16 14 0.44
17 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (16 bp):
TTAAATTTTAAAGTAA
Found at i:29802021 original size:8 final size:8
Alignment explanation
Indices: 29802002--29802052 Score: 61
Period size: 8 Copynumber: 6.4 Consensus size: 8
29801992 TCCTTAAATT
29802002 TTAAAGTAA
1 TTAAA-TAA
29802011 TTAAATAA
1 TTAAATAA
29802019 TTAAATAA
1 TTAAATAA
*
29802027 TT-AAT-T
1 TTAAATAA
29802033 TTAAAGTAA
1 TTAAA-TAA
29802042 TTAAATAA
1 TTAAATAA
29802050 TTA
1 TTA
29802053 TTAGTGAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
6 2 0.05
7 5 0.14
8 20 0.54
9 10 0.27
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (8 bp):
TTAAATAA
Found at i:29804317 original size:5 final size:5
Alignment explanation
Indices: 29804307--29804332 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
29804297 TGAGCATTCG
29804307 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
29804333 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:29805284 original size:29 final size:30
Alignment explanation
Indices: 29805224--29805284 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
29805214 AGAGGAGAGG
***
29805224 GGAGTAAAAGTTTTGGAGGGAAAGTGGGAA
1 GGAGTAAAAGTTTTGGAGGGAAAGTAAAAA
29805254 GGAGTAAAAG-TTT-GAGGGAAAAGTAAAAA
1 GGAGTAAAAGTTTTGGAGGG-AAAGTAAAAA
29805283 GG
1 GG
29805285 TTTTGGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 5 0.19
29 12 0.44
30 10 0.37
ACGTcount: A:0.43, C:0.00, G:0.39, T:0.18
Consensus pattern (30 bp):
GGAGTAAAAGTTTTGGAGGGAAAGTAAAAA
Found at i:29805343 original size:9 final size:9
Alignment explanation
Indices: 29805329--29805362 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
29805319 AGTTTGATAC
29805329 TCGAATTAT
1 TCGAATTAT
29805338 TCGAATTAT
1 TCGAATTAT
*
29805347 TCGAGTTAT
1 TCGAATTAT
29805356 TCGAATT
1 TCGAATT
29805363 CGAAAACTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (9 bp):
TCGAATTAT
Found at i:29805554 original size:15 final size:15
Alignment explanation
Indices: 29805534--29805562 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29805524 GTATTGTTGT
29805534 TTGATAACACGGTGA
1 TTGATAACACGGTGA
29805549 TTGATAACACGGTG
1 TTGATAACACGGTG
29805563 TGTAAGGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (15 bp):
TTGATAACACGGTGA
Found at i:29807469 original size:18 final size:18
Alignment explanation
Indices: 29807443--29807478 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29807433 ATTTTGTTGT
*
29807443 ACTGAAAAATTAAACTAA
1 ACTGAAAAACTAAACTAA
*
29807461 ACTGGAAAACTAAACTAA
1 ACTGAAAAACTAAACTAA
29807479 TTAGTACTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.14, G:0.08, T:0.19
Consensus pattern (18 bp):
ACTGAAAAACTAAACTAA
Found at i:29811643 original size:40 final size:41
Alignment explanation
Indices: 29811588--29811779 Score: 257
Period size: 40 Copynumber: 4.8 Consensus size: 41
29811578 ATTTGAATGA
*
29811588 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATTT
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTGATAT
*
29811628 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATTT
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTGATAT
*
29811668 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGATAT
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTGATAT
* * * *
29811709 -ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTGATAT
* * * *
29811749 G-CCCGGGTTAAGACCCGAAGGCAATTGTGCT
1 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCT
29811780 TGTGGTAATA
Statistics
Matches: 140, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
40 135 0.96
41 5 0.04
ACGTcount: A:0.21, C:0.22, G:0.31, T:0.26
Consensus pattern (41 bp):
GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTGATAT
Found at i:29817019 original size:79 final size:78
Alignment explanation
Indices: 29816917--29817140 Score: 274
Period size: 79 Copynumber: 2.8 Consensus size: 78
29816907 GCTCCTCGTT
* *
29816917 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
29816982 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
*
29816997 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
*
29817060 AATTAGTATCTCGCA
64 AATTAGTAACTCGCA
* * * * *
29817075 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
29817139 GA
63 GA
29817141 CATCATTCAA
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
78 38 0.30
79 53 0.42
80 34 0.27
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:29817034 original size:39 final size:40
Alignment explanation
Indices: 29816917--29817140 Score: 275
Period size: 40 Copynumber: 5.7 Consensus size: 40
29816907 GCTCCTCGTT
* *
29816917 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
29816957 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
29816997 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
29817036 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
29817075 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
29817116 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29817141 CATCATTCAA
Statistics
Matches: 167, Mismatches: 9, Indels: 16
0.87 0.05 0.08
Matches are distributed among these distances:
38 2 0.01
39 73 0.44
40 75 0.45
41 17 0.10
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:29823190 original size:40 final size:41
Alignment explanation
Indices: 29823132--29823282 Score: 200
Period size: 40 Copynumber: 3.8 Consensus size: 41
29823122 ATGTGAATGA
* * *
29823132 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATTT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
29823172 GATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
* * *
29823213 -ATCCGAGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
* * *
29823253 G-CCCGGGTTAAGACCCGAAGGCAATTGTGC
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGC
29823283 TTGTGGTAAT
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
40 93 0.95
41 5 0.05
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.24
Consensus pattern (41 bp):
GATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
Found at i:29823295 original size:80 final size:79
Alignment explanation
Indices: 29823133--29823302 Score: 191
Period size: 80 Copynumber: 2.1 Consensus size: 79
29823123 TGTGAATGAG
* * * * * *
29823133 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGACCCGAAGGCATT
1 ATCC-GGCTAAGACCCGAAGGCATTCGTGCGAGTGATATGACCCGGGCTAAGACCCGAAGGCAAT
*
29823198 TGTGCGAGTTGATAT
65 TGTGCGAGTGGATAT
* *
29823213 ATCCGAGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATG-CCCGGGTTAAGACCCGAAGGCAA
1 ATCCG-GCTAAGACCCGAAGGCATTCGTGCGAG-TGATATGACCCGGGCTAAGACCCGAAGGCAA
**
29823277 TTGTGCTTGTGG-TAAT
64 TTGTGCGAGTGGAT-AT
29823293 ATCCGGCTAA
1 ATCCGGCTAA
29823303 ATTCCGAAGA
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
79 7 0.09
80 64 0.84
81 5 0.07
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (79 bp):
ATCCGGCTAAGACCCGAAGGCATTCGTGCGAGTGATATGACCCGGGCTAAGACCCGAAGGCAATT
GTGCGAGTGGATAT
Found at i:29828639 original size:3 final size:3
Alignment explanation
Indices: 29828631--29828670 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
29828621 AAACAAACCT
29828631 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
29828671 TGTAATACCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:29828836 original size:19 final size:19
Alignment explanation
Indices: 29828812--29828925 Score: 156
Period size: 19 Copynumber: 5.8 Consensus size: 19
29828802 AATCTTCAGG
29828812 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29828831 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
29828850 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29828869 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29828888 GATATGCAATCTTAAAGATAT
1 GATATGCAATCTT--AGATAT
* *
29828909 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
29828926 GATTTAATAT
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
19 64 0.76
20 3 0.04
21 8 0.10
22 9 0.11
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:29833829 original size:14 final size:14
Alignment explanation
Indices: 29833810--29833836 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29833800 AGTGACATAG
29833810 ATGTGTTTAGAGGC
1 ATGTGTTTAGAGGC
29833824 ATGTGTTTAGAGG
1 ATGTGTTTAGAGG
29833837 TCCATCTACA
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:0.22, C:0.04, G:0.37, T:0.37
Consensus pattern (14 bp):
ATGTGTTTAGAGGC
Found at i:29833896 original size:19 final size:19
Alignment explanation
Indices: 29833872--29833963 Score: 157
Period size: 19 Copynumber: 4.8 Consensus size: 19
29833862 AATCTTCAGG
29833872 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29833891 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
29833910 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29833929 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29833948 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
29833964 AGATATGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:29833989 original size:22 final size:22
Alignment explanation
Indices: 29833872--29833986 Score: 94
Period size: 19 Copynumber: 5.7 Consensus size: 22
29833862 AATCTTCAGG
29833872 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
*
29833891 GATATGCAATCTTAG-ATATAAT
1 GATATGCAATCTTAGAAGAT-AT
29833913 -ATAT--AATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
29833929 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
29833948 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
29833970 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
29833987 GATTTAATAT
Statistics
Matches: 82, Mismatches: 4, Indels: 16
0.80 0.04 0.16
Matches are distributed among these distances:
16 2 0.02
17 7 0.09
19 44 0.54
21 7 0.09
22 10 0.12
23 12 0.15
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:29836534 original size:23 final size:23
Alignment explanation
Indices: 29836508--29836551 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
29836498 TTCTCCTCTC
29836508 CTCTCTGTTCTT-TTTTCTTTTTA
1 CTCT-TGTTCTTGTTTTCTTTTTA
* *
29836531 CTCTTTTTTTTGTTTTCTTTT
1 CTCTTGTTCTTGTTTTCTTTT
29836552 CGTTGCTGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (23 bp):
CTCTTGTTCTTGTTTTCTTTTTA
Found at i:29836896 original size:6 final size:6
Alignment explanation
Indices: 29836882--29836918 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
29836872 ATATTGGACC
*
29836882 ATTACA ATTATA ATTATA ATTATA ATTA-A ATT-TA ATT
1 ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA ATT
29836919 TATAGTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
5 8 0.28
6 21 0.72
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (6 bp):
ATTATA
Found at i:29846017 original size:17 final size:17
Alignment explanation
Indices: 29845995--29846066 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 17
29845985 CGACGGACGG
*
29845995 TATTGCCTGGTGAACAA
1 TATTGCCTGGCGAACAA
* *
29846012 TATTGCTTGGCGAACAG
1 TATTGCCTGGCGAACAA
** * * *
29846029 TATCACTTAGCGGACAA
1 TATTGCCTGGCGAACAA
* *
29846046 CATTGCCTGGCGGACAA
1 TATTGCCTGGCGAACAA
29846063 TATT
1 TATT
29846067 ACTTGGCGGA
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (17 bp):
TATTGCCTGGCGAACAA
Found at i:29846057 original size:34 final size:34
Alignment explanation
Indices: 29846008--29846076 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
29845998 TGCCTGGTGA
* * *
29846008 ACAATATTGCTTGGCGAACAGTATCACTTAGCGG
1 ACAACATTGCCTGGCGAACAATATCACTTAGCGG
* * *
29846042 ACAACATTGCCTGGCGGACAATATTACTTGGCGG
1 ACAACATTGCCTGGCGAACAATATCACTTAGCGG
29846076 A
1 A
29846077 TACTATTGCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (34 bp):
ACAACATTGCCTGGCGAACAATATCACTTAGCGG
Found at i:29846088 original size:17 final size:17
Alignment explanation
Indices: 29846008--29846089 Score: 74
Period size: 17 Copynumber: 4.8 Consensus size: 17
29845998 TGCCTGGTGA
*
29846008 ACAATATTGCTTGGCGA
1 ACAATATTGCTTGGCGG
* ** *
29846025 ACAGTATCACTTAGCGG
1 ACAATATTGCTTGGCGG
* *
29846042 ACAACATTGCCTGGCGG
1 ACAATATTGCTTGGCGG
*
29846059 ACAATATTACTTGGCGG
1 ACAATATTGCTTGGCGG
* *
29846076 ATACTATTGCTTGG
1 ACAATATTGCTTGG
29846090 TGACATGATT
Statistics
Matches: 48, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 48 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (17 bp):
ACAATATTGCTTGGCGG
Found at i:29846948 original size:35 final size:35
Alignment explanation
Indices: 29846902--29847041 Score: 156
Period size: 35 Copynumber: 4.0 Consensus size: 35
29846892 TTGAGGAAAA
*
29846902 ATCCCACCACAACACCAATACTTC-TTTCATAACAC
1 ATCCCACCACAACACCAATACTTCATTT-ATCACAC
* *
29846937 ATCCCACCACAACATCAATACTTCATTTATCATAC
1 ATCCCACCACAACACCAATACTTCATTTATCACAC
** *
29846972 ATCCCACCACAACACTGATACTTCACTTATCACAC
1 ATCCCACCACAACACCAATACTTCATTTATCACAC
*** * **
29847007 ATCTTGCCACAACATCAATACTTCATCCATCACAC
1 ATCCCACCACAACACCAATACTTCATTTATCACAC
29847042 TTCTTTCATA
Statistics
Matches: 87, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
35 84 0.97
36 3 0.03
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (35 bp):
ATCCCACCACAACACCAATACTTCATTTATCACAC
Found at i:29847017 original size:70 final size:70
Alignment explanation
Indices: 29846902--29847032 Score: 183
Period size: 70 Copynumber: 1.9 Consensus size: 70
29846892 TTGAGGAAAA
*
29846902 ATCCCACCACAACACCAATACTTCTTTCATAACACATCCCACCACAACATCAATACTTCATTTAT
1 ATCCCACCACAACACCAATACTTCCTTCATAACACATCCCACCACAACATCAATACTTCATTTAT
29846967 CATAC
66 CATAC
** * ***
29846972 ATCCCACCACAACACTGATACTTCACTT-ATCACACATCTTGCCACAACATCAATACTTCAT
1 ATCCCACCACAACACCAATACTTC-CTTCATAACACATCCCACCACAACATCAATACTTCAT
29847033 CCATCACACT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
70 51 0.96
71 2 0.04
ACGTcount: A:0.36, C:0.37, G:0.02, T:0.26
Consensus pattern (70 bp):
ATCCCACCACAACACCAATACTTCCTTCATAACACATCCCACCACAACATCAATACTTCATTTAT
CATAC
Found at i:29853220 original size:27 final size:27
Alignment explanation
Indices: 29853138--29853222 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 27
29853128 AACTAGTTAG
* * *
29853138 GAAAGAATAGCC-TTGTGACAAACTCT
1 GAAAGAATAACCTTTGTGGCGAACTCT
29853164 GAAAGAAT-ACCTTTTGTAGTGGCGAACTCT
1 GAAAGAATAACC--TT-T-GTGGCGAACTCT
29853194 GAAAGAATAACCTTTGTGGCGAACTCT
1 GAAAGAATAACCTTTGTGGCGAACTCT
29853221 GA
1 GA
29853223 GAAAATAGCT
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
25 2 0.04
26 8 0.16
27 14 0.28
28 2 0.04
29 3 0.06
30 18 0.36
31 3 0.06
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (27 bp):
GAAAGAATAACCTTTGTGGCGAACTCT
Found at i:29853239 original size:27 final size:28
Alignment explanation
Indices: 29853158--29853239 Score: 91
Period size: 27 Copynumber: 2.9 Consensus size: 28
29853148 CCTTGTGACA
29853158 AACTCTGAAAGAAT-ACCTTTTGTAGTGGCG
1 AACTCTGAAAGAATAACC--TT-TAGTGGCG
29853188 AACTCTGAAAGAATAACCTTT-GTGGCG
1 AACTCTGAAAGAATAACCTTTAGTGGCG
*
29853215 AACTCTGAGAA-AAT-AGCTTTAGTGG
1 AACTCTGA-AAGAATAACCTTTAGTGG
29853240 TGAATTATGA
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
26 5 0.10
27 21 0.44
28 3 0.06
29 2 0.04
30 14 0.29
31 3 0.06
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (28 bp):
AACTCTGAAAGAATAACCTTTAGTGGCG
Found at i:29878348 original size:25 final size:23
Alignment explanation
Indices: 29878311--29878387 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 23
29878301 TGCTATATAA
29878311 TCAACCGCACACTTAGTGCCAAT
1 TCAACCGCACACTTAGTGCCAAT
29878334 TACAACTCGCACAC-TAGTGCTGC-AT
1 T-CAAC-CGCACACTTAGTGC--CAAT
*
29878359 TTAACCGCACACTTAGTGCCAAT
1 TCAACCGCACACTTAGTGCCAAT
29878382 CTCAAC
1 -TCAAC
29878388 TAAATTTTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
22 1 0.02
23 10 0.22
24 23 0.51
25 10 0.22
26 1 0.02
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (23 bp):
TCAACCGCACACTTAGTGCCAAT
Found at i:29878802 original size:12 final size:12
Alignment explanation
Indices: 29878785--29878811 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
29878775 TGGGCATACT
29878785 TATGTATATATA
1 TATGTATATATA
29878797 TATGTATATATA
1 TATGTATATATA
29878809 TAT
1 TAT
29878812 ACTTCGGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:29886551 original size:28 final size:28
Alignment explanation
Indices: 29886483--29886581 Score: 137
Period size: 27 Copynumber: 3.5 Consensus size: 28
29886473 TATATTAAGT
*
29886483 CCGCACACTCAGTGCTATATAATC-AAC
1 CCGCACACTTAGTGCTATATAATCAAAC
*
29886510 TCGCACACTTAGTGCTATATAATCAAAC
1 CCGCACACTTAGTGCTATATAATCAAAC
* * *
29886538 CCGCACACTTAGTGCTGTACAATTTAAAC
1 CCGCACACTTAGTGCTATATAA-TCAAAC
29886567 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
29886582 CAATCTCATG
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 22 0.34
28 22 0.34
29 20 0.31
ACGTcount: A:0.31, C:0.30, G:0.13, T:0.25
Consensus pattern (28 bp):
CCGCACACTTAGTGCTATATAATCAAAC
Found at i:29887045 original size:12 final size:12
Alignment explanation
Indices: 29887028--29887054 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
29887018 TGGGCATACT
29887028 TATGTATATATA
1 TATGTATATATA
29887040 TATGTATATATA
1 TATGTATATATA
29887052 TAT
1 TAT
29887055 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:29904039 original size:29 final size:29
Alignment explanation
Indices: 29904000--29904078 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
29903990 CTTAATAATC
*
29904000 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
29904030 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
* *
29904059 AGCCCACACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
29904079 ATCTCACAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 3 0.07
29 37 0.86
30 3 0.07
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:29904541 original size:12 final size:12
Alignment explanation
Indices: 29904524--29904550 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
29904514 TGGGCATACT
29904524 TATGTATATATA
1 TATGTATATATA
29904536 TATGTATATATA
1 TATGTATATATA
29904548 TAT
1 TAT
29904551 ACTTCGGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:29908059 original size:12 final size:13
Alignment explanation
Indices: 29908033--29908065 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
29908023 AGTTTCGAAG
29908033 AAAAAAATTCGTGA
1 AAAAAAATTC-TGA
29908047 AAAAAAATT-TGA
1 AAAAAAATTCTGA
29908059 AAAAAAA
1 AAAAAAA
29908066 GGATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
14 9 0.47
ACGTcount: A:0.70, C:0.03, G:0.09, T:0.18
Consensus pattern (13 bp):
AAAAAAATTCTGA
Found at i:29910237 original size:18 final size:19
Alignment explanation
Indices: 29910193--29910237 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
29910183 TTGAAAAATC
*
29910193 AAAAGAAAATGAGAGAGAG
1 AAAAGAAAATGAGAAAGAG
29910212 AAAA-AAAATGA-AAAGA-
1 AAAAGAAAATGAGAAAGAG
29910228 ATAAAGAAAA
1 A-AAAGAAAA
29910238 GAGTAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 1 0.04
17 7 0.30
18 11 0.48
19 4 0.17
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (19 bp):
AAAAGAAAATGAGAAAGAG
Found at i:29910240 original size:29 final size:31
Alignment explanation
Indices: 29910186--29910255 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 31
29910176 AGTTCTATTG
* * *
29910186 AAAAATCAAAAGAAAATGAGAGAGAG-A-AA
1 AAAAATGAAAAGAAAAAGAGAAAGAGTAGAA
29910215 AAAAATGAAAAGAATAAAGA-AAAGAGTAGAA
1 AAAAATGAAAAGAA-AAAGAGAAAGAGTAGAA
29910246 AAAAA-GAAAA
1 AAAAATGAAAA
29910256 ACAAAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 18 0.51
30 10 0.29
31 7 0.20
ACGTcount: A:0.73, C:0.01, G:0.19, T:0.07
Consensus pattern (31 bp):
AAAAATGAAAAGAAAAAGAGAAAGAGTAGAA
Found at i:29926025 original size:79 final size:79
Alignment explanation
Indices: 29925894--29926125 Score: 455
Period size: 79 Copynumber: 2.9 Consensus size: 79
29925884 AGTTTTACCT
29925894 TTAATTCTTTATTTTCTGTTGCGTAACCTGATTTAAGGAAACAATGTTGATTACTATTTTGAATC
1 TTAATTCTTTATTTTCTGTTGCGTAACCTGATTTAAGGAAACAATGTTGATTACTATTTTGAATC
29925959 TAGATTCTACCCAC
66 TAGATTCTACCCAC
29925973 TTAATTCTTTATTTTCTGTTGCGTAACCTGATTTAAGGAAACAATGTTGATTACTATTTTGAATC
1 TTAATTCTTTATTTTCTGTTGCGTAACCTGATTTAAGGAAACAATGTTGATTACTATTTTGAATC
*
29926038 TAGATTCTAGCCAC
66 TAGATTCTACCCAC
29926052 TTAATTCTTTATTTTCTGTTGCGTAACCTGATTTAAGGAAACAATGTTGATTACTATTTTGAATC
1 TTAATTCTTTATTTTCTGTTGCGTAACCTGATTTAAGGAAACAATGTTGATTACTATTTTGAATC
29926117 TAGATTCTA
66 TAGATTCTA
29926126 TTCACCAACC
Statistics
Matches: 152, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 152 1.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (79 bp):
TTAATTCTTTATTTTCTGTTGCGTAACCTGATTTAAGGAAACAATGTTGATTACTATTTTGAATC
TAGATTCTACCCAC
Found at i:29929190 original size:100 final size:100
Alignment explanation
Indices: 29929011--29929210 Score: 303
Period size: 100 Copynumber: 2.0 Consensus size: 100
29929001 CCTCAGGTCA
* * *
29929011 AAGGCAGGAAACCTATATTGCCTTTCCTACTTCCTTACCCCAAGTTCCACTTTCTCCTCCCTATC
1 AAGGCAAGAAACCTATATTGCCTCTCCTACTTCCTTACCCCAAGTTCCACTTGCTCCTCCCTATC
*
29929076 TTCTACTTCAACCACCCTAGTAGATGGCTCTTCGC
66 TTCTACTTCAACCACCCTAGTAGACGGCTCTTCGC
* * * *
29929111 AAGGCAAGCAACCTCTATTTCCTCTCCTACTTCCTTACTCCAAGTTCCACTTGCTCCTCCCTATC
1 AAGGCAAGAAACCTATATTGCCTCTCCTACTTCCTTACCCCAAGTTCCACTTGCTCCTCCCTATC
*
29929176 TTCTA-TTCCGACCACCCTAGTAGACGGCTCTTCGC
66 TTCTACTT-CAACCACCCTAGTAGACGGCTCTTCGC
29929211 CCTATCTTAC
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
99 2 0.02
100 88 0.98
ACGTcount: A:0.20, C:0.38, G:0.11, T:0.32
Consensus pattern (100 bp):
AAGGCAAGAAACCTATATTGCCTCTCCTACTTCCTTACCCCAAGTTCCACTTGCTCCTCCCTATC
TTCTACTTCAACCACCCTAGTAGACGGCTCTTCGC
Found at i:29931946 original size:15 final size:16
Alignment explanation
Indices: 29931923--29931955 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
29931913 ATTGTGATCG
*
29931923 AAGTTAAAT-TTAAAA
1 AAGTAAAATGTTAAAA
29931938 AAGTAAAATGTTAAAA
1 AAGTAAAATGTTAAAA
29931954 AA
1 AA
29931956 TAATATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (16 bp):
AAGTAAAATGTTAAAA
Found at i:29940286 original size:4 final size:4
Alignment explanation
Indices: 29940277--29940303 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
29940267 GTTTATACCT
29940277 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
29940304 TTATATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:29940527 original size:16 final size:17
Alignment explanation
Indices: 29940501--29940534 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
29940491 TTTTATTATT
29940501 TAATGTTATTTATATAA
1 TAATGTTATTTATATAA
*
29940518 TAAT-TTATTTGTATAA
1 TAATGTTATTTATATAA
29940534 T
1 T
29940535 CGATCAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
TAATGTTATTTATATAA
Found at i:29946210 original size:4 final size:4
Alignment explanation
Indices: 29946201--29946227 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
29946191 TGTTATACCT
29946201 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
29946228 TTATATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:29952136 original size:4 final size:4
Alignment explanation
Indices: 29952127--29952153 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
29952117 GTTTATACCT
29952127 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
29952154 TTATATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:29958236 original size:6 final size:7
Alignment explanation
Indices: 29958217--29958259 Score: 63
Period size: 7 Copynumber: 6.3 Consensus size: 7
29958207 AAAAAGGGGG
29958217 TGAAAAA
1 TGAAAAA
29958224 TGAAAAA
1 TGAAAAA
29958231 TGAAAAA
1 TGAAAAA
29958238 TG-AAAA
1 TGAAAAA
29958244 TGAAAAA
1 TGAAAAA
29958251 -GTAAAAA
1 TG-AAAAA
29958258 TG
1 TG
29958260 GAGAGGCTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
6 7 0.21
7 25 0.76
8 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.16, T:0.16
Consensus pattern (7 bp):
TGAAAAA
Found at i:29958243 original size:20 final size:20
Alignment explanation
Indices: 29958220--29958259 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
29958210 AAGGGGGTGA
29958220 AAAATGAAAAA-TGAAAAATG
1 AAAATGAAAAAGT-AAAAATG
29958240 AAAATGAAAAAGTAAAAATG
1 AAAATGAAAAAGTAAAAATG
29958260 GAGAGGCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAATGAAAAAGTAAAAATG
Found at i:29959607 original size:87 final size:87
Alignment explanation
Indices: 29959461--29959855 Score: 583
Period size: 87 Copynumber: 4.5 Consensus size: 87
29959451 CAGATCAGTG
* * * *
29959461 AAGATAGCAGATCTTGCCTTCCTACATCGACAGCAAAACAGATCGAAAGCAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
* *
29959526 TTGGTTGCAGTGGAGCGGGTTA
66 TCGGTTGCAGTGGAGCAGGTTA
* *
29959548 AAGATAGTAGATCTTGCCTTCTTACATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
* *
29959613 TCAGTTGCAGTGGAGCGGGTTA
66 TCGGTTGCAGTGGAGCAGGTTA
* * * *
29959635 AAGATAGCAAATCTTGCCTTCCTGCATTGACAGCGAAACAGATCGAAAAAAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
*
29959700 TCGGTTGCAGTGGAGCAAGTTA
66 TCGGTTGCAGTGGAGCAGGTTA
* * *
29959722 AAGATTGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCC
1 AAGATAGCAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
29959787 TCGGTTGCAGTGGAGCAGGTTA
66 TCGGTTGCAGTGGAGCAGGTTA
* * * * *
29959809 AAGATAGCAAATCTTGCCTTTCTACGTCGACAGTGAAGCAGATCGAA
1 AAGATAGCAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAA
29959856 GATTACAAGT
Statistics
Matches: 278, Mismatches: 30, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 278 1.00
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (87 bp):
AAGATAGCAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
TCGGTTGCAGTGGAGCAGGTTA
Found at i:29959609 original size:43 final size:42
Alignment explanation
Indices: 29959560--29959783 Score: 109
Period size: 43 Copynumber: 5.2 Consensus size: 42
29959550 GATAGTAGAT
*
29959560 CTTGCCTTCTTACATTGACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCAT-CATTGACAGCGAAGCAGATCGAAAACAAAGC
* * * * * ** *
29959603 CTTGCCTCCATCAGTTG-CAGTGGAGCGGGTTAAAGATAGCAAA-T
1 CTTGCCTTCATCA-TTGACAGCGAAGCAGATCGAA-A-A-CAAAGC
* * *
29959647 CTTGCCTTCCTGCATTGACAGCGAAACAGATCGAAAAAAAAGC
1 CTTGCCTTCAT-CATTGACAGCGAAGCAGATCGAAAACAAAGC
* * * * * * *
29959690 CTTGCCTCCATCGGTTG-CAGTGGAGCA-AGT-TAAAGATTGCAGA-T
1 CTTGCCTTCATC-ATTGACAGCGAAGCAGA-TCGAAA-A---CAAAGC
*
29959734 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCAT-CATTGACAGCGAAGCAGATCGAAAACAAAGC
29959777 CTTGCCT
1 CTTGCCT
29959784 CCCTCGGTTG
Statistics
Matches: 125, Mismatches: 38, Indels: 36
0.63 0.19 0.18
Matches are distributed among these distances:
41 4 0.03
42 29 0.23
43 33 0.26
44 26 0.21
45 29 0.23
46 4 0.03
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (42 bp):
CTTGCCTTCATCATTGACAGCGAAGCAGATCGAAAACAAAGC
Found at i:29959827 original size:44 final size:44
Alignment explanation
Indices: 29959603--29959827 Score: 117
Period size: 44 Copynumber: 5.2 Consensus size: 44
29959593 AAAACAAAGC
* * *
29959603 CTTGCCTCCATCAGTTGCAGTGGAGCGGGTTAAAGATAGCAAAT
1 CTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAAAT
* * * * * * * *
29959647 CTTGCCTTCCT-GCATTGACAGCGAAACAGATCGAAA-A-A--AAAGC
1 CTTGCCTCCCTCG-GTTG-CAGTGGAGCAGGT-TAAAGATAGCAAA-T
* * * *
29959690 CTTGCCTCCATCGGTTGCAGTGGAGCAAGTTAAAGATTGCAGAT
1 CTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAAAT
* * * * * ** *
29959734 CTTGCCTTCCT-GCATTGACAGCGAAGCAGATCGAA-A-A-CAAAGC
1 CTTGCCTCCCTCG-GTTG-CAGTGGAGCAGGTTAAAGATAGCAAA-T
29959777 CTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAAAT
1 CTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAAAT
29959821 CTTGCCT
1 CTTGCCT
29959828 TTCTACGTCG
Statistics
Matches: 122, Mismatches: 43, Indels: 32
0.62 0.22 0.16
Matches are distributed among these distances:
41 3 0.02
42 27 0.22
43 27 0.22
44 36 0.30
45 26 0.21
46 3 0.02
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (44 bp):
CTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAAAT
Found at i:29960056 original size:131 final size:130
Alignment explanation
Indices: 29959860--29960353 Score: 643
Period size: 131 Copynumber: 3.8 Consensus size: 130
29959850 ATCGAAGATT
* * * * * *
29959860 ACAAGTCCTATATCCCTGGCCAACACTGGAATAGGTTGGGAAATTACAAATCTTGTCTCCCTAAG
1 ACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTT-GGAAATTGCAGATCTTGTCTCCCTAAG
*
29959925 CAATAGTGGAGCAGATCGAGGACGGC-AGATCTTATCTTCCCCAGAAGTAGGGAAACAGATTTAA
65 CAATAGTGGAGCAGATCGAAGACGGCGA-ATCTTATCTTCCCCAG-AGTAGGGAAACAGATTTAA
29959989 GCC
128 GCC
* * * *
29959992 ACAAGTCCTATGTCCTTGACCAGCAGTAGAATAGGTTGGAAATTGCAGATCTTATCTCCTTAAGC
1 ACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAGC
* * *
29960057 AATAGTGGAGCAGATCGAAGATGGCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGT
66 AATAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCA-GAGTAGGGAAACAGATTTAAGC
29960122 C
130 C
* ***
29960123 ACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATCGCAGATCTTGTCTCTAGAAGC
1 ACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAGC
* * * * * * * *
29960188 AGTAGTAGAGCAGATCGAGGACGGCGAATCTTATCTT--CAAGTGTAAGGAAGCAAATTTAAGCC
66 AATAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGAGTAGGGAAACAGATTTAAGCC
* * * *
29960251 ACAAGTCCTATGTCCCTGACCAGTAGTGAAATAGTTTGGAAATTGCAGATGTTGTCTCCCTAAGC
1 ACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAGC
* *
29960316 AGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTC
66 AATAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTC
29960354 AAGTGTAAAG
Statistics
Matches: 316, Mismatches: 43, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
128 109 0.34
129 2 0.01
131 173 0.55
132 32 0.10
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (130 bp):
ACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAGC
AATAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGAGTAGGGAAACAGATTTAAGCC
Found at i:29960328 original size:259 final size:262
Alignment explanation
Indices: 29959860--29960353 Score: 683
Period size: 259 Copynumber: 1.9 Consensus size: 262
29959850 ATCGAAGATT
* * **
29959860 ACAAGTCCTATATCCCTGGCCAACACTGGAATAGGTTGGGAAATTACAAATCTTGTCTCCCTAAG
1 ACAAGTCCTATATCCCTGACCAACACTGGAATAGGTTGGGAAATCACAAATCTTGTCTCCAGAAG
* * * *
29959925 CAATAGTGGAGCAGATCGAGGACGGCAGATCTTATCTTCCCCAGAAGTAGGGAAACAGATTTAAG
66 CAATAGTAGAGCAGATCGAGGACGGCAGATCTTATCTT-CCAAGAAGTAAGGAAACAAATTTAAG
* *
29959990 CCACAAGTCCTATGTCCTTGACCAGCAGTAGAATAGGTTGGAAATTGCAGATCTTATCTCCTTAA
130 CCACAAGTCCTATGTCCCTGACCAGCAGTAGAATAGGTTGGAAATTGCAGATCTTATCTCCCTAA
* * *
29960055 GCAATAGTGGAGCAGATCGAAGATGGCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAA
195 GCAATAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAA
29960120 GTC
260 GTC
* * * * * *
29960123 ACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTT-GGAAATCGCAGATCTTGTCTCTAGAAG
1 ACAAGTCCTATATCCCTGACCAACACTGGAATAGGTTGGGAAATCACAAATCTTGTCTCCAGAAG
* * *
29960187 CAGTAGTAGAGCAGATCGAGGACGGC-GAATCTTATCTT-CAAG-TGTAAGGAAGCAAATTTAAG
66 CAATAGTAGAGCAGATCGAGGACGGCAG-ATCTTATCTTCCAAGAAGTAAGGAAACAAATTTAAG
* * * *
29960249 CCACAAGTCCTATGTCCCTGACCAGTAGT-GAAATAGTTTGGAAATTGCAGATGTTGTCTCCCTA
130 CCACAAGTCCTATGTCCCTGACCAGCAGTAG-AATAGGTTGGAAATTGCAGATCTTATCTCCCTA
*
29960313 AGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTC
194 AGCAATAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTC
29960354 AAGTGTAAAG
Statistics
Matches: 202, Mismatches: 27, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
258 1 0.00
259 109 0.54
260 3 0.01
261 1 0.00
262 55 0.27
263 33 0.16
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (262 bp):
ACAAGTCCTATATCCCTGACCAACACTGGAATAGGTTGGGAAATCACAAATCTTGTCTCCAGAAG
CAATAGTAGAGCAGATCGAGGACGGCAGATCTTATCTTCCAAGAAGTAAGGAAACAAATTTAAGC
CACAAGTCCTATGTCCCTGACCAGCAGTAGAATAGGTTGGAAATTGCAGATCTTATCTCCCTAAG
CAATAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
TC
Found at i:29968172 original size:15 final size:15
Alignment explanation
Indices: 29968140--29968177 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
29968130 AGATTAATTC
*
29968140 TTAATTAAGATTTTA
1 TTAATTAAGATTTGA
29968155 TTAACTTAAG-TTTGA
1 TTAA-TTAAGATTTGA
29968170 TTAATTAA
1 TTAATTAA
29968178 CAAAAGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 4 0.19
15 12 0.57
16 5 0.24
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (15 bp):
TTAATTAAGATTTGA
Found at i:29975825 original size:51 final size:50
Alignment explanation
Indices: 29975692--29975886 Score: 230
Period size: 51 Copynumber: 3.9 Consensus size: 50
29975682 GTGAAAGTGA
* *
29975692 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAAAATA-AT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-AAATAGTT
* * *
29975742 AGGTCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAAATAGCTT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAAATAG-TT
* * * * ** *
29975793 TGATTACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGA
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAAATAGT-T
* *
29975844 TGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCA
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCA
29975887 GTATCATTAA
Statistics
Matches: 120, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
49 5 0.04
50 39 0.32
51 76 0.63
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (50 bp):
TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAAATAGTT
Found at i:29975832 original size:101 final size:102
Alignment explanation
Indices: 29975697--29975879 Score: 307
Period size: 101 Copynumber: 1.8 Consensus size: 102
29975687 AGTGATGGTC
29975697 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAAAATAAT-A-GGTCACATGTGTAGTAC
1 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACC-AAATAATGATGGTCACATGTGTAGTAC
29975760 TATGTGCAGGCTACTATGCGTACCAAATAGCTTTGATT
65 TATGTGCAGGCTACTATGCGTACCAAATAGCTTTGATT
* ** *
29975798 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGGTCACATGTGTAGTACT
1 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAAATAATGATGGTCACATGTGTAGTACT
29975863 ATGTGCAGGCTACTATG
66 ATGTGCAGGCTACTATG
29975880 TGAACCAGTA
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
100 4 0.05
101 37 0.49
102 35 0.46
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (102 bp):
ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAAATAATGATGGTCACATGTGTAGTACT
ATGTGCAGGCTACTATGCGTACCAAATAGCTTTGATT
Found at i:29975881 original size:26 final size:26
Alignment explanation
Indices: 29975801--29975881 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
29975791 TTTGATTACG
29975801 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* *
29975827 CGTGTA-T-CGGATAGTG-ATGG-TCAC-A
1 TGTGTAGTAC-TAT-GTGCA-GGCT-ACTA
29975852 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
29975878 TGTG
1 TGTG
29975882 AACCAGTATC
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
24 1 0.02
25 18 0.43
26 22 0.52
27 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:29983313 original size:25 final size:25
Alignment explanation
Indices: 29983285--29983396 Score: 120
Period size: 25 Copynumber: 4.5 Consensus size: 25
29983275 CAAGTAACTA
29983285 GCCACAAAAGCTTCCCAAATAAATC
1 GCCACAAAAGCTTCCCAAATAAATC
* * * *
29983310 GCCACAAAGGTTTCCCAAACAATTC
1 GCCACAAAAGCTTCCCAAATAAATC
* *
29983335 GCCACAAAGGCTT-CCAAGTAAATC
1 GCCACAAAAGCTTCCCAAATAAATC
* *
29983359 ACCAC-AAAGACTTCCCAAATAATTC
1 GCCACAAAAG-CTTCCCAAATAAATC
*
29983384 ACCACAAAAGCTT
1 GCCACAAAAGCTT
29983397 GGTTTGGTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
23 3 0.04
24 15 0.21
25 50 0.69
26 4 0.06
ACGTcount: A:0.41, C:0.31, G:0.10, T:0.18
Consensus pattern (25 bp):
GCCACAAAAGCTTCCCAAATAAATC
Found at i:29983367 original size:49 final size:50
Alignment explanation
Indices: 29983285--29983396 Score: 154
Period size: 49 Copynumber: 2.3 Consensus size: 50
29983275 CAAGTAACTA
* **
29983285 GCCACAAAAGCTTCCCAAATAAATCGCCACAAAGGTTTCCCAAACAATTC
1 GCCACAAAAGCTTCCCAAATAAATCACCACAAAGACTTCCCAAACAATTC
* * *
29983335 GCCACAAAGGCTT-CCAAGTAAATCACCACAAAGACTTCCCAAATAATTC
1 GCCACAAAAGCTTCCCAAATAAATCACCACAAAGACTTCCCAAACAATTC
*
29983384 ACCACAAAAGCTT
1 GCCACAAAAGCTT
29983397 GGTTTGGTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
49 42 0.78
50 12 0.22
ACGTcount: A:0.41, C:0.31, G:0.10, T:0.18
Consensus pattern (50 bp):
GCCACAAAAGCTTCCCAAATAAATCACCACAAAGACTTCCCAAACAATTC
Found at i:29988573 original size:25 final size:25
Alignment explanation
Indices: 29988540--29988599 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
29988530 TACCAAAAAA
*
29988540 GCTTCCCAAATAAATCGT-CATAAAG
1 GCTTTCCAAATAAATC-TCCATAAAG
*
29988565 GCTTTCCAACTAAATCTCCATAAAG
1 GCTTTCCAAATAAATCTCCATAAAG
29988590 GCTTTCCAAA
1 GCTTTCCAAA
29988600 CAATTTGCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 1 0.03
25 30 0.97
ACGTcount: A:0.37, C:0.27, G:0.10, T:0.27
Consensus pattern (25 bp):
GCTTTCCAAATAAATCTCCATAAAG
Found at i:30002242 original size:21 final size:21
Alignment explanation
Indices: 30002212--30002253 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
30002202 TAACATAGAA
30002212 TTTTTTTTAATTTTT-TTGTT
1 TTTTTTTTAATTTTTATTGTT
30002232 TTTTGTTTTAATTTTTATTGTT
1 TTTT-TTTTAATTTTTATTGTT
30002254 AATTGTGTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.81
Consensus pattern (21 bp):
TTTTTTTTAATTTTTATTGTT
Found at i:30002247 original size:22 final size:20
Alignment explanation
Indices: 30002212--30002253 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
30002202 TAACATAGAA
*
30002212 TTTTTTTTAATTTTTTTGTT
1 TTTTTTTTAATTTTATTGTT
30002232 TTTTGTTTTAATTTTTATTGTT
1 TTTT-TTTTAA-TTTTATTGTT
30002254 AATTGTGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 6 0.32
22 9 0.47
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.81
Consensus pattern (20 bp):
TTTTTTTTAATTTTATTGTT
Found at i:30002259 original size:22 final size:21
Alignment explanation
Indices: 30002216--30002259 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
30002206 ATAGAATTTT
**
30002216 TTTTAATTTTTTTGTTTTTTG
1 TTTTAATTTTTTTGTTAATTG
30002237 TTTTAATTTTTATTGTTAATTG
1 TTTTAATTTTT-TTGTTAATTG
30002259 T
1 T
30002260 GTGCTTGAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.75
Consensus pattern (21 bp):
TTTTAATTTTTTTGTTAATTG
Found at i:30004312 original size:11 final size:12
Alignment explanation
Indices: 30004296--30004344 Score: 50
Period size: 11 Copynumber: 4.3 Consensus size: 12
30004286 TGAGCTAAAG
30004296 AAAAGAAAAGA-
1 AAAAGAAAAGAC
* *
30004307 AAAAGAAAGGAT
1 AAAAGAAAAGAC
*
30004319 AATAGAAAA-AC
1 AAAAGAAAAGAC
30004330 AAAAG-AAAGAC
1 AAAAGAAAAGAC
30004341 AAAA
1 AAAA
30004345 TGTTGGTTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
10 3 0.10
11 21 0.68
12 7 0.23
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (12 bp):
AAAAGAAAAGAC
Found at i:30005525 original size:27 final size:28
Alignment explanation
Indices: 30005441--30005538 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
30005431 CATGAGATTG
* * *
30005441 GCACTAAGTGTGCGGGTTTAAATTGT-TCA
1 GCACTAAGTGTGCGAGTTT-GATTATAT-A
30005470 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
30005498 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
30005525 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
30005539 GACTTAATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 24 0.38
28 21 0.33
29 19 0.30
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:30005552 original size:29 final size:27
Alignment explanation
Indices: 30005469--30005553 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 27
30005459 TAAATTGTTC
* *
30005469 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTAATTATAT
* *
30005497 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTAATTATAT
*
30005524 AGCACTGAGTGTGCGGACTTAATATATAT
1 AGCACTAAGTGTGC-GACTTAAT-TATAT
30005553 A
1 A
30005554 TTTTTGAATC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 23 0.45
28 22 0.43
29 6 0.12
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTAATTATAT
Found at i:30022869 original size:18 final size:19
Alignment explanation
Indices: 30022824--30022872 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
30022814 GAATATTTAC
*
30022824 ATAAAAATTAAACTAAGTAA
1 ATAAAAA-TAAACTAAATAA
30022844 A-AATAAATAAA-TAAATAA
1 ATAA-AAATAAACTAAATAA
30022862 ATAAAAATAAA
1 ATAAAAATAAA
30022873 AATAAAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 8 0.31
20 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAATAAACTAAATAA
Found at i:30029337 original size:18 final size:19
Alignment explanation
Indices: 30029292--30029340 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
30029282 GAATATTTAC
*
30029292 ATAAAAATTAAACTAAGTAA
1 ATAAAAA-TAAACTAAATAA
30029312 A-AATAAATAAA-TAAATAA
1 ATAA-AAATAAACTAAATAA
30029330 ATAAAAATAAA
1 ATAAAAATAAA
30029341 AATAAAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 8 0.31
20 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAATAAACTAAATAA
Done.