Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 169 of 186
Found at i:56100007 original size:30 final size:30
Alignment explanation
Indices: 56099967--56100033 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
56099957 AGAGACCATG
56099967 GATGAGTTCCCTTACACATTCGGCTTTCAAA
1 GATGA-TTCCCTTACACATTCGGCTTTCAAA
56099998 GATGATTCCCTTACACATTCGGCTTTCAAA
1 GATGATTCCCTTACACATTCGGCTTTCAAA
56100028 GATGAT
1 GATGAT
56100034 AAAAATCATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 31 0.86
31 5 0.14
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (30 bp):
GATGATTCCCTTACACATTCGGCTTTCAAA
Found at i:56100319 original size:13 final size:13
Alignment explanation
Indices: 56100301--56100325 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56100291 TCAAACGATT
56100301 AAATTTTCACACG
1 AAATTTTCACACG
56100314 AAATTTTCACAC
1 AAATTTTCACAC
56100326 ATATAACCTA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:56104577 original size:19 final size:20
Alignment explanation
Indices: 56104542--56104579 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
56104532 AGAAAAAAAA
56104542 ACAACCTATAACATATATTT
1 ACAACCTATAACATATATTT
56104562 ACAA-CTAT-ACACTATATT
1 ACAACCTATAACA-TATATT
56104580 CTTTAACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.18
19 10 0.59
20 4 0.24
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (20 bp):
ACAACCTATAACATATATTT
Found at i:56107191 original size:13 final size:13
Alignment explanation
Indices: 56107162--56107190 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
56107152 TCTTTATTAC
56107162 TTTTGAAAAGTGA
1 TTTTGAAAAGTGA
56107175 TTTTGAAAAGTG-
1 TTTTGAAAAGTGA
56107187 TTTT
1 TTTT
56107191 TAGGAGTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (13 bp):
TTTTGAAAAGTGA
Found at i:56112421 original size:31 final size:31
Alignment explanation
Indices: 56112382--56112450 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
56112372 CTTAACATAC
**
56112382 CAATGACTTAAATAAAAACTTTTGAATAGTT
1 CAATGACTTAAATAAAAACTTTCAAATAGTT
*
56112413 CAGTGACTTAAATAAAAACTTTCAAATAGTT
1 CAATGACTTAAATAAAAACTTTCAAATAGTT
56112444 CAATGAC
1 CAATGAC
56112451 CAAATTGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (31 bp):
CAATGACTTAAATAAAAACTTTCAAATAGTT
Found at i:56115809 original size:27 final size:27
Alignment explanation
Indices: 56115779--56115830 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
56115769 GGACATGGGT
* *
56115779 TGTCACACGGTCATTCCACACACAGGA
1 TGTCACACAGTCATGCCACACACAGGA
*
56115806 TGTCACACAGTCGTGCCACACACAG
1 TGTCACACAGTCATGCCACACACAG
56115831 TCGTGTGTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.17
Consensus pattern (27 bp):
TGTCACACAGTCATGCCACACACAGGA
Found at i:56128930 original size:43 final size:42
Alignment explanation
Indices: 56128853--56128955 Score: 138
Period size: 43 Copynumber: 2.4 Consensus size: 42
56128843 NNNNNNNCAG
* *
56128853 GGTCTTACACGAATCA-AATACGATGCCAATGTCCCAGACAT
1 GGTCTTACACGAAACACAATACGATGCCAACGTCCCAGACAT
*
56128894 GGTCTTACACGTAAACACAAGT-CGATGCCAACGTCCCAGACGT
1 GGTCTTACACG-AAACACAA-TACGATGCCAACGTCCCAGACAT
56128937 GGTCTTACACGATAACACA
1 GGTCTTACACGA-AACACA
56128956 TATCGGAAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
41 11 0.20
42 5 0.09
43 38 0.69
44 1 0.02
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.20
Consensus pattern (42 bp):
GGTCTTACACGAAACACAATACGATGCCAACGTCCCAGACAT
Found at i:56129932 original size:29 final size:29
Alignment explanation
Indices: 56129899--56129957 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
56129889 TATATATATA
56129899 AATCACATATCATCATTATGCCATCCACT
1 AATCACATATCATCATTATGCCATCCACT
*
56129928 AATCACATATCATTATTATGCCATCCACT
1 AATCACATATCATCATTATGCCATCCACT
56129957 A
1 A
56129958 CCTATTACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (29 bp):
AATCACATATCATCATTATGCCATCCACT
Found at i:56132480 original size:20 final size:21
Alignment explanation
Indices: 56132457--56132513 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
56132447 GAAAAAGTAC
* *
56132457 TAAACATAACCTAA-AAACAT
1 TAAAAATAAACTAAGAAACAT
*
56132477 TAAAAATAAACTAAGACACAT
1 TAAAAATAAACTAAGAAACAT
56132498 TAAAAATAAACTAAGA
1 TAAAAATAAACTAAGA
56132514 CTCATTTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 12 0.36
21 21 0.64
ACGTcount: A:0.63, C:0.14, G:0.04, T:0.19
Consensus pattern (21 bp):
TAAAAATAAACTAAGAAACAT
Found at i:56132499 original size:21 final size:21
Alignment explanation
Indices: 56132473--56132519 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
56132463 TAACCTAAAA
56132473 ACATTAAAAATAAACTAAGAC
1 ACATTAAAAATAAACTAAGAC
56132494 ACATTAAAAATAAACTAAGAC
1 ACATTAAAAATAAACTAAGAC
*
56132515 TCATT
1 ACATT
56132520 TTACAACAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.57, C:0.15, G:0.04, T:0.23
Consensus pattern (21 bp):
ACATTAAAAATAAACTAAGAC
Found at i:56135457 original size:92 final size:90
Alignment explanation
Indices: 56135218--56135493 Score: 293
Period size: 91 Copynumber: 3.0 Consensus size: 90
56135208 TTTCAGAGAT
* * * *
56135218 TTTGGCAGGTTATCGGGGGAGAATATTTAGCCTACAGGTTTTGTACTATGCGTATCTAGCGTGTT
1 TTTGGCATGTTATC-GGGGAGAATATTTAGCCTAC-GGTTTTGCACTATGTGCATCTAGCGTGTT
* * *
56135283 ATCGGTTGTAATAACTTTTATGAACAA
64 ATCGGTTGAAATAACTCTTATGAGCAA
* * * * *
56135310 TTTGGCAT-TTATAGGAGGAGAACATTTAGCCTAAGGGTTTTACACTATGTGCATCTAACGTGTT
1 TTTGGCATGTTATCGG-GGAGAATATTTAGCCT-ACGGTTTTGCACTATGTGCATCTAGCGTGTT
* * * *
56135374 ATTGATTGAAATAGCTCTTATTAGCAA
64 ATCGGTTGAAATAACTCTTATGAGCAA
* * * * *
56135401 TTTGGCATGTTATCGGGGAAGAATATTTAACCTACGTGCTTTGCACTATGTGCATCTGGCGTATA
1 TTTGGCATGTTATCGGGG-AGAATATTTAGCCTACG-GTTTTGCACTATGTGCATCTAGCGTGTT
*
56135466 ATCGGTTGAAATATCTCTTATGAGCAA
64 ATCGGTTGAAATAACTCTTATGAGCAA
56135493 T
1 T
56135494 CTAGTGTGTT
Statistics
Matches: 149, Mismatches: 30, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
90 2 0.01
91 75 0.50
92 72 0.48
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (90 bp):
TTTGGCATGTTATCGGGGAGAATATTTAGCCTACGGTTTTGCACTATGTGCATCTAGCGTGTTAT
CGGTTGAAATAACTCTTATGAGCAA
Found at i:56135543 original size:38 final size:38
Alignment explanation
Indices: 56135466--56135545 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
56135456 CTGGCGTATA
* * ***
56135466 ATCGGTTGAAATATCTCTTATGAGCAATCTAGTGTGTT
1 ATCGGTTGAAATAGCTCTTATAAGCAATCTAGCACGTT
* *
56135504 ATCGGTTGGAATAGCTCTTATAAGCAATCTGGCACGTT
1 ATCGGTTGAAATAGCTCTTATAAGCAATCTAGCACGTT
56135542 ATCG
1 ATCG
56135546 AATGGATACC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (38 bp):
ATCGGTTGAAATAGCTCTTATAAGCAATCTAGCACGTT
Found at i:56137070 original size:10 final size:10
Alignment explanation
Indices: 56137043--56137088 Score: 56
Period size: 11 Copynumber: 4.3 Consensus size: 10
56137033 TAGATTTGCG
56137043 TTTATGTTTAT
1 TTTAT-TTTAT
*
56137054 GTTTATTTCAT
1 -TTTATTTTAT
56137065 TTTATTTTATT
1 TTTATTTTA-T
56137076 TTTATTTTAT
1 TTTATTTTAT
56137086 TTT
1 TTT
56137089 CTACATAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 12 0.39
11 14 0.45
12 5 0.16
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.76
Consensus pattern (10 bp):
TTTATTTTAT
Found at i:56137071 original size:5 final size:5
Alignment explanation
Indices: 56137043--56137088 Score: 56
Period size: 5 Copynumber: 8.6 Consensus size: 5
56137033 TAGATTTGCG
*
56137043 TTTAT GTTTAT GTTTAT TTCAT TTTAT TTTATT TTTAT TTTAT TTT
1 TTTAT -TTTAT -TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTT
56137089 CTACATAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
5 21 0.57
6 16 0.43
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:56137082 original size:16 final size:15
Alignment explanation
Indices: 56137043--56137088 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
56137033 TAGATTTGCG
56137043 TTTATGTTTATGTTTAT
1 TTTAT-TTTAT-TTTAT
*
56137060 TTCATTTTATTTTATT
1 TTTATTTTATTTTA-T
56137076 TTTATTTTATTTT
1 TTTATTTTATTTT
56137089 CTACATAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 4 0.15
16 18 0.69
17 4 0.15
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.76
Consensus pattern (15 bp):
TTTATTTTATTTTAT
Found at i:56144353 original size:100 final size:100
Alignment explanation
Indices: 56144180--56145097 Score: 882
Period size: 100 Copynumber: 9.2 Consensus size: 100
56144170 CATAGTTTGT
* * * * *
56144180 AATTAAAATATTGAAGCCACAACGGCGAATCTTA-CTCTCCTAGGCGGTGCAATGGAACAAATTG
1 AATTAAAAGATTGAAGCCACAACGGCGAATCTTACCT-TCCCAGGCGATGCAGTGGAACAGATTG
* ** ** *
56144244 AAGCCACAACGGCGAATCTCACTTCCCCGGTATTGT
65 AAGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
* * *
56144280 AATTAAAATATTGAGGCCACAACGGCGAATCTTACCTTCCCAGGCGATGTAGTGGAACAGATTGA
1 AATTAAAAGATTGAAGCCACAACGGCGAATCTTACCTTCCCAGGCGATGCAGTGGAACAGATTGA
*
56144345 AGCTACAACGGTGAATCTTGCTTCCCCGACATTGC
66 AGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
* * * *
56144380 AATTAAAAGATTGAAGCCACAACAGCAAATCTTACTTTCCCAGGCGGTGCAGTGGAACAGATTGA
1 AATTAAAAGATTGAAGCCACAACGGCGAATCTTACCTTCCCAGGCGATGCAGTGGAACAGATTGA
* *
56144445 AGCTACAACGGTGAATCTCGCTTCCCCGACATTGC
66 AGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
* ** * * * **
56144480 AATTAAAA-ATTGAAGTCACAACGGTAAATCTTACTTTCCCAGGTGGTGCAACGGAACAGATTGA
1 AATTAAAAGATTGAAGCCACAACGGCGAATCTTACCTTCCCAGGCGATGCAGTGGAACAGATTGA
* * *
56144544 AGCTACAACGACAAATCTCGCTTCCCCGACATTGC
66 AGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
* * * * *
56144579 AATTAAAAGATTGAAGCCACAACGGCAAATCTTACTTTCCCAGAC-AGTGCAATGGAACAGATTA
1 AATTAAAAGATTGAAGCCACAACGGCGAATCTTACCTTCCCAGGCGA-TGCAGTGGAACAGATTG
* *
56144643 AAGCTACAATGGTGAATCTTGCTTCCCCGACATTGC
65 AAGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
* * * * * * * *
56144679 AATTGAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAAGTGGTGCAGTGGAGCAAATTAA
1 AATTAAAAGATTGAAGCCACAACGGCGAATCTTACCTTCCCAGGCGATGCAGTGGAACAGATTGA
* * * *
56144744 AGCTACGACGGCGAATCTTACTTCCCTGATATTGC
66 AGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
* * * * *
56144779 AATTAAAAATATTGAAGCCGCAACGGCGAATCTTA-CTTCCCTGGC-AGTACAGTGGAGCAGATT
1 AATT-AAAAGATTGAAGCCACAACGGCGAATCTTACCTTCCCAGGCGA-TGCAGTGGAACAGATT
* * * **
56144842 AAAGCTACAACGGTGAATCTTGCTTCCCTGATTTTGC
64 GAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
* * * * * * * * *
56144879 AATTTAAAAGATTGAAGTCGCAATGACGAATCTTA-CTTCTCTGGC-AGTGCAATGGAGCATATT
1 AA-TTAAAAGATTGAAGCCACAACGGCGAATCTTACCTTCCCAGGCGA-TGCAGTGGAACAGATT
* * * * * * * *
56144942 AAAGATACGACGACAAATTTTACTTCCCCGATATTGC
64 GAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
* * * ** *
56144979 AATTTAAAAGATTGAAGCCGCAATGACGAATCTTA-CTTCCTTGGC-AGTGTAGTGGAACAGATT
1 AA-TTAAAAGATTGAAGCCACAACGGCGAATCTTACCTTCCCAGGCGA-TGCAGTGGAACAGATT
** * *
56145042 GAAGCTACAACGATGAATTTTGTTTCCCCGACATTGC
64 GAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
*
56145079 AGTTTAAAAAGATTGAAGC
1 A-ATT-AAAAGATTGAAGC
56145098 TATACATTGC
Statistics
Matches: 705, Mismatches: 104, Indels: 17
0.85 0.13 0.02
Matches are distributed among these distances:
99 90 0.13
100 571 0.81
101 44 0.06
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.25
Consensus pattern (100 bp):
AATTAAAAGATTGAAGCCACAACGGCGAATCTTACCTTCCCAGGCGATGCAGTGGAACAGATTGA
AGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
Found at i:56144730 original size:299 final size:299
Alignment explanation
Indices: 56144180--56145097 Score: 1052
Period size: 299 Copynumber: 3.1 Consensus size: 299
56144170 CATAGTTTGT
* * *
56144180 AATTAAAATATTGAAGCCACAACGGCGAATCTTACTCTCCTAGGCGGTGCAATGGAACAAATTGA
1 AATTAAAATATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGGTGCAATGGAACAGATTGA
* * * * * *
56144245 AGCCACAACGGCGAATCTCACTTCCCCGGTATTGTAATTAAAATATTGAGGCCACAACGGCGAAT
66 AGCTACAACGGCGAATCTCGCTTCCCCGATATTGCAATTAAAAGATTGAAGCCACAACGGCGAAT
* * *
56144310 CTTACCTTCCCAGGC-GATGTAGTGGAACAGATTGAAGCTACAACGGTGAATCTTGCTTCCCCGA
131 CTTA-CTTCCCAGGCAG-TGCAATGGAACAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGA
* *
56144374 CATTGCAATTAAAAGATTGAAGCCACAACAGCAAATCTTACTTTCCCAGGCGGTGCAGTGGAACA
194 CATTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGGTGCAGTGGAACA
*
56144439 GATTGAAGCTACAACGGTGAATCTCGCTTCCCCGACATTGC
259 GATTGAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGC
* ** * *
56144480 AATTAAAA-ATTGAAGTCACAACGGTAAATCTTACTTTCCCAGGTGGTGCAACGGAACAGATTGA
1 AATTAAAATATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGGTGCAATGGAACAGATTGA
* * * *
56144544 AGCTACAACGACAAATCTCGCTTCCCCGACATTGCAATTAAAAGATTGAAGCCACAACGGCAAAT
66 AGCTACAACGGCGAATCTCGCTTCCCCGATATTGCAATTAAAAGATTGAAGCCACAACGGCGAAT
* *
56144609 CTTACTTTCCCAGACAGTGCAATGGAACAGATTAAAGCTACAATGGTGAATCTTGCTTCCCCGAC
131 CTTAC-TTCCCAGGCAGTGCAATGGAACAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGAC
* * * * *
56144674 ATTGCAATTGAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAAGTGGTGCAGTGGAGCAA
195 ATTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGGTGCAGTGGAACAG
* * * * * *
56144739 ATTAAAGCTACGACGGCGAATCTTACTTCCCTGATATTGC
260 ATTGAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGC
* * * * * * *
56144779 AATTAAAAATATTGAAGCCGCAACGGCGAATCTTAC-TTCCCTGGCAGTACAGTGGAGCAGATTA
1 AATT-AAAATATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGGTGCAATGGAACAGATTG
* * * * * * * *
56144843 AAGCTACAACGGTGAATCTTGCTTCCCTGATTTTGCAATTTAAAAGATTGAAGTCGCAATGACGA
65 AAGCTACAACGGCGAATCTCGCTTCCCCGATATTGCAA-TTAAAAGATTGAAGCCACAACGGCGA
* * * * * * *** * *
56144908 ATCTTACTTCTCTGGCAGTGCAATGGAGCATATTAAAGATACGACGACAAATTTTACTTCCCCGA
129 ATCTTACTTCCCAGGCAGTGCAATGGAACAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGA
* * * * ** * *
56144973 TATTGCAATTTAAAAGATTGAAGCCGCAATGACGAATCTTAC-TTCCTTGGCAGTGTAGTGGAAC
194 CATTGCAA-TTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGGTGCAGTGGAAC
* * *
56145037 AGATTGAAGCTACAACGATGAATTTTGTTTCCCCGACATTGC
258 AGATTGAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGC
* *
56145079 AGTTTAAAAAGATTGAAGC
1 A-ATT-AAAATATTGAAGC
56145098 TATACATTGC
Statistics
Matches: 513, Mismatches: 98, Indels: 13
0.82 0.16 0.02
Matches are distributed among these distances:
298 1 0.00
299 254 0.50
300 164 0.32
301 94 0.18
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.25
Consensus pattern (299 bp):
AATTAAAATATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGGTGCAATGGAACAGATTGA
AGCTACAACGGCGAATCTCGCTTCCCCGATATTGCAATTAAAAGATTGAAGCCACAACGGCGAAT
CTTACTTCCCAGGCAGTGCAATGGAACAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACA
TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGGTGCAGTGGAACAGA
TTGAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGC
Found at i:56144842 original size:200 final size:199
Alignment explanation
Indices: 56144180--56145097 Score: 996
Period size: 200 Copynumber: 4.6 Consensus size: 199
56144170 CATAGTTTGT
* * * *
56144180 AATTAAAATATTGAAGCCACAACGGCGAATCTTAC-TCTCCTAGGCGGTGCAATGGAACAAATTG
1 AATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTC-CCT-GGCAGTGCAGTGGAACAGATTG
* * ** ** * * *
56144244 AAGCCACAACGGCGAATCTCACTTCCCCGGTATTGTAATTAAAATATTGAGGCCACAACGGCGAA
64 AAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAAGCCACAACGGCGAA
* * * * * *** *
56144309 TCTTACCTTCCCAGGCGATGTAGTGGAACAGATTGAAGCTACAACGGTGAATCTTGCTTCCCCGA
129 TCTTACTTTCCCAGGCGGTGCAATGGAACAGATTAAAGCTACAACGACAAATCTTACTTCCCCGA
56144374 CATTGC
194 CATTGC
* * * *
56144380 AATTAAAAGATTGAAGCCACAACAGCAAATCTTACTTTCCCAGGCGGTGCAGTGGAACAGATTGA
1 AATTAAAAGATTGAAGCCACAACGGCGAATCTTAC-TTCCCTGGCAGTGCAGTGGAACAGATTGA
* * **
56144445 AGCTACAACGGTGAATCTCGCTTCCCCGACATTGCAATTAAAA-ATTGAAGTCACAACGGTAAAT
65 AGCTACAACGGTGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAAGCCACAACGGCGAAT
* * * **
56144509 CTTACTTTCCCAGGTGGTGCAACGGAACAGATTGAAGCTACAACGACAAATCTCGCTTCCCCGAC
130 CTTACTTTCCCAGGCGGTGCAATGGAACAGATTAAAGCTACAACGACAAATCTTACTTCCCCGAC
56144574 ATTGC
195 ATTGC
* * * * *
56144579 AATTAAAAGATTGAAGCCACAACGGCAAATCTTACTTTCCCAGACAGTGCAATGGAACAGATTAA
1 AATTAAAAGATTGAAGCCACAACGGCGAATCTTAC-TTCCCTGGCAGTGCAGTGGAACAGATTGA
* *
56144644 AGCTACAATGGTGAATCTTGCTTCCCCGACATTGCAATTGAAAGATTGAAGCCACAACGGCGAAT
65 AGCTACAACGGTGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAAGCCACAACGGCGAAT
* * * * * * * * * *
56144709 CTTACTTTCCCAAGTGGTGCAGTGGAGCAAATTAAAGCTACGACGGCGAATCTTACTTCCCTGAT
130 CTTACTTTCCCAGGCGGTGCAATGGAACAGATTAAAGCTACAACGACAAATCTTACTTCCCCGAC
56144774 ATTGC
195 ATTGC
* * * * *
56144779 AATTAAAAATATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGCAGTACAGTGGAGCAGATTAA
1 AATT-AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTGA
* ** * * * *
56144844 AGCTACAACGGTGAATCTTGCTTCCCTGATTTTGCAATTTAAAAGATTGAAGTCGCAATGACGAA
65 AGCTACAACGGTGAATCTTGCTTCCCCGACATTGCAA-TTAAAAGATTGAAGCCACAACGGCGAA
* * * * * * * *
56144909 TCTTAC-TTCTCTGGCAGTGCAATGGAGCATATTAAAGATACGACGACAAATTTTACTTCCCCGA
129 TCTTACTTTCCCAGGCGGTGCAATGGAACAGATTAAAGCTACAACGACAAATCTTACTTCCCCGA
*
56144973 TATTGC
194 CATTGC
* * * * *
56144979 AATTTAAAAGATTGAAGCCGCAATGACGAATCTTACTTCCTTGGCAGTGTAGTGGAACAGATTGA
1 AA-TTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTGA
* * * *
56145044 AGCTACAACGATGAATTTTGTTTCCCCGACATTGCAGTTTAAAAAGATTGAAGC
65 AGCTACAACGGTGAATCTTGCTTCCCCGACATTGCA-ATT-AAAAGATTGAAGC
56145098 TATACATTGC
Statistics
Matches: 615, Mismatches: 95, Indels: 15
0.85 0.13 0.02
Matches are distributed among these distances:
199 177 0.29
200 364 0.59
201 72 0.12
202 2 0.00
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.25
Consensus pattern (199 bp):
AATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTGAA
GCTACAACGGTGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAAGCCACAACGGCGAATC
TTACTTTCCCAGGCGGTGCAATGGAACAGATTAAAGCTACAACGACAAATCTTACTTCCCCGACA
TTGC
Found at i:56144870 original size:50 final size:50
Alignment explanation
Indices: 56144193--56145053 Score: 381
Period size: 50 Copynumber: 17.2 Consensus size: 50
56144183 TAAAATATTG
* * * *
56144193 AAGCCACAACGGCGAATCTTAC-TCTCCTAGGCGGTGCAATGGAACAAATTG
1 AAGCCACAACGGCGAATCTTACTTC-CCT-GACAGTGCAATGGAACAGATTA
* * ** * * * * * *
56144244 AAGCCACAACGGCGAATCTCACTTCCCCGGTATTGTAAT-TAAAATATTG
1 AAGCCACAACGGCGAATCTTACTTCCCTGACAGTGCAATGGAACAGATTA
* * * * * *
56144293 AGGCCACAACGGCGAATCTTACCTTCCCAGGC-GATGTAGTGGAACAGATTG
1 AAGCCACAACGGCGAATCTTA-CTTCCCTGACAG-TGCAATGGAACAGATTA
* * * * * * * *
56144344 AAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCAAT-TAAAAGATTG
1 AAGCCACAACGGCGAATCTTACTTCCCTGACAGTGCAATGGAACAGATTA
* * * * * * *
56144393 AAGCCACAACAGCAAATCTTACTTTCCCAGGCGGTGCAGTGGAACAGATTG
1 AAGCCACAACGGCGAATCTTAC-TTCCCTGACAGTGCAATGGAACAGATTA
* * ** * * * * *
56144444 AAGCTACAACGGTGAATCTCGCTTCCCCGACATTGCAAT-TAA-AAATTG
1 AAGCCACAACGGCGAATCTTACTTCCCTGACAGTGCAATGGAACAGATTA
* ** * *** * *
56144492 AAGTCACAACGGTAAATCTTACTTTCCCAGGTGGTGCAACGGAACAGATTG
1 AAGCCACAACGGCGAATCTTAC-TTCCCTGACAGTGCAATGGAACAGATTA
* * * ** * * * * *
56144543 AAGCTACAACGACAAATCTCGCTTCCCCGACATTGCAAT-TAAAAGATTG
1 AAGCCACAACGGCGAATCTTACTTCCCTGACAGTGCAATGGAACAGATTA
* *
56144592 AAGCCACAACGGCAAATCTTACTTTCCCAGACAGTGCAATGGAACAGATTA
1 AAGCCACAACGGCGAATCTTAC-TTCCCTGACAGTGCAATGGAACAGATTA
* * * * * * * *
56144643 AAGCTACAATGGTGAATCTTGCTTCCCCGACATTGCAATTGAA-AGATTG
1 AAGCCACAACGGCGAATCTTACTTCCCTGACAGTGCAATGGAACAGATTA
* ** * * *
56144692 AAGCCACAACGGCGAATCTTACTTTCCC-AAGTGGTGCAGTGGAGCAAATTA
1 AAGCCACAACGGCGAATCTTAC-TTCCCTGA-CAGTGCAATGGAACAGATTA
* * * * ** * * *
56144743 AAGCTACGACGGCGAATCTTACTTCCCTGATATTGCAATTAAAAATATTG
1 AAGCCACAACGGCGAATCTTACTTCCCTGACAGTGCAATGGAACAGATTA
* * * * *
56144793 AAGCCGCAACGGCGAATCTTACTTCCCTGGCAGTACAGTGGAGCAGATTA
1 AAGCCACAACGGCGAATCTTACTTCCCTGACAGTGCAATGGAACAGATTA
* * * *** ** * *
56144843 AAGCTACAACGGTGAATCTTGCTTCCCTGATTTTGCAATTTAAAAGATTG
1 AAGCCACAACGGCGAATCTTACTTCCCTGACAGTGCAATGGAACAGATTA
* * * * * * * *
56144893 AAGTCGCAATGACGAATCTTACTTCTCTGGCAGTGCAATGGAGCATATTA
1 AAGCCACAACGGCGAATCTTACTTCCCTGACAGTGCAATGGAACAGATTA
** * * * * * * * ** * *
56144943 AAGATACGACGACAAATTTTACTTCCCCGATATTGCAATTTAAAAGATTG
1 AAGCCACAACGGCGAATCTTACTTCCCTGACAGTGCAATGGAACAGATTA
* * * * * * * *
56144993 AAGCCGCAATGACGAATCTTACTTCCTTGGCAGTGTAGTGGAACAGATTG
1 AAGCCACAACGGCGAATCTTACTTCCCTGACAGTGCAATGGAACAGATTA
*
56145043 AAGCTACAACG
1 AAGCCACAACG
56145054 ATGAATTTTG
Statistics
Matches: 585, Mismatches: 209, Indels: 33
0.71 0.25 0.04
Matches are distributed among these distances:
48 22 0.04
49 114 0.19
50 306 0.52
51 141 0.24
52 2 0.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (50 bp):
AAGCCACAACGGCGAATCTTACTTCCCTGACAGTGCAATGGAACAGATTA
Found at i:56145210 original size:44 final size:42
Alignment explanation
Indices: 56145152--56145477 Score: 296
Period size: 44 Copynumber: 7.6 Consensus size: 42
56145142 TCATATCAAG
*
56145152 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAACTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAA-AAACCAA
* * * *
56145196 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAAAC-CA-A
* * * * * * *
56145240 TCTTATCTCTCTAAAGTTGCAGTAGAGTAGAT-CACATCCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAAACCAA
*
56145281 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAACTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAA-AAACCAA
* * * * *
56145325 TCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAATCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAAAC-CA-A
* * * * * *
56145369 TCTTATCTCTCTAAAGTTGCAGTAGAGCAGAT-CACATCCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAAACCAA
*
56145410 TCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAA-AAACCAA
* * *
56145454 TCATATCTTCCAGAAGTTGCAGTG
1 TCTTATCTCCCTGAAGTTGCAGTG
56145478 AAGCGGATTA
Statistics
Matches: 226, Mismatches: 46, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
41 56 0.25
42 12 0.05
43 18 0.08
44 140 0.62
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.27
Consensus pattern (42 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAAACCAA
Found at i:56145290 original size:85 final size:85
Alignment explanation
Indices: 56145122--56145529 Score: 319
Period size: 85 Copynumber: 4.8 Consensus size: 85
56145112 ATTATATCTT
* * * * * *
56145122 TGAAGTTGCAGTAGAGTAGA-TCATATCA-AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT
1 TGAAGTTGCAGTGGAGCAGATTAAAATCACAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-T
* * * *
56145185 GAAGAAACTAATCCTATCTCCC
65 TAA-AATCCAATCTTATCTCCC
* * * *
56145207 TGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTAAAGTTGCAGTAGAGTAGA-
1 TGAAGTTGCAGTGGAGCAGATTAAAATCACA-ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGAT
* *
56145271 TCACATCCAATCTTATCTCCC
65 TAAAATCCAATCTTATCTCCC
* * *
56145292 TGAAGTTGCAGTGGAGCAGACTGAAGAA--ACTAATCCTATCTCCCTGAAGTTGCAGT-GAAGCG
1 TGAAGTTGCAGTGGAGCAGA-TTAA-AATCAC-AATCTTATCTCCCTGAAGTTGCAGTAG-AGCA
*
56145354 GATTAAAATCACAGATCTTATCTCTC
62 GATTAAAATC-CA-ATCTTATCTCCC
* * * * * *
56145380 TAAAGTTGCAGTAGAGCAGA-TCACATC-CAATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATT
1 TGAAGTTGCAGTGGAGCAGATTAAAATCACAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATT
* * *
56145443 GAAGAAACCAATCATATCTTCC
66 -AA-AATCCAATCTTATCTCCC
* * * * * * * *
56145465 AGAAGTTGCAGTGAAGCGGATTAAAATGATAGGTCTTATCTCTCTGAAGTTGCAGAAGAGCAGAT
1 TGAAGTTGCAGTGGAGCAGATTAAAATCACA-ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGAT
56145530 CACATCAGAC
Statistics
Matches: 253, Mismatches: 52, Indels: 33
0.75 0.15 0.10
Matches are distributed among these distances:
84 1 0.00
85 132 0.52
86 27 0.11
87 9 0.04
88 84 0.33
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (85 bp):
TGAAGTTGCAGTGGAGCAGATTAAAATCACAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATT
AAAATCCAATCTTATCTCCC
Found at i:56145337 original size:129 final size:129
Alignment explanation
Indices: 56145124--56145535 Score: 673
Period size: 129 Copynumber: 3.2 Consensus size: 129
56145114 TATATCTTTG
* *
56145124 AAGTTGCAGTAGAGTAGATCATAT-CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA
1 AAGTTGCAGTAGAGCAGATCACATCCAA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA
*
56145188 GAAACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTA
65 GAAACTAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAATCACAGATCTTATCTCTCTA
*
56145253 AAGTTGCAGTAGAGTAGATCACATCCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
1 AAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
56145318 AAACTAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAATCACAGATCTTATCTCTCTA
66 AAACTAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAATCACAGATCTTATCTCTCTA
* *
56145382 AAGTTGCAGTAGAGCAGATCACATCCAATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAG
1 AAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
* * * * * * * *
56145447 AAACCAATCATATCTTCCAGAAGTTGCAGTGAAGCGGATTAAAATGATAGGTCTTATCTCTCTG
66 AAACTAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAATCACAGATCTTATCTCTCTA
*
56145511 AAGTTGCAGAAGAGCAGATCACATC
1 AAGTTGCAGTAGAGCAGATCACATC
56145536 AGACTTTATG
Statistics
Matches: 268, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
129 265 0.99
130 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (129 bp):
AAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
AAACTAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAATCACAGATCTTATCTCTCTA
Found at i:56148807 original size:9 final size:9
Alignment explanation
Indices: 56148793--56148823 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
56148783 GTTAAATGAA
56148793 TCGAGTTAT
1 TCGAGTTAT
*
56148802 TCGAGTTAA
1 TCGAGTTAT
56148811 TCGAGTTAT
1 TCGAGTTAT
56148820 TCGA
1 TCGA
56148824 ATCAACTCGA
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:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:56151559 original size:35 final size:34
Alignment explanation
Indices: 56151510--56151580 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 34
56151500 TACTGATTTA
56151510 ATATAAATATATAAT-TATTATT-TAACATATATAT
1 ATATAAATATATAATAT-TTATTATAACA-ATATAT
* *
56151544 ATATAACTAATATAATATTTTTTATAACAATATAT
1 ATATAAAT-ATATAATATTTATTATAACAATATAT
56151579 AT
1 AT
56151581 TCTAACCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
34 7 0.22
35 19 0.59
36 6 0.19
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (34 bp):
ATATAAATATATAATATTTATTATAACAATATAT
Found at i:56157981 original size:13 final size:13
Alignment explanation
Indices: 56157963--56157991 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
56157953 AACATTTCCC
56157963 TCGTTGGGTTAAT
1 TCGTTGGGTTAAT
56157976 TCGTTGGGTTAAT
1 TCGTTGGGTTAAT
56157989 TCG
1 TCG
56157992 AGGGTTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.10, G:0.31, T:0.45
Consensus pattern (13 bp):
TCGTTGGGTTAAT
Found at i:56162748 original size:18 final size:17
Alignment explanation
Indices: 56162725--56162774 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
56162715 ACTAGAAATC
56162725 ATATTTTTATTGTTTTGT
1 ATATTTTTATTGTTTT-T
*
56162743 ATA-TTTTCTT-TTTTT
1 ATATTTTTATTGTTTTT
56162758 ATGATTTTTA-TGTTTTT
1 AT-ATTTTTATTGTTTTT
56162775 TATGATTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
15 3 0.11
16 6 0.22
17 15 0.56
18 3 0.11
ACGTcount: A:0.16, C:0.02, G:0.08, T:0.74
Consensus pattern (17 bp):
ATATTTTTATTGTTTTT
Found at i:56162775 original size:18 final size:18
Alignment explanation
Indices: 56162727--56162781 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
56162717 TAGAAATCAT
*
56162727 ATTTTTATTGTTTTGTAT-
1 ATTTTTA-TGTTTTTTATG
*
56162745 A-TTTTCT-TTTTTTATG
1 ATTTTTATGTTTTTTATG
56162761 ATTTTTATGTTTTTTATG
1 ATTTTTATGTTTTTTATG
56162779 ATT
1 ATT
56162782 AGATGACGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 7 0.23
16 2 0.06
17 9 0.29
18 13 0.42
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.73
Consensus pattern (18 bp):
ATTTTTATGTTTTTTATG
Found at i:56162936 original size:3 final size:3
Alignment explanation
Indices: 56162883--56162917 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
56162873 TCTTGATTTA
56162883 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
56162918 ACTTTTTCTA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:56174428 original size:27 final size:24
Alignment explanation
Indices: 56174381--56174429 Score: 71
Period size: 27 Copynumber: 1.9 Consensus size: 24
56174371 GCACAAAGTG
56174381 CAAAGTGCAAATAACGATAAGCAC
1 CAAAGTGCAAATAACGATAAGCAC
56174405 CAAAGTGCGAAATAATACGATAAGC
1 CAAAGTGC-AAAT-A-ACGATAAGC
56174430 GCGCTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.36
25 4 0.18
26 1 0.05
27 9 0.41
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.14
Consensus pattern (24 bp):
CAAAGTGCAAATAACGATAAGCAC
Found at i:56175609 original size:13 final size:13
Alignment explanation
Indices: 56175587--56175620 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
56175577 GTATTCAATT
*
56175587 CAATCCAATTACC
1 CAATCTAATTACC
56175600 CAATCTAATTACC
1 CAATCTAATTACC
*
56175613 CAACCTAA
1 CAATCTAA
56175621 CCCAATCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (13 bp):
CAATCTAATTACC
Found at i:56175748 original size:9 final size:9
Alignment explanation
Indices: 56175736--56175776 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
56175726 TGAATTAGGT
56175736 TAATTCGGG
1 TAATTCGGG
*
56175745 TAATTCGGT
1 TAATTCGGG
*
56175754 TAATTCGAG
1 TAATTCGGG
*
56175763 TAATTCGGT
1 TAATTCGGG
56175772 TAATT
1 TAATT
56175777 TAGTTAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (9 bp):
TAATTCGGG
Found at i:56175754 original size:18 final size:18
Alignment explanation
Indices: 56175728--56175794 Score: 82
Period size: 18 Copynumber: 3.7 Consensus size: 18
56175718 TGTATGATTG
* *
56175728 AATTAGGTTAATTCGGGT
1 AATTCGGTTAATTCGAGT
56175746 AATTCGGTTAATTCGAGT
1 AATTCGGTTAATTCGAGT
*
56175764 AATTCGGTTAATT-TAGTT
1 AATTCGGTTAATTCGAG-T
*
56175782 AATTTGGTTAATT
1 AATTCGGTTAATT
56175795 TTTAACCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
17 2 0.05
18 42 0.95
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (18 bp):
AATTCGGTTAATTCGAGT
Found at i:56175793 original size:27 final size:27
Alignment explanation
Indices: 56175728--56175794 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
56175718 TGTATGATTG
*
56175728 AATTAGGTTAATTCGGGTAATTCGGTT
1 AATTAGGTTAATTCGGGTAATTCAGTT
* * *
56175755 AATTCGAG-TAATTCGGTTAATTTAGTT
1 AATTAG-GTTAATTCGGGTAATTCAGTT
*
56175782 AATTTGGTTAATT
1 AATTAGGTTAATT
56175795 TTTAACCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
26 1 0.03
27 31 0.94
28 1 0.03
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (27 bp):
AATTAGGTTAATTCGGGTAATTCAGTT
Found at i:56179606 original size:21 final size:21
Alignment explanation
Indices: 56179570--56179629 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
56179560 ATAAAAATAT
56179570 AAAAATTTATTAAAAATTAGAAA
1 AAAAATTTA-T-AAAATTAGAAA
56179593 AAAAATTTATAAAATATAGAAA
1 AAAAATTTATAAAAT-TAGAAA
*
56179615 AAAAA-TTGTAAAATT
1 AAAAATTTATAAAATT
56179630 TTATAAAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
20 1 0.03
21 13 0.37
22 12 0.34
23 9 0.26
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
AAAAATTTATAAAATTAGAAA
Found at i:56179637 original size:22 final size:22
Alignment explanation
Indices: 56179570--56179621 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 22
56179560 ATAAAAATAT
56179570 AAAAATTTATTAAAA-ATTAGAAA
1 AAAAATTTA-TAAAATA-TAGAAA
56179593 AAAAATTTATAAAATATAGAAA
1 AAAAATTTATAAAATATAGAAA
56179615 AAAAATT
1 AAAAATT
56179622 GTAAAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (22 bp):
AAAAATTTATAAAATATAGAAA
Found at i:56180247 original size:92 final size:91
Alignment explanation
Indices: 56180090--56180256 Score: 223
Period size: 92 Copynumber: 1.8 Consensus size: 91
56180080 CAGTCAAAAT
* *
56180090 GTCTTTTTGATGCATTTTAACAATTCAAATACTTAATAGAGTGCAAAAAAAAAACAGGCGCTTAA
1 GTCTTTTTGATGCATTTGAACAATTCAAATACCTAATAGAGTGCAAAAAAAAAACAGGCGCTTAA
56180155 TTTTTTATTTTTTGAAAAAGTTTAAAG
66 TTTTTT-TTTTTTGAAAAAGTTTAAAG
* * * *
56180182 GTCTTTTTGATGCATGTTGAA-AGTTCTAGTACCTAATTGAGTGCAAAAAAAAAGTA-AGG-GCT
1 GTCTTTTTGATGCAT-TTGAACAATTCAAATACCTAATAGAGTGCAAAAAAAAA--ACAGGCGCT
56180244 TAATTTTTTTTTT
63 TAATTTTTTTTTT
56180257 AAGTTTGAGA
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
91 4 0.06
92 54 0.82
93 7 0.11
94 1 0.02
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.40
Consensus pattern (91 bp):
GTCTTTTTGATGCATTTGAACAATTCAAATACCTAATAGAGTGCAAAAAAAAAACAGGCGCTTAA
TTTTTTTTTTTTGAAAAAGTTTAAAG
Found at i:56180470 original size:62 final size:63
Alignment explanation
Indices: 56180365--56180490 Score: 218
Period size: 62 Copynumber: 2.0 Consensus size: 63
56180355 AATTGAGTAA
56180365 AAGGTGATACCAATTCAATCAAAACTTTAAATAATAGTATAAATAAATTATATAACCCTCACC
1 AAGGTGATACCAATTCAATCAAAACTTTAAATAATAGTATAAATAAATTATATAACCCTCACC
* * *
56180428 AAGGTGATACCAATTCAGTC-AAACTTTAAATAATAGTGTAAATAACTTATATAACCCTCACC
1 AAGGTGATACCAATTCAATCAAAACTTTAAATAATAGTATAAATAAATTATATAACCCTCACC
56180490 A
1 A
56180491 CTACAAAAGT
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
62 41 0.68
63 19 0.32
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (63 bp):
AAGGTGATACCAATTCAATCAAAACTTTAAATAATAGTATAAATAAATTATATAACCCTCACC
Found at i:56182647 original size:3 final size:3
Alignment explanation
Indices: 56182633--56182666 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
56182623 GCAATCGCCT
56182633 TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
56182667 TGGTGAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:56185905 original size:31 final size:31
Alignment explanation
Indices: 56185862--56185924 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
56185852 TTATTCTATA
56185862 AAGGCTGATGTTGTAGATACCACAAATATGT
1 AAGGCTGATGTTGTAGATACCACAAATATGT
*
56185893 AAGGTTGATGTTGTAGATACCACAAATATGT
1 AAGGCTGATGTTGTAGATACCACAAATATGT
56185924 A
1 A
56185925 GAGGGATATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (31 bp):
AAGGCTGATGTTGTAGATACCACAAATATGT
Found at i:56190414 original size:22 final size:23
Alignment explanation
Indices: 56190362--56190415 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
56190352 GCTGATAAAT
* *
56190362 AGTAGGCTCTATTAAGCTGAAAC
1 AGTAAGCTCTAATAAGCTGAAAC
* *
56190385 GGTAAGCTCTAATGAGCTG-AAC
1 AGTAAGCTCTAATAAGCTGAAAC
56190407 AGTAAGCTC
1 AGTAAGCTC
56190416 ATACGAGTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (23 bp):
AGTAAGCTCTAATAAGCTGAAAC
Found at i:56190444 original size:46 final size:47
Alignment explanation
Indices: 56190386--56190477 Score: 132
Period size: 48 Copynumber: 2.0 Consensus size: 47
56190376 AGCTGAAACG
* *
56190386 GTAAGCTCTAATGAGCTG-AACAGTAAGCTCATACGAGTTGAAATTT
1 GTAAACTCTAATGAGCTGAAACAGTAAGCTCATACGAGCTGAAATTT
* *
56190432 GTAAACTCTAATGAGCTGAAAACAGTAGGCTCTTACGAGCTGAAAT
1 GTAAACTCTAATGAGCTG-AAACAGTAAGCTCATACGAGCTGAAAT
56190478 ATCGGTAAGC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 17 0.43
48 23 0.57
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (47 bp):
GTAAACTCTAATGAGCTGAAACAGTAAGCTCATACGAGCTGAAATTT
Found at i:56190464 original size:24 final size:24
Alignment explanation
Indices: 56190349--56190476 Score: 84
Period size: 24 Copynumber: 5.4 Consensus size: 24
56190339 AAACTCCTCC
* * *
56190349 TGAGCTGATAAATAGTAGGCTCTAT
1 TGAGCTGA-AAACAGTAAGCTCTAA
* *
56190374 TAAGCTG-AAACGGTAAGCTCTAA
1 TGAGCTGAAAACAGTAAGCTCTAA
56190397 TGAGCTG--AACAGTAAGCTC-ATA
1 TGAGCTGAAAACAGTAAGCTCTA-A
* * *** *
56190419 CGAGTTGAAATTTGTAAACTCTAA
1 TGAGCTGAAAACAGTAAGCTCTAA
* *
56190443 TGAGCTGAAAACAGTAGGCTCTTA
1 TGAGCTGAAAACAGTAAGCTCTAA
*
56190467 CGAGCTGAAA
1 TGAGCTGAAA
56190477 TATCGGTAAG
Statistics
Matches: 77, Mismatches: 22, Indels: 9
0.71 0.20 0.08
Matches are distributed among these distances:
21 1 0.01
22 17 0.22
23 18 0.23
24 34 0.44
25 7 0.09
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.26
Consensus pattern (24 bp):
TGAGCTGAAAACAGTAAGCTCTAA
Found at i:56190721 original size:67 final size:67
Alignment explanation
Indices: 56190646--56191005 Score: 549
Period size: 67 Copynumber: 5.4 Consensus size: 67
56190636 AATAATTCAA
* *
56190646 TTTCTCAAATCACATATATATAATCTATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
1 TTTCTCAAATCACATACATATAATCGATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
56190711 AC
66 AC
* * * * * *
56190713 CTTCTCAAAACAAATGCATATAATCGATTTAATTAAATACATACATTTAAATACTCAATTCACAT
1 TTTCTCAAATCACATACATATAATCGATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
56190778 AC
66 AC
*
56190780 TTTCTCAAATCACATACATATAATCGATTTAATTAAATACATACATTTAAATACTCAATTCGCAT
1 TTTCTCAAATCACATACATATAATCGATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
56190845 AC
66 AC
* * * * * *
56190847 TTTCTCAAATCATATACATATAATCCATGCAATTAAATATATACATTTAATTACTCAATTCACAT
1 TTTCTCAAATCACATACATATAATCGATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
56190912 AC
66 AC
* *
56190914 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAATTACTCAATTCGCAT
1 TTTCTCAAATCACATACATATAATCGATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
56190979 AC
66 AC
* *
56190981 TTTCTCAAATCATATACAAATAATC
1 TTTCTCAAATCACATACATATAATC
56191006 AATAGTTTCT
Statistics
Matches: 266, Mismatches: 27, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 266 1.00
ACGTcount: A:0.42, C:0.20, G:0.02, T:0.36
Consensus pattern (67 bp):
TTTCTCAAATCACATACATATAATCGATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
AC
Found at i:56192978 original size:29 final size:30
Alignment explanation
Indices: 56192946--56193004 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
56192936 ACCAATAAAA
56192946 GCCG-TTTTTTTCAAAATTTACCGGAATGG
1 GCCGATTTTTTTCAAAATTTACCGGAATGG
* **
56192975 GCCGATTTTTTTTATTATTTACCGGAATGG
1 GCCGATTTTTTTCAAAATTTACCGGAATGG
56193005 TCCACTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.42
Consensus pattern (30 bp):
GCCGATTTTTTTCAAAATTTACCGGAATGG
Found at i:56193361 original size:51 final size:51
Alignment explanation
Indices: 56193301--56193466 Score: 287
Period size: 51 Copynumber: 3.3 Consensus size: 51
56193291 TCCTCTTTAA
56193301 TCCTCTCAATTTCCTTCCAAAATTCTCTTAAACCCATATTTAATTTCAATT
1 TCCTCTCAATTTCCTTCCAAAATTCTCTTAAACCCATATTTAATTTCAATT
56193352 TCCTCTCAATTTCCTTCCAAAATTCTCTTAAACCCATATTTAATTTCAATT
1 TCCTCTCAATTTCCTTCCAAAATTCTCTTAAACCCATATTTAATTTCAATT
* * **
56193403 TCCTCTCAATTTCCTTCCAAACTTCTCTCAAATTCATATTTAATTTCAATT
1 TCCTCTCAATTTCCTTCCAAAATTCTCTTAAACCCATATTTAATTTCAATT
*
56193454 TCCCCTCAATTTC
1 TCCTCTCAATTTC
56193467 ATTTTTTAAA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 110 1.00
ACGTcount: A:0.28, C:0.29, G:0.00, T:0.43
Consensus pattern (51 bp):
TCCTCTCAATTTCCTTCCAAAATTCTCTTAAACCCATATTTAATTTCAATT
Found at i:56193501 original size:30 final size:31
Alignment explanation
Indices: 56193467--56193533 Score: 118
Period size: 30 Copynumber: 2.2 Consensus size: 31
56193457 CCTCAATTTC
56193467 ATTTTTTAAAATAATTTTA-AATTTTTTTAT
1 ATTTTTTAAAATAATTTTATAATTTTTTTAT
*
56193497 ATTTTTTAAAATAATTTTATATTTTTTTTAT
1 ATTTTTTAAAATAATTTTATAATTTTTTTAT
56193528 ATTTTT
1 ATTTTT
56193534 ATCAATGGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 19 0.54
31 16 0.46
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (31 bp):
ATTTTTTAAAATAATTTTATAATTTTTTTAT
Found at i:56193508 original size:20 final size:19
Alignment explanation
Indices: 56193481--56193523 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
56193471 TTTAAAATAA
**
56193481 TTTTAAATTTTTTTATATT
1 TTTTAAATAATTTTATATT
56193500 TTTTAAAATAATTTTATATT
1 TTTT-AAATAATTTTATATT
56193520 TTTT
1 TTTT
56193524 TTATATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTAAATAATTTTATATT
Found at i:56193632 original size:18 final size:18
Alignment explanation
Indices: 56193609--56193671 Score: 51
Period size: 18 Copynumber: 3.5 Consensus size: 18
56193599 TAAGTATTAA
56193609 ATTTAATTTTTAAATATT
1 ATTTAATTTTTAAATATT
**
56193627 ATTTAAGATTTTTTTAT-TT
1 ATTT-A-ATTTTTAAATATT
*
56193646 ATGT-ATTTTTAAATAATT
1 ATTTAATTTTTAAAT-ATT
56193664 A-TTAATTT
1 ATTTAATTT
56193672 ATTATTTGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
16 8 0.24
17 1 0.03
18 11 0.32
19 6 0.18
20 8 0.24
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
ATTTAATTTTTAAATATT
Found at i:56195411 original size:55 final size:55
Alignment explanation
Indices: 56195345--56195526 Score: 305
Period size: 55 Copynumber: 3.3 Consensus size: 55
56195335 AACCCTAACC
56195345 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
* *
56195400 TAATTTTACATAATTTGATAATTTTACTAACCATTGACACAATTTTTGGAATTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
56195455 TAATTTTACATAATTTGATAATTTTACTAACCATTAACA-AATTTTTTTTGG-CTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAA---TTTTTGGACTTAA
56195511 TAATTTTACATAATTT
1 TAATTTTACATAATTT
56195527 TACATAATGT
Statistics
Matches: 120, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
54 2 0.02
55 91 0.76
56 20 0.17
57 7 0.06
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.46
Consensus pattern (55 bp):
TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
Found at i:56195525 original size:10 final size:10
Alignment explanation
Indices: 56195510--56195534 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
56195500 TTTTGGCTTA
56195510 ATAATTTTAC
1 ATAATTTTAC
56195520 ATAATTTTAC
1 ATAATTTTAC
56195530 ATAAT
1 ATAAT
56195535 GTTAGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:56196417 original size:124 final size:123
Alignment explanation
Indices: 56196080--56196423 Score: 530
Period size: 124 Copynumber: 2.8 Consensus size: 123
56196070 AACTTGCTAT
* * * **
56196080 TGTAGCAAAATCGCGTCCAAGAGGGCGCGATTTCACAATTCCTTCTCAAATAGCATTATGGTAGA
1 TGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGA
* *
56196145 AGCGATTTTATACTATTTGCTCAGAAATGT-AAAAAAAATATTTTTTACATGACCAAC
66 AGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATATTTATTACATGACCAAC
56196202 TGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGA
1 TGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGA
* * * * *
56196267 AGCGATTTTATACTATTAGCTAAGAAACGTCAGAAAAAATTATTTATTACATTACCTAC
66 AGCGATTTTATACTATTTGCTCAGAAACGTCA-AAAAAAATATTTATTACATGACCAAC
56196326 TGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGA
1 TGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGA
* *
56196391 AGTGATTTTATATTATTTGAC-CAGAAACGTCAA
66 AGCGATTTTATACTATTTG-CTCAGAAACGTCAA
56196424 CTCGAAATAA
Statistics
Matches: 203, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
122 87 0.43
123 2 0.01
124 113 0.56
125 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (123 bp):
TGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGA
AGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATATTTATTACATGACCAAC
Found at i:56201506 original size:27 final size:27
Alignment explanation
Indices: 56201476--56201530 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
56201466 AATTGGAGTT
56201476 TGTCAATTCCGCAATTTAACTCAAAAC
1 TGTCAATTCCGCAATTTAACTCAAAAC
56201503 TGTCAATTCCGCAATTTAACTCAAAAC
1 TGTCAATTCCGCAATTTAACTCAAAAC
56201530 T
1 T
56201531 TCACCTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.31
Consensus pattern (27 bp):
TGTCAATTCCGCAATTTAACTCAAAAC
Found at i:56202321 original size:15 final size:15
Alignment explanation
Indices: 56202297--56202335 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
56202287 GTTACTTGTA
56202297 CAAT-GAACCACAAC
1 CAATGGAACCACAAC
56202311 CAATGGAACCACAAC
1 CAATGGAACCACAAC
*
56202326 TAATGGAACC
1 CAATGGAACC
56202336 TGATGTGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.46, C:0.31, G:0.13, T:0.10
Consensus pattern (15 bp):
CAATGGAACCACAAC
Found at i:56206308 original size:21 final size:21
Alignment explanation
Indices: 56206283--56206324 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
56206273 TCGACGATTC
56206283 CCTCTTTGACGAGATGACATT
1 CCTCTTTGACGAGATGACATT
* *
56206304 CCTCTTTGATGATATGACATT
1 CCTCTTTGACGAGATGACATT
56206325 TTTCTGTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (21 bp):
CCTCTTTGACGAGATGACATT
Found at i:56207083 original size:94 final size:94
Alignment explanation
Indices: 56206915--56207106 Score: 269
Period size: 94 Copynumber: 2.0 Consensus size: 94
56206905 TCGTCCTTTT
* * * *
56206915 ATTGTTCAATTTTGTTTTGAGAAAGGAAGTGAGATTTTGCATCATGAATCCCAAATAGTTCTAAT
1 ATTGTTCAAGTTTATTTTGAGAAAGGAAGTGAGACTTTGCATCATGAATCCCAAATAGTTCGAAT
* *
56206980 TTTTGTATGAAAATAAGGAAGACGAA-AGG
66 CTTTATATGAAAATAAGGAAGAC-AAGAGG
* ** *
56207009 ATTGTTCAAGTTTATTTTGAGAAAGGAAGTGAGACTTTGCATCATGGATTTCAAATAGTTCGAGT
1 ATTGTTCAAGTTTATTTTGAGAAAGGAAGTGAGACTTTGCATCATGAATCCCAAATAGTTCGAAT
*
56207074 CTTTATATGAAAGTAAGGAAGACAAGAGG
66 CTTTATATGAAAATAAGGAAGACAAGAGG
56207103 ATTG
1 ATTG
56207107 AACTCAAGCC
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
93 2 0.02
94 84 0.98
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.33
Consensus pattern (94 bp):
ATTGTTCAAGTTTATTTTGAGAAAGGAAGTGAGACTTTGCATCATGAATCCCAAATAGTTCGAAT
CTTTATATGAAAATAAGGAAGACAAGAGG
Found at i:56208118 original size:28 final size:30
Alignment explanation
Indices: 56208078--56208140 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
56208068 AATCATAATT
56208078 AAAGTTTGAAGTA-TATAATTACATA-AAATA
1 AAAGTTT-AAGTATTA-AATTACATATAAATA
56208108 AAAGTTT-AGTATTAAATTACATATTAAATA
1 AAAGTTTAAGTATTAAATTACATA-TAAATA
56208138 AAA
1 AAA
56208141 ATATGTAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
28 13 0.43
29 2 0.07
30 15 0.50
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (30 bp):
AAAGTTTAAGTATTAAATTACATATAAATA
Found at i:56218806 original size:19 final size:20
Alignment explanation
Indices: 56218768--56218806 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
56218758 AAAAAATGAC
* *
56218768 CTGTAGTAGAGAGGGGGAAA
1 CTGTAGAAGAGAGAGGGAAA
56218788 CTGTAGAAGAGA-AGGGAAA
1 CTGTAGAAGAGAGAGGGAAA
56218807 AGAGAGTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.41, C:0.05, G:0.41, T:0.13
Consensus pattern (20 bp):
CTGTAGAAGAGAGAGGGAAA
Found at i:56228774 original size:16 final size:16
Alignment explanation
Indices: 56228749--56228790 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
56228739 GCTAATTTTT
56228749 TTTTTGAATTTT-TACA
1 TTTTTGAATTTTATA-A
*
56228765 TTTTTAAATTTTATAA
1 TTTTTGAATTTTATAA
56228781 TTTTTGAATT
1 TTTTTGAATT
56228791 ATTTGTTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (16 bp):
TTTTTGAATTTTATAA
Found at i:56239989 original size:24 final size:24
Alignment explanation
Indices: 56239954--56240174 Score: 222
Period size: 23 Copynumber: 9.5 Consensus size: 24
56239944 TTTGTTACAT
*
56239954 AATGCTGTCCAATTTTGATGCATA
1 AATGCTGCCCAATTTTGATGCATA
* *
56239978 AATGCTGCCCAA-TTTGTTACAT-
1 AATGCTGCCCAATTTTGATGCATA
* * *
56240000 AATGTTGTCCAATTTTGATGCTTA
1 AATGCTGCCCAATTTTGATGCATA
* *
56240024 AATGCTGCCCAA-TTTGTTACAT-
1 AATGCTGCCCAATTTTGATGCATA
*
56240046 AATGCTGTCCAATTTTGATGCATA
1 AATGCTGCCCAATTTTGATGCATA
* * *
56240070 AAAGCTGCCCAA-TTTGTTACAT-
1 AATGCTGCCCAATTTTGATGCATA
* *
56240092 AATGCTGTCCAATTTTGATGCTTA
1 AATGCTGCCCAATTTTGATGCATA
* *
56240116 AATGCTGCCCAA-TTTGTTACATA
1 AATGCTGCCCAATTTTGATGCATA
* * *
56240139 TATGCTGTCCAATTTTGATGCTTA
1 AATGCTGCCCAATTTTGATGCATA
56240163 AATGCTGCCCAA
1 AATGCTGCCCAA
56240175 ACTGTTTTAT
Statistics
Matches: 154, Mismatches: 36, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
22 31 0.20
23 63 0.41
24 60 0.39
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (24 bp):
AATGCTGCCCAATTTTGATGCATA
Found at i:56239993 original size:46 final size:46
Alignment explanation
Indices: 56239940--56240174 Score: 425
Period size: 46 Copynumber: 5.1 Consensus size: 46
56239930 ATGAGTTGAA
*
56239940 CCAATTTGTTACATAATGCTGTCCAATTTTGATGCATAAATGCTGC
1 CCAATTTGTTACATAATGCTGTCCAATTTTGATGCTTAAATGCTGC
*
56239986 CCAATTTGTTACATAATGTTGTCCAATTTTGATGCTTAAATGCTGC
1 CCAATTTGTTACATAATGCTGTCCAATTTTGATGCTTAAATGCTGC
* *
56240032 CCAATTTGTTACATAATGCTGTCCAATTTTGATGCATAAAAGCTGC
1 CCAATTTGTTACATAATGCTGTCCAATTTTGATGCTTAAATGCTGC
56240078 CCAATTTGTTACATAATGCTGTCCAATTTTGATGCTTAAATGCTGC
1 CCAATTTGTTACATAATGCTGTCCAATTTTGATGCTTAAATGCTGC
56240124 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
1 CCAATTTGTTACATA-ATGCTGTCCAATTTTGATGCTTAAATGCTGC
56240171 CCAA
1 CCAA
56240175 ACTGTTTTAT
Statistics
Matches: 181, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
46 146 0.81
47 35 0.19
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (46 bp):
CCAATTTGTTACATAATGCTGTCCAATTTTGATGCTTAAATGCTGC
Found at i:56252505 original size:54 final size:54
Alignment explanation
Indices: 56252441--56252548 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
56252431 AGTAGGCTTG
56252441 ATCGTAGATGAAGCCGCAGGCTCCACCGGAAGAATTGCATTTCCAGCATTCATC
1 ATCGTAGATGAAGCCGCAGGCTCCACCGGAAGAATTGCATTTCCAGCATTCATC
56252495 ATCGTAGATGAAGCCGCAGGCTCCACCGGAAGAATTGCATTTCCAGCATTCATC
1 ATCGTAGATGAAGCCGCAGGCTCCACCGGAAGAATTGCATTTCCAGCATTCATC
56252549 TGCATAGTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (54 bp):
ATCGTAGATGAAGCCGCAGGCTCCACCGGAAGAATTGCATTTCCAGCATTCATC
Found at i:56253182 original size:6 final size:6
Alignment explanation
Indices: 56253171--56253210 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
56253161 TAAACAAAAC
* * *
56253171 AGAGGA AGAGGA AGAGGA AGAGGC AGAGGC AGAGGC AGAG
1 AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAG
56253211 ATGATGAGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.42, C:0.07, G:0.50, T:0.00
Consensus pattern (6 bp):
AGAGGA
Found at i:56253188 original size:12 final size:12
Alignment explanation
Indices: 56253170--56253210 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
56253160 ATAAACAAAA
56253170 CAGAGGAAGAGG
1 CAGAGGAAGAGG
*
56253182 AAGAGGAAGAGG
1 CAGAGGAAGAGG
*
56253194 CAGAGGCAGAGG
1 CAGAGGAAGAGG
56253206 CAGAG
1 CAGAG
56253211 ATGATGAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.41, C:0.10, G:0.49, T:0.00
Consensus pattern (12 bp):
CAGAGGAAGAGG
Found at i:56254429 original size:3 final size:3
Alignment explanation
Indices: 56254421--56254453 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
56254411 ATGCTACTCT
56254421 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
56254454 AAGGATGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:56261670 original size:18 final size:19
Alignment explanation
Indices: 56261639--56261676 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
56261629 AAAATAAGAG
56261639 AAATAATAAGTTTTA-AAA
1 AAATAATAAGTTTTATAAA
56261657 AAATACATAA-TTTTATAAA
1 AAATA-ATAAGTTTTATAAA
56261676 A
1 A
56261677 TAGACACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (19 bp):
AAATAATAAGTTTTATAAA
Found at i:56272202 original size:24 final size:25
Alignment explanation
Indices: 56272169--56272220 Score: 97
Period size: 24 Copynumber: 2.1 Consensus size: 25
56272159 AACTCTAAAT
56272169 ACTGAAGAGTAGACCTGAACAATAA
1 ACTGAAGAGTAGACCTGAACAATAA
56272194 ACTG-AGAGTAGACCTGAACAATAA
1 ACTGAAGAGTAGACCTGAACAATAA
56272218 ACT
1 ACT
56272221 TAGTTTAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.46, C:0.17, G:0.19, T:0.17
Consensus pattern (25 bp):
ACTGAAGAGTAGACCTGAACAATAA
Found at i:56275622 original size:13 final size:13
Alignment explanation
Indices: 56275604--56275631 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
56275594 GTATATTGGT
56275604 TATTATGCATGTC
1 TATTATGCATGTC
56275617 TATTATGCATGTC
1 TATTATGCATGTC
56275630 TA
1 TA
56275632 AGTTCAACGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.46
Consensus pattern (13 bp):
TATTATGCATGTC
Found at i:56288251 original size:21 final size:21
Alignment explanation
Indices: 56288225--56288265 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
56288215 AGACGAGCAA
* *
56288225 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
56288246 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
56288266 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:56295379 original size:3 final size:3
Alignment explanation
Indices: 56295373--56295403 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
56295363 AAGAAGCTTT
56295373 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
56295404 GTCATATCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:56305442 original size:16 final size:16
Alignment explanation
Indices: 56305421--56305453 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
56305411 TCACAATACT
56305421 AGAGTAAATAAATTTG
1 AGAGTAAATAAATTTG
*
56305437 AGAGTATATAAATTTG
1 AGAGTAAATAAATTTG
56305453 A
1 A
56305454 AAACTTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.33
Consensus pattern (16 bp):
AGAGTAAATAAATTTG
Found at i:56305608 original size:20 final size:22
Alignment explanation
Indices: 56305565--56305609 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
56305555 TAACAAGTTT
* *
56305565 TTAAGATTTTTTATTTTTATAA
1 TTAAGATTTTTTATTTTCAAAA
56305587 TTAAGA-TTTTT-TTTTCAAAA
1 TTAAGATTTTTTATTTTCAAAA
56305607 TTA
1 TTA
56305610 TGAATTGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 5 0.24
22 6 0.29
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (22 bp):
TTAAGATTTTTTATTTTCAAAA
Found at i:56305853 original size:31 final size:31
Alignment explanation
Indices: 56305818--56305876 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
56305808 ATTCAACTCG
56305818 AATAACTCAAA-GTACTTATTTAAATTGACCC
1 AATAACTCAAATG-ACTTATTTAAATTGACCC
*
56305849 AATAACTCAAATGACTTATTTAACTTGA
1 AATAACTCAAATGACTTATTTAAATTGA
56305877 ATCAACTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34
Consensus pattern (31 bp):
AATAACTCAAATGACTTATTTAAATTGACCC
Found at i:56307691 original size:6 final size:6
Alignment explanation
Indices: 56307657--56307690 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
56307647 ATTCAGCCTC
*
56307657 GATTTG GATTTG GATTTG GATTTG GATTCG GATT
1 GATTTG GATTTG GATTTG GATTTG GATTTG GATT
56307691 CAGATTCTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.03, G:0.32, T:0.47
Consensus pattern (6 bp):
GATTTG
Found at i:56307696 original size:18 final size:18
Alignment explanation
Indices: 56307657--56307696 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
56307647 ATTCAGCCTC
* **
56307657 GATTTGGATTTGGATTTG
1 GATTTGGATTCGGATTCA
56307675 GATTTGGATTCGGATTCA
1 GATTTGGATTCGGATTCA
56307693 GATT
1 GATT
56307697 CTGCAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.20, C:0.05, G:0.30, T:0.45
Consensus pattern (18 bp):
GATTTGGATTCGGATTCA
Found at i:56314134 original size:24 final size:24
Alignment explanation
Indices: 56314100--56314148 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
56314090 ATTTAGAGAA
*
56314100 TTTTGTGTTTATGTTTT-GAGGGTT
1 TTTTGTGTTTAGGTTTTCG-GGGTT
*
56314124 TTTTGTTTTTAGGTTTTCGGGGTT
1 TTTTGTGTTTAGGTTTTCGGGGTT
56314148 T
1 T
56314149 AGTTTTTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.06, C:0.02, G:0.29, T:0.63
Consensus pattern (24 bp):
TTTTGTGTTTAGGTTTTCGGGGTT
Found at i:56314414 original size:19 final size:19
Alignment explanation
Indices: 56314392--56314433 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
56314382 AATTCATCTA
56314392 CATTTAACTAA-TATCATAT
1 CATTTAACTAATTATCA-AT
* *
56314411 CATTTCAGTAATTATCAAT
1 CATTTAACTAATTATCAAT
56314430 CATT
1 CATT
56314434 CATATTCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.43
Consensus pattern (19 bp):
CATTTAACTAATTATCAAT
Found at i:56315694 original size:14 final size:14
Alignment explanation
Indices: 56315675--56315715 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
56315665 ATAAATAATG
56315675 TATAAAGTCATA-AA
1 TATAAAGT-ATACAA
56315689 TATAAAGTATACAA
1 TATAAAGTATACAA
*
56315703 TATTAA-TATACAA
1 TATAAAGTATACAA
56315716 GTTTTGGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (14 bp):
TATAAAGTATACAA
Found at i:56316801 original size:17 final size:17
Alignment explanation
Indices: 56316779--56316814 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
56316769 TTATTTTGTT
56316779 ATTATTTACCAAAGTAC
1 ATTATTTACCAAAGTAC
56316796 ATTATTTACCAAAGTAC
1 ATTATTTACCAAAGTAC
56316813 AT
1 AT
56316815 AATTGAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.36
Consensus pattern (17 bp):
ATTATTTACCAAAGTAC
Found at i:56320944 original size:22 final size:21
Alignment explanation
Indices: 56320897--56320955 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
56320887 AGATTCTATT
* *
56320897 TTTTAAGATTTAAGAGTAGAAT
1 TTTTAAAATTTAA-AGTAGAAA
*
56320919 TTTTAAAATTTAAAGTTGGAAA
1 TTTTAAAATTTAAAG-TAGAAA
* *
56320941 TTTTGAAGTTTAAAG
1 TTTTAAAATTTAAAG
56320956 AAACATATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 2 0.06
22 29 0.94
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.42
Consensus pattern (21 bp):
TTTTAAAATTTAAAGTAGAAA
Found at i:56321059 original size:6 final size:6
Alignment explanation
Indices: 56321048--56321083 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
56321038 ATAATTTTTG
56321048 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT
1 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT
56321084 ATGTGTGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (6 bp):
GAAAAT
Found at i:56323054 original size:48 final size:48
Alignment explanation
Indices: 56322976--56323072 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
56322966 GTAATTATAA
* *
56322976 CACTTTAACATATTTATGTTATGGGTCCGTTAAAAGTACATTACAAAT
1 CACTCTAACATATTTATGTTATGGGCCCGTTAAAAGTACATTACAAAT
56323024 CACTCTAACATATTTATGTTATGGGCCCGTTAAAAGTACATTACAAAT
1 CACTCTAACATATTTATGTTATGGGCCCGTTAAAAGTACATTACAAAT
56323072 C
1 C
56323073 TTTCCCTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (48 bp):
CACTCTAACATATTTATGTTATGGGCCCGTTAAAAGTACATTACAAAT
Found at i:56324218 original size:48 final size:48
Alignment explanation
Indices: 56324140--56324236 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
56324130 GTAATTATAA
* *
56324140 CACTTTAACATATTTATGTTATGGGTCCGTTAAAAGTACATTACAAAT
1 CACTCTAACATATTTATGTTATGGGCCCGTTAAAAGTACATTACAAAT
56324188 CACTCTAACATATTTATGTTATGGGCCCGTTAAAAGTACATTACAAAT
1 CACTCTAACATATTTATGTTATGGGCCCGTTAAAAGTACATTACAAAT
56324236 C
1 C
56324237 TTTCCCTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (48 bp):
CACTCTAACATATTTATGTTATGGGCCCGTTAAAAGTACATTACAAAT
Found at i:56325559 original size:5 final size:5
Alignment explanation
Indices: 56325549--56325574 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
56325539 TAGGGTCAAG
56325549 AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA A
56325575 TTTATTTGTA
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:56328053 original size:19 final size:19
Alignment explanation
Indices: 56328026--56328066 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
56328016 TCTAGTTAAA
56328026 TAAAAAATTATAATAATAT
1 TAAAAAATTATAATAATAT
* *
56328045 TAAACAATTATAATTATAT
1 TAAAAAATTATAATAATAT
56328064 TAA
1 TAA
56328067 TATTAAATAA
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:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAAAATTATAATAATAT
Found at i:56328323 original size:16 final size:16
Alignment explanation
Indices: 56328288--56328325 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
56328278 AGTTTATAAT
*
56328288 ATTT-TATATTATGTT
1 ATTTATATATTATGTA
*
56328303 TTTTATATATTATGTA
1 ATTTATATATTATGTA
56328319 ATTTATA
1 ATTTATA
56328326 ACACATTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (16 bp):
ATTTATATATTATGTA
Found at i:56329973 original size:21 final size:22
Alignment explanation
Indices: 56329939--56329991 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
56329929 TTTAAATTTA
* * *
56329939 ATTTTACTTATAATTTAATCTAT
1 ATTTTA-TTTTAATATAATATAT
*
56329962 -TTTTATTTTAATATCATATAT
1 ATTTTATTTTAATATAATATAT
56329983 ATTTTATTT
1 ATTTTATTT
56329992 GTTACTATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTTTATTTTAATATAATATAT
Found at i:56334084 original size:42 final size:42
Alignment explanation
Indices: 56334038--56334140 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 42
56334028 GTTTAACTCA
* * *
56334038 TTTGAGTTTCCGTTCAACCCTAATGGGTTTCCGTTCATCTCT
1 TTTGAGCTTCCGTTCAACCCTAATGGGATTCCGTTCAGCTCT
* * * *
56334080 TTTGAGCTACTGTTTAACCCTTATGGGATTCCGTTCAGCTCT
1 TTTGAGCTTCCGTTCAACCCTAATGGGATTCCGTTCAGCTCT
* *
56334122 TATGAACTTCCGTTCAACC
1 TTTGAGCTTCCGTTCAACC
56334141 TTTACGGGTT
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (42 bp):
TTTGAGCTTCCGTTCAACCCTAATGGGATTCCGTTCAGCTCT
Found at i:56335515 original size:44 final size:44
Alignment explanation
Indices: 56335452--56335615 Score: 211
Period size: 44 Copynumber: 3.6 Consensus size: 44
56335442 TCACATTTAT
* *
56335452 CACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
*
56335496 CACTTATCACTTGTCACTGATCAGATAAATGTAGCTAAAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
* *
56335540 CACTTATCAATCGTCACTTGTCATTGATTAGATAAGTGTAGCTAAAGCTAC
1 CAC-T-T--A---TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
*
56335591 CACTTATCACTTGTTACTGATCAGA
1 CACTTATCACTTGTCACTGATCAGA
56335616 AGTACTCAAA
Statistics
Matches: 104, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
44 60 0.58
45 1 0.01
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 1 0.01
51 38 0.37
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (44 bp):
CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:56335557 original size:51 final size:51
Alignment explanation
Indices: 56335502--56335599 Score: 169
Period size: 51 Copynumber: 1.9 Consensus size: 51
56335492 CTACCACTTA
56335502 TCACTTGTCACTGATCAGATAAATGTAGCTAAAGCTACCACTTATCAATCG
1 TCACTTGTCACTGATCAGATAAATGTAGCTAAAGCTACCACTTATCAATCG
* * *
56335553 TCACTTGTCATTGATTAGATAAGTGTAGCTAAAGCTACCACTTATCA
1 TCACTTGTCACTGATCAGATAAATGTAGCTAAAGCTACCACTTATCA
56335600 CTTGTTACTG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (51 bp):
TCACTTGTCACTGATCAGATAAATGTAGCTAAAGCTACCACTTATCAATCG
Found at i:56351923 original size:33 final size:33
Alignment explanation
Indices: 56351881--56351945 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
56351871 AAAAACACTT
56351881 CTGGAGCAATGTATCCAGCAGTTCCTCTAGCAC
1 CTGGAGCAATGTATCCAGCAGTTCCTCTAGCAC
56351914 CTGGAGCAATGTATCCAGCAGTTCCTCTAGCA
1 CTGGAGCAATGTATCCAGCAGTTCCTCTAGCA
56351946 GTTCCTCAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.25
Consensus pattern (33 bp):
CTGGAGCAATGTATCCAGCAGTTCCTCTAGCAC
Found at i:56358942 original size:17 final size:17
Alignment explanation
Indices: 56358915--56358947 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
56358905 AAAGTTTAGG
56358915 GGGGAAATAAAAAGTTTT
1 GGGGAAAT-AAAAGTTTT
56358933 GGGG-AATAAAAGTTT
1 GGGGAAATAAAAGTTT
56358948 GAGGAAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.53
17 3 0.20
18 4 0.27
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.27
Consensus pattern (17 bp):
GGGGAAATAAAAGTTTT
Found at i:56365969 original size:16 final size:16
Alignment explanation
Indices: 56365950--56365980 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
56365940 CTATCTTCGT
56365950 TTTCATTTTCCTTCTC
1 TTTCATTTTCCTTCTC
56365966 TTTCATTTTCCTTCT
1 TTTCATTTTCCTTCT
56365981 ATCTTAAATG
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:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTCATTTTCCTTCTC
Found at i:56373978 original size:23 final size:21
Alignment explanation
Indices: 56373938--56374073 Score: 102
Period size: 21 Copynumber: 6.5 Consensus size: 21
56373928 TGGCCCATTT
* *
56373938 TTTTAATAAATAACAAAAAATTA
1 TTTTAA-AAATTA-AAAAAAGTA
56373961 TTTTAAAAATTAAAAAAAGTA
1 TTTTAAAAATTAAAAAAAGTA
***
56373982 TTTTAAAAA-TATTTTAAA--A
1 TTTTAAAAATTA-AAAAAAGTA
**
56374001 TTAAAAAAATTAAAAAAAGTA
1 TTTTAAAAATTAAAAAAAGTA
**
56374022 TTTTAAAAATATTTTAAAAA-TA
1 TTTT-AAAA-ATTAAAAAAAGTA
*
56374044 TTTT-AAAATTTAAAAAAGTA
1 TTTTAAAAATTAAAAAAAGTA
56374064 TTTTAAAAAT
1 TTTTAAAAAT
56374074 ATTTTAAAAT
Statistics
Matches: 90, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
19 20 0.22
20 13 0.14
21 28 0.31
22 15 0.17
23 14 0.16
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (21 bp):
TTTTAAAAATTAAAAAAAGTA
Found at i:56373994 original size:11 final size:11
Alignment explanation
Indices: 56373953--56374082 Score: 100
Period size: 11 Copynumber: 12.4 Consensus size: 11
56373943 ATAAATAACA
56373953 AAAAATTATTTT
1 AAAAA-TATTTT
**
56373965 -AAAA-ATTAA
1 AAAAATATTTT
56373974 AAAAAGTATTTT
1 AAAAA-TATTTT
56373986 AAAAATATTTT
1 AAAAATATTTT
56373997 --AAA-A--TT
1 AAAAATATTTT
* **
56374003 AAAAAAATTAA
1 AAAAATATTTT
56374014 AAAAAGTATTTT
1 AAAAA-TATTTT
56374026 AAAAATATTTT
1 AAAAATATTTT
56374037 AAAAATATTTT
1 AAAAATATTTT
*
56374048 --AAA-ATTTA
1 AAAAATATTTT
56374056 AAAAAGTATTTT
1 AAAAA-TATTTT
56374068 AAAAATATTTT
1 AAAAATATTTT
56374079 AAAA
1 AAAA
56374083 TTAAAAAATA
Statistics
Matches: 94, Mismatches: 11, Indels: 27
0.71 0.08 0.20
Matches are distributed among these distances:
6 2 0.02
8 8 0.09
9 10 0.11
10 7 0.07
11 42 0.45
12 25 0.27
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:56374069 original size:31 final size:30
Alignment explanation
Indices: 56374021--56374092 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 30
56374011 TAAAAAAAGT
*
56374021 ATTTTAAAAATATTTTAAAAATATTTTAAA
1 ATTTAAAAAATATTTTAAAAATATTTTAAA
56374051 ATTTAAAAAAGTATTTTAAAAATATTTTAAA
1 ATTTAAAAAA-TATTTTAAAAATATTTTAAA
56374082 A-TTAAAAAATA
1 ATTTAAAAAATA
56374093 AATATATTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
29 2 0.05
30 17 0.43
31 21 0.52
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (30 bp):
ATTTAAAAAATATTTTAAAAATATTTTAAA
Found at i:56395419 original size:52 final size:52
Alignment explanation
Indices: 56395362--56395467 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
56395352 AGAGTGAAGT
56395362 TAACATTATATACATATTTAAATCAATTATTTTTTATACACTTGCATCAAAC
1 TAACATTATATACATATTTAAATCAATTATTTTTTATACACTTGCATCAAAC
56395414 TAACATTATATACATATTTAAATCAATTATTTTTTATACACTTGCATCAAAC
1 TAACATTATATACATATTTAAATCAATTATTTTTTATACACTTGCATCAAAC
56395466 TA
1 TA
56395468 CACCTGAGTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.41, C:0.15, G:0.02, T:0.42
Consensus pattern (52 bp):
TAACATTATATACATATTTAAATCAATTATTTTTTATACACTTGCATCAAAC
Found at i:56395451 original size:26 final size:26
Alignment explanation
Indices: 56395370--56395453 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
56395360 GTTAACATTA
56395370 TATACATATTTAAATCAATTATTTTT
1 TATACATATTTAAATCAATTATTTTT
* ** * ** *
56395396 TATAC--ACTTGCATCAAACTAACATTA
1 TATACATATTTAAATC-AA-TTATTTTT
56395422 TATACATATTTAAATCAATTATTTTT
1 TATACATATTTAAATCAATTATTTTT
56395448 TATACA
1 TATACA
56395454 CTTGCATCAA
Statistics
Matches: 40, Mismatches: 14, Indels: 8
0.65 0.23 0.13
Matches are distributed among these distances:
24 6 0.15
25 2 0.05
26 24 0.60
27 2 0.05
28 6 0.15
ACGTcount: A:0.40, C:0.13, G:0.01, T:0.45
Consensus pattern (26 bp):
TATACATATTTAAATCAATTATTTTT
Found at i:56397109 original size:31 final size:29
Alignment explanation
Indices: 56397045--56397113 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
56397035 ATAATAATAT
** *
56397045 AAGTGACTAAAACGTAACATTTTAAACAT
1 AAGTGACTAAAACGTAACATGGTAAACAA
56397074 AAGTGACTAAAACGTAACATGAGGTAAACAA
1 AAGTGACTAAAACGTAACAT--GGTAAACAA
56397105 AAGTGACTA
1 AAGTGACTA
56397114 TTTTTGTAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 20 0.57
31 15 0.43
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAACGTAACATGGTAAACAA
Found at i:56430442 original size:45 final size:45
Alignment explanation
Indices: 56430387--56430477 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
56430377 ATTTATACAT
*
56430387 GCTTTTTTTCTCTTTATGTATTTGGAATTATGGATCTATTTGCCA
1 GCTTTTTTTCTCTTTATGGATTTGGAATTATGGATCTATTTGCCA
56430432 GCTTTTTTTCTCTTTATGGATTTGGAATTATGGATCTATTTGCCA
1 GCTTTTTTTCTCTTTATGGATTTGGAATTATGGATCTATTTGCCA
56430477 G
1 G
56430478 AATTCATAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.52
Consensus pattern (45 bp):
GCTTTTTTTCTCTTTATGGATTTGGAATTATGGATCTATTTGCCA
Found at i:56430875 original size:19 final size:19
Alignment explanation
Indices: 56430851--56430894 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
56430841 TTCAAACACT
*
56430851 AGAAAAGTAAATCATTTTC
1 AGAAAAATAAATCATTTTC
56430870 AGAAAAATAAATCATTTTC
1 AGAAAAATAAATCATTTTC
*
56430889 CGAAAA
1 AGAAAA
56430895 TCATTTTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.27
Consensus pattern (19 bp):
AGAAAAATAAATCATTTTC
Found at i:56436000 original size:11 final size:11
Alignment explanation
Indices: 56435984--56436008 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
56435974 TATGTTTTAA
56435984 AAAAATAAAAT
1 AAAAATAAAAT
56435995 AAAAATAAAAT
1 AAAAATAAAAT
56436006 AAA
1 AAA
56436009 GAACACACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:56436637 original size:7 final size:7
Alignment explanation
Indices: 56436625--56436665 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
56436615 TAAACAAAAA
56436625 AATTTTG
1 AATTTTG
56436632 AATTTTG
1 AATTTTG
56436639 AATTTTG
1 AATTTTG
*
56436646 AATTTTA
1 AATTTTG
*
56436653 AATTTTA
1 AATTTTG
56436660 AATTTT
1 AATTTT
56436666 ATAACAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (7 bp):
AATTTTG
Found at i:56444544 original size:40 final size:40
Alignment explanation
Indices: 56444461--56444680 Score: 268
Period size: 40 Copynumber: 5.5 Consensus size: 40
56444451 ACCCAAGTAT
** * *
56444461 CTTCGGGAT-TTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGG-TCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
56444499 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
56444539 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
56444579 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * *
56444619 CTTCGGATCTTAGTCCGGATATAGTCACTAGCATAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
56444659 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
56444681 CATTCGAATA
Statistics
Matches: 156, Mismatches: 21, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
37 1 0.01
38 11 0.07
39 16 0.10
40 127 0.81
41 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:56455591 original size:39 final size:39
Alignment explanation
Indices: 56455547--56455695 Score: 138
Period size: 39 Copynumber: 3.7 Consensus size: 39
56455537 TCATCACACA
56455547 AATTTAATTAGAGACTTAAAATATAATGTAACTTAATAT
1 AATTTAATTAGAGACTTAAAATATAATGTAACTTAATAT
** * * *
56455586 AATTTAATTAGAGGGTTCAACATAATTTAATTGTTAACTTAACAG
1 AATTTAATTAGAGACTT--A-A-AATATAA-TG-TAACTTAATAT
* * * *
56455631 AATTTACTTAGAGATTTAAAATATAATTTAACTTACTAT
1 AATTTAATTAGAGACTTAAAATATAATGTAACTTAATAT
* *
56455670 AATTTATTTAAAGACTT-AAATATAAT
1 AATTTAATTAGAGACTTAAAATATAAT
56455696 TTCAAACAAC
Statistics
Matches: 88, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
38 9 0.10
39 37 0.42
40 1 0.01
41 7 0.08
42 2 0.02
43 7 0.08
44 2 0.02
45 23 0.26
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (39 bp):
AATTTAATTAGAGACTTAAAATATAATGTAACTTAATAT
Found at i:56459984 original size:60 final size:60
Alignment explanation
Indices: 56459916--56460159 Score: 479
Period size: 60 Copynumber: 4.1 Consensus size: 60
56459906 ACTAAACGGT
56459916 GGGAAGGAGTTTAAATGAAATTCAAACTGTGCTAAGGGCTAAAATTAAGGAGCAAAATAA
1 GGGAAGGAGTTTAAATGAAATTCAAACTGTGCTAAGGGCTAAAATTAAGGAGCAAAATAA
56459976 GGGAAGGAGTTTAAATGAAATTCAAACTGTGCTAAGGGCTAAAATTAAGGAGCAAAATAA
1 GGGAAGGAGTTTAAATGAAATTCAAACTGTGCTAAGGGCTAAAATTAAGGAGCAAAATAA
56460036 GGGAAGGAGTTTAAATGAAATTCAAACTGTGCTAAGGGCTAAAATTAAGGAGCAAAATAA
1 GGGAAGGAGTTTAAATGAAATTCAAACTGTGCTAAGGGCTAAAATTAAGGAGCAAAATAA
*
56460096 GGGAAGGAGTTTAAATGAAATTCAAACTGTGCTAAGGGCTAAAATTAAGGAGCAAAACAA
1 GGGAAGGAGTTTAAATGAAATTCAAACTGTGCTAAGGGCTAAAATTAAGGAGCAAAATAA
56460156 GGGA
1 GGGA
56460160 TTCGAATATA
Statistics
Matches: 183, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 183 1.00
ACGTcount: A:0.45, C:0.09, G:0.26, T:0.21
Consensus pattern (60 bp):
GGGAAGGAGTTTAAATGAAATTCAAACTGTGCTAAGGGCTAAAATTAAGGAGCAAAATAA
Found at i:56463250 original size:92 final size:92
Alignment explanation
Indices: 56463093--56463278 Score: 354
Period size: 92 Copynumber: 2.0 Consensus size: 92
56463083 ATTTATCTTG
* *
56463093 ATCTAGATAGGTAATTTCATTCAATTAAATACTTTAGTATTCAATTTAATCCACATTTCATATTT
1 ATCTAAATACGTAATTTCATTCAATTAAATACTTTAGTATTCAATTTAATCCACATTTCATATTT
56463158 ATGAAAAATTACAAATTCACCCCTAAC
66 ATGAAAAATTACAAATTCACCCCTAAC
56463185 ATCTAAATACGTAATTTCATTCAATTAAATACTTTAGTATTCAATTTAATCCACATTTCATATTT
1 ATCTAAATACGTAATTTCATTCAATTAAATACTTTAGTATTCAATTTAATCCACATTTCATATTT
56463250 ATGAAAAATTACAAATTCACCCCTAAC
66 ATGAAAAATTACAAATTCACCCCTAAC
56463277 AT
1 AT
56463279 TTTAACTTTT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (92 bp):
ATCTAAATACGTAATTTCATTCAATTAAATACTTTAGTATTCAATTTAATCCACATTTCATATTT
ATGAAAAATTACAAATTCACCCCTAAC
Found at i:56467249 original size:30 final size:30
Alignment explanation
Indices: 56467215--56467274 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
56467205 ATTTAATACG
56467215 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
56467245 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
56467275 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:56473749 original size:46 final size:46
Alignment explanation
Indices: 56473597--56473865 Score: 161
Period size: 46 Copynumber: 5.7 Consensus size: 46
56473587 ACACTTGTGT
* * * **
56473597 GAGCTAGTGTAAGACATGACTGGGACATGCATCGGCCACATTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATGA
* * * ** *
56473643 GAGCCAATGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGACGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCAAGATGA
* ** * *
56473691 GTGTTAGAGTAAGACATGTCTGAGACATGCATCGGCCTCAAGATGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATG-A
* * *
56473738 -AGCCAGTGTAAGACATGTCTGGGACATGTATC-GACT-ACGA-GA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATGA
* ** * *
56473780 TGTGTTAGTGTAAGACCATGTTTGGGACATGGCATCGG-CACAAGTATGATA
1 -GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCAAG-ATG--A
** *
56473831 GAGCTTGTGTAAGACCATGTCTAGGACATGACATC
1 GAGCCAGTGTAAGA-CATGTCTGGGACATG-CATC
56473866 AGCACCTGAC
Statistics
Matches: 167, Mismatches: 42, Indels: 24
0.72 0.18 0.10
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 13 0.08
45 16 0.10
46 56 0.34
47 28 0.17
48 21 0.13
49 2 0.01
50 28 0.17
51 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATGA
Found at i:56482587 original size:39 final size:40
Alignment explanation
Indices: 56482375--56482591 Score: 350
Period size: 40 Copynumber: 5.5 Consensus size: 40
56482365 CAGATGATAA
56482375 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
56482415 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
56482455 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
56482495 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
56482535 CCGGGCT-AGTCCCGAAGACATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
56482574 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
56482592 TACTTGGTTT
Statistics
Matches: 168, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
38 5 0.03
39 37 0.22
40 126 0.75
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:56492891 original size:16 final size:16
Alignment explanation
Indices: 56492872--56492902 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56492862 CCCCAGGCAA
56492872 AATATTTACAATTTAC
1 AATATTTACAATTTAC
*
56492888 AATATTTATAATTTA
1 AATATTTACAATTTA
56492903 GTTCTAAGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATTTACAATTTAC
Found at i:56502531 original size:100 final size:101
Alignment explanation
Indices: 56502357--56502537 Score: 267
Period size: 100 Copynumber: 1.8 Consensus size: 101
56502347 TATTCACGAC
*
56502357 AGGTTTTAAACATTTATTATTAATCATTCTTGAAACTAACTATTATCACGATGAAGGCAAGTGTA
1 AGGTTTTAAACATTTATAATTAATCATTCTTGAAACTAACTATTATCACGATGAAGGCAAGTGTA
56502422 CCTATCGAACAGTAGTTGAGCGCGAGATTTTGTGAT
66 CCTATCGAACAGTAGTTGAGCGCGAGATTTTGTGAT
* * * * ***
56502458 AGGTTTTCAATATTTATAATTACTCTTTCTTG-AACTAACTATTATTGTGATGTAA-GCAAGTGT
1 AGGTTTTAAACATTTATAATTAATCATTCTTGAAACTAACTATTATCACGATG-AAGGCAAGTGT
56502521 ACCTATCGAACAGTAGT
65 ACCTATCGAACAGTAGT
56502538 ATAGTTTTAG
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
100 42 0.59
101 29 0.41
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (101 bp):
AGGTTTTAAACATTTATAATTAATCATTCTTGAAACTAACTATTATCACGATGAAGGCAAGTGTA
CCTATCGAACAGTAGTTGAGCGCGAGATTTTGTGAT
Found at i:56506266 original size:27 final size:27
Alignment explanation
Indices: 56506201--56506287 Score: 88
Period size: 27 Copynumber: 3.2 Consensus size: 27
56506191 GTGACGAAGT
* * *
56506201 CACCAGATAAAGAT-ATTATGGTAGAGC
1 CACCAGA-ACAGATAATTGTGGCAGAGC
56506228 CACCAGAACAGAT-ATATGTGGCAGAGC
1 CACCAGAACAGATAAT-TGTGGCAGAGC
* * *
56506255 CACCGGATCAGATAATTGTGGCATAGC
1 CACCAGAACAGATAATTGTGGCAGAGC
56506282 CACCAG
1 CACCAG
56506288 GACACAGGAC
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
26 7 0.14
27 42 0.82
28 2 0.04
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
CACCAGAACAGATAATTGTGGCAGAGC
Found at i:56519916 original size:41 final size:41
Alignment explanation
Indices: 56519867--56519979 Score: 181
Period size: 41 Copynumber: 2.8 Consensus size: 41
56519857 CGGCATTTTA
56519867 TAGCGGCGCTTTTGGCAAAACGCCGCTAAAAACCAGAGCAT
1 TAGCGGCGCTTTTGGCAAAACGCCGCTAAAAACCAGAGCAT
* *
56519908 TAGTGGCGCTTTTGGAAAAACGCCGCTAAAAACCAGAGCAT
1 TAGCGGCGCTTTTGGCAAAACGCCGCTAAAAACCAGAGCAT
* * *
56519949 TAGCGGCGCTTTCGACAAAACGCCACTAAAA
1 TAGCGGCGCTTTTGGCAAAACGCCGCTAAAA
56519980 GTCATATAAC
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 65 1.00
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.18
Consensus pattern (41 bp):
TAGCGGCGCTTTTGGCAAAACGCCGCTAAAAACCAGAGCAT
Found at i:56520142 original size:25 final size:25
Alignment explanation
Indices: 56520108--56520157 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
56520098 AGAGATAGTA
56520108 TTGAATTTAAAATATCGAATTAATT
1 TTGAATTTAAAATATCGAATTAATT
56520133 TTGAATTTAAAATATCGAATTAATT
1 TTGAATTTAAAATATCGAATTAATT
56520158 ATCATTATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (25 bp):
TTGAATTTAAAATATCGAATTAATT
Found at i:56521752 original size:201 final size:201
Alignment explanation
Indices: 56521407--56521809 Score: 788
Period size: 201 Copynumber: 2.0 Consensus size: 201
56521397 ATTCAGTTTC
*
56521407 TGATAAAAATTGGCTGAATATTATGAGGCTGCTGCTTTATAGGTGTTCGAGAAGAAGTCCAACAG
1 TGATAAAAATTGGCTGAAGATTATGAGGCTGCTGCTTTATAGGTGTTCGAGAAGAAGTCCAACAG
56521472 GAAAATAATGGGGGTATGTATATCTGATTCTAACATTAATTTTATTTGAATGAGGGGATACTATT
66 GAAAATAATGGGGGTATGTATATCTGATTCTAACATTAATTTTATTTGAATGAGGGGATACTATT
56521537 ACGTAGATATAACTGCTTGGAGACACGATATGTTTGCAAGTAGAGACACAATATAACTGCATAAT
131 ACGTAGATATAACTGCTTGGAGACACGATATGTTTGCAAGTAGAGACACAATATAACTGCATAAT
56521602 TTGGCT
196 TTGGCT
56521608 TGATAAAAATTGGCTGAAGATTATGAGGCTGCTGCTTTATAGGTGTTCGAGAAGAAGTCCAACAG
1 TGATAAAAATTGGCTGAAGATTATGAGGCTGCTGCTTTATAGGTGTTCGAGAAGAAGTCCAACAG
56521673 GAAAATAATGGGGGTATGTATATCTGATTCTAACATTAATTTTATTTGAATGAGGGGATACTATT
66 GAAAATAATGGGGGTATGTATATCTGATTCTAACATTAATTTTATTTGAATGAGGGGATACTATT
*
56521738 ACGTAGATATAACTGCTTGGAGACACGATATGTTTGCAAGTGGAGACACAATATAACTGCATAAT
131 ACGTAGATATAACTGCTTGGAGACACGATATGTTTGCAAGTAGAGACACAATATAACTGCATAAT
56521803 TTGGCT
196 TTGGCT
56521809 T
1 T
56521810 TTCTGACAAA
Statistics
Matches: 200, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
201 200 1.00
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.32
Consensus pattern (201 bp):
TGATAAAAATTGGCTGAAGATTATGAGGCTGCTGCTTTATAGGTGTTCGAGAAGAAGTCCAACAG
GAAAATAATGGGGGTATGTATATCTGATTCTAACATTAATTTTATTTGAATGAGGGGATACTATT
ACGTAGATATAACTGCTTGGAGACACGATATGTTTGCAAGTAGAGACACAATATAACTGCATAAT
TTGGCT
Found at i:56524042 original size:17 final size:18
Alignment explanation
Indices: 56524020--56524053 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
56524010 TACATGTGGG
56524020 GGAATATGGAG-TCAACT
1 GGAATATGGAGTTCAACT
56524037 GGAATATGGAGTTCAAC
1 GGAATATGGAGTTCAAC
56524054 ATTTTGGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.24
Consensus pattern (18 bp):
GGAATATGGAGTTCAACT
Found at i:56524437 original size:43 final size:43
Alignment explanation
Indices: 56524376--56524603 Score: 244
Period size: 43 Copynumber: 5.3 Consensus size: 43
56524366 GATCATTATT
* * * * * *
56524376 TTTAGCGGCATCTGTGAAAAAAGCGCTGCTAAAGGTTATGATC
1 TTTAGCGGCGTTTTTGAAAAAAGCGCCGCTAAAGGTCATGGTC
*
56524419 TTTAGCGGCGTTTTTGAAAAAAGCGTCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTTTGAAAAAAGCGCCGCTAAAGGTCATGGTC
** * *
56524462 TTTAGCGGCGTTTACGAAAAAAGCGCCACTAAAGGTCATGGTT
1 TTTAGCGGCGTTTTTGAAAAAAGCGCCGCTAAAGGTCATGGTC
* * * * *
56524505 TTTAGCGGTGTTTTT--TAAAAGCGCCACTAAAAGTCCTGGTC
1 TTTAGCGGCGTTTTTGAAAAAAGCGCCGCTAAAGGTCATGGTC
* * ** *
56524546 TTTAGCAGCATTTGCGAAAAAAGCGCCGCTAAAGTTCATGGTC
1 TTTAGCGGCGTTTTTGAAAAAAGCGCCGCTAAAGGTCATGGTC
*
56524589 TTTAGCGGCCTTTTT
1 TTTAGCGGCGTTTTT
56524604 TTCAAAAAAA
Statistics
Matches: 150, Mismatches: 33, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
41 32 0.21
43 118 0.79
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTTTGAAAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:56524569 original size:84 final size:85
Alignment explanation
Indices: 56524376--56524603 Score: 278
Period size: 84 Copynumber: 2.7 Consensus size: 85
56524366 GATCATTATT
* * * * *
56524376 TTTAGCGGCATCTGTGAAAAAAGCGCTGCTAAAGGTTATGATCTTTAGCGGCGTTTTTGAAAAAA
1 TTTAGCGGCATTTGCGAAAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTTT-AAAAAA
* * *
56524441 GCGTCGCTAAAGGTCATGGTC
65 GCGCCACTAAAAGTCATGGTC
* * * * * *
56524462 TTTAGCGGCGTTTACGAAAAAAGCGCCACTAAAGGTCATGGTTTTTAGCGGTGTTTTT-TAAAAG
1 TTTAGCGGCATTTGCGAAAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTTTAAAAAAG
*
56524526 CGCCACTAAAAGTCCTGGTC
66 CGCCACTAAAAGTCATGGTC
* * *
56524546 TTTAGCAGCATTTGCGAAAAAAGCGCCGCTAAAGTTCATGGTCTTTAGCGGCCTTTTT
1 TTTAGCGGCATTTGCGAAAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTTT
56524604 TTCAAAAAAA
Statistics
Matches: 119, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
84 71 0.60
86 48 0.40
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (85 bp):
TTTAGCGGCATTTGCGAAAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTTTAAAAAAG
CGCCACTAAAAGTCATGGTC
Found at i:56530305 original size:20 final size:20
Alignment explanation
Indices: 56530263--56530316 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
56530253 TCTCGCAATT
*
56530263 TTTATA-TTTTTAATTTCAT
1 TTTATATTTTTTAATTTCAC
56530282 TTTATATTTTTTAATTT-AGC
1 TTTATATTTTTTAATTTCA-C
*
56530302 TTTA-ATGTTTTAATT
1 TTTATATTTTTTAATT
56530317 CTGTTTCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTATATTTTTTAATTTCAC
Found at i:56530936 original size:20 final size:19
Alignment explanation
Indices: 56530886--56530937 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
56530876 CATATGCAAA
56530886 ATATTTATTATTTTATATT
1 ATATTTATTATTTTATATT
*
56530905 ATATTTCCTTATTTT-TATT
1 ATATTT-ATTATTTTATATT
56530924 CATATTATATTATT
1 -ATATT-TATTATT
56530938 ATACATAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 10 0.36
20 17 0.61
21 1 0.04
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (19 bp):
ATATTTATTATTTTATATT
Done.