Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 179 of 292
Found at i:53425666 original size:19 final size:20
Alignment explanation
Indices: 53425642--53425679 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
53425632 GGTACCACCA
53425642 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
53425661 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
53425680 ACTACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:53426018 original size:93 final size:93
Alignment explanation
Indices: 53425908--53426078 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
53425898 GCCCCTAAGT
* *
53425908 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
53425973 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * * *
53426001 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTTAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
53426066 CGAGTTCGGATGC
66 CGAGTTCGGATGC
53426079 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:53426075 original size:46 final size:46
Alignment explanation
Indices: 53425903--53426075 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
53425893 AACCCGCCCC
* * * *
53425903 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
53425949 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
53425997 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
*
53426042 TAAGTGAACTCGGACTCAACTTAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
53426076 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 59 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:53426531 original size:30 final size:30
Alignment explanation
Indices: 53426497--53426556 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
53426487 ATTTAATACG
53426497 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
53426527 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
53426557 GGCTCAGGAA
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:53429233 original size:28 final size:27
Alignment explanation
Indices: 53429170--53429239 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
53429160 ATAGTGAGTC
*
53429170 CGCACACTTAGTGCTATATAATTAACT
1 CGCACACTTAGTGCTATATAATAAACT
53429197 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAAT-AAACT
53429225 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
53429240 GTACAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATAAACT
Found at i:53436349 original size:19 final size:20
Alignment explanation
Indices: 53436325--53436362 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
53436315 GGTACCACCA
53436325 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
53436344 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
53436363 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:53436641 original size:30 final size:30
Alignment explanation
Indices: 53436607--53436666 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
53436597 ATTTAATACG
*
53436607 AACTTTGGA-AAAATTACACTTTTTCCCCTA
1 AACTTT-GACAAAATTACACTTTTGCCCCTA
* *
53436637 AACTTTTACATAATTACACTTTTGCCCCTA
1 AACTTTGACAAAATTACACTTTTGCCCCTA
53436667 GGCTCGGGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (30 bp):
AACTTTGACAAAATTACACTTTTGCCCCTA
Found at i:53438824 original size:44 final size:44
Alignment explanation
Indices: 53438775--53438865 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 44
53438765 GTAGGTTAAA
* * *
53438775 TAATATTAAAATATCCTATATTAATCAAATTTTAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAAATTTTAAGTGGGAAAC
*
53438819 TAATATTAAAATAACCTACACTAATCAGATTTTAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAAATTTTAAGTGGGAAAC
53438863 TAA
1 TAA
53438866 AAACAGAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAAATTTTAAGTGGGAAAC
Found at i:53448402 original size:34 final size:34
Alignment explanation
Indices: 53448364--53448432 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
53448354 TAGCTAAAAC
*
53448364 TCTCTAACACACCACATATACATATCCTGATGAA
1 TCTCTAACACACCACACATACATATCCTGATGAA
*
53448398 TCTCTAACACACCATACATACATATCCTGATGAA
1 TCTCTAACACACCACACATACATATCCTGATGAA
53448432 T
1 T
53448433 GGAGCTTAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.38, C:0.29, G:0.06, T:0.28
Consensus pattern (34 bp):
TCTCTAACACACCACACATACATATCCTGATGAA
Found at i:53448687 original size:19 final size:18
Alignment explanation
Indices: 53448663--53448705 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
53448653 TTCAGAACAA
53448663 TCATTTA-TCAAATATCAT
1 TCATTTAGT-AAATATCAT
53448681 CTCATTTTAGTAAATATCAT
1 -TCA-TTTAGTAAATATCAT
53448701 TCATT
1 TCATT
53448706 CATATTCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.09
19 6 0.27
20 13 0.59
21 1 0.05
ACGTcount: A:0.35, C:0.16, G:0.02, T:0.47
Consensus pattern (18 bp):
TCATTTAGTAAATATCAT
Found at i:53450169 original size:23 final size:23
Alignment explanation
Indices: 53450139--53450272 Score: 114
Period size: 23 Copynumber: 5.8 Consensus size: 23
53450129 CTGATGAACA
*
53450139 ATAAGCTCTATTGAGCTGAAAAG
1 ATAAGCTCTATCGAGCTGAAAAG
* *
53450162 ATAAGCTCTATCGAGTTGAAACG
1 ATAAGCTCTATCGAGCTGAAAAG
* *
53450185 ATAAGCTCTATCGAGTTGAACAG
1 ATAAGCTCTATCGAGCTGAAAAG
* *
53450208 -TAAGCTC-ACACGAGCTGAAACG
1 ATAAGCTCTA-TCGAGCTGAAAAG
* * *
53450230 GTAAGCTCCAAT-GAGCTGAAAAC
1 ATAAGCT-CTATCGAGCTGAAAAG
53450253 AGTAAGCTCTTAT-GAGCTGA
1 A-TAAGCTC-TATCGAGCTGA
53450273 TATATCGATA
Statistics
Matches: 91, Mismatches: 14, Indels: 11
0.78 0.12 0.09
Matches are distributed among these distances:
21 1 0.01
22 16 0.18
23 57 0.63
24 16 0.18
25 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (23 bp):
ATAAGCTCTATCGAGCTGAAAAG
Found at i:53450227 original size:45 final size:46
Alignment explanation
Indices: 53450139--53450297 Score: 137
Period size: 45 Copynumber: 3.4 Consensus size: 46
53450129 CTGATGAACA
* * *
53450139 ATAAGCTCTATTGAGCTGAAAAGATAAGCTCTATCGAGTTGAAACG
1 ATAAGCTCTATCGAGCTGAAAAGATAAGCTCTAACGAGCTGAAACG
* *
53450185 ATAAGCTCTATCGAGTTGAACAG-TAAGCTC-ACACGAGCTGAAACG
1 ATAAGCTCTATCGAGCTGAAAAGATAAGCTCTA-ACGAGCTGAAACG
* * * * *
53450230 GTAAGCTCCAAT-GAGCTGAAAACAGTAAGCTCTTATGAGCTGATATATCG
1 ATAAGCT-CTATCGAGCTGAAAAGA-TAAGCTCTAACGAGCTGA-A-A-CG
53450280 ATAAGCT-TATTCGAGCTG
1 ATAAGCTCTA-TCGAGCTG
53450298 TTGTGAGTCC
Statistics
Matches: 89, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
44 1 0.01
45 32 0.36
46 23 0.26
47 15 0.17
48 2 0.02
49 2 0.02
50 14 0.16
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (46 bp):
ATAAGCTCTATCGAGCTGAAAAGATAAGCTCTAACGAGCTGAAACG
Found at i:53450257 original size:24 final size:24
Alignment explanation
Indices: 53450203--53450272 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
53450193 TATCGAGTTG
*
53450203 AACAGTAAGCT-CACACGAGCTG-A
1 AACAGTAAGCTCCA-ATGAGCTGAA
*
53450226 AACGGTAAGCTCCAATGAGCTGAA
1 AACAGTAAGCTCCAATGAGCTGAA
**
53450250 AACAGTAAGCTCTTATGAGCTGA
1 AACAGTAAGCTCCAATGAGCTGA
53450273 TATATCGATA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
23 17 0.43
24 23 0.57
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (24 bp):
AACAGTAAGCTCCAATGAGCTGAA
Found at i:53451849 original size:42 final size:43
Alignment explanation
Indices: 53451788--53451870 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 43
53451778 TATGATTTAC
* *
53451788 GTGTAAGACCATGTTTGGGACA-TCGACATC-ATATTTGATTCT
1 GTGTAAGACCATATCTGGGACAGT-GACATCGATATTTGATTCT
* *
53451830 GTGTAAGACCCTATCTGGGACAGTGGCATCGATATTTGATT
1 GTGTAAGACCATATCTGGGACAGTGACATCGATATTTGATT
53451871 AAATGTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 24 0.69
43 11 0.31
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (43 bp):
GTGTAAGACCATATCTGGGACAGTGACATCGATATTTGATTCT
Found at i:53454641 original size:8 final size:8
Alignment explanation
Indices: 53454625--53454664 Score: 71
Period size: 8 Copynumber: 5.0 Consensus size: 8
53454615 CTCATATATG
*
53454625 TTCATAAT
1 TTCACAAT
53454633 TTCACAAT
1 TTCACAAT
53454641 TTCACAAT
1 TTCACAAT
53454649 TTCACAAT
1 TTCACAAT
53454657 TTCACAAT
1 TTCACAAT
53454665 CATACATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (8 bp):
TTCACAAT
Found at i:53463235 original size:21 final size:22
Alignment explanation
Indices: 53463205--53463266 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
53463195 ATTTTGTTTT
53463205 ATTATATTTAAAAAA-ATTAAA
1 ATTATATTTAAAAAATATTAAA
*
53463226 ATTATTTTTAAAAAATATT--A
1 ATTATATTTAAAAAATATTAAA
*
53463246 TTTCACTATTTAAAAAATATT
1 ATT-A-TATTTAAAAAATATT
53463267 GTTCTATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 3 0.09
21 15 0.43
22 17 0.49
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTATATTTAAAAAATATTAAA
Found at i:53463273 original size:19 final size:21
Alignment explanation
Indices: 53463232--53463274 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
53463222 TAAAATTATT
*
53463232 TTTAAAAAATATTATTTCACTA
1 TTTAAAAAATATTAGTT-ACTA
53463254 TTTAAAAAATATT-GTT-CTA
1 TTTAAAAAATATTAGTTACTA
53463273 TT
1 TT
53463275 AATTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
21 2 0.10
22 13 0.65
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTAAAAAATATTAGTTACTA
Found at i:53467382 original size:3 final size:3
Alignment explanation
Indices: 53467374--53467517 Score: 222
Period size: 3 Copynumber: 48.3 Consensus size: 3
53467364 TACTTATACG
*
53467374 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
53467422 -AA TTAA TCA TT- TT- TTCA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
53467466 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
53467514 TTA T
1 TTA T
53467518 GTTTCTTTAA
Statistics
Matches: 132, Mismatches: 5, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
2 5 0.04
3 123 0.93
4 4 0.03
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:53467589 original size:17 final size:18
Alignment explanation
Indices: 53467547--53467589 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
53467537 ACCTAAAATT
*
53467547 TTTATATACATTTATTTTA
1 TTTATAT-CATTTATTCTA
53467566 TTT-TATCATTTA-TCTA
1 TTTATATCATTTATTCTA
53467582 TTTATATC
1 TTTATATC
53467590 CTTTTATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 6 0.27
17 10 0.45
18 3 0.14
19 3 0.14
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATATCATTTATTCTA
Found at i:53469386 original size:9 final size:9
Alignment explanation
Indices: 53469372--53469396 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
53469362 TGAAAAAAAT
53469372 ATGGGATCA
1 ATGGGATCA
53469381 ATGGGATCA
1 ATGGGATCA
53469390 ATGGGAT
1 ATGGGAT
53469397 GACGAGATCA
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:0.32, C:0.08, G:0.36, T:0.24
Consensus pattern (9 bp):
ATGGGATCA
Found at i:53479822 original size:45 final size:43
Alignment explanation
Indices: 53479755--53479970 Score: 200
Period size: 45 Copynumber: 4.9 Consensus size: 43
53479745 ACAAATTACA
* *
53479755 AATCTTATCTCTCTGAAGTTGCAGTGGAGTAGATTGAAGATAGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-C
* * *
53479799 AGACCTTATCTCCCTGAAGTTGCAGTGGAGCATATTGAAGTTAC
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAC
* * * * *
53479843 AAGTCTTATCTCCCTAAAATTACAGTGGAGCAGACTGAATATAGC
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-C
* * * * * ** *
53479888 GAATCTTATCTCTCTAAATTTGTAATAAAGCAGATTGAAGCTAC
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAC
*
53479932 TAATCTTAT-TCCTTGAAGTTGCAGTGGAGCAGATTGAAG
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG
53479971 CAACAAATCC
Statistics
Matches: 136, Mismatches: 32, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
43 23 0.17
44 44 0.32
45 67 0.49
46 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAC
Found at i:53479844 original size:96 final size:96
Alignment explanation
Indices: 53479651--53479827 Score: 230
Period size: 96 Copynumber: 1.8 Consensus size: 96
53479641 GGGCAGGTTG
* * * *
53479651 AAATTACAAGTCTTATCTCCTTGAAGTTGCAGCGGAGCAAACTGAAGATAGTAAATCTCATTTCA
1 AAATTACAAATCTTATCTCCTTGAAGTTGCAGCGGAGCAAACTGAAGATAGCAAACCTCATCTCA
*
53479716 TTGAAGTTGCAGTGGAACAGATTAAAGCTAC
66 CTGAAGTTGCAGTGGAACAGATTAAAGCTAC
* * * * * *
53479747 AAATTACAAATCTTATCT-CTCTGAAGTTGCAGTGGAGTAGATTGAAGATAGCAGACCTTATCTC
1 AAATTACAAATCTTATCTCCT-TGAAGTTGCAGCGGAGCAAACTGAAGATAGCAAACCTCATCTC
*
53479811 CCTGAAGTTGCAGTGGA
65 ACTGAAGTTGCAGTGGA
53479828 GCATATTGAA
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
95 2 0.03
96 66 0.97
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (96 bp):
AAATTACAAATCTTATCTCCTTGAAGTTGCAGCGGAGCAAACTGAAGATAGCAAACCTCATCTCA
CTGAAGTTGCAGTGGAACAGATTAAAGCTAC
Found at i:53480395 original size:16 final size:16
Alignment explanation
Indices: 53480374--53480408 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
53480364 CAAAGCCAAA
*
53480374 AAACCAGACCCAAAGT
1 AAACCAGACCCAAACT
*
53480390 AAACCAGGCCCAAACT
1 AAACCAGACCCAAACT
53480406 AAA
1 AAA
53480409 ACATTTTCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.31, G:0.11, T:0.06
Consensus pattern (16 bp):
AAACCAGACCCAAACT
Found at i:53481316 original size:3 final size:3
Alignment explanation
Indices: 53481308--53481371 Score: 71
Period size: 3 Copynumber: 21.3 Consensus size: 3
53481298 TTTTGCTACT
*
53481308 TTA TTA TTA -AA TTA GTTA TTA TTA TTA TTA TTA -TA TTTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
53481353 TTA -TA TTTA TTA TTA TTA T
1 TTA TTA -TTA TTA TTA TTA T
53481372 ATTTCTTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
2 5 0.09
3 41 0.77
4 7 0.13
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:53481371 original size:15 final size:15
Alignment explanation
Indices: 53481329--53481375 Score: 94
Period size: 15 Copynumber: 3.1 Consensus size: 15
53481319 TTAGTTATTA
53481329 TTATTATTATTATAT
1 TTATTATTATTATAT
53481344 TTATTATTATTATAT
1 TTATTATTATTATAT
53481359 TTATTATTATTATAT
1 TTATTATTATTATAT
53481374 TT
1 TT
53481376 CTTTTTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATTATTATTATAT
Found at i:53485182 original size:19 final size:19
Alignment explanation
Indices: 53485158--53485196 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
53485148 GTTAGGAATA
53485158 TCTACATCTAACTCTGATC
1 TCTACATCTAACTCTGATC
*
53485177 TCTACATCTGACTCTGATC
1 TCTACATCTAACTCTGATC
53485196 T
1 T
53485197 GTTCTGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (19 bp):
TCTACATCTAACTCTGATC
Found at i:53490005 original size:20 final size:20
Alignment explanation
Indices: 53489977--53490023 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
53489967 CAGCGTTGAC
53489977 CACGGGCTGGAGTAATCTCA
1 CACGGGCTGGAGTAATCTCA
*
53489997 CATGGGCTGGAGTAATCTCA
1 CACGGGCTGGAGTAATCTCA
53490017 CACGGGC
1 CACGGGC
53490024 GTGTCCCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.26, G:0.32, T:0.19
Consensus pattern (20 bp):
CACGGGCTGGAGTAATCTCA
Found at i:53490407 original size:14 final size:14
Alignment explanation
Indices: 53490388--53490415 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53490378 ATACTTGACT
53490388 TGTTCTTAATTATG
1 TGTTCTTAATTATG
53490402 TGTTCTTAATTATG
1 TGTTCTTAATTATG
53490416 ACTTGTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.57
Consensus pattern (14 bp):
TGTTCTTAATTATG
Found at i:53497823 original size:29 final size:28
Alignment explanation
Indices: 53497757--53497825 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 28
53497747 TTATTATTTG
* *
53497757 AGACTGTATCTG-AATGGGATTAGGCCC
1 AGACTGTATATGTAATGGGATCAGGCCC
* *
53497784 AAACTGAATATGTAATGGGCA-CAGGCCCC
1 AGACTGTATATGTAATGGG-ATCAGG-CCC
53497813 AGACTGTATATGT
1 AGACTGTATATGT
53497826 TTGATTCTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 9 0.27
28 9 0.27
29 15 0.45
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (28 bp):
AGACTGTATATGTAATGGGATCAGGCCC
Found at i:53501462 original size:23 final size:23
Alignment explanation
Indices: 53501436--53501481 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
53501426 TATGTATATG
*
53501436 AACCAAGAAATACATTGAAATAA
1 AACCAACAAATACATTGAAATAA
* *
53501459 AACCGACCAATACATTGAAATAA
1 AACCAACAAATACATTGAAATAA
53501482 GGAAAGTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.57, C:0.17, G:0.09, T:0.17
Consensus pattern (23 bp):
AACCAACAAATACATTGAAATAA
Found at i:53503364 original size:5 final size:5
Alignment explanation
Indices: 53503347--53503383 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
53503337 TCTAAGATTT
53503347 TATTA TA-TA TATTA TATTA TATTA TATTA TATTA TAT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT
53503384 AATTGATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:53503399 original size:13 final size:12
Alignment explanation
Indices: 53503356--53503409 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
53503346 TTATTATATA
53503356 TATTAT-ATTA-
1 TATTATAATTAT
*
53503366 TATTATATTATAT
1 TATTATAAT-TAT
53503379 TA-TATAATTGAT
1 TATTATAATT-AT
53503391 TATTATAATTAT
1 TATTATAATTAT
53503403 TAATTAT
1 T-ATTAT
53503410 TATGGTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
10 6 0.17
11 2 0.06
12 14 0.39
13 14 0.39
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (12 bp):
TATTATAATTAT
Found at i:53503903 original size:24 final size:23
Alignment explanation
Indices: 53503863--53503907 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
53503853 ATTTATTTAC
53503863 TTATTATTTAAGAAATAATAATTA
1 TTATTATTTAAGAAAT-ATAATTA
*
53503887 TTATTA-TTAAGTTAATATAAT
1 TTATTATTTAAG-AAATATAAT
53503908 AATATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
TTATTATTTAAGAAATATAATTA
Found at i:53505017 original size:12 final size:12
Alignment explanation
Indices: 53505000--53505024 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53504990 GCCGACTACT
53505000 GTTACTGTTACC
1 GTTACTGTTACC
53505012 GTTACTGTTACC
1 GTTACTGTTACC
53505024 G
1 G
53505025 ATTCGACACT
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:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:53505052 original size:45 final size:45
Alignment explanation
Indices: 53505002--53505097 Score: 131
Period size: 45 Copynumber: 2.1 Consensus size: 45
53504992 CGACTACTGT
*
53505002 TACTGTTACCGTTACTGTTACCGATTC-GACACTTTGGGTGTCGAA
1 TACTGTTACCGTTACTGTTACAGATTCAG-CACTTTGGGTGTCGAA
* * * *
53505047 TACTGTTACTGTTACTGTTACAGATTCAGCATTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGGGTGTCGAA
53505092 TACTGT
1 TACTGT
53505098 CACTGATTAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
45 44 0.98
46 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGGGTGTCGAA
Found at i:53514688 original size:25 final size:24
Alignment explanation
Indices: 53514582--53514702 Score: 165
Period size: 24 Copynumber: 5.0 Consensus size: 24
53514572 GCTTTATCAT
*
53514582 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
53514607 ATAACTAGGGCA-AAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
53514630 ATAAATGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
53514654 ATAACTGGGGCATAAGCCCTTTATC
1 ATAACTGGGGCATAAGCCCTTT-TA
53514679 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
53514703 CACTTCCTCC
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
23 16 0.19
24 40 0.47
25 30 0.35
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:53514700 original size:49 final size:48
Alignment explanation
Indices: 53514573--53514702 Score: 165
Period size: 49 Copynumber: 2.6 Consensus size: 48
53514563 AGCATAGCTG
*
53514573 CTTTATCATATAACTGGAGGCCT-AGCCTCTTTTAATAACTAGGGCAAAGCC
1 CTTTATC--ATAACTGG-GGCATAAGCC-CTTTTAATAACTAGGGCAAAGCC
* * *
53514624 CTTT-TAATAAATGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCC
1 CTTTATCATAACTGGGGCATAAGCCCTTTTAATAACTAGGGCA-AAGCC
53514672 CTTTATCATAACTGGGGCATAAGCCCTTTTA
1 CTTTATCATAACTGGGGCATAAGCCCTTTTA
53514703 CACTTCCTCC
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
47 21 0.30
48 20 0.29
49 24 0.34
50 1 0.01
51 4 0.06
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (48 bp):
CTTTATCATAACTGGGGCATAAGCCCTTTTAATAACTAGGGCAAAGCC
Found at i:53514776 original size:20 final size:20
Alignment explanation
Indices: 53514751--53514817 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
53514741 TTATGAATAC
53514751 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
53514771 ATCATGTGCATATCATACGT
1 ATCATGTGCATATCATACAT
*
53514791 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
53514811 ACCATGT
1 ATCATGT
53514818 TTATCAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:53517222 original size:11 final size:11
Alignment explanation
Indices: 53517206--53517230 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53517196 TATATTGAGC
53517206 ATGATGATAGT
1 ATGATGATAGT
53517217 ATGATGATAGT
1 ATGATGATAGT
53517228 ATG
1 ATG
53517231 CATGTCATGA
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:0.36, C:0.00, G:0.28, T:0.36
Consensus pattern (11 bp):
ATGATGATAGT
Found at i:53517512 original size:41 final size:40
Alignment explanation
Indices: 53517467--53517543 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
53517457 TGTTATTGAA
* * *
53517467 TACTGCATGGCTGCTACTGATACTGTGATGGGCTAAGGCTC
1 TACTGCATAGCTGATACTG-TACTGAGATGGGCTAAGGCTC
**
53517508 TACTGCATATTTGATACTGTACTGAGATGGGCTAAG
1 TACTGCATAGCTGATACTGTACTGAGATGGGCTAAG
53517544 ACTTAAACCG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 16 0.52
41 15 0.48
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.31
Consensus pattern (40 bp):
TACTGCATAGCTGATACTGTACTGAGATGGGCTAAGGCTC
Found at i:53517835 original size:6 final size:6
Alignment explanation
Indices: 53517824--53517851 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
53517814 TAAATTTGGG
53517824 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
53517852 TTGTAGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:53535863 original size:7 final size:7
Alignment explanation
Indices: 53535851--53535881 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
53535841 CTCAAAATAA
53535851 AATGTCC
1 AATGTCC
53535858 AATGTCC
1 AATGTCC
53535865 AATGTCC
1 AATGTCC
*
53535872 AAAGTCC
1 AATGTCC
53535879 AAT
1 AAT
53535882 TACAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (7 bp):
AATGTCC
Found at i:53538996 original size:68 final size:68
Alignment explanation
Indices: 53538886--53539055 Score: 189
Period size: 68 Copynumber: 2.5 Consensus size: 68
53538876 GAAAGTATGG
* * * * * *
53538886 CATCATATTATGTAAGACCATAGCTGGACTACGACAACATATGAAGTCT-GTAAGGACAGTAAAC
1 CATCATATTGTGTAAGACCATAGCTGGGCTATGGCAAAATATGAAGT-TAGTAAGGACAGGAAAC
53538950 ATGA
65 ATGA
* * *
53538954 CATCATATTGTGTATGACCATAGCTGGGCTATGGCAAAATATGAAGTTAGTCAGGATAGGAAACA
1 CATCATATTGTGTAAGACCATAGCTGGGCTATGGCAAAATATGAAGTTAGTAAGGACAGGAAACA
53539019 TGA
66 TGA
* * * * * *
53539022 CAACTTATAGTGTAAGGCCATAGTTAGGCTATGG
1 CATCATATTGTGTAAGACCATAGCTGGGCTATGG
53539056 TAGCATATAA
Statistics
Matches: 85, Mismatches: 16, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
67 1 0.01
68 84 0.99
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (68 bp):
CATCATATTGTGTAAGACCATAGCTGGGCTATGGCAAAATATGAAGTTAGTAAGGACAGGAAACA
TGA
Found at i:53546213 original size:3 final size:3
Alignment explanation
Indices: 53546205--53546248 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
53546195 CACTTATGTA
* * *
53546205 ATC ATC ATC ATC ATC ATC ACC ATC ACC ATC ATC ATT ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
53546249 TTTCTTCTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:53547826 original size:13 final size:13
Alignment explanation
Indices: 53547802--53547839 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
53547792 TTGAAAAGTG
53547802 TTTTGAAAAAATAC
1 TTTTG-AAAAATAC
*
53547816 TTTTGAGAAATAC
1 TTTTGAAAAATAC
53547829 TTTTGAAAAAT
1 TTTTGAAAAAT
53547840 TTGGTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (13 bp):
TTTTGAAAAATAC
Found at i:53548043 original size:28 final size:30
Alignment explanation
Indices: 53548011--53548076 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
53548001 ATTATAACTT
53548011 ATTTTTAATA-TTTTAA-T-ATATAATATTA
1 ATTTTTAATATTTTTAAGTAAT-TAATATTA
*
53548039 ATTTTAAATATTTTTAAGTAATTAATATTA
1 ATTTTTAATATTTTTAAGTAATTAATATTA
53548069 ATTATTTA
1 ATT-TTTA
53548077 TTAAATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 9 0.28
29 6 0.19
30 12 0.38
31 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (30 bp):
ATTTTTAATATTTTTAAGTAATTAATATTA
Found at i:53552887 original size:47 final size:47
Alignment explanation
Indices: 53552831--53552920 Score: 110
Period size: 47 Copynumber: 1.9 Consensus size: 47
53552821 GAAATAAAAT
* * **
53552831 AGAATTTGTGCTAATTGTACATTTAGAAA-TAATTACAATTTAATAGA
1 AGAAGTTGTGATAATTACACATTTA-AAAGTAATTACAATTTAATAGA
* *
53552878 AGAAGTTGTGATAATTACATATTTAAAAGTAATTAGAATTTAA
1 AGAAGTTGTGATAATTACACATTTAAAAGTAATTACAATTTAA
53552921 ATTACAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
46 3 0.08
47 33 0.92
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.38
Consensus pattern (47 bp):
AGAAGTTGTGATAATTACACATTTAAAAGTAATTACAATTTAATAGA
Found at i:53553561 original size:20 final size:19
Alignment explanation
Indices: 53553504--53553564 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
53553494 AACTTAAACT
*
53553504 TTTTTTAAAATTATA-AAA
1 TTTTTTAAAATAATATAAA
* *
53553522 ATATTTAAAATAAGGT-TAAA
1 TTTTTTAAAATAA--TATAAA
53553542 TTTTTTAAAATAATTATAAA
1 TTTTTTAAAATAA-TATAAA
53553562 TTT
1 TTT
53553565 GTAAAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
18 10 0.30
19 1 0.03
20 22 0.67
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (19 bp):
TTTTTTAAAATAATATAAA
Found at i:53553876 original size:37 final size:37
Alignment explanation
Indices: 53553825--53553900 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
53553815 ATTAAAGAAT
* *
53553825 GTGTATAAAGTATTTTTTTACATGTGTAGTCTAAAAA
1 GTGTATAAAGTATTTTCTTACATGTGTAGCCTAAAAA
* *
53553862 GTGTATCAATTATTTTCTTACATGTGTAGCCTAAAAA
1 GTGTATAAAGTATTTTCTTACATGTGTAGCCTAAAAA
53553899 GT
1 GT
53553901 TAAAATAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (37 bp):
GTGTATAAAGTATTTTCTTACATGTGTAGCCTAAAAA
Found at i:53557091 original size:29 final size:29
Alignment explanation
Indices: 53557049--53557107 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
53557039 GGGCTAATTC
53557049 AGTGGAATGCCTACCGAAGATCCTCACAT
1 AGTGGAATGCCTACCGAAGATCCTCACAT
*
53557078 AGTGGAATGCCTACCGAAGATCCTTACAT
1 AGTGGAATGCCTACCGAAGATCCTCACAT
53557107 A
1 A
53557108 CACTTAAGAC
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:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (29 bp):
AGTGGAATGCCTACCGAAGATCCTCACAT
Found at i:53562851 original size:17 final size:18
Alignment explanation
Indices: 53562825--53562858 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
53562815 TTTTTGTTTA
53562825 AATAAATTAATA-GCATT
1 AATAAATTAATATGCATT
*
53562842 AATAATTTAATATGCAT
1 AATAAATTAATATGCAT
53562859 ATACTTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (18 bp):
AATAAATTAATATGCATT
Found at i:53563427 original size:20 final size:21
Alignment explanation
Indices: 53563386--53563427 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
53563376 GACCTATTTT
*
53563386 GTTCATTAATTATTTTTAAGA
1 GTTCATTAATTATTTATAAGA
53563407 GTTC-TTAATT-TTTATAGAGA
1 GTTCATTAATTATTTATA-AGA
53563427 G
1 G
53563428 GGTGGTAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 5 0.26
20 10 0.53
21 4 0.21
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.50
Consensus pattern (21 bp):
GTTCATTAATTATTTATAAGA
Found at i:53570276 original size:21 final size:21
Alignment explanation
Indices: 53570250--53570289 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
53570240 GACGATTCAA
*
53570250 CAAGTGTGAAATTTCGGTTAG
1 CAAGTGTGAAATTTAGGTTAG
53570271 CAAGTGTGAAATTTAGGTT
1 CAAGTGTGAAATTTAGGTT
53570290 GAACCTTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.07, G:0.28, T:0.35
Consensus pattern (21 bp):
CAAGTGTGAAATTTAGGTTAG
Found at i:53573122 original size:31 final size:31
Alignment explanation
Indices: 53573074--53573147 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
53573064 GGGCCACACA
*
53573074 GGCGTGT-AGGCCCACACGGGCATGTCACATG
1 GGCGTGTGA-GCCTACACGGGCATGTCACATG
*
53573105 GGCTTGTGAGCCTACACGGGCATGTCACATG
1 GGCGTGTGAGCCTACACGGGCATGTCACATG
53573136 GGCGTGTGAGCC
1 GGCGTGTGAGCC
53573148 CATTTTTCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
31 38 0.97
32 1 0.03
ACGTcount: A:0.18, C:0.27, G:0.36, T:0.19
Consensus pattern (31 bp):
GGCGTGTGAGCCTACACGGGCATGTCACATG
Found at i:53581220 original size:15 final size:14
Alignment explanation
Indices: 53581198--53581239 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
53581188 GAGATTGGAG
53581198 AGGGGATTTTCGGC
1 AGGGGATTTTCGGC
*
53581212 AGAGGGATTTTAGG-
1 AG-GGGATTTTCGGC
*
53581226 TGGGGATTTTCGGC
1 AGGGGATTTTCGGC
53581240 TTTAGGGGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 10 0.43
14 3 0.13
15 10 0.43
ACGTcount: A:0.17, C:0.10, G:0.43, T:0.31
Consensus pattern (14 bp):
AGGGGATTTTCGGC
Found at i:53581220 original size:27 final size:28
Alignment explanation
Indices: 53581185--53581239 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
53581175 TGGCCGAATA
53581185 AGAGAGATTGGA-GAGGGGATTTTCGGC
1 AGAGAGATTGGAGGAGGGGATTTTCGGC
* ** *
53581212 AGAGGGATTTTAGGTGGGGATTTTCGGC
1 AGAGAGATTGGAGGAGGGGATTTTCGGC
53581240 TTTAGGGGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.22, C:0.07, G:0.44, T:0.27
Consensus pattern (28 bp):
AGAGAGATTGGAGGAGGGGATTTTCGGC
Found at i:53582542 original size:11 final size:11
Alignment explanation
Indices: 53582506--53582561 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
53582496 CATGGTATGT
53582506 ATGATATGCAC
1 ATGATATGCAC
* *
53582517 ATGACATG--T
1 ATGATATGCAC
53582526 ATGATATGCAC
1 ATGATATGCAC
*
53582537 ATGATATG--T
1 ATGATATGCAC
53582546 ATGATATGCAC
1 ATGATATGCAC
53582557 ATGAT
1 ATGAT
53582562 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:53582561 original size:20 final size:20
Alignment explanation
Indices: 53582495--53582561 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
53582485 ATTTTGATAA
*
53582495 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
53582515 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
53582535 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
53582555 ACATGAT
1 ACATGAT
53582562 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:53582637 original size:23 final size:23
Alignment explanation
Indices: 53582611--53582750 Score: 239
Period size: 23 Copynumber: 6.1 Consensus size: 23
53582601 GAGGAAGTGA
53582611 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
53582634 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
53582657 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
53582680 AAAGGGCTTATG-CCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
53582702 AAAGGGCTTATGCCCCAGTT-TT
1 AAAGGGCTTATGCCCCAGTTATT
* *
53582724 AAAAGGGCTTTTTCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
53582748 AAA
1 AAA
53582751 AGAGGCTAGG
Statistics
Matches: 112, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
22 24 0.21
23 86 0.77
24 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:53582721 original size:68 final size:69
Alignment explanation
Indices: 53582611--53582750 Score: 239
Period size: 68 Copynumber: 2.0 Consensus size: 69
53582601 GAGGAAGTGA
53582611 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAG
1 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTT-TTAAAAGGGCTTATGCCCCAG
53582675 TTATT
65 TTATT
* *
53582680 AAAGGGCTTATG-CCCAGTTATTAAAGGGCTTATGCCCCAGTTTTAAAAGGGCTTTTTCCCCAGT
1 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTTTAAAAGGGCTTATGCCCCAGT
53582744 TATT
66 TATT
53582748 AAA
1 AAA
53582751 AGAGGCTAGG
Statistics
Matches: 68, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
67 2 0.03
68 54 0.79
69 12 0.18
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (69 bp):
AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTTTAAAAGGGCTTATGCCCCAGT
TATT
Found at i:53582999 original size:31 final size:31
Alignment explanation
Indices: 53582964--53583027 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
53582954 CGTTTACAGT
53582964 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
53582995 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
53583026 AA
1 AA
53583028 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:53590495 original size:25 final size:25
Alignment explanation
Indices: 53590466--53590513 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
53590456 TTATAACATG
* * *
53590466 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
53590491 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
53590514 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:53590597 original size:11 final size:11
Alignment explanation
Indices: 53590561--53590616 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
53590551 CATGGTATGT
53590561 ATGATATGCAC
1 ATGATATGCAC
* *
53590572 ATGACATG--T
1 ATGATATGCAC
53590581 ATGATATGCAC
1 ATGATATGCAC
*
53590592 ATGATATG--T
1 ATGATATGCAC
53590601 ATGATATGCAC
1 ATGATATGCAC
53590612 ATGAT
1 ATGAT
53590617 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:53590616 original size:20 final size:20
Alignment explanation
Indices: 53590550--53590616 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
53590540 ATTTTGATAA
*
53590550 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
53590570 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
53590590 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
53590610 ACATGAT
1 ACATGAT
53590617 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:53590739 original size:23 final size:24
Alignment explanation
Indices: 53590665--53590759 Score: 142
Period size: 23 Copynumber: 4.0 Consensus size: 24
53590655 GGAGGAAGTG
53590665 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
53590689 T-AAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
53590712 TAAAAGGGCTT-TGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
53590735 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 TAAAAG-GGCTTATGCC-CCAGTTAT
53590760 ATGATAAAGC
Statistics
Matches: 66, Mismatches: 1, Indels: 7
0.89 0.01 0.09
Matches are distributed among these distances:
23 42 0.64
24 16 0.24
25 8 0.12
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:53590988 original size:31 final size:31
Alignment explanation
Indices: 53590953--53591016 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
53590943 CGTTTACAGT
53590953 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
53590984 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
53591015 AA
1 AA
53591017 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:53592896 original size:5 final size:5
Alignment explanation
Indices: 53592888--53592912 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
53592878 AAAATAAAAA
53592888 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
53592913 GGTTGATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:53599439 original size:21 final size:21
Alignment explanation
Indices: 53599413--53599518 Score: 131
Period size: 21 Copynumber: 5.0 Consensus size: 21
53599403 AGAACATGCC
* *
53599413 AACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCGTGAGAGCTG
53599434 AACAGAAGCTCGTGAGAGCTG
1 AACAGAAGCTCGTGAGAGCTG
* * *
53599455 AATATAAGCTCGTGAGTGCTG
1 AACAGAAGCTCGTGAGAGCTG
*
53599476 AACATAAGCTCGTGAGAGCTG
1 AACAGAAGCTCGTGAGAGCTG
* * *
53599497 AAGAGAAGCTTGTAAGAGCTG
1 AACAGAAGCTCGTGAGAGCTG
53599518 A
1 A
53599519 TCCACCCAAT
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 74 1.00
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.19
Consensus pattern (21 bp):
AACAGAAGCTCGTGAGAGCTG
Found at i:53604463 original size:62 final size:62
Alignment explanation
Indices: 53604378--53604494 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 62
53604368 GTCACTGACT
* * *
53604378 GTGTGGTTCTATACCATAAACAGTAAGTTACACAGCCTAGGCACACACCCGTGTCTCCAGCC
1 GTGTGGTTCTATACCACAAACAGTAAGTTACACAGCCCAGACACACACCCGTGTCTCCAGCC
* * ** *
53604440 GTGTGGTTTTATACCACAAACAGTGAGTTACATTGCCCAGACACACACTCGTGTC
1 GTGTGGTTCTATACCACAAACAGTAAGTTACACAGCCCAGACACACACCCGTGTC
53604495 CGTTGCCCGT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 47 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (62 bp):
GTGTGGTTCTATACCACAAACAGTAAGTTACACAGCCCAGACACACACCCGTGTCTCCAGCC
Found at i:53607675 original size:20 final size:20
Alignment explanation
Indices: 53607650--53607695 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
53607640 ATTGGGCCTT
53607650 GCCCATATT-AACACAGTTGG
1 GCCCATATTCAACACAGTT-G
*
53607670 GCCCAT-TTCAATACAGTTG
1 GCCCATATTCAACACAGTTG
53607689 GCCCATA
1 GCCCATA
53607696 ACAAAACAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
GCCCATATTCAACACAGTTG
Found at i:53607704 original size:19 final size:20
Alignment explanation
Indices: 53607662--53607705 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
53607652 CCATATTAAC
** *
53607662 ACAGTTGGGCCCATTTCAAT
1 ACAGTTGGGCCCATAACAAA
53607682 ACAGTT-GGCCCATAACAAA
1 ACAGTTGGGCCCATAACAAA
53607701 ACAGT
1 ACAGT
53607706 CTCATATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ACAGTTGGGCCCATAACAAA
Found at i:53612710 original size:25 final size:25
Alignment explanation
Indices: 53612682--53612732 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
53612672 TAATTACTAC
53612682 AATTAAA-AATAATATTTAAAAAATT
1 AATTAAATAATAA-ATTTAAAAAATT
* *
53612707 AATTAAATATTAAATTTATAAAATT
1 AATTAAATAATAAATTTAAAAAATT
53612732 A
1 A
53612733 CATATTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
AATTAAATAATAAATTTAAAAAATT
Found at i:53612895 original size:25 final size:24
Alignment explanation
Indices: 53612859--53612921 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 24
53612849 GTGTTTTATA
53612859 GGAAGAGT-AAAGAGAAAAAAAGAGG
1 GGAAG-GTGAAAGAGAAAAAAA-AGG
53612884 GGAAGGTGAAAGA-AAAAAAAAGG
1 GGAAGGTGAAAGAGAAAAAAAAGG
53612907 GG-A-G-GAAAGAGAAAA
1 GGAAGGTGAAAGAGAAAA
53612922 GTTTGAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
20 6 0.17
21 5 0.14
22 1 0.03
23 5 0.14
24 9 0.25
25 10 0.28
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.03
Consensus pattern (24 bp):
GGAAGGTGAAAGAGAAAAAAAAGG
Found at i:53616066 original size:20 final size:20
Alignment explanation
Indices: 53616037--53616074 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
53616027 TTTATACATT
*
53616037 TATTTTTAGGAATTTATTCG
1 TATTTCTAGGAATTTATTCG
53616057 TATTTCTAGGAATTTATT
1 TATTTCTAGGAATTTATT
53616075 TGTACTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.05, G:0.13, T:0.55
Consensus pattern (20 bp):
TATTTCTAGGAATTTATTCG
Found at i:53619608 original size:126 final size:125
Alignment explanation
Indices: 53619419--53619685 Score: 326
Period size: 126 Copynumber: 2.1 Consensus size: 125
53619409 TACCGAATTT
* * *
53619419 CCAAATACGAAATATTGTCTCATTTTAATTTAAGAAAACATCGATGAAATGTCAAAAGGATATTC
1 CCAAACACGAAATATTGCCTCATTTTAATTTAAGAAAACATCGACGAAATGTCAAAAGGATATTC
* *
53619484 CGTATCTTAGTCGAATGAAAAATCGAAACCCAGCACGAT-AGGATACGA-TCTCTCAAACTC
66 CGTATCTTAGTCGAACGAAAAATCGAAACCCAGCACGATAAGG-CACGATTC-CTCAAACTC
* * **
53619544 CCTAAACACGAAATATTGCCTCATTTTAATTTTAA-AAAGCATGGACGAAAAT-TTTAAAGGATA
1 CC-AAACACGAAATATTGCCTCATTTTAA-TTTAAGAAAACATCGACG-AAATGTCAAAAGGATA
** * * * *
53619607 TTTTGTATTTTAGTTGAACGAAAAATCGAAACCTAGCACGATAAGGCACGATTCCTCGAACTC
63 TTCCGTATCTTAGTCGAACGAAAAATCGAAACCCAGCACGATAAGGCACGATTCCTCAAACTC
53619670 CCAAACACGAAATATT
1 CCAAACACGAAATATT
53619686 TCCTTATGTT
Statistics
Matches: 122, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
125 16 0.13
126 92 0.75
127 14 0.11
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (125 bp):
CCAAACACGAAATATTGCCTCATTTTAATTTAAGAAAACATCGACGAAATGTCAAAAGGATATTC
CGTATCTTAGTCGAACGAAAAATCGAAACCCAGCACGATAAGGCACGATTCCTCAAACTC
Found at i:53619831 original size:21 final size:23
Alignment explanation
Indices: 53619784--53619837 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
53619774 CATTCAAGAT
**
53619784 AAAATAATATATAAAACTCTTTA
1 AAAATAATATATAAAACTAATTA
*
53619807 AAAATAATATAT-AAA-TAATTC
1 AAAATAATATATAAAACTAATTA
53619828 AAAAT-ATATA
1 AAAATAATATA
53619838 ATGTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 8 0.29
22 3 0.11
23 12 0.43
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTA
Found at i:53620081 original size:23 final size:23
Alignment explanation
Indices: 53620015--53620081 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 23
53620005 TATAAGAAAA
*
53620015 ATAAT-AAT-GAAA-ATAATATT
1 ATAATAAATAGAAATATAATAAT
53620035 AGTATATAAATAGAAATA-AA-AAT
1 A-TA-ATAAATAGAAATATAATAAT
53620058 ATAATAAATAGAAATATAATAAT
1 ATAATAAATAGAAATATAATAAT
53620081 A
1 A
53620082 GTAGAAATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
20 1 0.03
21 15 0.38
22 6 0.15
23 10 0.26
24 6 0.15
25 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (23 bp):
ATAATAAATAGAAATATAATAAT
Found at i:53620088 original size:17 final size:15
Alignment explanation
Indices: 53620048--53620093 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
53620038 ATATAAATAG
*
53620048 AAATAAAAATATAAT
1 AAATAGAAATATAAT
53620063 AAATAGAAATATAAT
1 AAATAGAAATATAAT
53620078 AATAGTAGAAATATAA
1 AA-A-TAGAAATATAA
53620094 ATAGATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 16 0.57
16 1 0.04
17 11 0.39
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (15 bp):
AAATAGAAATATAAT
Found at i:53620103 original size:14 final size:13
Alignment explanation
Indices: 53620063--53620164 Score: 59
Period size: 14 Copynumber: 7.2 Consensus size: 13
53620053 AAAATATAAT
53620063 AAATAGA-AATATA
1 AAATAGATAA-ATA
*
53620076 ATAATAGTAGAAATA
1 A-AATAG-ATAAATA
53620091 TAAATAGATAAATA
1 -AAATAGATAAATA
53620105 AAATTAGATAAATA
1 AAA-TAGATAAATA
53620119 ATAATAGTATTAGAATA
1 A-AATAG-A-TA-AATA
53620136 ACAA-A-ATAAATA
1 A-AATAGATAAATA
53620148 TAAATAGA-AACATA
1 -AAATAGATAA-ATA
53620162 AAA
1 AAA
53620165 ATAATAGCAA
Statistics
Matches: 74, Mismatches: 2, Indels: 26
0.73 0.02 0.25
Matches are distributed among these distances:
12 6 0.08
13 13 0.18
14 30 0.41
15 12 0.16
16 6 0.08
17 7 0.09
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (13 bp):
AAATAGATAAATA
Found at i:53620122 original size:29 final size:30
Alignment explanation
Indices: 53620058--53620179 Score: 76
Period size: 29 Copynumber: 4.2 Consensus size: 30
53620048 AAATAAAAAT
53620058 ATAATAAATAGAAATATAATAATAGTAGAA
1 ATAATAAATAGAAATATAATAATAGTAGAA
*
53620088 AT-ATAAATAGATAA-ATAA-AATTAG-ATAA
1 ATAATAAATAGA-AATATAATAA-TAGTAGAA
* * * * ** *
53620116 ATAAT-AATAGTATTAGAATAACAAAATAA
1 ATAATAAATAGAAATATAATAATAGTAGAA
* * * *
53620145 AT-ATAAATAGAAACATAAAAATAATAGCA
1 ATAATAAATAGAAATATAATAATAGTAGAA
53620174 ATAATA
1 ATAATA
53620180 TATTAAATTA
Statistics
Matches: 69, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
27 1 0.01
28 18 0.26
29 43 0.62
30 7 0.10
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.26
Consensus pattern (30 bp):
ATAATAAATAGAAATATAATAATAGTAGAA
Found at i:53620978 original size:23 final size:22
Alignment explanation
Indices: 53620936--53620983 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
53620926 TATTTATTGA
*
53620936 TTACATAATTATTTAGTTTACT
1 TTACATAATTATTTAATTTACT
*
53620958 TTACAT-ATTATATTAAATTTATT
1 TTACATAATTAT-TT-AATTTACT
53620981 TTA
1 TTA
53620984 AGCTTACCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 5 0.23
22 8 0.36
23 9 0.41
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.56
Consensus pattern (22 bp):
TTACATAATTATTTAATTTACT
Found at i:53621269 original size:3 final size:3
Alignment explanation
Indices: 53621263--53621292 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
53621253 AGAAGAAGAA
53621263 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
53621293 TGATTGGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:53623595 original size:2 final size:2
Alignment explanation
Indices: 53623590--53623624 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
53623580 TATATATATA
53623590 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
53623625 TTAATTCTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:53628822 original size:35 final size:35
Alignment explanation
Indices: 53628776--53628917 Score: 214
Period size: 35 Copynumber: 4.0 Consensus size: 35
53628766 ATAATCTTCA
53628776 ATGATATGCAATCTTAGATATGATACAATCTTAGAT
1 ATGAT-TGCAATCTTAGATATGATACAATCTTAGAT
* *
53628812 ATTATTGCAATCTTAGATATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGATATGA-TACAATCTTAGAT
*
53628848 ATGA-TACAATCTTAGATATGATACAATCTTAGAT
1 ATGATTGCAATCTTAGATATGATACAATCTTAGAT
53628882 ATGATTGCAATCTTAGATATGATATACAATCTTAGA
1 ATGATTGCAATCTTAGATATG--ATACAATCTTAGA
53628918 AGATATGATT
Statistics
Matches: 96, Mismatches: 6, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
34 16 0.17
35 48 0.50
36 19 0.20
37 13 0.14
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.37
Consensus pattern (35 bp):
ATGATTGCAATCTTAGATATGATACAATCTTAGAT
Found at i:53628824 original size:18 final size:18
Alignment explanation
Indices: 53628784--53628917 Score: 202
Period size: 18 Copynumber: 7.6 Consensus size: 18
53628774 CAATGATATG
53628784 CAATCTTAGATATGA-TA
1 CAATCTTAGATATGATTA
* *
53628801 CAATCTTAGATATTATTG
1 CAATCTTAGATATGATTA
*
53628819 CAATCTTAGATATGATTG
1 CAATCTTAGATATGATTA
53628837 CAATCTTAGATATGA-TA
1 CAATCTTAGATATGATTA
53628854 CAATCTTAGATATGA-TA
1 CAATCTTAGATATGATTA
*
53628871 CAATCTTAGATATGATTG
1 CAATCTTAGATATGATTA
53628889 CAATCTTAGATATGATATA
1 CAATCTTAGATATGAT-TA
53628908 CAATCTTAGA
1 CAATCTTAGA
53628918 AGATATGATT
Statistics
Matches: 108, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
17 47 0.44
18 50 0.46
19 11 0.10
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (18 bp):
CAATCTTAGATATGATTA
Found at i:53628871 original size:70 final size:71
Alignment explanation
Indices: 53628784--53628917 Score: 243
Period size: 70 Copynumber: 1.9 Consensus size: 71
53628774 CAATGATATG
* *
53628784 CAATCTTAGATATGATACAATCTTAGATATTATTGCAATCTTAGATATGAT-TGCAATCTTAGAT
1 CAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGATATGATATACAATCTTAGAT
53628848 ATGATA
66 ATGATA
53628854 CAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGATATGATATACAATCTTAGA
1 CAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGATATGATATACAATCTTAGA
53628918 AGATATGATT
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
70 50 0.82
71 11 0.18
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (71 bp):
CAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGATATGATATACAATCTTAGAT
ATGATA
Found at i:53640425 original size:19 final size:19
Alignment explanation
Indices: 53640401--53640446 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
53640391 TGTGAAGTTT
*
53640401 AATGCAGATG-ATGCAATG
1 AATGCAAATGCATGCAATG
*
53640419 CAATGCAAATGCATGGAATG
1 -AATGCAAATGCATGCAATG
53640439 AATGCAAA
1 AATGCAAA
53640447 AGAAAGTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.20
Consensus pattern (19 bp):
AATGCAAATGCATGCAATG
Found at i:53642063 original size:125 final size:126
Alignment explanation
Indices: 53641934--53642233 Score: 358
Period size: 126 Copynumber: 2.4 Consensus size: 126
53641924 GTAAATTGCC
* * ** * * *
53641934 ACCCACCACGATTGGGCACGATTTAC-CAAA-TTTCTAAATACGAAATATTGTCTCATTTTAA-T
1 ACCCAGCACGATAGGGCACGATTT-CTCAAACTCCCCAAACACGAAATATTGCCTCATTTTAATT
* * *
53641996 TTAAGAAAACATGGATGAAA-TGTCAAAAGGATATTCCGTATCTTAGTCGAATGAAAAATCGAA
65 TTAA-AAAACATGGACGAAATTGTCAAAA-GACATTCCGTATCTTAGTCGAACGAAAAATCGAA
* *
53642059 ACCCAGCACGATAGGACACGATCTCTCAAACTCCCCAAACACGAAATATTGCCTCATTTTAATTT
1 ACCCAGCACGATAGGGCACGATTTCTCAAACTCCCCAAACACGAAATATTGCCTCATTTTAATTT
* * * * *
53642124 TAAAAAGCATGGACGAAATTTTCAAAAGACATTTCGTATTTTAGTTGAACGAAAAATCGAA
66 TAAAAAACATGGACGAAATTGTCAAAAGACATTCCGTATCTTAGTCGAACGAAAAATCGAA
* * *
53642185 ACCCAGCATGATAGGGCACGATTCCTCGAACT-CCCAAACACGAAATATT
1 ACCCAGCACGATAGGGCACGATTTCTCAAACTCCCCAAACACGAAATATT
53642234 TCCTTATGTT
Statistics
Matches: 149, Mismatches: 22, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
124 1 0.01
125 41 0.28
126 95 0.64
127 12 0.08
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (126 bp):
ACCCAGCACGATAGGGCACGATTTCTCAAACTCCCCAAACACGAAATATTGCCTCATTTTAATTT
TAAAAAACATGGACGAAATTGTCAAAAGACATTCCGTATCTTAGTCGAACGAAAAATCGAA
Found at i:53642607 original size:23 final size:23
Alignment explanation
Indices: 53642541--53642607 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 23
53642531 TATAAGAAAA
*
53642541 ATAAT-AAT-GAAA-ATAATATT
1 ATAATAAATAGAAATATAATAAT
53642561 AGTATATAAATAGAAATA-AA-AAT
1 A-TA-ATAAATAGAAATATAATAAT
53642584 ATAATAAATAGAAATATAATAAT
1 ATAATAAATAGAAATATAATAAT
53642607 A
1 A
53642608 GTAGAAATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
20 1 0.03
21 15 0.38
22 6 0.15
23 10 0.26
24 6 0.15
25 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (23 bp):
ATAATAAATAGAAATATAATAAT
Found at i:53642614 original size:17 final size:15
Alignment explanation
Indices: 53642574--53642619 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
53642564 ATATAAATAG
*
53642574 AAATAAAAATATAAT
1 AAATAGAAATATAAT
53642589 AAATAGAAATATAAT
1 AAATAGAAATATAAT
53642604 AATAGTAGAAATATAA
1 AA-A-TAGAAATATAA
53642620 ATAGATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 16 0.57
16 1 0.04
17 11 0.39
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (15 bp):
AAATAGAAATATAAT
Found at i:53642629 original size:14 final size:13
Alignment explanation
Indices: 53642589--53642681 Score: 57
Period size: 14 Copynumber: 6.5 Consensus size: 13
53642579 AAAATATAAT
53642589 AAATAGA-AATATA
1 AAATAGATAA-ATA
*
53642602 ATAATAGTAGAAATA
1 A-AATAG-ATAAATA
53642617 TAAATAGATAAATA
1 -AAATAGATAAATA
53642631 AAATTAGATAAATA
1 AAA-TAGATAAATA
53642645 ATAATAGTATTAGAATA
1 A-AATAG-A-TA-AATA
53642662 ACAA-A-ATAAATA
1 A-AATAGATAAATA
53642674 TAAATAGA
1 -AAATAGA
53642682 AGCATAAAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 23
0.73 0.02 0.25
Matches are distributed among these distances:
12 6 0.09
13 8 0.12
14 27 0.41
15 12 0.18
16 6 0.09
17 7 0.11
ACGTcount: A:0.63, C:0.01, G:0.09, T:0.27
Consensus pattern (13 bp):
AAATAGATAAATA
Found at i:53642648 original size:29 final size:30
Alignment explanation
Indices: 53642584--53642648 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 30
53642574 AAATAAAAAT
53642584 ATAATAAATAGAAATATAATAATAGTAGAA
1 ATAATAAATAGAAATATAATAATAGTAGAA
*
53642614 AT-ATAAATAGATAA-ATAA-AATTAG-ATAA
1 ATAATAAATAGA-AATATAATAA-TAGTAGAA
53642642 ATAATAA
1 ATAATAA
53642649 TAGTATTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
28 7 0.23
29 20 0.65
30 4 0.13
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.28
Consensus pattern (30 bp):
ATAATAAATAGAAATATAATAATAGTAGAA
Found at i:53643506 original size:23 final size:22
Alignment explanation
Indices: 53643464--53643511 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
53643454 TATTTATTGA
*
53643464 TTACATAATTATTTAGTTTACT
1 TTACATAATTATTTAATTTACT
*
53643486 TTACAT-ATTATATTAAATTTATT
1 TTACATAATTAT-TT-AATTTACT
53643509 TTA
1 TTA
53643512 AGCTTACCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 5 0.23
22 8 0.36
23 9 0.41
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.56
Consensus pattern (22 bp):
TTACATAATTATTTAATTTACT
Found at i:53645738 original size:31 final size:31
Alignment explanation
Indices: 53645697--53645762 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
53645687 CCTTTTCATA
*
53645697 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
** *
53645728 TTTCAAATTTCATATTACTGGGCCGAAGTCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
53645759 TTTC
1 TTTC
53645763 TATAAACGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:53646064 original size:23 final size:24
Alignment explanation
Indices: 53645954--53646166 Score: 290
Period size: 24 Copynumber: 9.0 Consensus size: 24
53645944 GCTTTATCAT
*
53645954 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* * *
53645979 GTAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
* *
53646003 GTAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
* *
53646027 ATCACTAGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
53646050 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
53646074 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
53646098 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
53646121 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
53646144 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
53646167 GCACTTCCTC
Statistics
Matches: 171, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
23 65 0.38
24 95 0.56
25 11 0.06
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:53646067 original size:71 final size:70
Alignment explanation
Indices: 53645975--53646167 Score: 314
Period size: 71 Copynumber: 2.7 Consensus size: 70
53645965 CCTAGCCTCT
* * *
53645975 TTTAGTAACTGGGGCAAAAGCCCTTTTTGTAACTGGGGCATAAGCCCTTTTGATCACTAGGGCAT
1 TTTAATAACTGGGGCATAAGCCC-TTTTGTAACTGGGGCATAAGCCCTTTTGATAACTAGGGCAT
53646040 AAGCCC
65 AAGCCC
*
53646046 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCAT
1 TTTAATAACTGGGGCATAAGCCCTTTTG-TAACTGGGGCATAAGCCCTTTTGATAACTAGGGCAT
53646111 AAGCCC
65 AAGCCC
**
53646117 TTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTTG
1 TTTAATAACTGGGGCATAAGCCCTTTTGTAACTGGGGCATAAGCCCTTTTG
53646168 CACTTCCTCC
Statistics
Matches: 115, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
70 28 0.24
71 87 0.76
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.29
Consensus pattern (70 bp):
TTTAATAACTGGGGCATAAGCCCTTTTGTAACTGGGGCATAAGCCCTTTTGATAACTAGGGCATA
AGCCC
Found at i:53646238 original size:9 final size:9
Alignment explanation
Indices: 53646224--53646280 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
53646214 ATCTCATGTG
53646224 CATATCATA
1 CATATCATA
*
53646233 CATATCATGTG
1 CATATCA--TA
53646244 CATATCATA
1 CATATCATA
* *
53646253 CATGTCATGTG
1 CATATCA--TA
53646264 CATATCATA
1 CATATCATA
53646273 CATATCAT
1 CATATCAT
53646281 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:53646240 original size:20 final size:20
Alignment explanation
Indices: 53646212--53646282 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
53646202 GCATTTATGA
*
53646212 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
53646232 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
53646252 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
53646272 ACATATCATGT
1 ACATATCATGT
53646283 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:53646247 original size:11 final size:11
Alignment explanation
Indices: 53646217--53646271 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
53646207 TATGAACATC
53646217 TCATGTGCATA
1 TCATGTGCATA
*
53646228 TCA--TACATA
1 TCATGTGCATA
53646237 TCATGTGCATA
1 TCATGTGCATA
* *
53646248 TCA--TACATG
1 TCATGTGCATA
53646257 TCATGTGCATA
1 TCATGTGCATA
53646268 TCAT
1 TCAT
53646272 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:53646361 original size:25 final size:24
Alignment explanation
Indices: 53646319--53646366 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
53646309 ATATATAAAC
* * *
53646319 CCTAGGGGTATAATGGTCACTTTTA
1 CCTAGGGGCAAAACGGTCA-TTTTA
53646344 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
53646367 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (24 bp):
CCTAGGGGCAAAACGGTCATTTTA
Found at i:53649713 original size:31 final size:31
Alignment explanation
Indices: 53649672--53649737 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
53649662 CCTTTTCATA
*
53649672 TTTCATATTTCATAACACTAGGCCGAAGCCT
1 TTTCAAATTTCATAACACTAGGCCGAAGCCT
** *
53649703 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTAGGCCGAAGCCT
53649734 TTTC
1 TTTC
53649738 TATAAACGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTAGGCCGAAGCCT
Found at i:53650039 original size:23 final size:24
Alignment explanation
Indices: 53649929--53650141 Score: 290
Period size: 24 Copynumber: 9.0 Consensus size: 24
53649919 GCTTTATCAT
*
53649929 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* * *
53649954 GTAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
* *
53649978 GTAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
* *
53650002 ATCACTAGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
53650025 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
53650049 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
53650073 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
53650096 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
53650119 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
53650142 GCACTTCCTC
Statistics
Matches: 171, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
23 65 0.38
24 95 0.56
25 11 0.06
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:53650042 original size:71 final size:70
Alignment explanation
Indices: 53649950--53650142 Score: 314
Period size: 71 Copynumber: 2.7 Consensus size: 70
53649940 CCTAGCCTCT
* * *
53649950 TTTAGTAACTGGGGCAAAAGCCCTTTTTGTAACTGGGGCATAAGCCCTTTTGATCACTAGGGCAT
1 TTTAATAACTGGGGCATAAGCCC-TTTTGTAACTGGGGCATAAGCCCTTTTGATAACTAGGGCAT
53650015 AAGCCC
65 AAGCCC
*
53650021 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCAT
1 TTTAATAACTGGGGCATAAGCCCTTTTG-TAACTGGGGCATAAGCCCTTTTGATAACTAGGGCAT
53650086 AAGCCC
65 AAGCCC
**
53650092 TTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTTG
1 TTTAATAACTGGGGCATAAGCCCTTTTGTAACTGGGGCATAAGCCCTTTTG
53650143 CACTTCCTCC
Statistics
Matches: 115, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
70 28 0.24
71 87 0.76
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.29
Consensus pattern (70 bp):
TTTAATAACTGGGGCATAAGCCCTTTTGTAACTGGGGCATAAGCCCTTTTGATAACTAGGGCATA
AGCCC
Found at i:53650213 original size:9 final size:9
Alignment explanation
Indices: 53650199--53650255 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
53650189 ATCTCATGTG
53650199 CATATCATA
1 CATATCATA
*
53650208 CATATCATGTG
1 CATATCA--TA
53650219 CATATCATA
1 CATATCATA
* *
53650228 CATGTCATGTG
1 CATATCA--TA
53650239 CATATCATA
1 CATATCATA
53650248 CATATCAT
1 CATATCAT
53650256 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:53650215 original size:20 final size:20
Alignment explanation
Indices: 53650187--53650257 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
53650177 GCATTTATGA
*
53650187 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
53650207 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
53650227 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
53650247 ACATATCATGT
1 ACATATCATGT
53650258 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:53650222 original size:11 final size:11
Alignment explanation
Indices: 53650192--53650246 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
53650182 TATGAACATC
53650192 TCATGTGCATA
1 TCATGTGCATA
*
53650203 TCA--TACATA
1 TCATGTGCATA
53650212 TCATGTGCATA
1 TCATGTGCATA
* *
53650223 TCA--TACATG
1 TCATGTGCATA
53650232 TCATGTGCATA
1 TCATGTGCATA
53650243 TCAT
1 TCAT
53650247 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:53650336 original size:25 final size:24
Alignment explanation
Indices: 53650294--53650341 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
53650284 ATATATAAAC
* * *
53650294 CCTAGGGGTATAATGGTCACTTTTA
1 CCTAGGGGCAAAACGGTCA-TTTTA
53650319 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
53650342 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (24 bp):
CCTAGGGGCAAAACGGTCATTTTA
Found at i:53652985 original size:2 final size:2
Alignment explanation
Indices: 53652980--53653038 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
53652970 TATATATATA
53652980 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
53653022 TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG T
53653039 TTAATTCTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:53658211 original size:35 final size:36
Alignment explanation
Indices: 53658173--53658289 Score: 184
Period size: 35 Copynumber: 3.3 Consensus size: 36
53658163 CAATGATATG
* * *
53658173 CAATCTTAGATATGA-TACAATCTTAGATATTATTG
1 CAATCTTAGATATGATTGCAATCTTAGATATGATTA
53658208 CAATCTTAGATATGATTGCAATCTTAGATATGA-TA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATTA
53658243 CAATCTTAGATATGATTGCAATCTTAGATATGATATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGAT-TA
53658280 CAATCTTAGA
1 CAATCTTAGA
53658290 AGATATGATT
Statistics
Matches: 76, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
35 49 0.64
36 15 0.20
37 12 0.16
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.38
Consensus pattern (36 bp):
CAATCTTAGATATGATTGCAATCTTAGATATGATTA
Found at i:53658213 original size:18 final size:18
Alignment explanation
Indices: 53658165--53658289 Score: 182
Period size: 18 Copynumber: 6.9 Consensus size: 18
53658155 ATAATCTTCA
53658165 ATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
*
53658184 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
53658201 ATTATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
53658219 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
53658237 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
53658254 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
53658272 ATGATATACAATCTTAGA
1 ATGAT-TGCAATCTTAGA
53658290 AGATATGATT
Statistics
Matches: 96, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
17 31 0.32
18 50 0.52
19 15 0.16
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (18 bp):
ATGATTGCAATCTTAGAT
Found at i:53658229 original size:53 final size:54
Alignment explanation
Indices: 53658165--53658289 Score: 225
Period size: 53 Copynumber: 2.3 Consensus size: 54
53658155 ATAATCTTCA
*
53658165 ATGATATGCAATCTTAGATATGATACAATCTTAGATATTATTGCAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGAT
53658219 ATGAT-TGCAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGAT
*
53658272 ATGATATACAATCTTAGA
1 ATGATATGCAATCTTAGA
53658290 AGATATGATT
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
53 52 0.76
54 16 0.24
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (54 bp):
ATGATATGCAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGAT
Found at i:53660500 original size:46 final size:46
Alignment explanation
Indices: 53660441--53660536 Score: 192
Period size: 46 Copynumber: 2.1 Consensus size: 46
53660431 TAAAAAGCTC
53660441 AATATTTTCTGTTCTCATAGAGAGATTAACATTCTTATTAAAAGTT
1 AATATTTTCTGTTCTCATAGAGAGATTAACATTCTTATTAAAAGTT
53660487 AATATTTTCTGTTCTCATAGAGAGATTAACATTCTTATTAAAAGTT
1 AATATTTTCTGTTCTCATAGAGAGATTAACATTCTTATTAAAAGTT
53660533 AATA
1 AATA
53660537 AAATTTTTCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.43
Consensus pattern (46 bp):
AATATTTTCTGTTCTCATAGAGAGATTAACATTCTTATTAAAAGTT
Found at i:53662756 original size:24 final size:24
Alignment explanation
Indices: 53662724--53662773 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
53662714 TGTTAGAATT
53662724 ATCTATACTATATTTAAGATTTTG
1 ATCTATACTATATTTAAGATTTTG
*
53662748 ATCTCTACTATATTTAAGATTTTG
1 ATCTATACTATATTTAAGATTTTG
53662772 AT
1 AT
53662774 TGAGTTAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.50
Consensus pattern (24 bp):
ATCTATACTATATTTAAGATTTTG
Found at i:53664069 original size:13 final size:12
Alignment explanation
Indices: 53664051--53664085 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
53664041 GAAATTTTGC
53664051 TTTCTTTTCCCT
1 TTTCTTTTCCCT
*
53664063 ATTTCTTCTCCCT
1 -TTTCTTTTCCCT
53664076 TTTCTTTTCC
1 TTTCTTTTCC
53664086 ATCTTCATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTCTTTTCCCT
Found at i:53665024 original size:38 final size:38
Alignment explanation
Indices: 53664954--53665030 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 38
53664944 ATTATTGGTT
* * *
53664954 ACATGCCTACCGTTACTGTTGAACCGATTACATGTTAA
1 ACATGCCTACCGTTACTGATGAACAGATTACATGATAA
* *
53664992 ACATGTCTACTGTTACTGATGAACTAGA-TACATGATAA
1 ACATGCCTACCGTTACTGATGAAC-AGATTACATGATAA
53665030 A
1 A
53665031 AAATGCTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
38 31 0.94
39 2 0.06
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (38 bp):
ACATGCCTACCGTTACTGATGAACAGATTACATGATAA
Found at i:53665317 original size:91 final size:91
Alignment explanation
Indices: 53665162--53665332 Score: 263
Period size: 91 Copynumber: 1.9 Consensus size: 91
53665152 CTAATAGTTT
* * *
53665162 ACCTACAAACACTGGTGGTTTATCCACACACTTTTTGACAAATTTTATCTACAAACTCGTTGTGC
1 ACCTACAAACACTGGTGGTTTATCCACACAATTTCTGACAAATTTTATCTACAAACCCGTTGTGC
53665227 ATTCACAACCTACTGGTAGTGTATCA
66 ATTCACAACCTACTGGTAGTGTATCA
* ** *
53665253 ACCTACAAACACTGGTGGTTTATCCACA-AATTTACTGGCAGCTTTTATCTATAAACCCGTTGTG
1 ACCTACAAACACTGGTGGTTTATCCACACAATTT-CTGACAAATTTTATCTACAAACCCGTTGTG
53665317 CATTCACAACCTACTG
65 CATTCACAACCTACTG
53665333 ACAGCGTATT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
90 4 0.06
91 68 0.94
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.32
Consensus pattern (91 bp):
ACCTACAAACACTGGTGGTTTATCCACACAATTTCTGACAAATTTTATCTACAAACCCGTTGTGC
ATTCACAACCTACTGGTAGTGTATCA
Found at i:53665569 original size:18 final size:18
Alignment explanation
Indices: 53665548--53665585 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
53665538 CTAAAAATTG
53665548 TTATTATGTATGC-TTGAT
1 TTATTAT-TATGCATTGAT
*
53665566 TTATTATTTTGCATTGAT
1 TTATTATTATGCATTGAT
53665584 TT
1 TT
53665586 TCTTATGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.21, C:0.05, G:0.13, T:0.61
Consensus pattern (18 bp):
TTATTATTATGCATTGAT
Found at i:53667300 original size:12 final size:12
Alignment explanation
Indices: 53667283--53667307 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53667273 ACTTAATCAC
53667283 TTTAATATTAAA
1 TTTAATATTAAA
53667295 TTTAATATTAAA
1 TTTAATATTAAA
53667307 T
1 T
53667308 ATTATTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:53670234 original size:32 final size:32
Alignment explanation
Indices: 53670193--53670254 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
53670183 GAATAAAGTA
53670193 TGTGGTGTACATCGATACATCCTACACTGGTC
1 TGTGGTGTACATCGATACATCCTACACTGGTC
*
53670225 TGTGGTGTACATCGATGCATCCTACACTGG
1 TGTGGTGTACATCGATACATCCTACACTGG
53670255 CTTTGGATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (32 bp):
TGTGGTGTACATCGATACATCCTACACTGGTC
Found at i:53672683 original size:21 final size:20
Alignment explanation
Indices: 53672659--53672706 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
53672649 ATTTAGCCCA
* *
53672659 TTTTTCTAATTACAATTGAAT
1 TTTTTCTAACTA-AACTGAAT
* *
53672680 TTTTGCAAACTAAACTGAAT
1 TTTTTCTAACTAAACTGAAT
53672700 TTTTTCT
1 TTTTTCT
53672707 TTCTTTTCTC
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (20 bp):
TTTTTCTAACTAAACTGAAT
Done.