Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 16 of 216
Found at i:5076717 original size:2 final size:2
Alignment explanation
Indices: 5076710--5076741 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5076700 AGCTTAGTAA
*
5076710 AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5076742 CAATTGTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5080702 original size:19 final size:18
Alignment explanation
Indices: 5080660--5080702 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
5080650 GTGAATATTT
* *
5080660 TTATAATTTTTAATTATG
1 TTATAATTTTTAAATAAG
*
5080678 TAATAATTTTTTAAATAAG
1 TTATAA-TTTTTAAATAAG
5080697 TTATAA
1 TTATAA
5080703 GTTTAATCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (18 bp):
TTATAATTTTTAAATAAG
Found at i:5094285 original size:9 final size:9
Alignment explanation
Indices: 5094271--5094313 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
5094261 TTTGGTTAAA
5094271 AATTACCCG
1 AATTACCCG
5094280 AATTACCCG
1 AATTACCCG
*
5094289 AATTAACCG
1 AATTACCCG
*
5094298 AATTAACCG
1 AATTACCCG
5094307 AATTACC
1 AATTACC
5094314 GAAAAATACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.40, C:0.28, G:0.09, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:5096739 original size:18 final size:18
Alignment explanation
Indices: 5096716--5096752 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5096706 ATTTGTTGTA
5096716 ATATAATACCTAGTGAGC
1 ATATAATACCTAGTGAGC
5096734 ATATAATACCTAGTGAGC
1 ATATAATACCTAGTGAGC
5096752 A
1 A
5096753 GCTAGCTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (18 bp):
ATATAATACCTAGTGAGC
Found at i:5111310 original size:44 final size:43
Alignment explanation
Indices: 5111243--5111848 Score: 497
Period size: 44 Copynumber: 13.7 Consensus size: 43
5111233 AAGTCATAAA
* * *
5111243 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGAG-GAAGTAGATCGAAGAT
* * * * *
5111287 AGCAGGTCCTATCTTCCTATATTGATAGGAAGTGGATCCG-AGAT
1 AGCAGATCTTGTCTTCCTATATTG-GAGGAAGTAGAT-CGAAGAT
* * * *
5111331 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAA
1 AGCAGATCTTGTCTTCCTATATTGG-AG-GAAGTAGATCGAAGAT
* * * *
5111375 AGCAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGAG-GAAGTAGATCGAAGAT
* * * * * *
5111419 AGCAGGTCCTATCTTCCTACATTGATAGGAAGT-GTATCCAAGAT
1 AGCAGATCTTGTCTTCCTATATTG-GAGGAAGTAG-ATCGAAGAT
* * *
5111463 -GCAGATCTTGTCTTCCCATATT-GATGGCGAAGTAGATCGCAGAA
1 AGCAGATCTTGTCTTCCTATATTGGA--G-GAAGTAGATCGAAGAT
* * * *
5111507 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGT
1 AGCAGATCTTGTCTTCCTATATTGGAG-GAAGTAGATCGAAGAT
* * *
5111551 AGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGG-AGGAAGTAGATCGAAGAT
* * *
5111595 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCCTATATTGG-AG-GAAGTAGATCGAAGAT
* * *
5111639 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGAG-GAAGTAGATCGAAGAT
* * * * * *
5111683 AGCAGGTCCTATCTTCCTATATTGATAGGAAGTGGATCCAAGAT
1 AGCAGATCTTGTCTTCCTATATTG-GAGGAAGTAGATCGAAGAT
* * *
5111727 -GCAGATCTTGTCTTCCCATATTGGTGGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCCTATATTGGAGGAAGTAGATCGAAGAT
* * * *
5111769 AGCAGATCTGTATCTTCATGATATTGGTGTGAAATAGATCGAAGAT
1 AGCAGATCT-TGTCTTCCT-ATATTGGAG-GAAGTAGATCGAAGAT
*
5111815 AGCAGATCCTTGCCTTCCTATATTGGTAGGAAGT
1 AGCAGAT-CTTGTCTTCCTATATTGG-AGGAAGT
5111849 GGATTGAAAA
Statistics
Matches: 440, Mismatches: 98, Indels: 47
0.75 0.17 0.08
Matches are distributed among these distances:
41 1 0.00
42 14 0.03
43 91 0.21
44 216 0.49
45 87 0.20
46 29 0.07
47 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (43 bp):
AGCAGATCTTGTCTTCCTATATTGGAGGAAGTAGATCGAAGAT
Found at i:5111478 original size:132 final size:132
Alignment explanation
Indices: 5111241--5111852 Score: 1023
Period size: 132 Copynumber: 4.6 Consensus size: 132
5111231 TGAAGTCATA
5111241 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
* *
5111306 TATTGATAGGAAGTGGATCCGAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
5111371 AG
131 AG
*
5111373 AAAGCAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
* * * *
5111438 CATTGATAGGAAGTGTATCCAAGATGCAGATCTTGTCTTCCCATATTGATGGCGAAGTAGATCGC
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
5111503 AG
131 AG
* *
5111505 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
* *
5111570 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
5111635 AG
131 AG
5111637 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
5111702 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGT-G-GAAGTAGATCGA
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
5111765 AG
131 AG
* * * *
5111767 AAAGCAGATCTGTATCTTCATGATATTGGTGTGAAATAGATCGAAGATAGCAGATCCT-TGCCTT
1 AAAGCAGATCT-TGTCTTCATG-TATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTAT--CTT
*
5111831 CCTATATTGGTAGGAAGTGGAT
62 CCTATATTGATAGGAAGTGGAT
5111853 TGAAAAACAG
Statistics
Matches: 453, Mismatches: 23, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
130 25 0.06
131 11 0.02
132 393 0.87
133 24 0.05
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (132 bp):
AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
AG
Found at i:5111895 original size:89 final size:88
Alignment explanation
Indices: 5111458--5111903 Score: 290
Period size: 88 Copynumber: 5.1 Consensus size: 88
5111448 AAGTGTATCC
* * * * *
5111458 AAGATGCAGATCTTGTCTTCCCATATTGATGGCGAAGTAGATCGCAGAAAGCAGATCT-TGTCTT
1 AAGATGCAGATCTTGCCTTCCCATATTGGT-G-GAAGTAGATCGAAGAAAGCAGATCTCTATCTC
* *
5111522 CATG-TATTGGCGTGAAGTAGATCG
64 CATGATATTGGAGTGAAATAGATCG
* * ** * * * *
5111546 AAGGTAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAG-ATGCAGATCT-TGTCTT
1 AAGAT-GCAGATCTTGCCTTCCCATATTGGT-GGAAGTAGATCGAAGAAAGCAGATCTCTATC-T
* * * *
5111609 CC--CATATTGGTGGCGAAGTAGATCG
63 CCATGATATTGG-AGTGAAATAGATCG
* * *** * * *
5111634 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTC-CTATCTT
1 AAG-ATGCAGATCTTGCCTTCCCATATTGGTG-GAAGTAGATCGAAGAAAGCAGATCTCTATC-T
* * * *
5111698 CC-T-ATATTGATAG-GAAGTGGATCC
63 CCATGATATTG-GAGTGAAATAGATCG
* * *
5111722 AAGATGCAGATCTTGTCTTCCCATATTGGTGGAAGTAGATCGAAGAAAGCAGATCTGTATCTTCA
1 AAGATGCAGATCTTGCCTTCCCATATTGGTGGAAGTAGATCGAAGAAAGCAGATCTCTATCTCCA
*
5111787 TGATATTGGTGTGAAATAGATCG
66 TGATATTGGAGTGAAATAGATCG
* * *
5111810 AAGATAGCAGATCCTTGCCTTCCTATATTGGTAGGAAGTGGATTGAA-AAA-CAGA-CTCTATCT
1 AAGAT-GCAGAT-CTTGCCTTCCCATATTGGT-GGAAGTAGATCGAAGAAAGCAGATCTCTATCT
* * *
5111872 CCCTG-TATTTGGCAGTGGAATAGATTG
63 CCATGATA-TTGG-AGTGAAATAGATCG
5111899 AAGAT
1 AAGAT
5111904 CAAAGATGGC
Statistics
Matches: 286, Mismatches: 53, Indels: 37
0.76 0.14 0.10
Matches are distributed among these distances:
86 24 0.08
87 51 0.18
88 111 0.39
89 68 0.24
90 20 0.07
91 12 0.04
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (88 bp):
AAGATGCAGATCTTGCCTTCCCATATTGGTGGAAGTAGATCGAAGAAAGCAGATCTCTATCTCCA
TGATATTGGAGTGAAATAGATCG
Found at i:5112056 original size:40 final size:40
Alignment explanation
Indices: 5112006--5112322 Score: 300
Period size: 40 Copynumber: 7.8 Consensus size: 40
5111996 AAGATTTCAG
* * *
5112006 GTCTTATCTCCCTAAGTAATAGTGGAGCAGATCGCATCAA
1 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCACCAA
* * ** *
5112046 GTCTCATCTCCCTAAGCAGTAGTGGAGTAGA-CAAAACCACG
1 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-GCACCA-A
* * *
5112087 GATCTTATTTCCCTAAGCAATAGTGGAGCAGATCGCATCAA
1 G-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCACCAA
* *
5112128 GTCTTATCTCCCTAAGCAGTAGCGGAG-AGGA-CGAAACCACA
1 GTCTTATCTCCCTAAGCAGTAGTGGAGCA-GATCG-CACCA-A
*
5112169 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAA
1 G-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCACCAA
* * * *
5112210 GTCTTATCTCCTTAAGCAGTAGCGGAGCAGA-AGAAACCACA
1 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG-CACCA-A
* * *
5112251 GATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCACACCCA
1 G-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCACCAA
* **
5112292 TTCTTATCTCCCTAAATAGTAGTGGAGCAGA
1 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGA
5112323 CTAAAAACAC
Statistics
Matches: 225, Mismatches: 38, Indels: 28
0.77 0.13 0.10
Matches are distributed among these distances:
39 5 0.02
40 118 0.52
41 9 0.04
42 89 0.40
43 4 0.02
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (40 bp):
GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCACCAA
Found at i:5112109 original size:82 final size:82
Alignment explanation
Indices: 5112007--5112338 Score: 443
Period size: 82 Copynumber: 4.0 Consensus size: 82
5111997 AGATTTCAGG
* * *
5112007 TCTTATCTCCCTAAGTAATAGTGGAGCAGATCGCATCAAGTCTCATCTCCCTAAGCAGTAGTGGA
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGCGGA
* *
5112072 GTAGACAAAACCACGGA
66 GCAGACAAAACCACAGA
*
5112089 TCTTATTTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGCGGA
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGCGGA
*
5112154 G-AGGACGAAACCACAGA
66 GCA-GACAAAACCACAGA
* *
5112171 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCTTAAGCAGTAGCGGA
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGCGGA
5112236 GCAGA-AGAAACCACAGA
66 GCAGACA-AAACCACAGA
* * * * * * ** *
5112253 TCTTATCTCCCTAAGTAGTAGTGGAGCAGATCACACCCATTCTTATCTCCCTAAATAGTAGTGGA
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGCGGA
* *
5112318 GCAGACTAAAAACACAAA
66 GCAGAC-AAAACCACAGA
5112336 TCT
1 TCT
5112339 CATCCCCATG
Statistics
Matches: 224, Mismatches: 21, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
81 1 0.00
82 210 0.94
83 12 0.05
84 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.23
Consensus pattern (82 bp):
TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGCGGA
GCAGACAAAACCACAGA
Found at i:5112226 original size:122 final size:122
Alignment explanation
Indices: 5112089--5112322 Score: 271
Period size: 122 Copynumber: 1.9 Consensus size: 122
5112079 AAACCACGGA
* * * * *
5112089 TCTTATTTCCCTAAGCAATAGTGGAGCAGATCG-CATCA-AG-TCTTATCTCCCTAAGCAGTAGC
1 TCTTATCTCCCTAAGCAATAGCGGAGCAGA-AGAAACCACAGATCTTATCTCCCTAAGCAGTAGC
*
5112151 GGAG-AGGA-CGAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
65 GGAGCA-GATC-AAACC-CA-ATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGCATCAAG
* * * *
5112211 TCTTATCTCCTTAAGCAGTAGCGGAGCAGAAGAAACCACAGATCTTATCTCCCTAAGTAGTAGTG
1 TCTTATCTCCCTAAGCAATAGCGGAGCAGAAGAAACCACAGATCTTATCTCCCTAAGCAGTAGCG
* * *
5112276 GAGCAGATCACACCCATTCTTATCTCCCTAAATAGTAGTGGAGCAGA
66 GAGCAGATCAAACCCAATCTTATCTCCCTAAACAGTAGTGGAGCAGA
5112323 CTAAAAACAC
Statistics
Matches: 94, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
121 1 0.01
122 57 0.61
123 4 0.04
124 30 0.32
125 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (122 bp):
TCTTATCTCCCTAAGCAATAGCGGAGCAGAAGAAACCACAGATCTTATCTCCCTAAGCAGTAGCG
GAGCAGATCAAACCCAATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGCATCAAG
Found at i:5117474 original size:49 final size:47
Alignment explanation
Indices: 5117206--5117708 Score: 760
Period size: 47 Copynumber: 10.6 Consensus size: 47
5117196 CCCTTCGGGA
* * *
5117206 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
5117253 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
5117300 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
5117347 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
5117394 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
5117441 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
5117490 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
5117537 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
5117586 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
5117633 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
5117682 CTTATCACATATATATACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
5117709 TATTCAAATA
Statistics
Matches: 429, Mismatches: 19, Indels: 16
0.92 0.04 0.03
Matches are distributed among these distances:
46 1 0.00
47 291 0.68
49 136 0.32
50 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:5117530 original size:96 final size:96
Alignment explanation
Indices: 5117206--5117708 Score: 786
Period size: 96 Copynumber: 5.3 Consensus size: 96
5117196 CCCTTCGGGA
* * *
5117206 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATAC
5117269 ACTTTCACATTCATCACATTGGCCATTCGGC
66 ACTTTCACATTCATCACATTGGCCATTCGGC
* * * *
5117300 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ACATACA
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATA
5117362 CA-TGTTCACATTCATCACATTGGCCATTCGGC
65 CACT-TTCACATTCATCACATTGGCCATTCGGC
* *
5117394 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATA
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATA
5117458 CACTTTCACATTCATCACATTGGCCATTCGGC
65 CACTTTCACATTCATCACATTGGCCATTCGGC
*
5117490 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATAC
* *
5117555 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATTGGCCATTCGGC
* *
5117586 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATAC
*
5117651 ACTTTCACATTCATCACATTGGCCATTAGGC
66 ACTTTCACATTCATCACATTGGCCATTCGGC
*
5117682 CTTATCACATATATATACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
5117709 TATTCAAATA
Statistics
Matches: 386, Mismatches: 17, Indels: 10
0.93 0.04 0.02
Matches are distributed among these distances:
93 2 0.01
94 138 0.36
96 244 0.63
97 2 0.01
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.34
Consensus pattern (96 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:5119220 original size:56 final size:56
Alignment explanation
Indices: 5119153--5119272 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
5119143 TATTAGTTTA
5119153 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
5119209 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
5119265 TTGCCCAT
1 TTGCCCAT
5119273 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:5121940 original size:125 final size:125
Alignment explanation
Indices: 5121718--5122105 Score: 613
Period size: 125 Copynumber: 3.1 Consensus size: 125
5121708 ATTGCTCAAG
5121718 GTATCATCCATGGCTC-AATCATGTTTTTAA-AGCTAAGCTGCATTAGTTGAAGTCAACCCGGAA
1 GTATCATCCATGG-TCGAATCATGTTTTTAACA-CTAAGCTGCATTAGTTGAAGTCAACCCGGAA
5121781 AAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTCAT-TTATTC
64 AAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATT-ATCTTATTC
* *
5121843 GTATCATCCATGGTCGAATCATGTTTTTAACACTAAGCTGCATTAGTTGAAGTCAACCCTGAAGA
1 GTATCATCCATGGTCGAATCATGTTTTTAACACTAAGCTGCATTAGTTGAAGTCAACCCGGAAAA
* *
5121908 ACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTTTCTTATTT
66 ACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTATCTTATTC
* * * *
5121968 GTATCATCCATGGTTGAATCTTGTTTTTAACGCTAAGCTGCATTAGTTGAAATCAACCCGGAAAA
1 GTATCATCCATGGTCGAATCATGTTTTTAACACTAAGCTGCATTAGTTGAAGTCAACCCGGAAAA
* **
5122033 ACTATAATTTTACATGTTTCTATTCTAGTG-TATATTGCTTGAGCACCATTATCTTATTC
66 ACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTATCTTATTC
*
5122092 ATATCATCCATGGT
1 GTATCATCCATGGT
5122106 TGAGTCTTAT
Statistics
Matches: 244, Mismatches: 16, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
124 43 0.18
125 200 0.82
126 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (125 bp):
GTATCATCCATGGTCGAATCATGTTTTTAACACTAAGCTGCATTAGTTGAAGTCAACCCGGAAAA
ACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTATCTTATTC
Found at i:5122219 original size:100 final size:99
Alignment explanation
Indices: 5122040--5122219 Score: 270
Period size: 100 Copynumber: 1.8 Consensus size: 99
5122030 AAAACTATAA
* *
5122040 TTTTACATGTTTCTATTCTAGTGTATATTGCTTGAGCACCATTATCTTATTCATATCATCCATGG
1 TTTTACATGTTTCTATTCTAGTGTATATTGCTTGACCACCATTATCTTATTCATATCATCCATGA
** * *
5122105 TTGAGTCTTATTTTTCAACCTGAAAAAACTTTTC
66 TCAAATCATATTTTTCAACCTGAAAAAACTTTTC
* *
5122139 TTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTATCTTATTCGTGTCATCCATG
1 TTTTACATGTTTCTATTCTAGTG-TATATTGCTTGACCACCATTATCTTATTCATATCATCCATG
*
5122204 ATCAAATCATGTTTTT
65 ATCAAATCATATTTTT
5122220 TTATAGCTAA
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
99 23 0.32
100 48 0.68
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.46
Consensus pattern (99 bp):
TTTTACATGTTTCTATTCTAGTGTATATTGCTTGACCACCATTATCTTATTCATATCATCCATGA
TCAAATCATATTTTTCAACCTGAAAAAACTTTTC
Found at i:5122333 original size:351 final size:350
Alignment explanation
Indices: 5121770--5122426 Score: 1023
Period size: 351 Copynumber: 1.9 Consensus size: 350
5121760 TTAGTTGAAG
* *
5121770 TCAACCCGGAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTC
1 TCAACCCGAAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTC
* * *
5121835 ATTTATTCGTATCATCCATGGTCGAATCATGTTTTTAACACTAAGCTGCATTAGTTGAAGTCAAC
66 ATTTATTCGTATCATCCATGATCAAATCATGTTTTTAACACTAAGCTGCATTAGTTGAAATCAAC
* * *
5121900 CCTGAAGAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTTTCTTA
131 CCTGAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGAACCATTATCTTA
* * * * *
5121965 TTTGTATCATCCATGGTTGAATCTTGTTTTTAACGCTAAGCTGCATTAGTTGAAATCAACCCGGA
196 TTCGTATCATCCATGGTTGAATCATGTTTTTAAAGCTAAGCTGCATTAATTGAAATCAACCCGAA
5122030 AAAACTATAATTTTACATGTTTCTATTCTAGTG-TATATTGCTTGAGCACCATTATCTTATTCAT
261 AAAACTATAATTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTATCTTATTCAT
5122094 ATCATCCATGGTTGAGTCTTATTTT
326 ATCATCCATGGTTGAGTCTTATTTT
*
5122119 TCAACCTGAAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATT-
1 TCAACCCGAAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTC
* * * *
5122183 ATCTTATTCGTGTCATCCATGATCAAATCATGTTTTTTTATAGCTAAGCTGCGTTAGTTGAAATC
66 AT-TTATTCGTATCATCCATGATCAAATCATG-TTTTTAACA-CTAAGCTGCATTAGTTGAAATC
* * *
5122248 TA-CCTGGAAAAACTTTTCTTTTTCATGTTTGTATTCTAGTGATATATTGCTTGAGAACCATTAT
128 AACCCT-GAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGAACCATTAT
* *
5122312 CTTATTCGTATCATCCATGGTTGAGTCATGTTTTTAAAGCTAAGCTGCATTAATTGCAATCAACC
192 CTTATTCGTATCATCCATGGTTGAATCATGTTTTTAAAGCTAAGCTGCATTAATTGAAATCAACC
* **
5122377 CGAAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGA
257 CGAAAAAACTATAATTTTACATGTTTCTATTCTAGTGATATATTGCTTGA
5122427 ACAGCTTGAA
Statistics
Matches: 277, Mismatches: 26, Indels: 7
0.89 0.08 0.02
Matches are distributed among these distances:
348 2 0.01
349 87 0.31
350 10 0.04
351 166 0.60
352 12 0.04
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.42
Consensus pattern (350 bp):
TCAACCCGAAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTC
ATTTATTCGTATCATCCATGATCAAATCATGTTTTTAACACTAAGCTGCATTAGTTGAAATCAAC
CCTGAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGAACCATTATCTTA
TTCGTATCATCCATGGTTGAATCATGTTTTTAAAGCTAAGCTGCATTAATTGAAATCAACCCGAA
AAAACTATAATTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTATCTTATTCAT
ATCATCCATGGTTGAGTCTTATTTT
Found at i:5122423 original size:125 final size:126
Alignment explanation
Indices: 5122128--5122857 Score: 744
Period size: 125 Copynumber: 5.7 Consensus size: 126
5122118 TTCAACCTGA
*
5122128 AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTATCTTATTCG
1 AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTATCTTATTCG
* * ** * * * **
5122193 TGTCATCCATGATCAAATCATGTTTTTTTATAGCTAAGCTGCGTTAGTTGAAATCTACCTGG
66 TATCATCCATGGTTGAATCATG-TTTTTTAAAGCTAAGCTGCATTAGTTGAAATCAACCCAG
* * *
5122255 AAAAACTTTTCTTTTTCATGTTTGTATTCTAGTGATATATTGCTTGAGAACCATTATCTTATTCG
1 AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTATCTTATTCG
* * *
5122320 TATCATCCATGGTTGAGTCATG-TTTTTAAAGCTAAGCTGCATTAATTGCAATCAACCC-G
66 TATCATCCATGGTTGAATCATGTTTTTTAAAGCTAAGCTGCATTAGTTGAAATCAACCCAG
5122379 AAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAACAGCTTGAACACCATT
1 -AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTG---A----G--CACCATT
* ** * *
5122444 TTCTTTATTCGTATCATCCATAATTGAATCATGTTTTTCTATAGCTAAGCTGCATCAGTTGAAAT
56 ATC-TTATTCGTATCATCCATGGTTGAATCATGTTTTT-TAAAGCTAAGCTGCATTAGTTGAAAT
**
5122509 TGACCCAG
119 CAACCCAG
*
5122517 AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCA-CATTATCTTATTCG
1 AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTATCTTATTCG
** ** * **
5122581 TATCATTTATGGTCAAATCATGTTTTTTATATAGCTAAGCTGCATTGGTTGAAATTGACCCAG
66 TATCATCCATGGTTGAATCATGTTTTTTA-A-AGCTAAGCTGCATTAGTTGAAATCAACCCAG
* *
5122644 AAAAACTTTTCTTTTTTACATG----T-TTCTAGTGATATATTGCCTGAGCACCATTCA-ATTAT
1 AAAAACTTTTC--TTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATT-ATCTTAT
* * * ** *
5122703 TCATATCATCCATGGTAGGATGGTG-TTTTTAAAGCTAAGCTGCATTAGTTGAAATCAATCCAG
63 TCGTATCATCCATGGTTGAATCATGTTTTTTAAAGCTAAGCTGCATTAGTTGAAATCAACCCAG
* * * * * * ***
5122766 TAAAGCTTATCTTTTACATGTTCCTATTCCT-GTGATGTATTGCTCGAGCACTGGTATCTTATTC
1 AAAAACTTTTCTTTTACATGTTTCTATT-CTAGTGATATATTGCTTGAGCACCATTATCTTATTC
* * * *
5122830 ATGTCATCCATGGTTGAATAAGGTTTTT
65 GTATCATCCATGGTTGAATCATGTTTTT
5122858 ATAGCTTGGC
Statistics
Matches: 505, Mismatches: 70, Indels: 57
0.80 0.11 0.09
Matches are distributed among these distances:
120 9 0.02
122 35 0.07
123 1 0.00
124 31 0.06
125 145 0.29
126 35 0.07
127 124 0.25
128 3 0.01
129 9 0.02
132 1 0.00
134 9 0.02
135 26 0.05
136 4 0.01
137 72 0.14
138 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (126 bp):
AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTATCTTATTCG
TATCATCCATGGTTGAATCATGTTTTTTAAAGCTAAGCTGCATTAGTTGAAATCAACCCAG
Found at i:5122530 original size:137 final size:132
Alignment explanation
Indices: 5122128--5122814 Score: 627
Period size: 127 Copynumber: 5.4 Consensus size: 132
5122118 TTCAACCTGA
5122128 AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGA-C-----CACCATTATCT
1 AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCTTGAACACCATTATCT
* * ** *
5122187 TATTCGTGTCATCCATGATCAAATCATGTTTTTTTATAGCTAAGCTGCGTTAGTTGAAATCT-AC
66 TATTCGTATCATCCATGGTTGAATCATG-TTTTTTATAGCTAAGCTGCATTAGTTGAAAT-TGAC
**
5122251 CTGG
129 CCAG
* *
5122255 AAAAACTTTTCTTTTTCATGTTTGTATTCTAGTGATATATTGCTTGA----G-A-ACCATTATCT
1 AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCTTGAACACCATTATCT
* * * * **
5122314 TATTCGTATCATCCATGGTTGAGTCATG-TTTTTAAAGCTAAGCTGCATTAATTGCAATCAACCC
66 TATTCGTATCATCCATGGTTGAATCATGTTTTTTATAGCTAAGCTGCATTAGTTGAAATTGACCC
5122378 -G
131 AG
5122379 AAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAACAGCTTGAACACCATT
1 -AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTG---AGCTTGAACACCATT
* ** *
5122444 TTCTTTATTCGTATCATCCATAATTGAATCATGTTTTTCTATAGCTAAGCTGCATCAGTTGAAAT
62 ATC-TTATTCGTATCATCCATGGTTGAATCATGTTTTT-TATAGCTAAGCTGCATTAGTTGAAAT
5122509 TGACCCAG
125 TGACCCAG
5122517 AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGA-C-----CA-CATTATCT
1 AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCTTGAACACCATTATCT
** ** *
5122575 TATTCGTATCATTTATGGTCAAATCATGTTTTTTATATAGCTAAGCTGCATTGGTTGAAATTGAC
66 TATTCGTATCATCCATGGTTGAATCATG-TTTTT-TATAGCTAAGCTGCATTAGTTGAAATTGAC
5122640 CCAG
129 CCAG
*
5122644 AAAAACTTTTCTTTTTTACATG----T-TTCTAGTGATATATTGC-----C-TGAGCACCATTCA
1 AAAAACTTTTC--TTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCTTGAACACCATT-A
* * * * ** * **
5122698 -ATTATTCATATCATCCATGGTAGGATGGTG-TTTTTAAAGCTAAGCTGCATTAGTTGAAATCAA
63 TCTTATTCGTATCATCCATGGTTGAATCATGTTTTTTATAGCTAAGCTGCATTAGTTGAAATTGA
*
5122761 TCCAG
128 CCCAG
* * * * * *
5122766 TAAAGCTTATCTTTTACATGTTCCTATTCCT-GTGATGTATTGCTCGAGC
1 AAAAACTTTTCTTTTACATGTTTCTATT-CTAGTGATATATTGCTTGAGC
5122815 ACTGGTATCT
Statistics
Matches: 470, Mismatches: 53, Indels: 71
0.79 0.09 0.12
Matches are distributed among these distances:
120 10 0.02
122 37 0.08
123 4 0.01
124 21 0.04
125 112 0.24
126 26 0.06
127 132 0.28
128 3 0.01
129 9 0.02
130 1 0.00
132 1 0.00
133 2 0.00
134 9 0.02
135 26 0.06
136 4 0.01
137 72 0.15
138 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.41
Consensus pattern (132 bp):
AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCTTGAACACCATTATCT
TATTCGTATCATCCATGGTTGAATCATGTTTTTTATAGCTAAGCTGCATTAGTTGAAATTGACCC
AG
Found at i:5138529 original size:46 final size:46
Alignment explanation
Indices: 5138462--5138559 Score: 187
Period size: 46 Copynumber: 2.1 Consensus size: 46
5138452 CTATTCTACT
5138462 ATGTCTAGGTGATGAAGTATTATGAGAGTTAGCCGAAAAGACCATC
1 ATGTCTAGGTGATGAAGTATTATGAGAGTTAGCCGAAAAGACCATC
*
5138508 ATGTCTAGGTGATGAAGTATTATGAGAGTTCGCCGAAAAGACCATC
1 ATGTCTAGGTGATGAAGTATTATGAGAGTTAGCCGAAAAGACCATC
5138554 ATGTCT
1 ATGTCT
5138560 GGTTTGTAGC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (46 bp):
ATGTCTAGGTGATGAAGTATTATGAGAGTTAGCCGAAAAGACCATC
Found at i:5139906 original size:13 final size:13
Alignment explanation
Indices: 5139888--5139914 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5139878 GTGCATTCAT
5139888 TAGTTAATTTAGA
1 TAGTTAATTTAGA
5139901 TAGTTAATTTAGA
1 TAGTTAATTTAGA
5139914 T
1 T
5139915 TTTAATCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TAGTTAATTTAGA
Found at i:5144137 original size:21 final size:21
Alignment explanation
Indices: 5144111--5144151 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5144101 AGACGAGCAA
* *
5144111 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
5144132 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
5144152 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:5153767 original size:24 final size:23
Alignment explanation
Indices: 5153735--5153787 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
5153725 TTTTTTTCTA
*
5153735 TTGTATTCTACTATTCTTTTGCC
1 TTGTTTTCTACTATTCTTTTGCC
* * *
5153758 TCTGTTTTCTTCTATTGTTTTGTC
1 T-TGTTTTCTACTATTCTTTTGCC
5153782 TTGTTT
1 TTGTTT
5153788 GCAGGTTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.08, C:0.17, G:0.11, T:0.64
Consensus pattern (23 bp):
TTGTTTTCTACTATTCTTTTGCC
Found at i:5155289 original size:25 final size:23
Alignment explanation
Indices: 5155256--5155301 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
5155246 ATATTGCCAG
5155256 GCTCAAGTTTGACTTGAAATATTCA
1 GCTCAAGTTTGA-TTG-AATATTCA
*
5155281 GCTCGAGTTTGATTGAATATT
1 GCTCAAGTTTGATTGAATATT
5155302 TATTTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (23 bp):
GCTCAAGTTTGATTGAATATTCA
Found at i:5155684 original size:25 final size:25
Alignment explanation
Indices: 5155620--5155686 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
5155610 GTGAAGAGAA
* *
5155620 ATTATTTTAAAAATCAATTTTTTAAAT
1 ATTACTTTAAAAA-C-ATCTTTTAAAT
* *
5155647 ATAACTTTGAAAACATCTTTTAACAT
1 ATTACTTTAAAAACATCTTTTAA-AT
5155673 ATTA-TTTAAAAACA
1 ATTACTTTAAAAACA
5155687 ATTTACAAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
25 17 0.52
26 6 0.18
27 10 0.30
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.43
Consensus pattern (25 bp):
ATTACTTTAAAAACATCTTTTAAAT
Found at i:5156137 original size:11 final size:11
Alignment explanation
Indices: 5156130--5156171 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
5156120 TGGCAAAATG
5156130 ACAACAAAACA
1 ACAACAAAACA
**
5156141 ACAACAAAATT
1 ACAACAAAACA
*
5156152 GCAACAAAACA
1 ACAACAAAACA
5156163 ACAACAAAA
1 ACAACAAAA
5156172 AAATTTAGGC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.69, C:0.24, G:0.02, T:0.05
Consensus pattern (11 bp):
ACAACAAAACA
Found at i:5156148 original size:22 final size:22
Alignment explanation
Indices: 5156123--5156171 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
5156113 AATAGAATGG
5156123 CAAAA-TGACAACAAAACAACAA
1 CAAAATTG-CAACAAAACAACAA
5156145 CAAAATTGCAACAAAACAACAA
1 CAAAATTGCAACAAAACAACAA
5156167 CAAAA
1 CAAAA
5156172 AAATTTAGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 24 0.92
23 2 0.08
ACGTcount: A:0.67, C:0.22, G:0.04, T:0.06
Consensus pattern (22 bp):
CAAAATTGCAACAAAACAACAA
Found at i:5162695 original size:87 final size:87
Alignment explanation
Indices: 5162594--5162767 Score: 339
Period size: 87 Copynumber: 2.0 Consensus size: 87
5162584 TATATCAAGA
5162594 ACATAATACCTTATTTAAGAAAACTCAACTATAACATCATTTCTATGCATTTTCAATAATATCAA
1 ACATAATACCTTATTTAAGAAAACTCAACTATAACATCATTTCTATGCATTTTCAATAATATCAA
5162659 ACTTAAAAATATATTGAAATCT
66 ACTTAAAAATATATTGAAATCT
*
5162681 ACATAATACCTTATTTAAGAAAACTCTACTATAACATCATTTCTATGCATTTTCAATAATATCAA
1 ACATAATACCTTATTTAAGAAAACTCAACTATAACATCATTTCTATGCATTTTCAATAATATCAA
5162746 ACTTAAAAATATATTGAAATCT
66 ACTTAAAAATATATTGAAATCT
5162768 TGATGTTCTT
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.44, C:0.16, G:0.03, T:0.36
Consensus pattern (87 bp):
ACATAATACCTTATTTAAGAAAACTCAACTATAACATCATTTCTATGCATTTTCAATAATATCAA
ACTTAAAAATATATTGAAATCT
Found at i:5163089 original size:23 final size:22
Alignment explanation
Indices: 5163063--5163116 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
5163053 ATATACTAAA
*
5163063 TAAATAATAATAAAATATCTCAT
1 TAAATAATAATAAAATAT-TAAT
* *
5163086 TAAATATTAGTAAAATATTAAT
1 TAAATAATAATAAAATATTAAT
*
5163108 AAAATAATA
1 TAAATAATA
5163117 TTTATCTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (22 bp):
TAAATAATAATAAAATATTAAT
Found at i:5163103 original size:11 final size:11
Alignment explanation
Indices: 5163064--5163113 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
5163054 TATACTAAAT
*
5163064 AAATAATAATA
1 AAATATTAATA
* *
5163075 AAATATCTCATT
1 AAATAT-TAATA
*
5163087 AAATATTAGTA
1 AAATATTAATA
5163098 AAATATTAATA
1 AAATATTAATA
5163109 AAATA
1 AAATA
5163114 ATATTTATCT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
11 22 0.71
12 9 0.29
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (11 bp):
AAATATTAATA
Found at i:5170738 original size:3 final size:3
Alignment explanation
Indices: 5170730--5170768 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
5170720 CCATATATGG
5170730 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
5170769 CTGGTGTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:5176821 original size:9 final size:9
Alignment explanation
Indices: 5176796--5176829 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
5176786 CTAATTAATT
5176796 TTAAATTAA
1 TTAAATTAA
* *
5176805 TCATATTAA
1 TTAAATTAA
5176814 TTAAATTAA
1 TTAAATTAA
5176823 TTAAATT
1 TTAAATT
5176830 TAGATCCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (9 bp):
TTAAATTAA
Found at i:5178262 original size:4 final size:4
Alignment explanation
Indices: 5178255--5178285 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
5178245 ATCAACCAAT
*
5178255 CATA CATA CATA CATG CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CAT
5178286 TATTTGGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.45, C:0.26, G:0.03, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:5178276 original size:16 final size:16
Alignment explanation
Indices: 5178255--5178285 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5178245 ATCAACCAAT
5178255 CATACATACATACATG
1 CATACATACATACATG
5178271 CATACATACATACAT
1 CATACATACATACAT
5178286 TATTTGGGTT
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:0.45, C:0.26, G:0.03, T:0.26
Consensus pattern (16 bp):
CATACATACATACATG
Found at i:5191540 original size:40 final size:40
Alignment explanation
Indices: 5191484--5191573 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
5191474 ATTGGCCAAT
*
5191484 CGTTG-TTTTTGCTAATTT-ATTGCATATAAAATGTTTAAC
1 CGTTGATTTTTGCTAATTTCA-TGCATATAAAATGTTGAAC
* *
5191523 CGTTGATTTTTGTTAATTTCATGCATATAAATTGTTGAAC
1 CGTTGATTTTTGCTAATTTCATGCATATAAAATGTTGAAC
*
5191563 TGTTGATTTTT
1 CGTTGATTTTT
5191574 AAGTCAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
39 5 0.11
40 39 0.87
41 1 0.02
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.51
Consensus pattern (40 bp):
CGTTGATTTTTGCTAATTTCATGCATATAAAATGTTGAAC
Found at i:5198654 original size:34 final size:35
Alignment explanation
Indices: 5198594--5198660 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
5198584 CAAACACCAG
*
5198594 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* * *
5198629 AAAACATTTTCCCG-AAATTATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
5198661 TATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:5204726 original size:36 final size:37
Alignment explanation
Indices: 5204668--5204740 Score: 121
Period size: 36 Copynumber: 2.0 Consensus size: 37
5204658 CATGATTACC
* *
5204668 AAATAAAATTTACATAAACTAAATTTTAAATTTTAAA
1 AAATAAAATATACAAAAACTAAATTTTAAATTTTAAA
5204705 AAATAAAA-ATACAAAAACTAAATTTTAAATTTTAAA
1 AAATAAAATATACAAAAACTAAATTTTAAATTTTAAA
5204741 TTTTCAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 26 0.76
37 8 0.24
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.34
Consensus pattern (37 bp):
AAATAAAATATACAAAAACTAAATTTTAAATTTTAAA
Found at i:5211208 original size:28 final size:29
Alignment explanation
Indices: 5211173--5211227 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
5211163 AATATATATT
5211173 TTTATTTTTTA-ATTTTAAAATATTTTTA
1 TTTATTTTTTATATTTTAAAATATTTTTA
* *
5211201 TTT-TTTTTTATTTTTTTAAATATTTTT
1 TTTATTTTTTATATTTTAAAATATTTTT
5211228 TTTGTGTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (29 bp):
TTTATTTTTTATATTTTAAAATATTTTTA
Found at i:5211241 original size:22 final size:21
Alignment explanation
Indices: 5211202--5211242 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5211192 ATATTTTTAT
*
5211202 TTTTTTTTATTTTTTTAAATA
1 TTTTTTTTATTTTATTAAATA
*
5211223 TTTTTTTTGTGTTTATTAAA
1 TTTTTTTTAT-TTTATTAAA
5211243 AATAGGGTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (21 bp):
TTTTTTTTATTTTATTAAATA
Found at i:5212925 original size:45 final size:47
Alignment explanation
Indices: 5212874--5212964 Score: 132
Period size: 47 Copynumber: 2.0 Consensus size: 47
5212864 TTTGACATCG
**
5212874 TTTCTAC-TTTTTTTGA-TATTGTTTTTACCCGTAATATCAACTCAA
1 TTTCTACTTTTTTTTGAGTACCGTTTTTACCCGTAATATCAACTCAA
* *
5212919 TTTCTACTTTTTTTTTAGTACCGTTTTTACTCGTAATATCAACTCA
1 TTTCTACTTTTTTTTGAGTACCGTTTTTACCCGTAATATCAACTCA
5212965 TTAAAATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 7 0.17
46 8 0.20
47 25 0.62
ACGTcount: A:0.23, C:0.19, G:0.07, T:0.52
Consensus pattern (47 bp):
TTTCTACTTTTTTTTGAGTACCGTTTTTACCCGTAATATCAACTCAA
Found at i:5223323 original size:16 final size:16
Alignment explanation
Indices: 5223292--5223321 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5223282 TTATTTCATA
5223292 AATATTTCTAAAAAAT
1 AATATTTCTAAAAAAT
5223308 AATATTT-TAAAAAA
1 AATATTTCTAAAAAA
5223322 ATTAAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
AATATTTCTAAAAAAT
Found at i:5237366 original size:31 final size:31
Alignment explanation
Indices: 5237331--5237398 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
5237321 AGTCTTAATG
*
5237331 TGGGAAAAGTTGTGAAGTCTAGGCCCCAATA
1 TGGGAAAAGTTGTGAAGTCCAGGCCCCAATA
* *
5237362 TGGGAAAAGTTGTGAAGTCCAGGTCCCAATG
1 TGGGAAAAGTTGTGAAGTCCAGGCCCCAATA
5237393 TGGGAA
1 TGGGAA
5237399 CAATTGCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.31, C:0.15, G:0.32, T:0.22
Consensus pattern (31 bp):
TGGGAAAAGTTGTGAAGTCCAGGCCCCAATA
Found at i:5238230 original size:17 final size:18
Alignment explanation
Indices: 5238186--5238232 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
5238176 TATAATTAAT
5238186 TTTAAATAAAAATATTGAA
1 TTTAAAT-AAAATATTGAA
* * *
5238205 TTTATATAAAAT-TTTAG
1 TTTAAATAAAATATTGAA
5238222 TTTAAATAAAA
1 TTTAAATAAAA
5238233 AAATTCAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 13 0.54
18 5 0.21
19 6 0.25
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (18 bp):
TTTAAATAAAATATTGAA
Found at i:5247431 original size:83 final size:83
Alignment explanation
Indices: 5247292--5247463 Score: 326
Period size: 83 Copynumber: 2.1 Consensus size: 83
5247282 TGTGCCATTG
*
5247292 TATCTTGAAGCTCTTTGGTAACCTAAAATCGACAGATTCTCATAAGGTGAAATACAAAACCTCCC
1 TATCTTGAAGCTCTTTGGTAACCTAAAATCAACAGATTCTCATAAGGTGAAATACAAAACCTCCC
*
5247357 TAAATTTGTCATCACTAT
66 TAAATTTGTCATCACTAC
5247375 TATCTTGAAGCTCTTTGGTAACCTAAAATCAACAGATTCTCATAAGGTGAAATACAAAACCTCCC
1 TATCTTGAAGCTCTTTGGTAACCTAAAATCAACAGATTCTCATAAGGTGAAATACAAAACCTCCC
5247440 TAAATTTGTCATCACTAC
66 TAAATTTGTCATCACTAC
5247458 TATCTT
1 TATCTT
5247464 CACAGTCAAA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 87 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (83 bp):
TATCTTGAAGCTCTTTGGTAACCTAAAATCAACAGATTCTCATAAGGTGAAATACAAAACCTCCC
TAAATTTGTCATCACTAC
Found at i:5249625 original size:23 final size:22
Alignment explanation
Indices: 5249561--5249625 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
5249551 ACAAATACAG
5249561 GAGCACATAAGTGCTAAA-TCAA
1 GAGCAC-TAAGTGCTAAATTCAA
* *
5249583 GAGCACCAAAATGCTAAATTCAA
1 GAGCA-CTAAGTGCTAAATTCAA
5249606 GAGCACTGAAGTGCTAAATT
1 GAGCACT-AAGTGCTAAATT
5249626 AATGAACGCG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 15 0.42
23 21 0.58
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.20
Consensus pattern (22 bp):
GAGCACTAAGTGCTAAATTCAA
Found at i:5252662 original size:41 final size:41
Alignment explanation
Indices: 5252601--5252762 Score: 177
Period size: 41 Copynumber: 4.0 Consensus size: 41
5252591 TGAAAATAAG
*
5252601 ATGTTTCAGACTTTACGTCTAAG-AGGCTTGATGCCGATGAA
1 ATGTTTCAGACTTTATGTCT-AGCAGGCTTGATGCCGATGAA
5252642 ATGTTTCAGACTTTATGTCTAGCAGGCTTGATGCC-AGTGAA
1 ATGTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGA-TGAA
* ** *
5252683 TTACTTCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAA
1 ATGTTTCAGACTTTATGTCTAGCAGGC-TTGATGCCGATGAA
* * * * * *
5252724 ATGTATCGGGCTTTGTGCCTAGCAGGCTTTATGCCGATG
1 ATGTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGATG
5252763 TTTTATACAA
Statistics
Matches: 101, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
40 5 0.05
41 93 0.92
42 3 0.03
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (41 bp):
ATGTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGATGAA
Found at i:5252718 original size:82 final size:82
Alignment explanation
Indices: 5252605--5252758 Score: 204
Period size: 82 Copynumber: 1.9 Consensus size: 82
5252595 AATAAGATGT
* *
5252605 TTCAGACTTTACGTCTAAGAGGCTTGATGCCGATGAAATGTTTCAGACTTTATGTCTAGCAGGCT
1 TTCAGACTTTACGTCTAAGAGGCTTGATGCCGATGAAATGTATCAGACTTTATGCCTAGCAGGCT
5252670 TGATGCCAGTGAATTAC
66 TGATGCCAGTGAATTAC
* * * * *
5252687 TTCAGACTTTATGTCT-AGCAGGCTTTG-TGCCGGTGAAATGTATCGGGCTTTGTGCCTAGCAGG
1 TTCAGACTTTACGTCTAAG-AGGC-TTGATGCCGATGAAATGTATCAGACTTTATGCCTAGCAGG
*
5252750 CTTTATGCC
64 CTTGATGCC
5252759 GATGTTTTAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
81 2 0.03
82 57 0.92
83 3 0.05
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.34
Consensus pattern (82 bp):
TTCAGACTTTACGTCTAAGAGGCTTGATGCCGATGAAATGTATCAGACTTTATGCCTAGCAGGCT
TGATGCCAGTGAATTAC
Found at i:5254142 original size:35 final size:35
Alignment explanation
Indices: 5254096--5254165 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
5254086 CCATACTTGT
5254096 TATTCGAACACACAAAAAAATTTGTCTTAAGTTTC
1 TATTCGAACACACAAAAAAATTTGTCTTAAGTTTC
5254131 TATTCGAACACACAAAAAAATTTGTCTTAAGTTTC
1 TATTCGAACACACAAAAAAATTTGTCTTAAGTTTC
5254166 AATTAAGTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (35 bp):
TATTCGAACACACAAAAAAATTTGTCTTAAGTTTC
Found at i:5261161 original size:19 final size:19
Alignment explanation
Indices: 5261134--5261177 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
5261124 AAAAACAAAC
*
5261134 TATTTTATTACTATT-TTGT
1 TATTATATTACTATTATT-T
5261153 TATTATATTACTATTATTT
1 TATTATATTACTATTATTT
5261172 TATTAT
1 TATTAT
5261178 TTTATTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 21 0.91
20 2 0.09
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (19 bp):
TATTATATTACTATTATTT
Found at i:5261178 original size:11 final size:11
Alignment explanation
Indices: 5261134--5261178 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
5261124 AAAAACAAAC
*
5261134 TATTTTATTAC
1 TATTTTATTAT
*
5261145 TATTTTGTTAT
1 TATTTTATTAT
* *
5261156 TATATTACTAT
1 TATTTTATTAT
5261167 TATTTTATTAT
1 TATTTTATTAT
5261178 T
1 T
5261179 TTATTGAAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:5268572 original size:24 final size:24
Alignment explanation
Indices: 5268537--5268591 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
5268527 GCACATTAAA
5268537 AAAATAA-ATCT-ATATTAAATA-C
1 AAAATAATATCTAATA-TAAATATC
*
5268559 AAAATAATATTCTAATATAAATATT
1 AAAATAATA-TCTAATATAAATATC
5268584 AAAATAAT
1 AAAATAAT
5268592 GTTATGATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 7 0.25
23 1 0.04
24 9 0.32
25 11 0.39
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAATAATATCTAATATAAATATC
Found at i:5271365 original size:39 final size:37
Alignment explanation
Indices: 5271298--5271390 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
5271288 ACCAGAATGG
* *
5271298 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
5271337 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
5271374 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
5271391 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:5271587 original size:23 final size:24
Alignment explanation
Indices: 5271566--5271610 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
5271556 CACTTTCAAT
* *
5271566 TCAATCATT-TTTC-CACATTCAA
1 TCAATAATTATTTCACAAATTCAA
5271588 TCAATAATTATTTCACAAATTCA
1 TCAATAATTATTTCACAAATTCA
5271611 CACATTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.40
Consensus pattern (24 bp):
TCAATAATTATTTCACAAATTCAA
Found at i:5271604 original size:22 final size:23
Alignment explanation
Indices: 5271560--5271610 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
5271550 TTCTCACACT
*
5271560 TTCAATTCAATCATTTTTCCACA
1 TTCAATTCAATAATTTTTCCACA
*
5271583 TTCAA-TCAATAATTATTTCACAAA
1 TTCAATTCAATAATT-TTTC-CACA
5271607 TTCA
1 TTCA
5271611 CACATTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 8 0.33
23 9 0.38
24 7 0.29
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (23 bp):
TTCAATTCAATAATTTTTCCACA
Found at i:5272489 original size:15 final size:15
Alignment explanation
Indices: 5272471--5272508 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
5272461 TGTTCCTTTG
5272471 TTCTTTCTATTCTGT
1 TTCTTTCTATTCTGT
* *
5272486 TTCTTTCTGTTTTGT
1 TTCTTTCTATTCTGT
5272501 TTCTTTCT
1 TTCTTTCT
5272509 TTTTCTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.03, C:0.18, G:0.08, T:0.71
Consensus pattern (15 bp):
TTCTTTCTATTCTGT
Found at i:5272690 original size:31 final size:28
Alignment explanation
Indices: 5272654--5272721 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
5272644 TTGTCTTTAT
**
5272654 TTAATTTATTTCTTAATATAATATTTATAA
1 TTAATTTATTTAATAATAT-A-ATTTATAA
* *
5272684 TGTAATTAATTTAATAATATACTTTATAA
1 T-TAATTTATTTAATAATATAATTTATAA
5272713 TTAATTTAT
1 TTAATTTAT
5272722 ATATTTATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 8 0.25
30 2 0.06
31 15 0.47
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (28 bp):
TTAATTTATTTAATAATATAATTTATAA
Found at i:5272738 original size:21 final size:20
Alignment explanation
Indices: 5272700--5272738 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5272690 TAATTTAATA
*
5272700 ATATACTTTATAATTAATTT
1 ATATACTTTATAAATAATTT
*
5272720 ATATATTTATATAAATAAT
1 ATATACTT-TATAAATAAT
5272739 AATATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATACTTTATAAATAATTT
Found at i:5277679 original size:21 final size:21
Alignment explanation
Indices: 5277637--5277679 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5277627 TTCACTATAC
*
5277637 ATTCTTTCATCAGTATCATTT
1 ATTCTTTCATCAGCATCATTT
*
5277658 ATTCTTTCTTCAGACATC-TTT
1 ATTCTTTCATCAG-CATCATTT
5277679 A
1 A
5277680 ATCTATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTCTTTCATCAGCATCATTT
Found at i:5278848 original size:20 final size:20
Alignment explanation
Indices: 5278814--5278853 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5278804 TTCTATTCTG
*
5278814 TTTCTTTTCTGTTTTGTTTC
1 TTTCTTTTCTGTTTTATTTC
5278834 TTTCTTTTTCT-TTTTATTTC
1 TTTC-TTTTCTGTTTTATTTC
5278854 CTTTTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTCTTTTCTGTTTTATTTC
Found at i:5279068 original size:21 final size:20
Alignment explanation
Indices: 5279030--5279068 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5279020 TAATTTAATA
*
5279030 ATATACTTTATAATTAATTT
1 ATATACTTTATAAATAATTT
*
5279050 ATATATTTATATAAATAAT
1 ATATACTT-TATAAATAAT
5279069 AATATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATACTTTATAAATAATTT
Found at i:5281441 original size:12 final size:12
Alignment explanation
Indices: 5281424--5281452 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
5281414 GCATTGTTTT
5281424 TTTTTATATATA
1 TTTTTATATATA
5281436 TTTTTATATATA
1 TTTTTATATATA
5281448 TTTTT
1 TTTTT
5281453 TCATTCGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTTATATATA
Found at i:5282028 original size:23 final size:22
Alignment explanation
Indices: 5281981--5282028 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
5281971 ATACATACAG
5281981 ATTTTCACATATATATATATAT
1 ATTTTCACATATATATATATAT
* * *
5282003 ATTTTCCCATAGTTTATTTATAT
1 ATTTTCACATA-TATATATATAT
5282026 ATT
1 ATT
5282029 ATATTTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.54
Consensus pattern (22 bp):
ATTTTCACATATATATATATAT
Found at i:5282035 original size:13 final size:13
Alignment explanation
Indices: 5282017--5282046 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5282007 TCCCATAGTT
5282017 TATTTATATATTA
1 TATTTATATATTA
*
5282030 TATTTATATATTT
1 TATTTATATATTA
5282043 TATT
1 TATT
5282047 CTTTTCTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTTATATATTA
Found at i:5288714 original size:5 final size:5
Alignment explanation
Indices: 5288704--5288735 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
5288694 GATTATTGTG
5288704 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TA
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TA
5288736 TTATATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAAAT
Found at i:5299306 original size:85 final size:85
Alignment explanation
Indices: 5299159--5299931 Score: 807
Period size: 86 Copynumber: 8.9 Consensus size: 85
5299149 CAGATCAGTG
* *
5299159 AAGAAGCAAATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCTTTGCCTTCATT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATT
5299224 GGTTACAGTGGAGCTGGTTA
66 GGTTACAGTGGAGCTGGTTA
*
5299244 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGTCTTCATT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATT
*
5299309 GGTTACAGTGAAGCTGGTTA
66 GGTTACAGTGGAGCTGGTTA
* *
5299329 AAGAAGCAGATCTCGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCTTTCATT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATT
5299394 GGTTACAGTGGAGCTGGTTA
66 GGTTACAGTGGAGCTGGTTA
* *
5299414 AAGATAACAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATTGAAAACAAAGCCTTGCCTTCA
1 AAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAAC-AAGCCTTGCCTTCA
*
5299479 TTGGTTGCAGTGGAGCTGGTTA
64 TTGGTTACAGTGGAGCTGGTTA
* * *
5299501 AAGAGGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAAC-AAGCCTTGCCTTCAT
* * * *
5299566 CGGGTGCAGTGGAGCTTGTTA
65 TGGTTACAGTGGAGCTGGTTA
** * * * ** * *
5299587 AAGAAATAGATCTTGCCTT-ATGGCATTAACATCGAAGCAGATAAAAAACAAAGCCTTACCTCCA
1 AAGAAGCAGATCTTGCCTTCCT-GCGTTAACAGCGAAGCAGATCGAAAAC-AAGCCTTGCCTTCA
* * *
5299651 TCGGTTGCAGTAGAGCTGGTTA
64 TTGGTTACAGTGGAGCTGGTTA
* ** * * * **
5299673 AGGATAGCAGATCTTGCCTTCCTGTATTGACGGCGAAGCAGATCGAAGAAACCAGTTTTGCCTTT
1 AAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG-A-AAACAAGCCTTGCC-TT
** * * ****
5299738 C-TGTAATGACAGCGGAGCAAACTA
62 CAT-TGGTTACAGTGGAGCTGGTTA
* * * * * *
5299762 AAGATAACAGATATTGCCTTCCTACGTTGACAGCGAAGCAGATTGAAGACACAAACCTTGCCTCT
1 AAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAA-A-ACAAGCCTTGCCT-T
* ** * *
5299827 C-TCGGTTGTAGTGAAGCTGGTTG
62 CATTGGTTACAGTGGAGCTGGTTA
* * * * *
5299850 AAGATAACAGATCTTGCCTTCTTGCCTTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCT
1 AAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAA-A-ACAAGCCTTGCCT-T
*
5299915 C-TCGGTTACAGTGGAGC
62 CATTGGTTACAGTGGAGC
5299932 AGATTGAAGC
Statistics
Matches: 585, Mismatches: 91, Indels: 21
0.84 0.13 0.03
Matches are distributed among these distances:
85 167 0.29
86 192 0.33
87 68 0.12
88 94 0.16
89 64 0.11
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (85 bp):
AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATT
GGTTACAGTGGAGCTGGTTA
Found at i:5299910 original size:44 final size:44
Alignment explanation
Indices: 5299788--5299940 Score: 150
Period size: 43 Copynumber: 3.5 Consensus size: 44
5299778 CCTTCCTACG
*
5299788 TTGACAGCGAAGCAGATTGAAGACACAAACCTTGCCTCTCTCGG
1 TTGACAGCGAAGCAGATTGAAGACACAAACCTTGCCTCTCTCGC
* * * * * * * *
5299832 TTG-TAGTGAAGCTGGTTGAAGATAACAGATCTTGCCT-TCTTGCC
1 TTGACAGCGAAGCAGATTGAAGA-CACAAACCTTGCCTCTCTCG-C
* *
5299876 TTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGG
1 TTGACAGCGAAGCAGATTGAAGACACAAACCTTGCCTCTCTCGC
* *
5299920 TT-ACAGTGGAGCAGATTGAAG
1 TTGACAGCGAAGCAGATTGAAG
5299941 CTAGTAATCC
Statistics
Matches: 83, Mismatches: 22, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
43 35 0.42
44 30 0.36
45 18 0.22
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (44 bp):
TTGACAGCGAAGCAGATTGAAGACACAAACCTTGCCTCTCTCGC
Found at i:5299970 original size:44 final size:44
Alignment explanation
Indices: 5299920--5300323 Score: 231
Period size: 44 Copynumber: 9.2 Consensus size: 44
5299910 CCTCTCTCGG
*
5299920 TTACAGTGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TTACAGTGGAGCAGATTGAAGCTAGTAATCTTATCTCCCTGAGA
** ** * *
5299964 TTACAGTGGAGTGGATT-AAAATAAAG-GATCTTATCTCTCTGA-A
1 TTACAGTGGAGCAGATTGAAGCT--AGTAATCTTATCTCCCTGAGA
* * * * * *
5300007 GTTACAGTAGAGTAGATCGCATC-AG--GTCTTATCTCCCTGAGA
1 -TTACAGTGGAGCAGATTGAAGCTAGTAATCTTATCTCCCTGAGA
* *** * *
5300049 TTACAGTGGAACAGACCAAAG-AATTTCAGATCTTATCTCCCTGAGA
1 TTACAGTGGAGCAGATTGAAGCTA-GT-A-ATCTTATCTCCCTGAGA
* * *
5300095 TTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGA
1 TTACAGTGGAGCAGATTGAAGCTAGTAATCTTATCTCCCTGAGA
** * * *
5300139 TTACAGTGGAGCAGATT-AAAATAAATGATCTTATCTCTCTGA-A
1 TTACAGTGGAGCAGATTGAAGCT-AGTAATCTTATCTCCCTGAGA
* ** * * * * *
5300182 GGTACAGCAGAGTAGATCGCATC-AG--GTCTTATCTCCCTGAGA
1 -TTACAGTGGAGCAGATTGAAGCTAGTAATCTTATCTCCCTGAGA
*** * *
5300224 TTACAGTGGAGCAGACCAAAG-AATTTCAGATCTTATCTCCCTGAGA
1 TTACAGTGGAGCAGATTGAAGCTA-GT-A-ATCTTATCTCCCTGAGA
* * *
5300270 TTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TTACAGTGGAGCAGATTGAAGCTAGTAATCTTATCTCCCTGAGA
5300314 TTACAGTGGA
1 TTACAGTGGA
5300324 ACGGATTTTT
Statistics
Matches: 269, Mismatches: 68, Indels: 46
0.70 0.18 0.12
Matches are distributed among these distances:
41 55 0.20
42 4 0.01
43 10 0.04
44 126 0.47
45 6 0.02
46 66 0.25
47 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (44 bp):
TTACAGTGGAGCAGATTGAAGCTAGTAATCTTATCTCCCTGAGA
Found at i:5300055 original size:85 final size:84
Alignment explanation
Indices: 5299951--5300323 Score: 329
Period size: 87 Copynumber: 4.3 Consensus size: 84
5299941 CTAGTAATCC
** *
5299951 TATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
1 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAA-GATCTTATCTCTCTGAAGTTACAGCA
5300016 GAGTAGATCGCATCAGGTCT
65 GAGTAGATCGCATCAGGTCT
* ** ** *
5300036 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTG-AGATTACA
1 TATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-AA-TAAAGATCTTATCTCTCTGAAG-TTACA
* * * * * *
5300100 GCGGAGCAGATTGAAGAT-AGTAATCC
62 GCAGAGTAGATCG--CATCAG--GTCT
*
5300126 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAATGATCTTATCTCTCTGAAGGTACAGCA
1 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAA-GATCTTATCTCTCTGAAGTTACAGCA
5300191 GAGTAGATCGCATCAGGTCT
65 GAGTAGATCGCATCAGGTCT
** ** *
5300211 TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATTTCAGATCTTATCTCCCTG-AGATTACA
1 TATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-AA-TAAAGATCTTATCTCTCTGAAG-TTACA
* * * * * *
5300275 GCGGAGTAGATTGAAGCTAGTAATCC
62 GCAGAGTAGATCGCATC-AG--GTCT
5300301 TATCTCCCTGAGATTACAGTGGA
1 TATCTCCCTGAGATTACAGTGGA
5300324 ACGGATTTTT
Statistics
Matches: 230, Mismatches: 40, Indels: 31
0.76 0.13 0.10
Matches are distributed among these distances:
85 55 0.24
86 10 0.04
87 67 0.29
88 38 0.17
89 6 0.03
90 54 0.23
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (84 bp):
TATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAGATCTTATCTCTCTGAAGTTACAGCAG
AGTAGATCGCATCAGGTCT
Found at i:5300100 original size:46 final size:46
Alignment explanation
Indices: 5300028--5300280 Score: 206
Period size: 46 Copynumber: 5.7 Consensus size: 46
5300018 GTAGATCGCA
* *
5300028 TCAGGTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATT
1 TCAGATCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATT
* *** *
5300074 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG-ATAG
1 TCAGATCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAAT-T
* **
5300120 T-A-ATCCTATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-AA-T
1 TCAGATCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATT
** * * ** * * *
5300161 AAATGATCTTATCTCTCTGA-AGGTACAGCAGAGTAGATC---GCA--
1 TCA-GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGACCAAAGAATT
*
5300203 TCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATT
1 TCAGATCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATT
*
5300249 TCAGATCTTATCTCCCTGAGATTACAGCGGAG
1 TCAGATCTTATCTCCCTGAGATTACAGTGGAG
5300281 TAGATTGAAG
Statistics
Matches: 161, Mismatches: 32, Indels: 28
0.73 0.14 0.13
Matches are distributed among these distances:
41 26 0.16
42 3 0.02
43 6 0.04
44 56 0.35
45 3 0.02
46 67 0.42
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (46 bp):
TCAGATCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATT
Found at i:5300218 original size:175 final size:175
Alignment explanation
Indices: 5299920--5300323 Score: 727
Period size: 175 Copynumber: 2.3 Consensus size: 175
5299910 CCTCTCTCGG
* **
5299920 TTACAGTGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAA
1 TTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAA
* *
5299985 TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGAT
66 TAAAGGATCTTATCTCTCTGAAGGTACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGAT
5300050 TACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGA
131 TACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGA
*
5300095 TTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAA
1 TTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAA
*
5300160 TAAATGATCTTATCTCTCTGAAGGTACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGAT
66 TAAAGGATCTTATCTCTCTGAAGGTACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGAT
*
5300225 TACAGTGGAGCAGACCAAAGAATTTCAGATCTTATCTCCCTGAGA
131 TACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGA
*
5300270 TTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGA
1 TTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGA
5300324 ACGGATTTTT
Statistics
Matches: 219, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
175 219 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (175 bp):
TTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAA
TAAAGGATCTTATCTCTCTGAAGGTACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGAT
TACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGA
Found at i:5300319 original size:131 final size:129
Alignment explanation
Indices: 5300074--5300311 Score: 291
Period size: 131 Copynumber: 1.8 Consensus size: 129
5300064 CCAAAGAATT
***
5300074 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGA
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGACCAAAGATAGTAATCCTATCTCCCTGAGA
* * * *
5300139 TTACAGTGGAGCAGATTAAAATAAATGATCTTATCTCTCTGAAGGTACAGCAGAGTAGATCGCA
66 TTACAGCGGAGCAGATTAAAATAAATAATCCTATCTCCCTGAAGGTACAGCAGAGTAGATCGCA
* * * *
5300203 TCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAGA-ATTTCAGATCTTATCTCCCTG
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGACCAAAGATA-GT-A-ATCCTATCTCCCTG
* ** *
5300267 AGATTACAGCGGAGTAGATTGAAGCT-AGTAATCCTATCTCCCTGA
63 AGATTACAGCGGAGCAGATT-AAAATAAATAATCCTATCTCCCTGA
5300312 GATTACAGTG
Statistics
Matches: 90, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
128 1 0.01
129 39 0.43
130 1 0.01
131 46 0.51
132 3 0.03
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (129 bp):
TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGACCAAAGATAGTAATCCTATCTCCCTGAGA
TTACAGCGGAGCAGATTAAAATAAATAATCCTATCTCCCTGAAGGTACAGCAGAGTAGATCGCA
Found at i:5305805 original size:5 final size:5
Alignment explanation
Indices: 5305795--5305826 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
5305785 GATTATTGTG
5305795 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TA
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TA
5305827 TTATATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAAAT
Found at i:5308911 original size:25 final size:26
Alignment explanation
Indices: 5308869--5308918 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
5308859 ACAAATTAAA
* *
5308869 TAAACATATAAAAGATTGAAACATTT
1 TAAACATAAAAAAAATTGAAACATTT
5308895 TAAA-ATAAAAAAAATTGAAACATT
1 TAAACATAAAAAAAATTGAAACATT
5308919 GAATTTATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (26 bp):
TAAACATAAAAAAAATTGAAACATTT
Found at i:5309518 original size:18 final size:16
Alignment explanation
Indices: 5309495--5309538 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
5309485 ATTTAAGGTG
5309495 TAATTAATTTATAATTTA
1 TAATTAA-TTA-AATTTA
5309513 TAATTAATTAAATTTA
1 TAATTAATTAAATTTA
5309529 T--TTAATTAAA
1 TAATTAATTAAA
5309539 AACCTATTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.35
16 7 0.27
17 3 0.12
18 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATTAATTAAATTTA
Found at i:5309926 original size:13 final size:13
Alignment explanation
Indices: 5309904--5309940 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
5309894 GAGCCGGCCC
5309904 ATATTAAATATAT
1 ATATTAAATATAT
*
5309917 ATATTTAATATAT
1 ATATTAAATATAT
5309930 ATA--AAATATAT
1 ATATTAAATATAT
5309941 GTTTGATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 7 0.32
13 15 0.68
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATTAAATATAT
Found at i:5309959 original size:24 final size:23
Alignment explanation
Indices: 5309932--5310000 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 23
5309922 TAATATATAT
5309932 AAAATATATGTTTGATTAAAAATAA
1 AAAATATAT-TTTGATTAAAAAT-A
5309957 AAAATATATTTTGATTAAAAAT-
1 AAAATATATTTTGATTAAAAATA
* *
5309979 AATATATATATTTGAATAAAAA
1 AAAATATAT-TTTGATTAAAAA
5310001 ATATGTATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.20
23 11 0.27
24 13 0.32
25 9 0.22
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.38
Consensus pattern (23 bp):
AAAATATATTTTGATTAAAAATA
Found at i:5310003 original size:24 final size:23
Alignment explanation
Indices: 5309908--5310000 Score: 98
Period size: 23 Copynumber: 4.0 Consensus size: 23
5309898 CGGCCCATAT
* * *
5309908 TAAATATATATATTT-AATATATA
1 TAAA-ATATATATTTGATTAAAAA
*
5309931 TAAAATATATGTTTGATTAAAAA
1 TAAAATATATATTTGATTAAAAA
*
5309954 TAAAAAATATATTTTGATTAAAAA
1 TAAAATATATA-TTTGATTAAAAA
* *
5309978 TAATATATATATTTGAATAAAAA
1 TAAAATATATATTTGATTAAAAA
5310001 ATATGTATTT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
22 9 0.15
23 29 0.49
24 21 0.36
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (23 bp):
TAAAATATATATTTGATTAAAAA
Found at i:5311387 original size:2 final size:2
Alignment explanation
Indices: 5311380--5311410 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5311370 TTGTAACTTT
5311380 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5311411 GAAGATGAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5317159 original size:42 final size:42
Alignment explanation
Indices: 5317109--5317208 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
5317099 CTATACGAAT
* * *
5317109 GGCACTAAGTGTGCGAAACTAAAATGATGATGTTGAATAACG
1 GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACG
5317151 GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACG
1 GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACG
5317193 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
5317209 TACCAAGATC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.20
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACG
Found at i:5328087 original size:31 final size:31
Alignment explanation
Indices: 5328052--5328118 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
5328042 CCACTAACAA
* *
5328052 TTTTCAGTTATAGACGTAACGGAACTACCAT
1 TTTTCAGTTACAAACGTAACGGAACTACCAT
* ** *
5328083 TTTTC-GTTACAAACTTAACGGAGTTGCCAT
1 TTTTCAGTTACAAACGTAACGGAACTACCAT
5328113 TTTTCA
1 TTTTCA
5328119 TCCCCCTATC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (31 bp):
TTTTCAGTTACAAACGTAACGGAACTACCAT
Found at i:5328910 original size:47 final size:46
Alignment explanation
Indices: 5328857--5328955 Score: 119
Period size: 49 Copynumber: 2.1 Consensus size: 46
5328847 AAGGGACGAT
* *
5328857 AGGGGAGCGAATCAGAGTAG-GAGGAGAGATGGTGGGGAAGAAGGGGAA
1 AGGGGAGAGAATCAGAGGAGAG-GGAGAGATGGTGGGGAAG-A-GGGAA
* *
5328905 AGGGAGAGAGAATCAGGGGAGAGGGAGGGATGGTGGGGAAGAGGGAA
1 AGGG-GAGAGAATCAGAGGAGAGGGAGAGATGGTGGGGAAGAGGGAA
5328952 AGGG
1 AGGG
5328956 ATGGGAGAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
47 9 0.20
48 5 0.11
49 30 0.67
50 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.56, T:0.07
Consensus pattern (46 bp):
AGGGGAGAGAATCAGAGGAGAGGGAGAGATGGTGGGGAAGAGGGAA
Found at i:5329016 original size:30 final size:30
Alignment explanation
Indices: 5328982--5329046 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
5328972 AGGGAGATGG
5328982 AAAATGACAGCTCCGTTAAGTCTGTAACAA
1 AAAATGACAGCTCCGTTAAGTCTGTAACAA
** * * *
5329012 AAAATGGTAGCTCTGTTACGTCTGTAACAG
1 AAAATGACAGCTCCGTTAAGTCTGTAACAA
5329042 AAAAT
1 AAAAT
5329047 AGTTAGTGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.26
Consensus pattern (30 bp):
AAAATGACAGCTCCGTTAAGTCTGTAACAA
Found at i:5333011 original size:26 final size:29
Alignment explanation
Indices: 5332977--5333045 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
5332967 CCCGGCTTGA
5332977 ATAT-ATTATATTA-TAAA-AATAATTAT
1 ATATAATTATATTATTAAATAATAATTAT
*
5333003 AT-TAATTATATATATTAAATAATTATTAT
1 ATATAATTATAT-TATTAAATAATAATTAT
*
5333032 ATATATTTATATTA
1 ATATAATTATATTA
5333046 AATTACTAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
25 1 0.03
26 9 0.25
27 2 0.06
28 4 0.11
29 12 0.33
30 8 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
ATATAATTATATTATTAAATAATAATTAT
Found at i:5333046 original size:26 final size:26
Alignment explanation
Indices: 5332977--5333048 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 26
5332967 CCCGGCTTGA
*
5332977 ATATA-TTATATTATAAAAATAATTAT
1 ATATATTTATATTA-AATAATAATTAT
* *
5333003 ATTAATTATATATATTAAATAATTATTAT
1 A-T-A-TATTTATATTAAATAATAATTAT
5333032 ATATATTTATATTAAAT
1 ATATATTTATATTAAAT
5333049 TACTAACCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
26 14 0.37
27 2 0.05
28 2 0.05
29 13 0.34
30 7 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATATATTTATATTAAATAATAATTAT
Found at i:5333050 original size:20 final size:19
Alignment explanation
Indices: 5332977--5333050 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 19
5332967 CCCGGCTTGA
*
5332977 ATATATTATATTATAA--AA
1 ATATATTATATTA-AATTAT
5332995 ATA-ATTATATT-AATTAT
1 ATATATTATATTAAATTAT
*
5333012 ATATATTA-AATAATTATTAT
1 ATATATTATATTAA--ATTAT
5333032 ATATATTTATATTAAATTA
1 ATATA-TTATATTAAATTA
5333051 CTAACCTAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
15 2 0.04
17 14 0.31
18 8 0.18
20 14 0.31
21 3 0.07
22 4 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATATTATATTAAATTAT
Found at i:5336814 original size:11 final size:11
Alignment explanation
Indices: 5336798--5336822 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5336788 AAAAATAAAA
5336798 ATATTTATTAT
1 ATATTTATTAT
5336809 ATATTTATTAT
1 ATATTTATTAT
5336820 ATA
1 ATA
5336823 AATACTAAAT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATATTTATTAT
Found at i:5347380 original size:45 final size:44
Alignment explanation
Indices: 5347320--5347437 Score: 128
Period size: 50 Copynumber: 2.5 Consensus size: 44
5347310 ACAAGATTAC
* * *
5347320 TATTACGCCTCTATTCCATTACATTCAACCAAACCGTTAATTTGT
1 TATTACACATCTATTCCATTACATTCAA-CAAACAGTTAATTTGT
* *
5347365 TATTACACTTCTATTCCATTACACCTCTATTCAATAAACAGTTAATTTGT
1 TATTACACATCTATTCCATT--A---C-ATTCAACAAACAGTTAATTTGT
5347415 TATTACACATCTATTCCATTACA
1 TATTACACATCTATTCCATTACA
5347438 CCTCTATTCA
Statistics
Matches: 62, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
44 1 0.02
45 19 0.31
47 1 0.02
48 1 0.02
50 34 0.55
51 6 0.10
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (44 bp):
TATTACACATCTATTCCATTACATTCAACAAACAGTTAATTTGT
Found at i:5347387 original size:16 final size:16
Alignment explanation
Indices: 5347366--5347396 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5347356 TTAATTTGTT
*
5347366 ATTACACTTCTATTCC
1 ATTACACCTCTATTCC
5347382 ATTACACCTCTATTC
1 ATTACACCTCTATTC
5347397 AATAAACAGT
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:0.26, C:0.32, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:5347418 original size:50 final size:50
Alignment explanation
Indices: 5347350--5347449 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
5347340 ACATTCAACC
* *
5347350 AAACCGTTAATTTGTTATTACACTTCTATTCCATTACACCTCTATTCAAT
1 AAACAGTTAATTTGTTATTACACATCTATTCCATTACACCTCTATTCAAT
5347400 AAACAGTTAATTTGTTATTACACATCTATTCCATTACACCTCTATTCAAT
1 AAACAGTTAATTTGTTATTACACATCTATTCCATTACACCTCTATTCAAT
5347450 TACGCCTCTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (50 bp):
AAACAGTTAATTTGTTATTACACATCTATTCCATTACACCTCTATTCAAT
Found at i:5347457 original size:16 final size:16
Alignment explanation
Indices: 5347416--5347459 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
5347406 TTAATTTGTT
* *
5347416 ATTACACATCTATTCC
1 ATTACACCTCTATTCA
5347432 ATTACACCTCTATTCA
1 ATTACACCTCTATTCA
*
5347448 ATTACGCCTCTA
1 ATTACACCTCTA
5347460 ATCCAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.30, C:0.32, G:0.02, T:0.36
Consensus pattern (16 bp):
ATTACACCTCTATTCA
Found at i:5348603 original size:21 final size:23
Alignment explanation
Indices: 5348563--5348604 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
5348553 AACCTAGAGA
*
5348563 TTAAAAATCTTGGACTTGCATGG
1 TTAAAAATATTGGACTTGCATGG
5348586 TTAAAAA-ATTGG-CTTGCAT
1 TTAAAAATATTGGACTTGCAT
5348605 TCAGTTTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (23 bp):
TTAAAAATATTGGACTTGCATGG
Found at i:5352301 original size:11 final size:10
Alignment explanation
Indices: 5352279--5352311 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
5352269 ATAATCTGGA
5352279 AAGAG-AAGG
1 AAGAGAAAGG
5352288 AAGAGAAGAGG
1 AAGAGAA-AGG
5352299 AAGAGAAAGG
1 AAGAGAAAGG
5352309 AAG
1 AAG
5352312 GATTACCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.23
10 7 0.32
11 10 0.45
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (10 bp):
AAGAGAAAGG
Found at i:5359700 original size:15 final size:15
Alignment explanation
Indices: 5359676--5359709 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5359666 AACAATTACG
*
5359676 ATAATGCGAGCAAAA
1 ATAATACGAGCAAAA
5359691 ATAATACGAGCAAAA
1 ATAATACGAGCAAAA
5359706 ATAA
1 ATAA
5359710 AAAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (15 bp):
ATAATACGAGCAAAA
Found at i:5362198 original size:132 final size:132
Alignment explanation
Indices: 5361901--5363475 Score: 2704
Period size: 132 Copynumber: 11.9 Consensus size: 132
5361891 CTGTTTTTCA
** * * * *
5361901 ATCCACTTCCTACCAATATAGGAAGGCAGGATCTGCTATCTTCGATCTATTTCACACCAATATAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
* * *
5361966 GAATACAAGATCTGCTTTCTTCGATCTACTT--CCACCAATATGGGAAGACAAGATCTGCGTCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
*
5362029 CA
131 CG
5362031 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
*
5362096 GAAGACAAGATCTGCTTTCAGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
5362161 CG
131 CG
* *
5362163 ATCTACTTCCTACCAATATAGGAAGATAAGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
*
5362228 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
*
5362293 GG
131 CG
* * *
5362295 ATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
*
5362360 GAAGACAAGATCTGCTTTCAGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
5362425 CG
131 CG
* *
5362427 ATCTACTTCCTACCAATATAGGAAGATAAGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
* * * *
5362492 GAAGACAAGATCTTCTTTCTTCGATCTACTTCACCACCAATATGGGAAGATAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
*
5362557 GG
131 CG
* * *
5362559 ATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
*
5362624 GAAGACAAGATCTGCTTTCAGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
5362689 CG
131 CG
*
5362691 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTTGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
5362756 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
*
5362821 GG
131 CG
* * *
5362823 ATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
5362888 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
5362953 CG
131 CG
* *
5362955 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTTGATCTACTTCACGGCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
5363020 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
*
5363085 GG
131 CG
* * * *
5363087 ATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCTAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
*
5363152 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGTATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
5363217 CG
131 CG
* *
5363219 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTTGATCTACTTCACGCTAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
*
5363284 GAAGACAAGATCTACTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
5363349 CG
131 CG
*
5363351 ATCCACTTCTTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
*
5363416 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC
5363476 TTTAATGACT
Statistics
Matches: 1361, Mismatches: 82, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
130 87 0.06
132 1274 0.94
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (132 bp):
ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
CG
Found at i:5370166 original size:15 final size:15
Alignment explanation
Indices: 5370142--5370175 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5370132 AACAATTACG
*
5370142 ATAATGCGAGCAAAA
1 ATAATACGAGCAAAA
5370157 ATAATACGAGCAAAA
1 ATAATACGAGCAAAA
5370172 ATAA
1 ATAA
5370176 CAAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (15 bp):
ATAATACGAGCAAAA
Found at i:5375589 original size:106 final size:106
Alignment explanation
Indices: 5375393--5375605 Score: 286
Period size: 106 Copynumber: 2.0 Consensus size: 106
5375383 AAAATGAGCA
* ** * * *
5375393 TTCTTATTTTTGAGAATTTGAGACATCGTGCCCTAACTTACGGGGCGAGATTTTCTTCCCGATTA
1 TTCTTATTTTTGAGAATTCGAGACATCGTGCCCTAACTTACAAGACGAGATTTTCTTACAGATTA
5375458 ACTCGAAATACGAAGACATTCTTCATAAAATTTGATTTAAT
66 ACTCGAAATACGAAGACATTCTTCATAAAATTTGATTTAAT
* * *
5375499 TTCTTATTTTTGGGAATTCGAGTCATCGTGCCCTAACTTACAAGAC-ATGATTTTCTTACATATT
1 TTCTTATTTTTGAGAATTCGAGACATCGTGCCCTAACTTACAAGACGA-GATTTTCTTACAGATT
* * *
5375563 AACTTGAAATACGAATG-CATTTTTCATAAATTTTGATTTAAT
65 AACTCGAAATACGAA-GACATTCTTCATAAAATTTGATTTAAT
5375605 T
1 T
5375606 AGCGATATTT
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
105 1 0.01
106 91 0.98
107 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (106 bp):
TTCTTATTTTTGAGAATTCGAGACATCGTGCCCTAACTTACAAGACGAGATTTTCTTACAGATTA
ACTCGAAATACGAAGACATTCTTCATAAAATTTGATTTAAT
Found at i:5378497 original size:24 final size:23
Alignment explanation
Indices: 5378469--5378514 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
5378459 TAATAATCCT
*
5378469 TAAAATAAAT-CCACACAAATTTAA
1 TAAAAAAAATGCCA-AC-AATTTAA
5378493 TAAAAAAAATGCCAACAATTTA
1 TAAAAAAAATGCCAACAATTTA
5378515 TTTTGAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 11 0.55
25 3 0.15
ACGTcount: A:0.59, C:0.15, G:0.02, T:0.24
Consensus pattern (23 bp):
TAAAAAAAATGCCAACAATTTAA
Found at i:5379945 original size:18 final size:19
Alignment explanation
Indices: 5379924--5379961 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
5379914 CAAAAAAAGT
5379924 AAAATTATAAAAAT-ATTC
1 AAAATTATAAAAATAATTC
*
5379942 AAAATTATATAAATAATTC
1 AAAATTATAAAAATAATTC
5379961 A
1 A
5379962 TAAAAATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATTATAAAAATAATTC
Found at i:5384614 original size:10 final size:9
Alignment explanation
Indices: 5384582--5384733 Score: 67
Period size: 10 Copynumber: 15.3 Consensus size: 9
5384572 AAAAAAAAAC
5384582 TATAATTTAT
1 TATAATTT-T
* *
5384592 TAGAATATAT
1 TATAAT-TTT
5384602 TATATATTTT
1 TATA-ATTTT
5384612 TATAACATTTT
1 TAT-A-ATTTT
*
5384623 TA-AGTTTT
1 TATAATTTT
5384631 TATATATTTT
1 TATA-ATTTT
5384641 TATAATTTT
1 TATAATTTT
*
5384650 CTATAACTTT
1 -TATAATTTT
*
5384660 TATAAGTTTA
1 TATAA-TTTT
*
5384670 TATAAAATTT
1 TAT-AATTTT
5384680 TA-AGATTTT
1 TATA-ATTTT
*
5384689 AATATATTTT
1 TATA-ATTTT
5384699 TA-AATATTT
1 TATAAT-TTT
5384708 CTAATAATTTTTTT
1 -T-ATAA---TTTT
5384722 TATAATTTT
1 TATAATTTT
5384731 TAT
1 TAT
5384734 GTGAAAAATA
Statistics
Matches: 109, Mismatches: 16, Indels: 35
0.68 0.10 0.22
Matches are distributed among these distances:
8 9 0.08
9 28 0.26
10 47 0.43
11 14 0.13
12 6 0.06
13 1 0.01
14 3 0.03
15 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (9 bp):
TATAATTTT
Found at i:5384632 original size:19 final size:19
Alignment explanation
Indices: 5384608--5384689 Score: 71
Period size: 19 Copynumber: 4.3 Consensus size: 19
5384598 ATATTATATA
5384608 TTTTTATAACATTTTTAAG
1 TTTTTATAACATTTTTAAG
* *
5384627 TTTTTAT-ATATTTTTATAA
1 TTTTTATAACATTTTTA-AG
5384646 TTTTCTATAAC-TTTTATAAG
1 TTTT-TATAACATTTT-TAAG
* *
5384666 TTTATATAA-AATTTTAAG
1 TTTTTATAACATTTTTAAG
*
5384684 ATTTTA
1 TTTTTA
5384690 ATATATTTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
18 16 0.32
19 20 0.40
20 11 0.22
21 3 0.06
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.59
Consensus pattern (19 bp):
TTTTTATAACATTTTTAAG
Found at i:5384634 original size:29 final size:28
Alignment explanation
Indices: 5384601--5384700 Score: 96
Period size: 29 Copynumber: 3.5 Consensus size: 28
5384591 TTAGAATATA
5384601 TTATATATTTTTATAACATTTTTAAGTTT
1 TTATATATTTTTATAA-ATTTTTAAGTTT
**
5384630 TTATATATTTTTAT-AATTTTCTATAACTT
1 TTATATATTTTTATAAATTTT-TA-AGTTT
* *
5384659 TTATA-AGTTTATATAAAATTTTAAGATTT
1 TTATATA-TTTTTATAAATTTTTAAG-TTT
*
5384688 TAATATATTTTTA
1 TTATATATTTTTA
5384701 AATATTTCTA
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
27 5 0.09
28 5 0.09
29 41 0.72
30 6 0.11
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (28 bp):
TTATATATTTTTATAAATTTTTAAGTTT
Found at i:5384681 original size:39 final size:39
Alignment explanation
Indices: 5384601--5384681 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
5384591 TTAGAATATA
* * *
5384601 TTATATATTTTTATAACATTTTTAAGTTTTTATATATTT
1 TTATATATTTTTATAACATTTTTAAGTTTATATAAAATT
5384640 TTATA-ATTTTCTATAAC-TTTTATAAGTTTATATAAAATT
1 TTATATATTTT-TATAACATTTT-TAAGTTTATATAAAATT
5384679 TTA
1 TTA
5384682 AGATTTTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 9 0.24
39 28 0.76
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (39 bp):
TTATATATTTTTATAACATTTTTAAGTTTATATAAAATT
Found at i:5385168 original size:29 final size:29
Alignment explanation
Indices: 5385136--5385191 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
5385126 CTTTTCAATA
*
5385136 ATTTATAAATTTTTAT-AATTTTCTATATT
1 ATTTATAAATTTTCATCAATTTT-TATATT
*
5385165 ATTTATAAGTTTTCATCAATTTTTATA
1 ATTTATAAATTTTCATCAATTTTTATA
5385192 AGCTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (29 bp):
ATTTATAAATTTTCATCAATTTTTATATT
Found at i:5385189 original size:20 final size:18
Alignment explanation
Indices: 5385143--5385198 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 18
5385133 ATAATTTATA
5385143 AATTTTTATAA-TTTTCT
1 AATTTTTATAAGTTTTCT
5385160 ATATTATTTATAAGTTTTCAT
1 A-ATT-TTTATAAGTTTTC-T
5385181 CAATTTTTATAAGCTTTT
1 -AATTTTTATAAG-TTTT
5385199 AAATATGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 1 0.03
18 3 0.09
19 7 0.21
20 13 0.39
21 8 0.24
22 1 0.03
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (18 bp):
AATTTTTATAAGTTTTCT
Found at i:5385299 original size:656 final size:650
Alignment explanation
Indices: 5384286--5385883 Score: 1759
Period size: 656 Copynumber: 2.5 Consensus size: 650
5384276 TTGGACATAA
* **
5384286 AAAAATAAAAATAATAATTTATCAAT-AAAAAGAAGAATGTCCCGTAATTATTATTTTATTTGTG
1 AAAAATAAAAATAATAATTTATCAATAAAAAAG-AGAATGTCTCGTAATTATCGTTTTATTTGTG
* * * * *
5384350 GAAGATCAAGAACATTTTATTTAACATGAAAAATGATCCCAATGATTTAACGATTATTCCTATTA
65 AAAGATCAAGAATATTTTATTTAACATG-AAAATGATCCTAATGATTTGACGACTATTCCTATTA
* * * *
5384415 TTTAAAGGTTGGTC-TTGTTGTGTGTTCATTATGATTTTAGGGGGTTTAAATGTCCTTTT-AATA
129 TCTAAAAGTTGATCGGTGTTGTGTGTTCATTATGATTTTA-GGGGTTTAAATGTCCTTTTCAATA
** *
5384478 ATTTATATTTTTTTTTATAATTTTCTATATTATTTATAAGTTTTTATGAATTTTCATAAGCTTTT
193 ATTTATA--AATTTTTATAATTTTCTATATTATTTATAAGTTTTTATGAATTTTTATAAGCTTTT
* * * * *
5384543 AAACATGTTATTATATGTTTTATTAATTTAAAA-A-AA--AACTATAATTTATTAGAATATATTA
256 AAATATGTT-TTAT-TATTTTA-TAA---AAAATATAATTTATTAAAATTTATTAGAATATATTA
* *
5384604 TATATTTTTATAACATTTTTAAGTTTTTATATATTTTTATAATTTTCTAT-AACTTTTATAAGTT
315 TATATTTTTATAACATTTATAAGTTTTTATATATTTTTATAATTTTCTATAAATTTTTA-AAGTT
*
5384668 TATATAAAATTTTAAGATTTTAATATATTTTTAAATATTTCTAATAATTTTTTTTATAATTTTTA
379 TATATAAAATTTTAAGA-TTT--TATATTTTTAAATATTTCTAATAAATTTTTTTATAATTTTTA
* * * *
5384733 TGTGAAAAATATAATATTAAATCATATAAGTTGTTA-GTGTCACCATAT-GATTGGTCCGTTAAT
441 TGTG-AAAA-ATAAGATTAAATC--AGAAGTTGTCATGTGTCACCAT-TGGATTGGTCCGTCAAT
* * *
5384796 TTATTTTCACAAAT-AATATTATCAAAGATGGAAATCATTAATAGAGGGACTTAATTGA-TTTTT
501 TTATTTTCAC-AATCAACATGATCAAAGATGGAAACCATTAATAGAGGGACTTAATTGATTTTTT
** ** * * * * * * * *
5384859 TT-GGT-TTG-TGGGGGGTGAACTGGGTGTGAATAGTATAGGGGCTCAATACTGTACTGTATTTT
565 TTAACTAGCGATAGGGGCTAAACTAGGTGTGAATAGTACAGCGGCTCAATACTG-ACTATACTTT
* *
5384921 AAAAATTGGAGATAAAAATTTT
629 AAAAACTGGAGATAAAAATTAT
*
5384943 AAAAATAAAAA-AATAATTTATCAATAAAAAAGAGAATGTCTTGTAATTATCGTTTTATTTGTGA
1 AAAAATAAAAATAATAATTTATCAATAAAAAAGAGAATGTCTCGTAATTATCGTTTTATTTGTGA
* * * * * *
5385007 AAGATCGAGAATATTTTATTCAACATGAGAATAATCCTAATAATTTGACTAACTATTCCTATTAT
66 AAGATCAAGAATATTTTATTTAACATGAAAATGATCCTAATGATTTGAC-GACTATTCCTATTAT
* *
5385072 CTAAAAGTTGATTCGGTGTCGTGTGTTCATTAAGATTTTAGGGGTTTAAATGTCCTTTTCAATAA
130 CTAAAAGTTGA-TCGGTGTTGTGTGTTCATTATGATTTTAGGGGTTTAAATGTCCTTTTCAATAA
* *
5385137 TTTATAAATTTTTATAATTTTCTATATTATTTATAAGTTTTCATCAATTTTTATAAGCTTTTAAA
194 TTTATAAATTTTTATAATTTTCTATATTATTTATAAGTTTTTATGAATTTTTATAAGCTTTTAAA
* *
5385202 TATGTTTTATTAATTTATAAAAAATATAATTTATTAAAATTTATTAG-A-A-CTTATATATTTTT
259 TATGTTTTATTATTTTATAAAAAATATAATTTATTAAAATTTATTAGAATATATTATATATTTTT
* * * *
5385264 ATAATATTTATAAGGTTTTTTTTAGGTTTTTTTTATAATTTTCTATAAATTTTTAAATTTTATAT
324 ATAACATTTATAA-G-TTTTTATA---TATTTTTATAATTTTCTATAAATTTTTAAAGTTTATAT
*
5385329 AAAATTTTAAGATTTTGTATTTTTAAATATTTCTAATAAATTTTTTTATAATTTTTATGTGAAAA
384 AAAATTTTAAGATTTTATATTTTTAAATATTTCTAATAAATTTTTTTATAATTTTTATGTGAAAA
* * ** * **
5385394 GTAAGATTAAATCAGAAGTTGTCATGTGTCACCATTGGATTTGTTTGTCAATTTATTTTTACGGT
449 ATAAGATTAAATCAGAAGTTGTCATGTGTCACCATTGGATTGGTCCGTCAATTTATTTTCACAAT
* * * *
5385459 CAACGTGATTAAAGATGGAAACCGTTAATGGAGGGACTTAATTGATTTTTTTTAACTAGCGATAG
514 CAACATGATCAAAGATGGAAACCATTAATAGAGGGACTTAATTGATTTTTTTTAACTAGCGATAG
* * * *
5385524 GGGCTAAACTAGGTGTGAGTAGTGCATCGGCTCAATACTGACTATGCTTTAAAAACTGGAGATAA
579 GGGCTAAACTAGGTGTGAATAGTACAGCGGCTCAATACTGACTATACTTTAAAAACTGGAGATAA
5385589 AAATTAT
644 AAATTAT
* * * *
5385596 AAAAATTAAAAATAATAATTTATCAATAAAAAGGAGAATATCTCATAATTATCGTTTTATTTATG
1 AAAAA-TAAAAATAATAATTTATCAATAAAAAAGAGAATGTCTCGTAATTATCGTTTTATTTGT-
* ** * *
5385661 GAAA-AT-AAAAATATTTTATTTAATTTGAAAATGA-CCTTAATGATTTGACGGCTATTTCTATT
64 GAAAGATCAAGAATATTTTATTTAACATGAAAATGATCC-TAATGATTTGACGACTATTCCTATT
* * * * * *
5385723 ACCT-AATGATTGATCTGGTGTTGTGTGTTTATTATGATTTTAGGAGTTTAAATAT-TTTTTCAA
128 ATCTAAAAG-TTGATC-GGTGTTGTGTGTTCATTATGATTTTAGGGGTTTAAATGTCCTTTTCAA
* *
5385786 TAATTTAT-AA--TTT-T--TTTT-TA-ATT-TTTATAAGTTTTTATGAATTTTTATAACCCTTT
191 TAATTTATAAATTTTTATAATTTTCTATATTATTTATAAGTTTTTATGAATTTTTATAAGCTTTT
* * *
5385842 AAATAAGTTTTTATTATTTTTAAAAAAAATTATCATTTATTA
256 AAATATG-TTTTATTA-TTTTATAAAAAA-TATAATTTATTA
5385884 TATATTTTAT
Statistics
Matches: 801, Mismatches: 109, Indels: 73
0.81 0.11 0.07
Matches are distributed among these distances:
643 35 0.04
644 11 0.01
645 12 0.01
646 15 0.02
648 1 0.00
649 14 0.02
650 71 0.09
651 44 0.05
652 29 0.04
653 141 0.18
654 90 0.11
655 72 0.09
656 188 0.23
657 45 0.06
658 33 0.04
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (650 bp):
AAAAATAAAAATAATAATTTATCAATAAAAAAGAGAATGTCTCGTAATTATCGTTTTATTTGTGA
AAGATCAAGAATATTTTATTTAACATGAAAATGATCCTAATGATTTGACGACTATTCCTATTATC
TAAAAGTTGATCGGTGTTGTGTGTTCATTATGATTTTAGGGGTTTAAATGTCCTTTTCAATAATT
TATAAATTTTTATAATTTTCTATATTATTTATAAGTTTTTATGAATTTTTATAAGCTTTTAAATA
TGTTTTATTATTTTATAAAAAATATAATTTATTAAAATTTATTAGAATATATTATATATTTTTAT
AACATTTATAAGTTTTTATATATTTTTATAATTTTCTATAAATTTTTAAAGTTTATATAAAATTT
TAAGATTTTATATTTTTAAATATTTCTAATAAATTTTTTTATAATTTTTATGTGAAAAATAAGAT
TAAATCAGAAGTTGTCATGTGTCACCATTGGATTGGTCCGTCAATTTATTTTCACAATCAACATG
ATCAAAGATGGAAACCATTAATAGAGGGACTTAATTGATTTTTTTTAACTAGCGATAGGGGCTAA
ACTAGGTGTGAATAGTACAGCGGCTCAATACTGACTATACTTTAAAAACTGGAGATAAAAATTAT
Found at i:5385316 original size:20 final size:19
Alignment explanation
Indices: 5385293--5385344 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
5385283 TTTTAGGTTT
*
5385293 TTTTTATAATTTTCTATAAA
1 TTTTTA-AATTTTATATAAA
5385313 TTTTTAAATTTTATATAAA
1 TTTTTAAATTTTATATAAA
*
5385332 ATTTTAAGATTTT
1 TTTTTAA-ATTTT
5385345 GTATTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTTAAATTTTATATAAA
Found at i:5385812 original size:20 final size:20
Alignment explanation
Indices: 5385789--5385835 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
5385779 TTTTCAATAA
* * *
5385789 TTTATAATTTTTTTTTAATT
1 TTTATAAGTTTTTATGAATT
5385809 TTTATAAGTTTTTATGAATT
1 TTTATAAGTTTTTATGAATT
5385829 TTTATAA
1 TTTATAA
5385836 CCCTTTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (20 bp):
TTTATAAGTTTTTATGAATT
Found at i:5392560 original size:24 final size:24
Alignment explanation
Indices: 5392533--5392634 Score: 127
Period size: 24 Copynumber: 4.3 Consensus size: 24
5392523 ATTTCAAGAT
5392533 TTGAAATCTTGATTTTCTTCATTC
1 TTGAAATCTTGATTTTCTTCATTC
*
5392557 TTGAAATCTTGATTTTATTCATTC
1 TTGAAATCTTGATTTTCTTCATTC
* * ***
5392581 TTGAAATCATGAATTTCAAGA-T-
1 TTGAAATCTTGATTTTCTTCATTC
*
5392603 TTGAAATCTTGATTTTCTTGATTC
1 TTGAAATCTTGATTTTCTTCATTC
5392627 TTGAAATC
1 TTGAAATC
5392635 ATCAAAAACA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
22 17 0.26
23 2 0.03
24 46 0.71
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (24 bp):
TTGAAATCTTGATTTTCTTCATTC
Found at i:5393500 original size:31 final size:31
Alignment explanation
Indices: 5393465--5393523 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
5393455 TTATAACATA
* *
5393465 TTTCATATTCTGTTTTCAATTCACTATCGTT
1 TTTCACATTCTATTTTCAATTCACTATCGTT
5393496 TTTCACATTCTATTTTCAATTCACTATC
1 TTTCACATTCTATTTTCAATTCACTATC
5393524 TCATATTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.03, T:0.53
Consensus pattern (31 bp):
TTTCACATTCTATTTTCAATTCACTATCGTT
Found at i:5393691 original size:25 final size:23
Alignment explanation
Indices: 5393615--5393716 Score: 102
Period size: 22 Copynumber: 4.3 Consensus size: 23
5393605 CACTAATGAC
*
5393615 CAGAGAGCACTAAAGTGCT-ATA
1 CAGAGAGCACTAACGTGCTAATA
*
5393637 CAGAGAGCAC-AGATGTGCTAA-A
1 CAGAGAGCACTA-ACGTGCTAATA
*
5393659 CAGAGAGCACTGACGTGCTAAATA
1 CAGAGAGCACTAACGTGCT-AATA
*
5393683 TCAGAGAGCACCAACGTGCTAATAA
1 -CAGAGAGCACTAACGTGCTAAT-A
5393708 TCAGAGAGC
1 -CAGAGAGC
5393717 GCGCTAAAGT
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.01
22 33 0.49
23 3 0.04
24 4 0.06
25 27 0.40
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.16
Consensus pattern (23 bp):
CAGAGAGCACTAACGTGCTAATA
Found at i:5398381 original size:41 final size:41
Alignment explanation
Indices: 5398331--5398410 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
5398321 CCGAAATGTA
* * *
5398331 TCACTGGCATTAAGCCTGCTAGATGTAAAGTCTGTATTATT
1 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGTATTATT
5398372 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGTATTA
1 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGTATTA
5398411 CATTCAATCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (41 bp):
TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGTATTATT
Found at i:5398682 original size:12 final size:12
Alignment explanation
Indices: 5398665--5398718 Score: 63
Period size: 12 Copynumber: 4.2 Consensus size: 12
5398655 CTCAAAAACT
5398665 TATATATATACA
1 TATATATATACA
*
5398677 TATATATATTCGA
1 TATATATATAC-A
*
5398690 GTATTATACATACA
1 -TA-TATATATACA
5398704 TATATATATACA
1 TATATATATACA
5398716 TAT
1 TAT
5398719 CTTTGACTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 22 0.63
13 3 0.09
14 3 0.09
15 7 0.20
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (12 bp):
TATATATATACA
Found at i:5401426 original size:22 final size:22
Alignment explanation
Indices: 5401398--5401485 Score: 79
Period size: 22 Copynumber: 3.9 Consensus size: 22
5401388 ACTAATAAAC
*
5401398 AGAGAGCACTAAAGTGCTATAT
1 AGAGAGCACTAACGTGCTATAT
* * *
5401420 AGAGAGCAC-AGATGTGCTAAAC
1 AGAGAGCACTA-ACGTGCTATAT
*
5401442 AGAGAGCACTGACGTGCTAAATAT
1 AGAGAGCACTAACGTGCT--ATAT
*
5401466 CAGAGAGCACCAACGTGCTA
1 -AGAGAGCACTAACGTGCTA
5401486 ATAATCAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
21 1 0.02
22 32 0.62
23 1 0.02
24 2 0.04
25 16 0.31
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (22 bp):
AGAGAGCACTAACGTGCTATAT
Found at i:5401473 original size:25 final size:24
Alignment explanation
Indices: 5401397--5401523 Score: 120
Period size: 25 Copynumber: 5.3 Consensus size: 24
5401387 CACTAATAAA
* *
5401397 CAGAGAGCACTAAAGTGCT-ATAT
1 CAGAGAGCACCAACGTGCTAATAT
*
5401420 -AGAGAGCA-CAGATGTGCTAA-A-
1 CAGAGAGCACCA-ACGTGCTAATAT
**
5401441 CAGAGAGCACTGACGTGCTAAATAT
1 CAGAGAGCACCAACGTGCT-AATAT
5401466 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAAT-AT
* *
5401491 CAAAAAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAAT-AT
5401516 CAGAGAGC
1 CAGAGAGC
5401524 GCGCTAAAGT
Statistics
Matches: 85, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
21 1 0.01
22 29 0.34
23 3 0.04
24 4 0.05
25 48 0.56
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (24 bp):
CAGAGAGCACCAACGTGCTAATAT
Found at i:5403945 original size:24 final size:24
Alignment explanation
Indices: 5403913--5403962 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
5403903 TTGAATAAAC
5403913 TTAAATGAAAAGTCAAGAGTTATG
1 TTAAATGAAAAGTCAAGAGTTATG
*
5403937 TTAAATGAAAGGTCAAGAGTTATG
1 TTAAATGAAAAGTCAAGAGTTATG
5403961 TT
1 TT
5403963 TTTTTAATGG
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:0.42, C:0.04, G:0.22, T:0.32
Consensus pattern (24 bp):
TTAAATGAAAAGTCAAGAGTTATG
Found at i:5407814 original size:84 final size:84
Alignment explanation
Indices: 5407670--5407828 Score: 205
Period size: 84 Copynumber: 1.9 Consensus size: 84
5407660 GGAAGACTCG
* * * * *** *
5407670 TACAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCATTGTCCCAGGCA
1 TACAATACCAACGTCCCAGACATGGTCTTACACGTAAACACATATCGATGCCAACATCCCAGAC-
5407735 G-GGTCTTACATAAATCAAA
65 GTGGTCTTACATAAATCAAA
*
5407754 TACAATACCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTCGATGCCAACATCCCAGAC
1 TACAATACCAACGTCCCAGACATGGTCTTACACGTAAACACATA-TCGATGCCAACATCCCAGAC
5407818 GTGGTCTTACA
65 GTGGTCTTACA
5407829 CGAAAACACG
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
83 2 0.03
84 62 0.97
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (84 bp):
TACAATACCAACGTCCCAGACATGGTCTTACACGTAAACACATATCGATGCCAACATCCCAGACG
TGGTCTTACATAAATCAAA
Found at i:5407829 original size:43 final size:42
Alignment explanation
Indices: 5407674--5407837 Score: 156
Period size: 43 Copynumber: 3.9 Consensus size: 42
5407664 GACTCGTACA
* *
5407674 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACA-ATCG
** * *
5407717 ATGCCATTGTCCCAGGCAG-GGTCTTACA--TAAATCA-AATACA
1 ATGCCAACGTCCCAGAC-GTGGTCTTACACGTAAA-CACAAT-CG
* * *
5407758 ATACCAATGTCCCAGACATGGTCTTACACGTAAACACAAGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAA-TCG
* *
5407801 ATGCCAACATCCCAGACGTGGTCTTACACGAAAACAC
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACAC
5407838 GTATCAAAAT
Statistics
Matches: 98, Mismatches: 15, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
40 2 0.02
41 28 0.29
42 4 0.04
43 62 0.63
44 2 0.02
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAATCG
Found at i:5413582 original size:9 final size:8
Alignment explanation
Indices: 5413566--5413631 Score: 51
Period size: 8 Copynumber: 7.4 Consensus size: 8
5413556 TAACAAAAAT
5413566 AAATTTAA
1 AAATTTAA
5413574 AAATCTTAA
1 AAAT-TTAA
*
5413583 AAATTTTA
1 AAATTTAA
5413591 AAATTTAA
1 AAATTTAA
*
5413599 GCAAATATAA
1 --AAATTTAA
5413609 AAATGTTCTAGA
1 AAA--TT-TA-A
5413621 AAATTTAA
1 AAATTTAA
5413629 AAA
1 AAA
5413632 ATATCATTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
8 21 0.45
9 10 0.21
10 10 0.21
11 2 0.04
12 4 0.09
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (8 bp):
AAATTTAA
Found at i:5414219 original size:24 final size:24
Alignment explanation
Indices: 5414192--5414238 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5414182 TTTTGTATTT
* * *
5414192 TATATTTTAAAATGAAAGTATATA
1 TATATTTAAAAAGGAAAATATATA
5414216 TATATTTAAAAAGGAAAATATAT
1 TATATTTAAAAAGGAAAATATAT
5414239 TTTTAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (24 bp):
TATATTTAAAAAGGAAAATATATA
Found at i:5416680 original size:17 final size:17
Alignment explanation
Indices: 5416658--5416693 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5416648 AAGCAAAGTT
5416658 CATTATTTAACAACAAC
1 CATTATTTAACAACAAC
5416675 CATTATTTAACAACAAC
1 CATTATTTAACAACAAC
5416692 CA
1 CA
5416694 CCCCATCATT
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:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (17 bp):
CATTATTTAACAACAAC
Found at i:5417959 original size:40 final size:40
Alignment explanation
Indices: 5417909--5418045 Score: 247
Period size: 40 Copynumber: 3.4 Consensus size: 40
5417899 TCCGTACACT
* *
5417909 GGCATGAAGCCTGCTAGATGTATAGTCTAAATATTTCACC
1 GGCATTAAGCCTGCTAGATGTATAGTCTGAATATTTCACC
*
5417949 GGCATTAAGCCTGCTAGACGTATAGTCTGAATATTTCACC
1 GGCATTAAGCCTGCTAGATGTATAGTCTGAATATTTCACC
5417989 GGCATTAAGCCTGCTAGATGTATAGTCTGAATATTTCACC
1 GGCATTAAGCCTGCTAGATGTATAGTCTGAATATTTCACC
5418029 GGCATTAAGCCTGCTAG
1 GGCATTAAGCCTGCTAG
5418046 GCACAAGCCT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 93 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (40 bp):
GGCATTAAGCCTGCTAGATGTATAGTCTGAATATTTCACC
Done.