Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009405.1 Hibiscus syriacus cultivar Beakdansim tig00113337_pilon, whole genome shotgun sequence
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: 1310060
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:393905 original size:33 final size:33
Alignment explanation
Indices: 393868--393953 Score: 129
Period size: 33 Copynumber: 2.6 Consensus size: 33
393858 TTCAGAAAAT
393868 AAATCAACGTATTTGAGTCCTATTGAAACACTA
1 AAATCAACGTATTTGAGTCCTATTGAAACACTA
*
393901 AAATCAACGTATTTGAGTCATATTGAAACACTA
1 AAATCAACGTATTTGAGTCCTATTGAAACACTA
* *
393934 AAACTGAA-GCATTTGAGTCC
1 AAA-TCAACGTATTTGAGTCC
393954 AAGTAGGACT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 45 0.94
34 3 0.06
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (33 bp):
AAATCAACGTATTTGAGTCCTATTGAAACACTA
Found at i:394315 original size:2 final size:2
Alignment explanation
Indices: 394308--394334 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
394298 TTTACATTGT
394308 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 T
394335 TTATTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:394352 original size:18 final size:18
Alignment explanation
Indices: 394331--394374 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 18
394321 ATATATATAT
394331 ATATTTATTTATTTATTA
1 ATATTTATTTATTTATTA
394349 ATA-TTA-TTA--TATTA
1 ATATTTATTTATTTATTA
394363 ATATTT-TTTATT
1 ATATTTATTTATT
394375 ATTCTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 9
0.71 0.00 0.29
Matches are distributed among these distances:
14 8 0.36
15 5 0.23
16 3 0.14
17 3 0.14
18 3 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATATTTATTTATTTATTA
Found at i:394353 original size:14 final size:14
Alignment explanation
Indices: 394336--394375 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
394326 TATATATATT
394336 TATTTATTTATTAA
1 TATTTATTTATTAA
394350 TA-TTATTATATTAA
1 TATTTATT-TATTAA
394364 TATTT-TTTATTA
1 TATTTATTTATTA
394376 TTCTTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 10 0.42
14 12 0.50
15 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTTATTTATTAA
Found at i:397613 original size:16 final size:16
Alignment explanation
Indices: 397592--397626 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
397582 CACACCATGT
397592 AAATCTAAAATCACTC
1 AAATCTAAAATCACTC
397608 AAATCTAAAATCACTC
1 AAATCTAAAATCACTC
397624 AAA
1 AAA
397627 AGTTTCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATCTAAAATCACTC
Found at i:397940 original size:27 final size:27
Alignment explanation
Indices: 397902--397959 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
397892 TTGACCATTG
* **
397902 GACTTCAGCATGCTTGACCGATCGTTT
1 GACTTCAACATGCTTGACAAATCGTTT
397929 GACTTCAACATGCTTGACAAATCGTTT
1 GACTTCAACATGCTTGACAAATCGTTT
397956 GACT
1 GACT
397960 ATTCTTCTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (27 bp):
GACTTCAACATGCTTGACAAATCGTTT
Found at i:406972 original size:19 final size:19
Alignment explanation
Indices: 406948--406984 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
406938 ATGACCAACA
*
406948 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
406967 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
406985 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:407119 original size:20 final size:20
Alignment explanation
Indices: 407094--407181 Score: 176
Period size: 20 Copynumber: 4.4 Consensus size: 20
407084 AGTCCAAAAT
407094 CATTGCGATAGCACTGTTCA
1 CATTGCGATAGCACTGTTCA
407114 CATTGCGATAGCACTGTTCA
1 CATTGCGATAGCACTGTTCA
407134 CATTGCGATAGCACTGTTCA
1 CATTGCGATAGCACTGTTCA
407154 CATTGCGATAGCACTGTTCA
1 CATTGCGATAGCACTGTTCA
407174 CATTGCGA
1 CATTGCGA
407182 ATTTGCGATA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (20 bp):
CATTGCGATAGCACTGTTCA
Found at i:407356 original size:16 final size:17
Alignment explanation
Indices: 407329--407380 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
407319 TTTATTTATG
407329 ATAAACTATAAATTTTAA
1 ATAAA-TATAAATTTTAA
*
407347 AT-AATATAAA-ATTAA
1 ATAAATATAAATTTTAA
*
407362 ATAAATATAAATTCTAA
1 ATAAATATAAATTTTAA
407379 AT
1 AT
407381 TATTTATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 14 0.48
17 7 0.24
18 2 0.07
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAAATATAAATTTTAA
Found at i:407940 original size:21 final size:20
Alignment explanation
Indices: 407914--407974 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 20
407904 AATTCGCAAT
407914 GTGAACACTGCTATCGCAACG
1 GTGAACA-TGCTATCGCAACG
407935 GTGAACAGTGCTATCGCAACG
1 GTGAACA-TGCTATCGCAACG
407956 GTGAACA-GCTATCGCAACG
1 GTGAACATGCTATCGCAACG
407975 CGAATTTGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 12 0.31
21 27 0.69
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (20 bp):
GTGAACATGCTATCGCAACG
Found at i:408057 original size:20 final size:19
Alignment explanation
Indices: 408034--408079 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
408024 GAAAACTTAT
* *
408034 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
408054 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
408073 TTGCGAT
1 TTGCGAT
408080 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:408069 original size:19 final size:19
Alignment explanation
Indices: 408045--408081 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
408035 TGCGATACTG
*
408045 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
408064 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
408082 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:414236 original size:162 final size:165
Alignment explanation
Indices: 413969--414295 Score: 633
Period size: 162 Copynumber: 2.0 Consensus size: 165
413959 AAAATTCGAG
413969 CACGTCCGCACGATCACTTAAATGAGAAAGTGCAAAGGTGCCCCTTGGCTGATTGTTAAATGAAC
1 CACGTCCGCACGATCACTTAAATGAGAAAGTGCAAAGGTGCCCCTTGGCTGATTGTTAAATGAAC
414034 CAATTAAGTCAATAGCCCCAGTGGGAGGTTCATCTAGTTCATCATTGCAGCCAACTCTAACCATA
66 CAATTAAGTCAATAGCCCCAGTGGGAGGTTCATCTAGTTCATCATTGCAGCCAACTCTAACCATA
414099 ACATTGACA-TTCCGCTA-TT-TTTGAAGTCCAGC
131 ACATTGACATTTCCGCTATTTCTTTGAAGTCCAGC
414131 CACGTCCGCACGATCACTTAAATGAGAAAGTGCAAAGGTGCCCCTTGGCTGATTGTTAAATGAAC
1 CACGTCCGCACGATCACTTAAATGAGAAAGTGCAAAGGTGCCCCTTGGCTGATTGTTAAATGAAC
414196 CAATTAAGTCAATAGCCCCAGTGGGAGGTTCATCTAGTTCATCATTGCAGCCAACTCTAACCATA
66 CAATTAAGTCAATAGCCCCAGTGGGAGGTTCATCTAGTTCATCATTGCAGCCAACTCTAACCATA
414261 ACATTGACATTTCCGCTATTTCTTTGAAGTCCAGC
131 ACATTGACATTTCCGCTATTTCTTTGAAGTCCAGC
414296 AGCATCATTC
Statistics
Matches: 162, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
162 139 0.86
163 8 0.05
164 2 0.01
165 13 0.08
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (165 bp):
CACGTCCGCACGATCACTTAAATGAGAAAGTGCAAAGGTGCCCCTTGGCTGATTGTTAAATGAAC
CAATTAAGTCAATAGCCCCAGTGGGAGGTTCATCTAGTTCATCATTGCAGCCAACTCTAACCATA
ACATTGACATTTCCGCTATTTCTTTGAAGTCCAGC
Found at i:415858 original size:36 final size:36
Alignment explanation
Indices: 415797--415867 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
415787 AGATGAATAA
*
415797 TTGAATCGAAAGTGTCGATACTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGTCGATACTTCCTTTCATTCTTC
**
415833 TTGAATCGAAAGTG-CTGATGTTTCCTTTCATTCTT
1 TTGAATCGAAAGTGTC-GATACTTCCTTTCATTCTT
415868 TTTATTCACC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 1 0.03
36 30 0.97
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.44
Consensus pattern (36 bp):
TTGAATCGAAAGTGTCGATACTTCCTTTCATTCTTC
Found at i:418354 original size:3 final size:3
Alignment explanation
Indices: 418346--418372 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
418336 GTTATATAAC
418346 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
418373 TTGAAAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:424591 original size:17 final size:18
Alignment explanation
Indices: 424571--424608 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
424561 TTAAATAACC
424571 TAAAATAAAAATATA-AT
1 TAAAATAAAAATATATAT
* *
424588 TAAAATTAATATATATAT
1 TAAAATAAAAATATATAT
424606 TAA
1 TAA
424609 TACTATCGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATAAAAATATATAT
Found at i:426779 original size:15 final size:15
Alignment explanation
Indices: 426759--426788 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
426749 TTTCACCTAT
426759 TTTTTTAATTTTTAA
1 TTTTTTAATTTTTAA
*
426774 TTTTTTATTTTTTAA
1 TTTTTTAATTTTTAA
426789 AATTATTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTAATTTTTAA
Found at i:432023 original size:38 final size:37
Alignment explanation
Indices: 431968--432053 Score: 88
Period size: 38 Copynumber: 2.3 Consensus size: 37
431958 TTTTATATGT
*
431968 AATATTAATATATTATTTTAAT-ATCATTTTAATAAAA
1 AATATTAATATATTA-TTTAATGATAATTTTAATAAAA
* *
432005 AATATTAAT-TATTATATTTATTGATAATTTTAATAATAT
1 AATATTAATATA-T-TATTTAATGATAATTTTAATAA-AA
432044 AATA-TAATAT
1 AATATTAATAT
432054 TTTGTTTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
36 2 0.05
37 15 0.37
38 18 0.44
39 6 0.15
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (37 bp):
AATATTAATATATTATTTAATGATAATTTTAATAAAA
Found at i:432056 original size:21 final size:20
Alignment explanation
Indices: 432031--432100 Score: 50
Period size: 21 Copynumber: 3.3 Consensus size: 20
432021 TTTATTGATA
432031 ATTTTAATAATATAATATAAT
1 ATTTTAAT-ATATAATATAAT
** * *
432052 ATTTTGTTTTTATAATTATATT
1 ATTTT-AATATATAA-TATAAT
* *
432074 ATTATAATATATAATATTAT
1 ATTTTAATATATAATATAAT
432094 ACTTTTA
1 A-TTTTA
432101 TTTTTATAAT
Statistics
Matches: 35, Mismatches: 11, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
20 5 0.14
21 20 0.57
22 10 0.29
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (20 bp):
ATTTTAATATATAATATAAT
Found at i:432093 original size:29 final size:29
Alignment explanation
Indices: 432061--432118 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
432051 TATTTTGTTT
*
432061 TTATAATTATATTATTATAATATATAATA
1 TTATAATTATATTATTATAATAAATAATA
* * *
432090 TTATACTTTTATTTTTATAATAAATAATA
1 TTATAATTATATTATTATAATAAATAATA
432119 AATTATTAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (29 bp):
TTATAATTATATTATTATAATAAATAATA
Found at i:432283 original size:9 final size:9
Alignment explanation
Indices: 432271--432372 Score: 55
Period size: 9 Copynumber: 10.6 Consensus size: 9
432261 ATTTTAATTA
432271 ATAATTAAT
1 ATAATTAAT
432280 ATAATTAAT
1 ATAATTAAT
*
432289 AATATATTATT
1 -ATA-ATTAAT
432300 ATAATTGTAAT
1 ATAA-T-TAAT
432311 AAATAATTAAT
1 --ATAATTAAT
*
432322 ATAATTTAT
1 ATAATTAAT
*
432331 AATAATT-TT
1 -ATAATTAAT
*
432340 AT-TTTAAT
1 ATAATTAAT
* *
432348 AAAATTATT
1 ATAATTAAT
432357 ATAATCATAAT
1 ATAAT--TAAT
432368 ATAAT
1 ATAAT
432373 ATTTTAATAA
Statistics
Matches: 71, Mismatches: 11, Indels: 20
0.70 0.11 0.20
Matches are distributed among these distances:
7 2 0.03
8 4 0.06
9 27 0.38
10 13 0.18
11 20 0.28
12 1 0.01
13 4 0.06
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (9 bp):
ATAATTAAT
Found at i:432284 original size:16 final size:15
Alignment explanation
Indices: 432265--432333 Score: 56
Period size: 16 Copynumber: 4.7 Consensus size: 15
432255 ATTATTATTT
432265 TAATTAATAATTAATA
1 TAATTAATAATT-ATA
432281 TAATTAATAA-TATA
1 TAATTAATAATTATA
* *
432295 TTATT-ATAA-T-TG
1 TAATTAATAATTATA
*
432307 TAATAAATAATTAATA
1 TAATTAATAATT-ATA
*
432323 TAATTTATAAT
1 TAATTAATAAT
432334 AATTTTATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
12 4 0.10
13 9 0.21
14 8 0.19
15 1 0.02
16 20 0.48
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (15 bp):
TAATTAATAATTATA
Found at i:432316 original size:42 final size:40
Alignment explanation
Indices: 432248--432380 Score: 129
Period size: 42 Copynumber: 3.4 Consensus size: 40
432238 TTTAATATTT
432248 TAATAATATTATTAT--TTTAATTAATAATTAATATAATTAA
1 TAAT-ATATTATTATAATTTAA-TAATAATTAATATAATTAA
*
432288 TAATATATTATTATAATTGTAATAAATAATTAATATAATTTA
1 TAATATATTATTATAATT-TAAT-AATAATTAATATAATTAA
* *
432330 TAATA-ATT-TTAT--TTTAATAA-AATTATTATAA-TCA
1 TAATATATTATTATAATTTAATAATAATTAATATAATTAA
* *
432364 TAATATAATATTTTAAT
1 TAATATATTATTATAAT
432381 AATAATTTTG
Statistics
Matches: 80, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
34 7 0.09
35 12 0.15
36 5 0.06
37 4 0.05
38 3 0.04
39 10 0.12
40 8 0.10
41 6 0.08
42 25 0.31
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (40 bp):
TAATATATTATTATAATTTAATAATAATTAATATAATTAA
Found at i:441020 original size:2 final size:2
Alignment explanation
Indices: 441013--441050 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
441003 ATTTGAGTTG
441013 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
441051 TCTCTAATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:446554 original size:20 final size:20
Alignment explanation
Indices: 446516--446554 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
446506 CCAGTATATT
* *
446516 TTTACCGGTTATATTATAAA
1 TTTACCGGTTACATAATAAA
*
446536 TTTACCTGTTACATAATAA
1 TTTACCGGTTACATAATAA
446555 TTATCGATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.44
Consensus pattern (20 bp):
TTTACCGGTTACATAATAAA
Found at i:447131 original size:20 final size:20
Alignment explanation
Indices: 447084--447131 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
447074 ATCCGGTAGC
*
447084 TCTTTACCGGTTTTGTCATT
1 TCTTTACCGGTTTTATCATT
**
447104 TCGATACCGGTTTTATCATAT
1 TCTTTACCGGTTTTATCAT-T
447125 T-TTTACC
1 TCTTTACC
447132 TGTTATATTG
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.17, C:0.21, G:0.12, T:0.50
Consensus pattern (20 bp):
TCTTTACCGGTTTTATCATT
Found at i:447224 original size:182 final size:182
Alignment explanation
Indices: 446909--447360 Score: 661
Period size: 182 Copynumber: 2.5 Consensus size: 182
446899 TTTTTACTAT
* * * * * *
446909 CGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACATGTTATATTGTTATAGATTGATAT
1 CGGTTTTGTCATTTCGAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAT
* * *
446974 ATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTTCAAAAATGT
66 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAATGT
* * *
447039 CGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCTCTTTAC
131 CGATACTTATAATAAAGTATCGACACTATCAACATATCCAGTAGCGCTTTAA
* *
447091 CGGTTTTGTCATTTCGATACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTCGAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAT
** *
447156 ATTTTTATAAAGTATCGACGTTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
66 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAATGT
* *
447221 CGATACTTATAATAAAGTATCGATACTATCAACATATCTAGTAGCGCTTTAA
131 CGATACTTATAATAAAGTATCGACACTATCAACATATCCAGTAGCGCTTTAA
* ** * * *
447273 CTGTTTTGTCATTTATAGACCGGTTTTATCATTTTTTTTTACCTGTTTTATTATTATGGATCGAT
1 CGGTTTTGTCATTTCGAGACCGGTTTTATCA--TATTTTTACCTGTTATATTGTTATGGATCGAT
447338 ATATTTTTATAAAGTATCGACAC
64 ATATTTTTATAAAGTATCGACAC
447361 AATCAACATA
Statistics
Matches: 239, Mismatches: 29, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
182 190 0.79
184 49 0.21
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (182 bp):
CGGTTTTGTCATTTCGAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAT
ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAATGT
CGATACTTATAATAAAGTATCGACACTATCAACATATCCAGTAGCGCTTTAA
Found at i:447484 original size:112 final size:112
Alignment explanation
Indices: 447232--447693 Score: 708
Period size: 112 Copynumber: 4.1 Consensus size: 112
447222 GATACTTATA
* ** *
447232 ATAAAGTATCGATACTATCAACATATCTAGTAGCGCTTTAACTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * * *
447297 TTTATCATTTTTTTTTACCTGTTTTATTATTATGGATCGATATATTTTT
66 TTTGTCA--TTTTTTTACCTGTTATATTATTATGGATCAATACATTTTT
* * *
447346 ATAAAGTATCGACACAATCAACATATCTGGTAGCGCTTTACCTATTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
447411 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCAATACATTTTT
* *
447458 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
447523 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATAAATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCAATACATTTTT
* * *
447570 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTATCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
447635 TTTGTCATTTTTTTACTTGTTATATTATTATGGATTAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCAATACATTTTT
447682 ATAAAGTATCGA
1 ATAAAGTATCGA
447694 TACAAACCGA
Statistics
Matches: 327, Mismatches: 21, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
112 261 0.80
114 66 0.20
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTATTATGGATCAATACATTTTT
Found at i:451998 original size:35 final size:35
Alignment explanation
Indices: 451958--452036 Score: 158
Period size: 35 Copynumber: 2.3 Consensus size: 35
451948 CATACGGGAA
451958 CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
1 CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
451993 CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
1 CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
452028 CATACGAGC
1 CATACGAGC
452037 GTTCTCCCCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.27, C:0.34, G:0.20, T:0.19
Consensus pattern (35 bp):
CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
Found at i:454883 original size:26 final size:24
Alignment explanation
Indices: 454825--454883 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
454815 CTAATAAACC
*
454825 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
454849 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
454877 TAATAAT
1 TAATAAT
454884 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:455729 original size:28 final size:30
Alignment explanation
Indices: 455689--455751 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
455679 ATTTTTTATA
*
455689 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
455719 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
455747 TAATA
1 TAATA
455752 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:455758 original size:28 final size:28
Alignment explanation
Indices: 455693--455758 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
455683 TTTATATAAT
*
455693 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
455721 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
455749 ATAATTTATA
1 ATAATATATA
455759 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:455761 original size:21 final size:21
Alignment explanation
Indices: 455728--455776 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
455718 CTAATATAAT
455728 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
455749 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
455770 ATTAACT
1 A-TAACT
455777 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:456277 original size:15 final size:15
Alignment explanation
Indices: 456257--456435 Score: 144
Period size: 15 Copynumber: 11.1 Consensus size: 15
456247 CCATCCCCTC
456257 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
456272 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* * *
456287 CGTCCAATGCACCATCCCCT
1 C--CCCATG---CATTCCCA
456307 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
456322 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* *
456337 CGTCCCATGCATCCCCTC
1 C--CCCATGCATTCCC-A
456355 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* *
456370 CATCCCATG-TTGATCCCTC
1 C--CCCATGCAT--TCCC-A
456389 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* *
456404 CCCCATGCATCCCCTC
1 CCCCATGCATTCCC-A
456420 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
456435 C
1 C
456436 GTCCCATGTT
Statistics
Matches: 131, Mismatches: 18, Indels: 30
0.73 0.10 0.17
Matches are distributed among these distances:
15 53 0.40
16 30 0.23
17 29 0.22
18 11 0.08
19 1 0.01
20 7 0.05
ACGTcount: A:0.18, C:0.53, G:0.08, T:0.21
Consensus pattern (15 bp):
CCCCATGCATTCCCA
Found at i:456332 original size:50 final size:51
Alignment explanation
Indices: 456230--456370 Score: 245
Period size: 50 Copynumber: 2.8 Consensus size: 51
456220 CCATGCACAG
456230 TTCCCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCACCCCATGCA
1 TTCCCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCACCCCATGCA
456281 TTCCCACGTCCAATGCACCATCCCCT-CCCCATGCATTCCCACCCCATGCA
1 TTCCCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCACCCCATGCA
*
456331 TTCCCACGTCCCATG---CATCCCCTCCCCCATGCATTCCCAC
1 TTCCCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCAC
456371 ATCCCATGTT
Statistics
Matches: 88, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
47 8 0.09
48 16 0.18
50 38 0.43
51 26 0.30
ACGTcount: A:0.18, C:0.53, G:0.08, T:0.21
Consensus pattern (51 bp):
TTCCCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCACCCCATGCA
Found at i:456377 original size:50 final size:49
Alignment explanation
Indices: 456230--456443 Score: 224
Period size: 50 Copynumber: 4.3 Consensus size: 49
456220 CCATGCACAG
*
456230 TTCCCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCACCCCATGCA
1 TTCCCACGTCCCATG--CCATCCCCTCCCCCATGCATTCCCACCCCATGCA
*
456281 TTCCCACGTCCAATGCACCATCCCCT-CCCCATGCATTCCCACCCCATGCA
1 TTCCCACGTCCCATG--CCATCCCCTCCCCCATGCATTCCCACCCCATGCA
*
456331 TTCCCACGTCCCATG-CATCCCCTCCCCCATGCATTCCCACATCCCATG-T
1 TTCCCACGTCCCATGCCATCCCCTCCCCCATGCATTCCCAC--CCCATGCA
* * * * * *
456380 TGATCCCTC-CCCCATG-CATTCCC-ACCCCATGCATCCCCTCCCCCATGCA
1 T--TCCCACGTCCCATGCCATCCCCTCCCCCATGCATTCCC-ACCCCATGCA
456429 TTCCCACGTCCCATG
1 TTCCCACGTCCCATG
456444 TTGATTGCAT
Statistics
Matches: 144, Mismatches: 11, Indels: 19
0.83 0.06 0.11
Matches are distributed among these distances:
47 13 0.09
48 28 0.19
49 15 0.10
50 57 0.40
51 31 0.22
ACGTcount: A:0.18, C:0.52, G:0.08, T:0.21
Consensus pattern (49 bp):
TTCCCACGTCCCATGCCATCCCCTCCCCCATGCATTCCCACCCCATGCA
Found at i:456377 original size:65 final size:64
Alignment explanation
Indices: 456252--456443 Score: 203
Period size: 65 Copynumber: 2.9 Consensus size: 64
456242 ATGCACCATC
* * * * * *
456252 CCCTCCCCCATGCATTCCCACCCCATGCATTCCCACGTCCAATGCACCATCCC-C-TCCCCATGC
1 CCCTACCCCATGCATTCCCACCCCATGCATCCCCTC-CCCCATGCA--TTCCCACAT-CCCATG-
456315 AT-T
61 ATAT
*
456318 CCC-ACCCCATGCATTCCCACGTCCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTG
1 CCCTACCCCATGCATTCCCAC--CCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGAT-
456382 AT
63 AT
* *
456384 CCCTCCCCCATGCATTCCCACCCCATGCATCCCCTCCCCCATGCATTCCCACGTCCCATG
1 CCCTACCCCATGCATTCCCACCCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATG
456444 TTGATTGCAT
Statistics
Matches: 110, Mismatches: 9, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
64 5 0.05
65 61 0.55
66 15 0.14
67 29 0.26
ACGTcount: A:0.17, C:0.53, G:0.08, T:0.21
Consensus pattern (64 bp):
CCCTACCCCATGCATTCCCACCCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGATAT
Found at i:456393 original size:82 final size:82
Alignment explanation
Indices: 456258--456435 Score: 218
Period size: 82 Copynumber: 2.2 Consensus size: 82
456248 CATCCCCTCC
* *
456258 CCCATGCATTCCCACCCCATGCATTCCCACGTCCAATGCACCATCCCCTCCCCATGCATTCCCAC
1 CCCATGCATCCCCACCCCATGCATTCCCACATCCAATGCACCATCCCCTCCCCATGCATTCCCAC
456323 CCCATGCATTCCCACGT
66 CCCATGCATTCCCACGT
* * ***
456340 CCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATG-TTGAT-CCCTCCCCCATGCATTCCC
1 CCCATGCATCCCC-ACCCCATGCATTCCCACATCCAATGCACCATCCCCT-CCCCATGCATTCCC
* * *
456403 ACCCCATGCATCCCCTC-C
64 ACCCCATGCATTCCCACGT
*
456421 CCCATGCATTCCCAC
1 CCCATGCATCCCCAC
456436 GTCCCATGTT
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
80 1 0.01
81 16 0.20
82 43 0.52
83 22 0.27
ACGTcount: A:0.18, C:0.53, G:0.08, T:0.21
Consensus pattern (82 bp):
CCCATGCATCCCCACCCCATGCATTCCCACATCCAATGCACCATCCCCTCCCCATGCATTCCCAC
CCCATGCATTCCCACGT
Found at i:456444 original size:65 final size:66
Alignment explanation
Indices: 456322--456448 Score: 229
Period size: 65 Copynumber: 1.9 Consensus size: 66
456312 TGCATTCCCA
456322 CCCCATGCATTCCCACGTCCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTGATCCC
1 CCCCATGCATTCCCACG-CCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTGATCCC
456387 TC
65 TC
*
456389 CCCCATGCATTCCCAC-CCCATGCATCCCCTCCCCCATGCATTCCCACGTCCCATGTTGAT
1 CCCCATGCATTCCCACGCCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTGAT
456449 TGCATGGCGA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
65 43 0.73
67 16 0.27
ACGTcount: A:0.17, C:0.50, G:0.09, T:0.24
Consensus pattern (66 bp):
CCCCATGCATTCCCACGCCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTGATCCCT
C
Found at i:456523 original size:29 final size:29
Alignment explanation
Indices: 456481--456627 Score: 294
Period size: 29 Copynumber: 5.1 Consensus size: 29
456471 TAATACACAC
456481 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
456510 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
456539 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
456568 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
456597 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
456626 AG
1 AG
456628 ACCACTGTAT
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 118 1.00
ACGTcount: A:0.18, C:0.37, G:0.31, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCCA
Found at i:461592 original size:12 final size:13
Alignment explanation
Indices: 461574--461610 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
461564 GATATCAGAA
461574 ATCAAAACATAAT
1 ATCAAAACATAAT
461587 -TCAAAACAT-AT
1 ATCAAAACATAAT
461598 ATCAAAACATAAT
1 ATCAAAACATAAT
461611 CCAGATCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 2 0.09
12 18 0.82
13 2 0.09
ACGTcount: A:0.59, C:0.16, G:0.00, T:0.24
Consensus pattern (13 bp):
ATCAAAACATAAT
Found at i:461625 original size:24 final size:24
Alignment explanation
Indices: 461567--461630 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
461557 AAACGGAGAT
*
461567 ATCAGAAATCAAAACATAATTCAA
1 ATCAGAAATCAAAACATAATCCAA
* * * *
461591 AACATATATCAAAACATAATCCAG
1 ATCAGAAATCAAAACATAATCCAA
*
461615 ATCAGAAATCAGAACA
1 ATCAGAAATCAAAACA
461631 GAATTCAGGT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.56, C:0.19, G:0.06, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAAAACATAATCCAA
Found at i:461649 original size:48 final size:47
Alignment explanation
Indices: 461567--461675 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 47
461557 AAACGGAGAT
* *
461567 ATCAGAAATCAAAACATAATTCAAAACATATATCAAAACATAATCCA
1 ATCAGAAATCAGAACAGAATTCAAAACATATATCAAAACATAATCCA
*** * * *
461614 GATCAGAAATCAGAACAGAATTCAGGTCATGTATCAGAACATAATTCA
1 -ATCAGAAATCAGAACAGAATTCAAAACATATATCAAAACATAATCCA
*
461662 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
461676 TAAAATATTT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
47 1 0.02
48 50 0.98
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAAAACATATATCAAAACATAATCCA
Found at i:461673 original size:24 final size:25
Alignment explanation
Indices: 461619--461675 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
461609 ATCCAGATCA
* *
461619 GAAATCAGAACAGAATTCAGGTCAT
1 GAAATCAGAACAGAATTCAAGTCAG
* *
461644 G-TATCAGAACATAATTCAAGTC-G
1 GAAATCAGAACAGAATTCAAGTCAG
461667 GAAATCAGA
1 GAAATCAGA
461676 TAAAATATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 1 0.04
24 24 0.92
25 1 0.04
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (25 bp):
GAAATCAGAACAGAATTCAAGTCAG
Found at i:463449 original size:36 final size:36
Alignment explanation
Indices: 463402--463474 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
463392 GATAAATTAT
463402 AATCTACATATCCATGGATGATTCTTTTATCACTTA
1 AATCTACATATCCATGGATGATTCTTTTATCACTTA
* *
463438 AATCTACATATCGATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGATGATTCTTTTATCACTTA
463474 A
1 A
463475 TTCCAGAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (36 bp):
AATCTACATATCCATGGATGATTCTTTTATCACTTA
Found at i:466370 original size:60 final size:60
Alignment explanation
Indices: 466224--466397 Score: 147
Period size: 60 Copynumber: 2.9 Consensus size: 60
466214 ATATATCCCC
* * * * * * *
466224 AAACTATATCCGT-ATTTTAAATTGGTCTTTACACTTTTGAATATTTCAATTTCATTCTT
1 AAACTATAGCCCTCATTTTAAATTAGTCCTTAAACTTTTGAACATTTCAATTTCATCCTT
* * * * *
466283 AAATTATAGCTCTCATTCTAAAATAGTCCTTAAACTTTTGAACA-TTCTGATTTCATCCTT
1 AAACTATAGCCCTCATTTTAAATTAGTCCTTAAACTTTTGAACATTTC-AATTTCATCCTT
* ** * * *
466343 AAACTAT-GTCCCTCTTTTTAAATTAGTCCCCAAACTTTTGGATATTCCAATTTCA
1 AAACTATAG-CCCTCATTTTAAATTAGTCCTTAAACTTTTGAACATTTCAATTTCA
466398 CCTCCAAATT
Statistics
Matches: 88, Mismatches: 23, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
59 13 0.15
60 73 0.83
61 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.44
Consensus pattern (60 bp):
AAACTATAGCCCTCATTTTAAATTAGTCCTTAAACTTTTGAACATTTCAATTTCATCCTT
Found at i:466634 original size:29 final size:29
Alignment explanation
Indices: 466602--466658 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
466592 ATGAAATTGA
* *
466602 AATGCTCAAAAGTTTGAGG-ATTAATTTAG
1 AATGATCAAAAGTTT-AGGAATCAATTTAG
*
466631 AATGATTAAAAGTTTAGGAATCAATTTA
1 AATGATCAAAAGTTTAGGAATCAATTTA
466659 AAATAAGAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (29 bp):
AATGATCAAAAGTTTAGGAATCAATTTAG
Found at i:471514 original size:2 final size:2
Alignment explanation
Indices: 471507--471531 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
471497 CAAATTTTAT
471507 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 T
471532 TTCCATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:473486 original size:168 final size:171
Alignment explanation
Indices: 473208--473547 Score: 650
Period size: 168 Copynumber: 2.0 Consensus size: 171
473198 TATAAGGCAT
*
473208 ATTCGGCCTATCCACAATGCAGTTGTTGATCGTGTTGCATCTTTAGTTTAAGGTCCTTCCTTGCA
1 ATTCGGCCTATCCACAATGCAGTTGTTGATCGTGTTGCATCTTTAGTTTAAGGTCCTCCCTTGCA
473273 TGAAGTCCTTTTTGCTGATCCACCACCCCAGGTGGTTTCATTGATTCATGTTGAT-AA-A-CTTA
66 TGAAGTCCTTTTTGCTGATCCACCACCCCAGGTGGTTTCATTGATTCATGTTGATAAACAGCTTA
473335 GTGCTGCAGTTACTTGGTATAAGTCTGTTCTGGTTGTAAAA
131 GTGCTGCAGTTACTTGGTATAAGTCTGTTCTGGTTGTAAAA
473376 ATTCGGCCTATCCACAATGCAGTTGTTGATCGTGTTGCATCTTTAGTTTAAGGTCCTCCCTTGCA
1 ATTCGGCCTATCCACAATGCAGTTGTTGATCGTGTTGCATCTTTAGTTTAAGGTCCTCCCTTGCA
473441 TGAAGTCCTTTTTGCTGATCCACCACCCCAGGTGGTTTCATTGATTCATGTTGATAAACAGCTTA
66 TGAAGTCCTTTTTGCTGATCCACCACCCCAGGTGGTTTCATTGATTCATGTTGATAAACAGCTTA
473506 GTGCTGCAGTTACTTGGTATAAGTCTGTTCTGGTTGTAAAA
131 GTGCTGCAGTTACTTGGTATAAGTCTGTTCTGGTTGTAAAA
473547 A
1 A
473548 CAATAATAAT
Statistics
Matches: 168, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
168 119 0.71
169 2 0.01
170 1 0.01
171 46 0.27
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (171 bp):
ATTCGGCCTATCCACAATGCAGTTGTTGATCGTGTTGCATCTTTAGTTTAAGGTCCTCCCTTGCA
TGAAGTCCTTTTTGCTGATCCACCACCCCAGGTGGTTTCATTGATTCATGTTGATAAACAGCTTA
GTGCTGCAGTTACTTGGTATAAGTCTGTTCTGGTTGTAAAA
Found at i:473557 original size:3 final size:3
Alignment explanation
Indices: 473549--473598 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
473539 TTGTAAAAAC
473549 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
473597 AA
1 AA
473599 AATGCAGTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:474853 original size:15 final size:15
Alignment explanation
Indices: 474835--474865 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
474825 CTATAGACTA
*
474835 AAAATCTTGAATCTT
1 AAAATCTCGAATCTT
474850 AAAATCTCGAATCTT
1 AAAATCTCGAATCTT
474865 A
1 A
474866 CTAGTCTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.35
Consensus pattern (15 bp):
AAAATCTCGAATCTT
Found at i:478888 original size:19 final size:18
Alignment explanation
Indices: 478866--478901 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
478856 TAATTTTATT
*
478866 TATAATAAATAAATAATTG
1 TATAAT-AATAAAAAATTG
478885 TATAATAATAAAAAATT
1 TATAATAATAAAAAATT
478902 AGGTATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TATAATAATAAAAAATTG
Found at i:481587 original size:2 final size:2
Alignment explanation
Indices: 481580--481644 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
481570 CTCTATCATA
481580 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
481621 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
481645 GATAATAATT
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:485950 original size:31 final size:31
Alignment explanation
Indices: 485867--485950 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
485857 GAATTAAAAA
* * *
485867 AAATTAATTTGACCCTTAAATGTTATATAAG
1 AAATCAATTTGACTCTTAAATTTTATATAAG
* * *
485898 AAATCAATTTAACTCATAAATTTTATTTAA-
1 AAATCAATTTGACTCTTAAATTTTATATAAG
485928 AATATCAATTTGACTCTTAAATT
1 AA-ATCAATTTGACTCTTAAATT
485951 CTATCAAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 2 0.05
31 42 0.95
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.42
Consensus pattern (31 bp):
AAATCAATTTGACTCTTAAATTTTATATAAG
Found at i:492963 original size:2 final size:2
Alignment explanation
Indices: 492956--492980 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
492946 CTGTGCATTT
492956 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
492981 CTGGCTCCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:500924 original size:15 final size:15
Alignment explanation
Indices: 500899--500932 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
500889 AATGATATAA
500899 TTAAAAATTAAAA-T
1 TTAAAAATTAAAAGT
500913 TTAAATAATTAAAAGT
1 TTAAA-AATTAAAAGT
500929 TTAA
1 TTAA
500933 TATGTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 8 0.44
16 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
TTAAAAATTAAAAGT
Found at i:500943 original size:23 final size:22
Alignment explanation
Indices: 500889--500945 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 22
500879 TTAACGATAT
500889 AATG-ATATAATTAAAAATTAA
1 AATGTATATAATTAAAAATTAA
* * *
500910 AATTTAAATAATTAAAAGTTTAA
1 AATGTATATAATTAAAA-ATTAA
*
500933 TATGTATATAATT
1 AATGTATATAATT
500946 TAGTCTTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
21 3 0.11
22 11 0.39
23 14 0.50
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.40
Consensus pattern (22 bp):
AATGTATATAATTAAAAATTAA
Found at i:506247 original size:14 final size:14
Alignment explanation
Indices: 506230--506270 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
506220 GTTCGGTTAT
506230 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
506244 GTTCGGTTATGTTC
1 GTTCGTTTATGTTC
*
506258 GTTCATTTATGTT
1 GTTCGTTTATGTT
506271 TAACCCAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.10, C:0.12, G:0.22, T:0.56
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:513581 original size:14 final size:15
Alignment explanation
Indices: 513539--513632 Score: 63
Period size: 14 Copynumber: 6.4 Consensus size: 15
513529 AAAAAAAGGT
*
513539 AATAAAAACTA-ACAA
1 AATAAAAAC-AGATAA
*
513554 AATAGAAAACAGATGA
1 AATA-AAAACAGATAA
513570 AATAAAAA-AGATAA
1 AATAAAAACAGATAA
513584 AAT-AAAAC-GAATAA
1 AATAAAAACAG-ATAA
* * *
513598 AATAAAGACAAAGAA
1 AATAAAAACAGATAA
* *
513613 AATAATAATA-ATAA
1 AATAAAAACAGATAA
513627 AATAAA
1 AATAAA
513633 GATAACAAGT
Statistics
Matches: 62, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
13 5 0.08
14 23 0.37
15 23 0.37
16 11 0.18
ACGTcount: A:0.72, C:0.05, G:0.07, T:0.15
Consensus pattern (15 bp):
AATAAAAACAGATAA
Found at i:513659 original size:9 final size:9
Alignment explanation
Indices: 513642--513755 Score: 77
Period size: 9 Copynumber: 12.2 Consensus size: 9
513632 AGATAACAAG
*
513642 TAAATAAAA
1 TAAAAAAAA
*
513651 TAAACAAAA
1 TAAAAAAAA
513660 TAAAAATAAA
1 TAAAAA-AAA
*
513670 GAAACAAAAA
1 TAAA-AAAAA
*
513680 GAAAAATAAA
1 TAAAAA-AAA
*
513690 TAAATAAAA
1 TAAAAAAAA
513699 TAAAAAAACA
1 TAAAAAAA-A
513709 T-AAAAAAA
1 TAAAAAAAA
* * *
513717 TAAATAGAG
1 TAAAAAAAA
*
513726 TCAAGAAAAA
1 T-AAAAAAAA
*
513736 TAAATAAAA
1 TAAAAAAAA
*
513745 TAAATAAAA
1 TAAAAAAAA
513754 TA
1 TA
513756 CATGAAAATA
Statistics
Matches: 84, Mismatches: 15, Indels: 12
0.76 0.14 0.11
Matches are distributed among these distances:
8 2 0.02
9 53 0.63
10 27 0.32
11 2 0.02
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:513660 original size:31 final size:30
Alignment explanation
Indices: 513596--513673 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
513586 TAAAACGAAT
* *
513596 AAAATAAAGA-CAAAGAAAATAATAATAAT
1 AAAATAAAGATAAAAGAAAATAATAATAAC
*
513625 AAAATAAAGATAACAAGTAAATAA-AATAAAC
1 AAAATAAAGATAA-AAGAAAATAATAAT-AAC
*
513656 AAAATAAAAAT-AAAGAAA
1 AAAATAAAGATAAAAGAAA
513674 CAAAAAGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
29 15 0.37
30 5 0.12
31 21 0.51
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.15
Consensus pattern (30 bp):
AAAATAAAGATAAAAGAAAATAATAATAAC
Found at i:513662 original size:14 final size:14
Alignment explanation
Indices: 513569--513755 Score: 99
Period size: 14 Copynumber: 13.4 Consensus size: 14
513559 AAAACAGATG
513569 AAATAAAA-AAGATA
1 AAATAAAATAA-ATA
**
513583 AAATAAAACGAATA
1 AAATAAAATAAATA
* *
513597 AAATAAAGACAAAGA
1 AAATAAA-ATAAATA
513612 AAATAATAAT-AATA
1 AAATAA-AATAAATA
513626 AAATAAAGATAACA-A
1 AAATAAA-ATAA-ATA
*
513641 GTAAATAAAATAAACA
1 --AAATAAAATAAATA
*
513657 AAATAAAAATAAA-G
1 AAAT-AAAATAAATA
* *
513671 AAACAAAA-AGA-A
1 AAATAAAATAAATA
513683 AAAT-AAATAAATA
1 AAATAAAATAAATA
*
513696 AAATAAAA-AAACA
1 AAATAAAATAAATA
513709 TAAA-AAAATAAATA
1 -AAATAAAATAAATA
* *
513723 GAGTCAAGAA-AAAT-
1 AAAT-AA-AATAAATA
513737 AAATAAAATAAATA
1 AAATAAAATAAATA
513751 AAATA
1 AAATA
513756 CATGAAAATA
Statistics
Matches: 136, Mismatches: 17, Indels: 40
0.70 0.09 0.21
Matches are distributed among these distances:
11 3 0.02
12 9 0.07
13 25 0.18
14 53 0.39
15 30 0.22
16 9 0.07
17 7 0.05
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.16
Consensus pattern (14 bp):
AAATAAAATAAATA
Found at i:513768 original size:18 final size:18
Alignment explanation
Indices: 513569--513766 Score: 98
Period size: 19 Copynumber: 10.3 Consensus size: 18
513559 AAAACAGATG
513569 AAATAAA-AAAGATAAAATA
1 AAATAAATAAA-AT-AAATA
** *
513588 AAACGAATAAAATAAAGA
1 AAATAAATAAAATAAATA
*
513606 CAAAGAAAATAATAAT-AATA
1 -AAA-TAAATAA-AATAAATA
513626 AAATAAAGATAACAAGTAAATA
1 AAAT-AA-ATAA-AA-TAAATA
* *
513648 AAATAAACAAAATAAAAA
1 AAATAAATAAAATAAATA
* * * *
513666 TAAAGAAACAAAAAGAAAAA
1 -AAATAAA-TAAAATAAATA
*
513686 TAAATAAATAAAATAAAAA
1 -AAATAAATAAAATAAATA
513705 AACATAAA-AAAATAAATA
1 AA-ATAAATAAAATAAATA
* *
513723 GAGTCAAGA-AAAATAAATA
1 AAAT-AA-ATAAAATAAATA
*
513742 AAATAAATAAAATACATGA
1 AAATAAATAAAATAAAT-A
513761 AAATAA
1 AAATAA
513767 TAGTGAAAAT
Statistics
Matches: 142, Mismatches: 22, Indels: 30
0.73 0.11 0.15
Matches are distributed among these distances:
17 2 0.01
18 33 0.23
19 57 0.40
20 36 0.25
21 6 0.04
22 8 0.06
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.16
Consensus pattern (18 bp):
AAATAAATAAAATAAATA
Found at i:513873 original size:23 final size:22
Alignment explanation
Indices: 513832--513879 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
513822 TAGATATAAG
*
513832 ATAAGTATACAAAAAAATAGAT
1 ATAAGTAAACAAAAAAATAGAT
* *
513854 ATAAGATAAACAAAATAATATAT
1 ATAAG-TAAACAAAAAAATAGAT
513877 ATA
1 ATA
513880 TATATATACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.25
Consensus pattern (22 bp):
ATAAGTAAACAAAAAAATAGAT
Found at i:525950 original size:2 final size:2
Alignment explanation
Indices: 525943--525967 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
525933 TGCATCTCTT
525943 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 T
525968 GCAAGAACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:526513 original size:6 final size:6
Alignment explanation
Indices: 526502--526533 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
526492 ATAAATGGGG
526502 CCTTTT CCTTTT CCTTTT CCTTTT CCTTTT CC
1 CCTTTT CCTTTT CCTTTT CCTTTT CCTTTT CC
526534 ATCATTCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (6 bp):
CCTTTT
Found at i:533571 original size:20 final size:21
Alignment explanation
Indices: 533534--533576 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
533524 TTTTTTTCAA
533534 ACATTATTGCACCTAATTTTG
1 ACATTATTGCACCTAATTTTG
*
533555 ACATTGTTGCA-CTAATTTTG
1 ACATTATTGCACCTAATTTTG
533575 AC
1 AC
533577 GTTGCAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTATTGCACCTAATTTTG
Found at i:538182 original size:20 final size:21
Alignment explanation
Indices: 538157--538196 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
538147 TTCAAACTTA
538157 TGCACCTAA-TTTGACATTGT
1 TGCACCTAATTTTGACATTGT
538177 TGCACCTAATTTTGACATTG
1 TGCACCTAATTTTGACATTG
538197 CAATATTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (21 bp):
TGCACCTAATTTTGACATTGT
Found at i:539352 original size:18 final size:16
Alignment explanation
Indices: 539320--539350 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
539310 AATATTGAAA
539320 CTTGAACTCAAAAAAG
1 CTTGAACTCAAAAAAG
539336 CTTGAACTCAAAAAA
1 CTTGAACTCAAAAAA
539351 AAATTAGAAG
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:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
CTTGAACTCAAAAAAG
Found at i:539963 original size:70 final size:69
Alignment explanation
Indices: 539884--540022 Score: 253
Period size: 70 Copynumber: 2.0 Consensus size: 69
539874 TTTTTCGATC
539884 GATCGGATCAGTTCGATCGGTTAAACCAAT-AACCGATAATATGATCGGCTCGCTAATCGGTCCG
1 GATCGGATCAGTTCGATCGGTTAAACCAATAAACCGATAATATGA--GGCTCGCTAATCGGTCCG
539948 ATTCTG
64 ATTCTG
539954 GATCGGATCAGTTCGATCGGTTAAACCAATAAACCGATAATATGAGGCTCGCTAATCGGTCCGAT
1 GATCGGATCAGTTCGATCGGTTAAACCAATAAACCGATAATATGAGGCTCGCTAATCGGTCCGAT
540019 TCTG
66 TCTG
540023 AAAATATGCA
Statistics
Matches: 68, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
69 24 0.35
70 30 0.44
71 14 0.21
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (69 bp):
GATCGGATCAGTTCGATCGGTTAAACCAATAAACCGATAATATGAGGCTCGCTAATCGGTCCGAT
TCTG
Found at i:560296 original size:2 final size:2
Alignment explanation
Indices: 560289--560325 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
560279 AAATAAAACC
560289 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
560326 AAAAGGGGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:566112 original size:60 final size:60
Alignment explanation
Indices: 566019--566157 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 60
566009 AAATAGCGAC
* * * * * * * * *
566019 TATTAAAAGTTGCAAAATGATTCATTAATTATAGGGAGTTATTTTATTGAGTCCATCGAA
1 TATTAAAAGTTACAAAATGATCCATCAACTATAGAGAGTTACTCTATTAAGTCAATCGAA
* * * *
566079 TATTAAAAGTTACAAAATGATCCCTCAACTATAGAGAGTTGCTCTGTTAAGTCAATCGAT
1 TATTAAAAGTTACAAAATGATCCATCAACTATAGAGAGTTACTCTATTAAGTCAATCGAA
*
566139 TAGTAAAAGTTACAAAATG
1 TATTAAAAGTTACAAAATG
566158 TTGATTGAGG
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.34
Consensus pattern (60 bp):
TATTAAAAGTTACAAAATGATCCATCAACTATAGAGAGTTACTCTATTAAGTCAATCGAA
Found at i:571820 original size:20 final size:20
Alignment explanation
Indices: 571784--571825 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
571774 GTGGCACTTA
*
571784 ATATTTTTTTGTGTAATCAT
1 ATATTTTTTTGTGTAATAAT
*
571804 ATATTTATTTT-TTTAATAAT
1 ATATTT-TTTTGTGTAATAAT
571824 AT
1 AT
571826 GATTAGGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (20 bp):
ATATTTTTTTGTGTAATAAT
Found at i:572167 original size:40 final size:40
Alignment explanation
Indices: 572123--572216 Score: 143
Period size: 40 Copynumber: 2.4 Consensus size: 40
572113 ATACCTAAAG
572123 TTTAGTTTTTGTTTCATTTTAGAACCCCACCCTTAAAAAC
1 TTTAGTTTTTGTTTCATTTTAGAACCCCACCCTTAAAAAC
* * ** *
572163 TTTAGTTTTTATTTCATTTTAGTATTCCACCCTTAACAAC
1 TTTAGTTTTTGTTTCATTTTAGAACCCCACCCTTAAAAAC
572203 TTTAGTTTTTGTTT
1 TTTAGTTTTTGTTT
572217 TTTTAGTATC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.23, C:0.18, G:0.07, T:0.51
Consensus pattern (40 bp):
TTTAGTTTTTGTTTCATTTTAGAACCCCACCCTTAAAAAC
Found at i:577650 original size:14 final size:14
Alignment explanation
Indices: 577631--577687 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 14
577621 AATATTTTAA
577631 TAATATTATATTTT
1 TAATATTATATTTT
*
577645 TAATATTACA-TTT
1 TAATATTATATTTT
*
577658 TAATAATATAATTTT
1 TAATATTAT-ATTTT
*
577673 ACTTATATTATATTT
1 --TAATATTATATTT
577688 GATTAGTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 10 0.29
14 10 0.29
15 3 0.09
16 4 0.12
17 7 0.21
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (14 bp):
TAATATTATATTTT
Found at i:579702 original size:28 final size:28
Alignment explanation
Indices: 579643--579901 Score: 362
Period size: 28 Copynumber: 9.3 Consensus size: 28
579633 AACATTTTTT
*
579643 ATAATTACGAAAATATCACCTTTTTCGAA
1 ATAATTACCAAAATATCA-CTTTTTCGAA
* *
579672 ATAATTACGAAAATAGCACTTTTTCGAA
1 ATAATTACCAAAATATCACTTTTTCGAA
579700 ATAATTACCAAAATATCACTTTTTCGAA
1 ATAATTACCAAAATATCACTTTTTCGAA
*
579728 ATAATTACCAAATTATCACTTTTTCGAA
1 ATAATTACCAAAATATCACTTTTTCGAA
*
579756 ATAATTACCAAATTATCAC-TTTT-GAA
1 ATAATTACCAAAATATCACTTTTTCGAA
* *
579782 ATAATTACCAAAATATCATTTTTTTGAA
1 ATAATTACCAAAATATCACTTTTTCGAA
*
579810 ATAATTACCAAAATATTACTTTTTCGAA
1 ATAATTACCAAAATATCACTTTTTCGAA
* *
579838 ATAATTATCAAAATATCATTTTTTTCGAA
1 ATAATTACCAAAATATCA-CTTTTTCGAA
* *
579867 ATAATTACAAAAATATCA-TTTTTTGAA
1 ATAATTACCAAAATATCACTTTTTCGAA
*
579894 ATATTTAC
1 ATAATTAC
579902 GAAACTAACA
Statistics
Matches: 211, Mismatches: 16, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
26 20 0.09
27 23 0.11
28 126 0.60
29 42 0.20
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (28 bp):
ATAATTACCAAAATATCACTTTTTCGAA
Found at i:579798 original size:82 final size:82
Alignment explanation
Indices: 579622--579901 Score: 361
Period size: 82 Copynumber: 3.4 Consensus size: 82
579612 ATAGTCAACT
* * * *
579622 ATTACGAAAATAACATTTTTT---ATAATTACGAAAATATCACCTTTTTCGAAATAATTACGAAA
1 ATTACCAAAATATCATTTTTTGAAATAATTACCAAAATATCA-CTTTTTCGAAATAATTACCAAA
*
579684 ATAGCACTTTTTCGAAATA
65 ATATCAC-TTTTCGAAATA
* *
579703 ATTACCAAAATATCACTTTTTCGAAATAATTACCAAATTATCACTTTTTCGAAATAATTACCAAA
1 ATTACCAAAATATCA-TTTTTTGAAATAATTACCAAAATATCACTTTTTCGAAATAATTACCAAA
*
579768 TTATCACTTTT-GAAATA
65 ATATCACTTTTCGAAATA
* *
579785 ATTACCAAAATATCATTTTTTTGAAATAATTACCAAAATATTACTTTTTCGAAATAATTATCAAA
1 ATTACCAAAATATCA-TTTTTTGAAATAATTACCAAAATATCACTTTTTCGAAATAATTACCAAA
*
579850 ATATCATTTTTTTCGAAATA
65 ATATCA--CTTTTCGAAATA
* *
579870 ATTACAAAAATATCATTTTTTGAAATATTTAC
1 ATTACCAAAATATCATTTTTTGAAATAATTAC
579902 GAAACTAACA
Statistics
Matches: 175, Mismatches: 17, Indels: 11
0.86 0.08 0.05
Matches are distributed among these distances:
81 13 0.07
82 76 0.43
83 4 0.02
84 46 0.26
85 36 0.21
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (82 bp):
ATTACCAAAATATCATTTTTTGAAATAATTACCAAAATATCACTTTTTCGAAATAATTACCAAAA
TATCACTTTTCGAAATA
Found at i:579985 original size:28 final size:28
Alignment explanation
Indices: 579883--579987 Score: 140
Period size: 29 Copynumber: 3.7 Consensus size: 28
579873 ACAAAAATAT
*
579883 CATTTTTTGA-AATATTTACGAAACTAA
1 CATTTTTTAACAATATTTACGAAACTAA
* * *
579910 CACCTTCTTAACAGTATTTACGAAACTAA
1 CA-TTTTTTAACAATATTTACGAAACTAA
*
579939 CATTTGTTTAATAATATTTACGAAACTAA
1 CATTT-TTTAACAATATTTACGAAACTAA
579968 CATTTTTTAACAATATTTAC
1 CATTTTTTAACAATATTTAC
579988 AAAAATACCA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
27 2 0.03
28 21 0.32
29 43 0.65
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.40
Consensus pattern (28 bp):
CATTTTTTAACAATATTTACGAAACTAA
Found at i:580564 original size:20 final size:20
Alignment explanation
Indices: 580539--580591 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
580529 CACTTCATTT
580539 TATTTTATTCT-TAGTGCTAA
1 TATTTTATT-TATAGTGCTAA
*
580559 TATTTTATTTATAGTGCTAT
1 TATTTTATTTATAGTGCTAA
580579 TAATTTT-TTTATA
1 T-ATTTTATTTATA
580592 TTATATTGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 1 0.03
20 24 0.80
21 5 0.17
ACGTcount: A:0.26, C:0.06, G:0.08, T:0.60
Consensus pattern (20 bp):
TATTTTATTTATAGTGCTAA
Found at i:580862 original size:20 final size:19
Alignment explanation
Indices: 580821--580868 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
580811 ATAAAATAAA
*
580821 TAAAAATA-TTAGTTTAAT
1 TAAAAATATTTAGTTTAAC
*
580839 TAAAAATATTATATTTTAAC
1 TAAAAATATT-TAGTTTAAC
580859 T-AAAATATTT
1 TAAAAATATTT
580869 TATGTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 9 0.35
19 9 0.35
20 8 0.31
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
TAAAAATATTTAGTTTAAC
Found at i:580899 original size:14 final size:15
Alignment explanation
Indices: 580875--580903 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
580865 ATTTTATGTA
580875 TATATATAATATAAT
1 TATATATAATATAAT
580890 TATA-ATAATATAAT
1 TATATATAATATAAT
580904 ATTTTAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATATATAATATAAT
Found at i:581738 original size:20 final size:20
Alignment explanation
Indices: 581697--581739 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
581687 TTGTATTGAA
*
581697 TTTTATTCACTTTTAATTCT
1 TTTTATTCACTTTTAATACT
*
581717 TTTTATTACATTTTTAA-ACT
1 TTTTATT-CACTTTTAATACT
581737 TTT
1 TTT
581740 AAAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTATTCACTTTTAATACT
Found at i:581765 original size:21 final size:21
Alignment explanation
Indices: 581740--581783 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
581730 TTAAACTTTT
581740 AAAATAAATAAAA-TGTAATAA
1 AAAATAAATAAAAGTG-AATAA
*
581761 AAAATAATTAAAAGTGAATAA
1 AAAATAAATAAAAGTGAATAA
581782 AA
1 AA
581784 TTCAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (21 bp):
AAAATAAATAAAAGTGAATAA
Found at i:581982 original size:31 final size:31
Alignment explanation
Indices: 581947--582020 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 31
581937 ATTAATTTTT
581947 TTAAAATCAATAAAAATACAATA-AAAAAGAA
1 TTAAAATCAAT-AAAATACAATACAAAAAGAA
* * *
581978 TTAAAAGTAAATGAAATTCAATACAAAAAGAA
1 TTAAAA-TCAATAAAATACAATACAAAAAGAA
*
582010 TATAAAGTCAA
1 T-TAAAATCAA
582021 ATTTTTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
31 15 0.43
32 16 0.46
33 4 0.11
ACGTcount: A:0.65, C:0.07, G:0.07, T:0.22
Consensus pattern (31 bp):
TTAAAATCAATAAAATACAATACAAAAAGAA
Found at i:582017 original size:32 final size:32
Alignment explanation
Indices: 581960--582022 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
581950 AAATCAATAA
581960 AAATACAATAAAAAAGAATTAAAAGT-AAATG
1 AAATACAATAAAAAAGAATTAAAAGTCAAATG
*
581991 AAATTCAATACAAAAAGAA-TATAAAGTCAAAT
1 AAATACAATA-AAAAAGAATTA-AAAGTCAAAT
582023 TTTTTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 11 0.39
32 13 0.46
33 4 0.14
ACGTcount: A:0.65, C:0.06, G:0.08, T:0.21
Consensus pattern (32 bp):
AAATACAATAAAAAAGAATTAAAAGTCAAATG
Found at i:582064 original size:26 final size:27
Alignment explanation
Indices: 582024--582074 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
582014 AAGTCAAATT
582024 TTTTTTAAAAATATATAAA-ATTTATAA
1 TTTTTTAAAAATATA-AAATATTTATAA
*
582051 TTTTTT-AAATTATAAAATATTTAT
1 TTTTTTAAAAATATAAAATATTTAT
582075 TATTATCATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 3 0.14
26 13 0.59
27 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTTTTTAAAAATATAAAATATTTATAA
Found at i:584131 original size:148 final size:146
Alignment explanation
Indices: 583833--584133 Score: 462
Period size: 148 Copynumber: 2.0 Consensus size: 146
583823 TCCTCAAGGA
*
583833 TCATATTAAGAACCTACAAATGGGAAGACCAAACCATTCAACGATTCCGATACAATTTAAATGGC
1 TCATATTAAGAACCTACAAATGGGAAGACCAAACCATTCAACGATTCCGATACAAGTTAAATGGC
* ** *
583898 ATCTCTCAAGGCAAGCTACTGCTATAATTTTTGGGATGTTGCATATAATGATTGGAACATGAAGT
66 AACTCTCAAGGCAAGCTACTAATATAATTTTTGGGATGTTGCACATAATGATTGGAACATGAAGT
* *
583963 AACATTCATGTTAATG
131 AACATTCAAGTCAATG
*
583979 TCATATTAAGAACATACTACAACTGGGAAGA-C-AACCATTCAACGATTCCGATACAAGTTAAAT
1 TCATATTAAGAAC---CTACAAATGGGAAGACCAAACCATTCAACGATTCCGATACAAGTTAAAT
* *
584042 GGCAACTCTCAAGGCAAGCTACTAATATTAATTTTTGGGATGTTGCACATAATTATTGGAGCATG
63 GGCAACTCTCAAGGCAAGCTACTAATA-TAATTTTTGGGATGTTGCACATAATGATTGGAACATG
584107 AAGTAACATTCAAGTCAATG
127 AAGTAACATTCAAGTCAATG
584127 TCATATT
1 TCATATT
584134 TGTGTCCAAG
Statistics
Matches: 141, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
146 13 0.09
147 54 0.38
148 60 0.43
149 14 0.10
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (146 bp):
TCATATTAAGAACCTACAAATGGGAAGACCAAACCATTCAACGATTCCGATACAAGTTAAATGGC
AACTCTCAAGGCAAGCTACTAATATAATTTTTGGGATGTTGCACATAATGATTGGAACATGAAGT
AACATTCAAGTCAATG
Found at i:593101 original size:121 final size:120
Alignment explanation
Indices: 592862--593115 Score: 356
Period size: 122 Copynumber: 2.1 Consensus size: 120
592852 TAAGACTTAA
592862 AAAAT-AAAATGAATTTAATATTTTTTATTTAAATTATTTTTTACAAATATTTTAAAAATATAAT
1 AAAATAAAAAT-AATTTAATATTTTTTATTTAAATTATTTTTTACAAATATTTTAAAAATATAAT
* *
592926 ATACAAATTATATTAAAAATAAAATTATGTTAAAATTAGTTAGAGAATCCAAATCAC-
65 ATACAAATTATAGTAAAAAT-AAATTATATTAAAATTAGTTAGAGAATCCAAATC-CT
* *
592983 AAAATAAAAATAAGTTTAATATTTTTTATTTAAATTATTTTTTACAATTATTTT-TAAATAATAA
1 AAAATAAAAATAA-TTTAATATTTTTTATTTAAATTATTTTTTACAAATATTTTAAAAAT-ATAA
* *
593047 TATATAAATTATAGTAAGCAAAT-AA-TATATTAAAATTATTTAGAGAATCCAAATCCT
64 TATACAAATTATAGTAA--AAATAAATTATATTAAAATTAGTTAGAGAATCCAAATCCT
593104 AAAATAAAAATA
1 AAAATAAAAATA
593116 TTAAACTCAT
Statistics
Matches: 121, Mismatches: 6, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
120 1 0.01
121 51 0.42
122 65 0.54
124 4 0.03
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.41
Consensus pattern (120 bp):
AAAATAAAAATAATTTAATATTTTTTATTTAAATTATTTTTTACAAATATTTTAAAAATATAATA
TACAAATTATAGTAAAAATAAATTATATTAAAATTAGTTAGAGAATCCAAATCCT
Found at i:603169 original size:20 final size:20
Alignment explanation
Indices: 603122--603169 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
603112 TTGTTCATTG
*
603122 TTTTCTTCAGCCTGTTTCTT
1 TTTTCTTTAGCCTGTTTCTT
603142 TTTTCTTTAGCCTGTTTCTT
1 TTTTCTTTAGCCTGTTTCTT
603162 TTTTCTTT
1 TTTTCTTT
603170 TATCATCTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.04, C:0.21, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTTCTTTAGCCTGTTTCTT
Found at i:620070 original size:31 final size:31
Alignment explanation
Indices: 620008--620070 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
619998 TTCTAAACTA
* ** *
620008 TTTTTATCAAAATAAGTATTTAATTTTATTT
1 TTTTTATCAAAATAAGTACTTAAAGTAATTT
620039 TTTTTATCAAAAT-AGATACTTAAAGTAATTT
1 TTTTTATCAAAATAAG-TACTTAAAGTAATTT
620070 T
1 T
620071 AGTCAAAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (31 bp):
TTTTTATCAAAATAAGTACTTAAAGTAATTT
Found at i:620374 original size:21 final size:21
Alignment explanation
Indices: 620257--620394 Score: 77
Period size: 21 Copynumber: 6.7 Consensus size: 21
620247 CGCGAAATAA
**
620257 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
620277 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
* *
620297 AAAATCACAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
620318 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
620339 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * *
620360 AAAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
620380 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
620395 ACACATAAAT
Statistics
Matches: 87, Mismatches: 27, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
19 1 0.01
20 38 0.44
21 46 0.53
22 2 0.02
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:620423 original size:20 final size:20
Alignment explanation
Indices: 620361--620552 Score: 194
Period size: 20 Copynumber: 9.7 Consensus size: 20
620351 CGATTTTCCA
* ** *
620361 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
620381 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
620401 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
620421 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
620441 AAATCGCAACGCGTAT-GGT
1 AAATCGCAACGCGTATCCGT
*
620460 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
620480 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* ***
620500 AAATCGCAACG-ATAATAAAT
1 AAATCGCAACGCGT-ATCCGT
*
620520 AAAATCAC-ACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
620540 AAATCGCAACGCG
1 AAATCGCAACGCG
620553 ATATTTAAAG
Statistics
Matches: 140, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
19 25 0.18
20 106 0.76
21 9 0.06
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:620970 original size:33 final size:33
Alignment explanation
Indices: 620931--621001 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
620921 TTCACTTAGA
*
620931 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
620964 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
620997 TTTCA
1 TTTCA
621002 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:621125 original size:20 final size:20
Alignment explanation
Indices: 621081--621190 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
621071 TGCAGAAGAG
*
621081 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
621102 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
621122 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
621143 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
621157 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
621176 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
621191 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:621138 original size:41 final size:38
Alignment explanation
Indices: 621074--621190 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
621064 TTCAATTTGC
* *
621074 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
621112 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
621153 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
621186 AGAAT
1 AGAAT
621191 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:621160 original size:14 final size:14
Alignment explanation
Indices: 621141--621197 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
621131 GAGAAATGAA
621141 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
621155 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
621174 AATCGCAACGAGAG
1 AATCGCAACGAGAG
621188 AATCGCAACG
1 AATCGCAACG
621198 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:621173 original size:33 final size:33
Alignment explanation
Indices: 621133--621213 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
621123 CGCAACGAGA
621133 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
621166 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
621199 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
621214 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:621231 original size:19 final size:19
Alignment explanation
Indices: 621209--621306 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
621199 GAAACCAAAA
*
621209 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
621228 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
621242 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
621261 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
621275 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
621294 TCGCGTTGCGATT
1 TCGCGTTGCGATT
621307 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:621250 original size:14 final size:14
Alignment explanation
Indices: 621231--621320 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
621221 TTTCATTTCG
621231 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
621245 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
621264 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
621278 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
621297 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
621311 CGTTGCGATT
1 CGTTGCGATT
621321 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:621256 original size:33 final size:33
Alignment explanation
Indices: 621214--621328 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
621204 CAAAATCGCA
621214 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
621247 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
621280 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
621313 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
621329 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:623319 original size:92 final size:93
Alignment explanation
Indices: 623012--623477 Score: 879
Period size: 93 Copynumber: 5.1 Consensus size: 93
623002 TAGATTGCTT
*
623012 AGTAAATTTATTCGGTTGCTGCCAA-TCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
623076 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
623104 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
623169 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
623197 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
623261 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
623289 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTA-TCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
623353 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
623381 AGTAAAATTTGTTC-GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
1 AGT-AAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
623445 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
623473 AGTAA
1 AGTAA
623478 GCAATCCATT
Statistics
Matches: 369, Mismatches: 1, Indels: 9
0.97 0.00 0.02
Matches are distributed among these distances:
91 16 0.04
92 171 0.46
93 182 0.49
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:623564 original size:19 final size:19
Alignment explanation
Indices: 623524--623622 Score: 91
Period size: 19 Copynumber: 5.4 Consensus size: 19
623514 TAGTTTACTT
* *
623524 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
623544 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
623563 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
623582 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
**
623596 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
623615 TCGCAACG
1 TCGCAACG
623623 AAAGAATCGC
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
14 9 0.14
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 38 0.58
20 13 0.20
ACGTcount: A:0.45, C:0.26, G:0.18, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:623599 original size:14 final size:14
Alignment explanation
Indices: 623580--623636 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
623570 GCGAAATGAA
*
623580 AATCGCAACGACAG
1 AATCGCAACGAAAG
623594 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
623611 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
623627 AATCGCAACG
1 AATCGCAACG
623637 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:623603 original size:33 final size:33
Alignment explanation
Indices: 623561--623652 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
623551 GCGAAACCAA
*
623561 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
623594 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
623627 AATCGCAACGCGAAATG-AAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
623653 TGCATTTTGG
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 9 0.16
33 49 0.84
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:623698 original size:33 final size:33
Alignment explanation
Indices: 623656--623743 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 33
623646 ATCGCAATGC
623656 ATTTTGGTTTCGCGTTGCGA-TCTTGTCGTTGCG
1 ATTTTGGTTTCGCGTTGCGATTC-TGTCGTTGCG
623689 ATTTTGGTTTCGCGTTGCGATTCTGTCGTTGCG
1 ATTTTGGTTTCGCGTTGCGATTCTGTCGTTGCG
**
623722 ATTTTCATTTCGCGTTGCGATT
1 ATTTTGGTTTCGCGTTGCGATT
623744 TTGGTTTCGC
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
33 50 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.27, T:0.47
Consensus pattern (33 bp):
ATTTTGGTTTCGCGTTGCGATTCTGTCGTTGCG
Found at i:623706 original size:19 final size:19
Alignment explanation
Indices: 623656--623764 Score: 112
Period size: 19 Copynumber: 6.3 Consensus size: 19
623646 ATCGCAATGC
623656 ATTTTGGTTTCGCGTTGCG
1 ATTTTGGTTTCGCGTTGCG
*
623675 ATCTT-G--T--CGTTGCG
1 ATTTTGGTTTCGCGTTGCG
623689 ATTTTGGTTTCGCGTTGCG
1 ATTTTGGTTTCGCGTTGCG
*
623708 ATTCT-G--T--CGTTGCG
1 ATTTTGGTTTCGCGTTGCG
**
623722 ATTTTCATTTCGCGTTGCG
1 ATTTTGGTTTCGCGTTGCG
623741 ATTTTGGTTTCGCGTTGCG
1 ATTTTGGTTTCGCGTTGCG
623760 ATTTT
1 ATTTT
623765 TAAGTTTCGT
Statistics
Matches: 73, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
14 22 0.30
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 44 0.60
ACGTcount: A:0.07, C:0.17, G:0.28, T:0.48
Consensus pattern (19 bp):
ATTTTGGTTTCGCGTTGCG
Found at i:623773 original size:21 final size:19
Alignment explanation
Indices: 623682--623781 Score: 95
Period size: 19 Copynumber: 5.4 Consensus size: 19
623672 GCGATCTTGT
*
623682 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
*
623701 CGTTGCGATTCT-G--T--
1 CGTTGCGATTTTAGTTTCG
623715 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTT-AGTTTCG
*
623734 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
623753 CGTTGCGATTTTTAAGTTTCG
1 CGTTGCGA-TTTT-AGTTTCG
*
623774 TGTTGCGA
1 CGTTGCGA
623782 AAGTAAACTA
Statistics
Matches: 67, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
14 11 0.16
16 1 0.01
17 1 0.01
18 1 0.01
19 36 0.54
20 4 0.06
21 13 0.19
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:624011 original size:15 final size:13
Alignment explanation
Indices: 623978--624006 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
623968 TTTGTTTTCC
623978 TGTTTAAATATCA
1 TGTTTAAATATCA
623991 TGTTTAAATATCA
1 TGTTTAAATATCA
624004 TGT
1 TGT
624007 GTTTATTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.48
Consensus pattern (13 bp):
TGTTTAAATATCA
Found at i:626325 original size:12 final size:12
Alignment explanation
Indices: 626308--626332 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
626298 TTCTTCGGGA
626308 CTTTTTCTTCTT
1 CTTTTTCTTCTT
626320 CTTTTTCTTCTT
1 CTTTTTCTTCTT
626332 C
1 C
626333 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:626540 original size:24 final size:23
Alignment explanation
Indices: 626506--626551 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
626496 CTGAAACATC
*
626506 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCG-ATATTGACCAAT
*
626530 ATCAAAGTCCGATATTGACCAA
1 ATCAAAATCCGATATTGACCAA
626552 GACCAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (23 bp):
ATCAAAATCCGATATTGACCAAT
Found at i:627288 original size:20 final size:20
Alignment explanation
Indices: 627244--627411 Score: 209
Period size: 20 Copynumber: 8.5 Consensus size: 20
627234 TTAAGATTCT
627244 CGTTGCGATTTACGGATTA--
1 CGTTGCGATTTACGGA-TACG
* * *
627263 CGTTGCGATTTACAGATTCT
1 CGTTGCGATTTACGGATACG
*
627283 CGTTGCGATTTACGGATTA-T
1 CGTTGCGATTTACGGA-TACG
627303 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
627323 CGTTGCGATATA-GGATACG
1 CGTTGCGATTTACGGATACG
* **
627342 CATTGCGATTTACCCATACG
1 CGTTGCGATTTACGGATACG
*
627362 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACG
627382 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
627402 CGTTGCGATT
1 CGTTGCGATT
627412 ATGTGTTCGC
Statistics
Matches: 129, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
18 1 0.01
19 34 0.26
20 93 0.72
21 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:627348 original size:79 final size:79
Alignment explanation
Indices: 627244--627410 Score: 232
Period size: 79 Copynumber: 2.1 Consensus size: 79
627234 TTAAGATTCT
* * * * *
627244 CGTTGCGATTTACGGATTACGTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTA-TCGTTG
1 CGTTGCGATATACGGATTACGTTGCGATTTACACATACGCGTTGCGATTTACGGA-TACACGTTG
627308 CGATTTACGGATACG
65 CGATTTACGGATACG
*
627323 CGTTGCGATATA-GGA-TACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACACGTT
1 CGTTGCGATATACGGATTACG--TTGCGATTTACACATACGCGTTGCGATTTACGGATACACGTT
627386 GCGATTTACGGATACG
64 GCGATTTACGGATACG
627402 CGTTGCGAT
1 CGTTGCGAT
627411 TATGTGTTCG
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
77 4 0.05
78 5 0.06
79 70 0.89
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (79 bp):
CGTTGCGATATACGGATTACGTTGCGATTTACACATACGCGTTGCGATTTACGGATACACGTTGC
GATTTACGGATACG
Found at i:627423 original size:59 final size:59
Alignment explanation
Indices: 627226--627431 Score: 211
Period size: 59 Copynumber: 3.5 Consensus size: 59
627216 AAATTTCAGT
* * * * * * * *
627226 GTTGTGATTTAAGATTCTCGTTGCGATTTACGGAT-TACGTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGTTCGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGC
** * *
627284 GTTGCGATTTACGGATTATCGTTGCGATTTACGGATACGCGTTGCGATATA-GGATACGC
1 GTTGCGATTTACGG-TTCGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGC
* ** *
627343 ATTGCGATTTACCCATACGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGC
1 GTTGCGATTTA-CGGTTCGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGC
*
627403 GTTGCGA-TTATGTGTTCGCGTTGCGATTT
1 GTTGCGATTTACG-GTTCGCGTTGCGATTT
627432 TCATATCGCC
Statistics
Matches: 120, Mismatches: 23, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
58 11 0.09
59 83 0.69
60 26 0.22
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (59 bp):
GTTGCGATTTACGGTTCGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGC
Found at i:627427 original size:79 final size:79
Alignment explanation
Indices: 627263--627431 Score: 227
Period size: 79 Copynumber: 2.1 Consensus size: 79
627253 TTACGGATTA
* * * *
627263 CGTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACGGATACGCGTTG
1 CGTTGCGATTTACACATACGCGTTGCGATTTACGGATTAACGTTGCGATTTACGGATACGCGTTG
627328 CGATATAGGATACG
66 CGATATAGGATACG
* *
627342 CATTGCGATTTACCCATACGCGTTGCGATTTACGGA-TACACGTTGCGATTTACGGATACGCGTT
1 CGTTGCGATTTACACATACGCGTTGCGATTTACGGATTA-ACGTTGCGATTTACGGATACGCGTT
*
627406 GCGAT-TATGTG-TTCG
65 GCGATATA-G-GATACG
627421 CGTTGCGATTT
1 CGTTGCGATTT
627432 TCATATCGCC
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
78 4 0.05
79 74 0.94
80 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (79 bp):
CGTTGCGATTTACACATACGCGTTGCGATTTACGGATTAACGTTGCGATTTACGGATACGCGTTG
CGATATAGGATACG
Found at i:627753 original size:30 final size:30
Alignment explanation
Indices: 627693--627786 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 30
627683 CTTAGGTATC
* *
627693 TATTTTGAAGTAAAAAGATAACTTT-A-TACT
1 TATTTTGAA-AAAAAAAAT-ACTTTAAGTACT
627723 TATTTTGAAAAAAAAAATACTTTAAGTACT
1 TATTTTGAAAAAAAAAATACTTTAAGTACT
** * **
627753 TA-AATGAAAAAGAGTATACTTTAAGTACT
1 TATTTTGAAAAAAAAAATACTTTAAGTACT
627782 TATTT
1 TATTT
627787 GTTAATATAA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
28 5 0.10
29 32 0.62
30 15 0.29
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (30 bp):
TATTTTGAAAAAAAAAATACTTTAAGTACT
Found at i:633082 original size:148 final size:146
Alignment explanation
Indices: 632803--633104 Score: 561
Period size: 148 Copynumber: 2.1 Consensus size: 146
632793 AATCTGATTT
632803 AAAATGATAATGGAGAACTCAGTGCCTACATTGTAATCCTAAGGAGATCCTATTTCGGTTACAAT
1 AAAATGATAATGGAGAACTCAGTGCCTACATTGTAATCCTAAGGAGATCCTATTTCGGTTACAAT
*
632868 TGGTGTATAGAGCCTAAGTTTAAAGCCTAACCTTCTGTGTCCTGCTTCCTTTAACCACTCGAAAA
66 TGGTGTATAGAGCCTAAGTTTAAAGCCTAACCTTCTGTGTCCCGCTTCCTTTAACCACTCGAAAA
632933 AACAGAGCATTTAAAA
131 AACAGAGCATTTAAAA
632949 CAAAATGATAATGGAGAACTCAGTGCCTACACTTGTAATCCTAAGGAGATCCTATTTCGGTTACA
1 -AAAATGATAATGGAGAACTCAGTGCCTACA-TTGTAATCCTAAGGAGATCCTATTTCGGTTACA
633014 ATTGGTGTATAGAGCCTAAGTTTAAAGCCTAACCTTCTGTGTCCCGCTTCCTTTTAACCACTCG-
64 ATTGGTGTATAGAGCCTAAGTTTAAAGCCTAACCTTCTGTGTCCCGCTTCC-TTTAACCACTCGA
633078 AAAAACAGAGCATTTAAAA
128 AAAAACAGAGCATTTAAAA
633097 AAAATGAT
1 AAAATGAT
633105 TTCGTCATTA
Statistics
Matches: 152, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
147 38 0.25
148 102 0.67
149 12 0.08
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (146 bp):
AAAATGATAATGGAGAACTCAGTGCCTACATTGTAATCCTAAGGAGATCCTATTTCGGTTACAAT
TGGTGTATAGAGCCTAAGTTTAAAGCCTAACCTTCTGTGTCCCGCTTCCTTTAACCACTCGAAAA
AACAGAGCATTTAAAA
Found at i:634784 original size:119 final size:119
Alignment explanation
Indices: 634573--634807 Score: 445
Period size: 119 Copynumber: 2.0 Consensus size: 119
634563 GCCCATAATT
634573 CATAAGTTGAGGAAAGGGTTCACATTTGATGAAAGGTCTCCCAGGGCCATCCCATGGGAAATGAC
1 CATAAGTTGAGGAAAGGGTTCACATTTGATGAAAGGTCTCCCAGGGCCATCCCATGGGAAATGAC
*
634638 CTTGTAAATAGACAGGTGGTACCATTAGGGGTTAAATCAGAGGCGGAGGAATCG
66 CTTGTAAATAGACAGGTGGTACCATTAGGGGTGAAATCAGAGGCGGAGGAATCG
634692 CATAAGTTGAGGAAAGTGGTTCACATTTGATGAAAGGTCT-CCAGGGCCATCCCATGGGAAATGA
1 CATAAGTTGAGGAAAG-GGTTCACATTTGATGAAAGGTCTCCCAGGGCCATCCCATGGGAAATGA
634756 CCTTGTAAATAGACAGGTGGTACCATTAGGGGTGAAATCAGAGGCGGAGGAA
65 CCTTGTAAATAGACAGGTGGTACCATTAGGGGTGAAATCAGAGGCGGAGGAA
634808 ATCGTGAAAT
Statistics
Matches: 114, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
119 91 0.80
120 23 0.20
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.22
Consensus pattern (119 bp):
CATAAGTTGAGGAAAGGGTTCACATTTGATGAAAGGTCTCCCAGGGCCATCCCATGGGAAATGAC
CTTGTAAATAGACAGGTGGTACCATTAGGGGTGAAATCAGAGGCGGAGGAATCG
Found at i:655691 original size:21 final size:22
Alignment explanation
Indices: 655645--655693 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
655635 TAGACGGATT
*
655645 TCGTCGGAGATGGGGACATATT
1 TCGTCGGAGATGGGGACATATG
655667 TCGTCGGAGAT-GGGAC-TGATG
1 TCGTCGGAGATGGGGACAT-ATG
655688 TCGTCG
1 TCGTCG
655694 TAGAGAGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 13 0.52
22 11 0.44
ACGTcount: A:0.18, C:0.16, G:0.39, T:0.27
Consensus pattern (22 bp):
TCGTCGGAGATGGGGACATATG
Found at i:655869 original size:20 final size:20
Alignment explanation
Indices: 655841--655886 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
655831 TAAACGCGCT
*
655841 TTGCCAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
*
655861 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTCTGTG
655881 TTGCGA
1 TTGCGA
655887 TTTACATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.15, G:0.24, T:0.46
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:659493 original size:18 final size:18
Alignment explanation
Indices: 659462--659510 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
659452 ACATTCATAT
659462 TCTAGATC-AATGCATGA
1 TCTAGATCAAATGCATGA
659479 TCTAGATCAAATGCATGA
1 TCTAGATCAAATGCATGA
659497 TCTAGATCAAATGC
1 TCTAGATCAAATGC
659511 TACCTACTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 8 0.26
18 23 0.74
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (18 bp):
TCTAGATCAAATGCATGA
Done.