Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007888.1 Hibiscus syriacus cultivar Beakdansim tig00110270_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: 1558302
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1169211 original size:20 final size:21
Alignment explanation
Indices: 1169158--1169211 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1169148 TTGTGGCTCG
** *
1169158 AAGGATCGATCCTTTTGACCA
1 AAGGATCGATCCCCTTGACAA
1169179 AAGGATCTG-TCCCCTTGA-AA
1 AAGGATC-GATCCCCTTGACAA
1169199 AAGGATCGATCCC
1 AAGGATCGATCCC
1169212 TTGGATTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 1 0.04
20 12 0.43
21 14 0.50
22 1 0.04
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (21 bp):
AAGGATCGATCCCCTTGACAA
Found at i:1197691 original size:20 final size:20
Alignment explanation
Indices: 1197668--1197718 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1197658 ATGTGGGTCA
1197668 AGTATCGATACTCACAGGGT
1 AGTATCGATACTCACAGGGT
*
1197688 AGTATCGATACTCACATGGT
1 AGTATCGATACTCACAGGGT
*
1197708 AGTATCAATAC
1 AGTATCGATAC
1197719 ATATTTTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (20 bp):
AGTATCGATACTCACAGGGT
Found at i:1197918 original size:20 final size:20
Alignment explanation
Indices: 1197893--1197945 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
1197883 ACCCTAAAGA
1197893 CCAATATCGATACTGTAAGG
1 CCAATATCGATACTGTAAGG
1197913 CCAATATCGATACTGTAAGG
1 CCAATATCGATACTGTAAGG
1197933 CCAATATCGATAC
1 CCAATATCGATAC
1197946 CCTCAACTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (20 bp):
CCAATATCGATACTGTAAGG
Found at i:1200625 original size:42 final size:39
Alignment explanation
Indices: 1200572--1200713 Score: 137
Period size: 42 Copynumber: 3.5 Consensus size: 39
1200562 GCATTTTTTA
*
1200572 ACAAACACCGCAATAGAGTGGTAAATTAGCAGCGTTTATACC
1 ACAAACGCCGCAATAGA-TGGTAAATTAGC-GCGTTT-TACC
*
1200614 ACAAACGCCGCAATAGAT--TAACATATAGTGGCGTTTTAGCC
1 ACAAACGCCGCAATAGATGGTAA-AT-TAG-CGCGTTTTA-CC
* *
1200655 A-AAACGCCACAATAGATCGGTAAATTAGCGATGTTTCTACC
1 ACAAACGCCGCAATAGAT-GGTAAATTAGCG-CGTTT-TACC
1200696 ACAAACGCCGCAATAGAT
1 ACAAACGCCGCAATAGAT
1200714 TACACATATA
Statistics
Matches: 84, Mismatches: 6, Indels: 20
0.76 0.05 0.18
Matches are distributed among these distances:
39 3 0.04
40 20 0.24
41 23 0.27
42 35 0.42
43 3 0.04
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (39 bp):
ACAAACGCCGCAATAGATGGTAAATTAGCGCGTTTTACC
Found at i:1200786 original size:83 final size:82
Alignment explanation
Indices: 1200696--1200892 Score: 213
Period size: 83 Copynumber: 2.4 Consensus size: 82
1200686 TGTTTCTACC
*** *
1200696 ACAAACGCCGCAATAG-ATTACA-CATATAGTGGCGTTTATTCTTAAAACGCCGTAATAATGATA
1 ACAAACGCCGCAATAGTATTA-ATCA-ATAGTGGCGTTT-TTAGAAAAACGCCGCAATAATGATA
*
1200759 ATAAATAGTGGCA-TTTTTA
63 ATAAATAATGGCATTTTTTA
* * **
1200778 GACAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGAAAAACGCCGCAATAGTTTTAAT
1 -ACAAACGCCGCAATAGTATTAATCAATAGTGGCGTTTTTAGAAAAACGCCGCAATAATGATAAT
*
1200843 CAATAATGGCATTTTTTTA
65 AAATAATGGCA-TTTTTTA
* *
1200862 ACAAACGCCACAATAGT-GTAATCAATAGTGG
1 ACAAACGCCGCAATAGTATTAATCAATAGTGG
1200893 TATTTTTTTT
Statistics
Matches: 98, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
82 42 0.43
83 45 0.46
84 11 0.11
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.29
Consensus pattern (82 bp):
ACAAACGCCGCAATAGTATTAATCAATAGTGGCGTTTTTAGAAAAACGCCGCAATAATGATAATA
AATAATGGCATTTTTTA
Found at i:1200807 original size:41 final size:41
Alignment explanation
Indices: 1200740--1200899 Score: 198
Period size: 41 Copynumber: 3.9 Consensus size: 41
1200730 TTTATTCTTA
* * * *
1200740 AAACGCCGTAATAATGATAATAAATAGTGGCATTTTTAGAC
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTTAGAC
* *
1200781 AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGAA
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTTAGAC
* *
1200822 AAACGCCGCAATAGTTTTAATCAATAATGGCATTTTTTTA-AC
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCA--TTTTTAGAC
* *
1200864 AAACGCCACAATAGTG-TAATCAATAGTGGTATTTTT
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTT
1200900 TTTGTATAAA
Statistics
Matches: 103, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 5 0.05
41 77 0.75
42 15 0.15
43 6 0.06
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (41 bp):
AAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTTAGAC
Found at i:1200900 original size:41 final size:41
Alignment explanation
Indices: 1200696--1200901 Score: 183
Period size: 41 Copynumber: 5.0 Consensus size: 41
1200686 TGTTTCTACC
*
1200696 ACAAACGCCGCAATAGAT-TACA-CATATAGTGGCGTTTATTCTT-
1 ACAAACGCCGCAATAG-TGTA-ATCA-ATAGTGGCATTT-TT-TTA
* * *
1200739 A-AAACGCCGTAATAATGATAATAAATAGTGGCA--TTTTTA
1 ACAAACGCCGCAATAGTG-TAATCAATAGTGGCATTTTTTTA
* **
1200778 GACAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
1 -ACAAACGCCGCAATAGTG-TAATCAATAGTGGCATTTTTTTA
* *
1200821 A-AAACGCCGCAATAGTTTTAATCAATAATGGCATTTTTTTA
1 ACAAACGCCGCAATAG-TGTAATCAATAGTGGCATTTTTTTA
* *
1200862 ACAAACGCCACAATAGTGTAATCAATAGTGGTATTTTTTT
1 ACAAACGCCGCAATAGTGTAATCAATAGTGGCATTTTTTT
1200902 TGTATAAACG
Statistics
Matches: 133, Mismatches: 20, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
38 2 0.02
39 2 0.02
40 2 0.02
41 83 0.62
42 36 0.27
43 8 0.06
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (41 bp):
ACAAACGCCGCAATAGTGTAATCAATAGTGGCATTTTTTTA
Found at i:1202335 original size:42 final size:42
Alignment explanation
Indices: 1202289--1202372 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
1202279 GCCGCTAAAA
* * *
1202289 AGTTGTACTTTAGTGGTGTTTTTGA-CATAAACGCTGCAATAG
1 AGTTGTAATTTAGTGGCGTTTTT-ATAATAAACGCTGCAATAG
1202331 AGTTGTAATTTAGTGGCGTTTTTATAATAAACGCTGCAATAG
1 AGTTGTAATTTAGTGGCGTTTTTATAATAAACGCTGCAATAG
1202373 TATGTTCGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 1 0.03
42 37 0.97
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.38
Consensus pattern (42 bp):
AGTTGTAATTTAGTGGCGTTTTTATAATAAACGCTGCAATAG
Found at i:1206362 original size:43 final size:43
Alignment explanation
Indices: 1206301--1206545 Score: 253
Period size: 43 Copynumber: 5.7 Consensus size: 43
1206291 CGTTTTTAGC
* * *
1206301 AAAAACGCTGCAAAACATCAATACCTACTGCGACATTTGTGAG
1 AAAAACGCCGCAAAACATCAACACCTACTGCGGCATTTGTGAG
* **
1206344 AAAAACGCCGCAAAACATCAAAACCTACTGCGGTGTTTGTG-G
1 AAAAACGCCGCAAAACATCAACACCTACTGCGGCATTTGTGAG
*
1206386 GAAAACGCCGCAAAACATCAACACCTACTGCGGCATTTGTGAG
1 AAAAACGCCGCAAAACATCAACACCTACTGCGGCATTTGTGAG
* * * **
1206429 AAAAATGCCGCAAAACATCATA-ACCTATTGCGGCGTTTGT-CT
1 AAAAACGCCGCAAAACATCA-ACACCTACTGCGGCATTTGTGAG
* * * * **
1206471 AAAAACGCCGCTAAATATCAACACCTATTGCGGCATTTTTCTG
1 AAAAACGCCGCAAAACATCAACACCTACTGCGGCATTTGTGAG
* * * * *
1206514 ACAATCGCCGCTAAATATCAACACCTATTGCG
1 AAAAACGCCGCAAAACATCAACACCTACTGCG
1206546 ACGTTTGTCA
Statistics
Matches: 174, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.01
42 71 0.41
43 101 0.58
44 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (43 bp):
AAAAACGCCGCAAAACATCAACACCTACTGCGGCATTTGTGAG
Found at i:1206404 original size:85 final size:85
Alignment explanation
Indices: 1206301--1206567 Score: 302
Period size: 85 Copynumber: 3.1 Consensus size: 85
1206291 CGTTTTTAGC
* * *
1206301 AAAAACGCTGCAAAACATCAATACCTACTGCGACATTTGTGAGAAAAACGCCGCAAAACATCAAA
1 AAAAACGCCGCAAAACATCAACACCTACTGCGGCATTTGTGAGAAAAACGCCGCAAAACATCAAA
* *
1206366 ACCTACTGCGGTGTTTGTGG
66 ACCTACTGCGGCGTTTGTCG
* * *
1206386 GAAAACGCCGCAAAACATCAACACCTACTGCGGCATTTGTGAGAAAAATGCCGCAAAACATCATA
1 AAAAACGCCGCAAAACATCAACACCTACTGCGGCATTTGTGAGAAAAACGCCGCAAAACATCAAA
* *
1206451 ACCTATTGCGGCGTTTGTCT
66 ACCTACTGCGGCGTTTGTCG
* * * * ** * * * * *
1206471 AAAAACGCCGCTAAATATCAACACCTATTGCGGCATTTTTCTGACAATCGCCGCTAAATATCAAC
1 AAAAACGCCGCAAAACATCAACACCTACTGCGGCATTTGTGAGAAAAACGCCGCAAAACATCAAA
* *
1206536 ACCTATTGCGACGTTTGTC-
66 ACCTACTGCGGCGTTTGTCG
1206555 ACACAAACGCCGC
1 A-A-AAACGCCGC
1206568 TAAATATAAA
Statistics
Matches: 155, Mismatches: 25, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
84 1 0.01
85 145 0.94
86 9 0.06
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (85 bp):
AAAAACGCCGCAAAACATCAACACCTACTGCGGCATTTGTGAGAAAAACGCCGCAAAACATCAAA
ACCTACTGCGGCGTTTGTCG
Found at i:1206587 original size:43 final size:42
Alignment explanation
Indices: 1206346--1206574 Score: 194
Period size: 43 Copynumber: 5.4 Consensus size: 42
1206336 TTTGTGAGAA
* * * * * **
1206346 AAACGCCGCAAAACATCAAAACCTACTGCGGTGTTTGTGGGA-
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGT-CAAC
* * * * * *
1206388 AAACGCCGCAAAACATCAACACCTACTGCGGCATTTGTGAGAA
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCA-AC
* * *
1206431 AAATGCCGCAAAACATCATA-ACCTATTGCGGCGTTTGTCTAA-
1 AAACGCCGCTAAATATCA-ACACCTATTGCGGCGTTTGTC-AAC
* * *
1206473 AAACGCCGCTAAATATCAACACCTATTGCGGCATTTTTCTGAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTC-AAC
* *
1206516 AATCGCCGCTAAATATCAACACCTATTGCGACGTTTGTCACAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCA-AC
1206559 AAACGCCGCTAAATAT
1 AAACGCCGCTAAATAT
1206575 AAATACCAAT
Statistics
Matches: 160, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
41 2 0.01
42 70 0.44
43 86 0.54
44 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.23
Consensus pattern (42 bp):
AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCAAC
Found at i:1210283 original size:3 final size:3
Alignment explanation
Indices: 1210277--1210334 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
1210267 TATTATCACC
* * * *
1210277 ATT ATT A-T ATT ATT TTT ATT GTTT ATT ATT ATT ATT ATT AAT GTT
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT
*
1210322 GTT ATT ATT ATT A
1 ATT ATT ATT ATT A
1210335 GTAGTTTAGG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.91
4 2 0.04
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1210304 original size:24 final size:23
Alignment explanation
Indices: 1210277--1210332 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
1210267 TATTATCACC
**
1210277 ATTATTATATTATTTTTATTGTTT
1 ATTATTATATTATTAATATTG-TT
*
1210301 ATTATTATTATTATTAATGTTGTT
1 ATTATTA-TATTATTAATATTGTT
1210325 ATTATTAT
1 ATTATTAT
1210333 TAGTAGTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 1 0.04
24 16 0.57
25 11 0.39
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (23 bp):
ATTATTATATTATTAATATTGTT
Found at i:1211363 original size:2 final size:2
Alignment explanation
Indices: 1211356--1211417 Score: 58
Period size: 2 Copynumber: 32.5 Consensus size: 2
1211346 TCGGGCCGGG
* * * *
1211356 TA TA TA TA TA TA TA TA AA T- TA AA TA TA TA TA TA AA T- TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1211396 TA TA TA AA TA T- TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
1211418 TTAAATTTAA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
1 3 0.06
2 44 0.94
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1211383 original size:17 final size:17
Alignment explanation
Indices: 1211361--1211429 Score: 88
Period size: 17 Copynumber: 4.1 Consensus size: 17
1211351 CCGGGTATAT
1211361 ATATATATATAAATTAA
1 ATATATATATAAATTAA
1211378 ATATATATATAAATTAA
1 ATATATATATAAATTAA
* *
1211395 ATATATA-A-ATATTAT
1 ATATATATATAAATTAA
*
1211410 ATATATATTTAAATTTAA
1 ATATATATATAAA-TTAA
1211428 AT
1 AT
1211430 TAAATTTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
15 12 0.27
16 1 0.02
17 26 0.59
18 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATATATATAAATTAA
Found at i:1211399 original size:32 final size:33
Alignment explanation
Indices: 1211363--1211455 Score: 93
Period size: 32 Copynumber: 2.8 Consensus size: 33
1211353 GGGTATATAT
1211363 ATATATATAAATTAAATATATATATAAA-TTAA
1 ATATATATAAATTAAATATATATATAAATTTAA
* *
1211395 ATATATA-AATATTATATATATATTTAAATTTAA
1 ATATATATAA-ATTAAATATATATATAAATTTAA
* **
1211428 AT-TAAATTTATTAATATTATATATATAA
1 ATATATATAAATTAA-A-TATATATATAA
1211456 TAATTATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
31 2 0.04
32 30 0.61
33 7 0.14
34 10 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
ATATATATAAATTAAATATATATATAAATTTAA
Found at i:1211436 original size:17 final size:17
Alignment explanation
Indices: 1211370--1211437 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 17
1211360 TATATATATA
* * *
1211370 TAAATTAAATATATATA
1 TAAATTAAATTTAAATT
1211387 TAAATTAAATATATAAATAT
1 TAAATTAAAT-T-TAAAT-T
* *
1211407 TATATATATATTTAAATT
1 TAAAT-TAAATTTAAATT
1211425 TAAATTAAATTTA
1 TAAATTAAATTTA
1211438 TTAATATTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
17 17 0.43
18 5 0.12
19 9 0.22
20 5 0.12
21 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAATTAAATTTAAATT
Found at i:1211838 original size:12 final size:12
Alignment explanation
Indices: 1211817--1211850 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1211807 CTTAAATATA
*
1211817 CATATACATACG
1 CATATGCATACG
1211829 CATATGCATACG
1 CATATGCATACG
*
1211841 CATACGCATA
1 CATATGCATA
1211851 TAAGTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (12 bp):
CATATGCATACG
Found at i:1211838 original size:18 final size:18
Alignment explanation
Indices: 1211812--1211852 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1211802 GAGGTCTTAA
*
1211812 ATATACATATACATACGC
1 ATATACATACACATACGC
* *
1211830 ATATGCATACGCATACGC
1 ATATACATACACATACGC
1211848 ATATA
1 ATATA
1211853 AGTAAAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (18 bp):
ATATACATACACATACGC
Found at i:1212222 original size:21 final size:20
Alignment explanation
Indices: 1212198--1212263 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
1212188 AATTTTAAAC
1212198 GTCACTAATTTAAATCAGATT
1 GTCA-TAATTTAAATCAGATT
* *
1212219 GTCATAA--T-AAT-AAATC
1 GTCATAATTTAAATCAGATT
1212235 GTCACTAATTTAAATCAGATT
1 GTCA-TAATTTAAATCAGATT
1212256 GTCATAAT
1 GTCATAAT
1212264 AATAAATCGT
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
16 7 0.19
17 6 0.17
18 1 0.03
19 1 0.03
20 10 0.28
21 11 0.31
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (20 bp):
GTCATAATTTAAATCAGATT
Found at i:1212247 original size:37 final size:37
Alignment explanation
Indices: 1212193--1212280 Score: 169
Period size: 37 Copynumber: 2.4 Consensus size: 37
1212183 CTGCAAATTT
1212193 TAAA-CGTCACTAATTTAAATCAGATTGTCATAATAA
1 TAAATCGTCACTAATTTAAATCAGATTGTCATAATAA
1212229 TAAATCGTCACTAATTTAAATCAGATTGTCATAATAA
1 TAAATCGTCACTAATTTAAATCAGATTGTCATAATAA
1212266 TAAATCGTCACTAAT
1 TAAATCGTCACTAAT
1212281 ACTTCTATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 4 0.08
37 47 0.92
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (37 bp):
TAAATCGTCACTAATTTAAATCAGATTGTCATAATAA
Found at i:1212269 original size:21 final size:21
Alignment explanation
Indices: 1212208--1212271 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
1212198 GTCACTAATT
1212208 TAAATCAGATTGTCATAATAA
1 TAAATCAGATTGTCATAATAA
*
1212229 TAAATC-----GTCACTAAT-T
1 TAAATCAGATTGTCA-TAATAA
1212245 TAAATCAGATTGTCATAATAA
1 TAAATCAGATTGTCATAATAA
1212266 TAAATC
1 TAAATC
1212272 GTCACTAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
16 10 0.29
17 4 0.12
20 4 0.12
21 16 0.47
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.34
Consensus pattern (21 bp):
TAAATCAGATTGTCATAATAA
Found at i:1214319 original size:18 final size:18
Alignment explanation
Indices: 1214292--1214327 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1214282 CCAGAGTTTG
1214292 ATTATATGGTTTGTGTCA
1 ATTATATGGTTTGTGTCA
*
1214310 ATTATGTGGTTTGTGTCA
1 ATTATATGGTTTGTGTCA
1214328 TTGAGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (18 bp):
ATTATATGGTTTGTGTCA
Found at i:1217364 original size:21 final size:22
Alignment explanation
Indices: 1217331--1217371 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1217321 TTGGCGGATT
*
1217331 AGTTTTTAAAATTTTAATATAA
1 AGTTTTTAAAATTCTAATATAA
*
1217353 AGTTTTT-CAATTCTAATAT
1 AGTTTTTAAAATTCTAATAT
1217372 TGATGAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (22 bp):
AGTTTTTAAAATTCTAATATAA
Found at i:1224291 original size:18 final size:17
Alignment explanation
Indices: 1224237--1224285 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1224227 TTGGACTCCT
* *
1224237 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
1224255 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
1224273 AGTGCATTCGATG
1 AGTGCA-TCGATG
1224286 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:1224306 original size:64 final size:60
Alignment explanation
Indices: 1224237--1224416 Score: 166
Period size: 64 Copynumber: 2.8 Consensus size: 60
1224227 TTGGACTCCT
*
1224237 AGTGCATCGGTGCACTAAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA-AAAT-AG
1 AGTGCATCGATGCA-T-AGAGTGCATCGATGCATGAA-TGCATTCGATGTTTGAATAAATCAG
* * * * *
1224298 CCTGGTGCATCGATGCATGGATTGTGCATCGATGCATCAAATGGATTCGATGTTTTAATTAAATC
1 ---AGTGCATCGATGCATAGA--GTGCATCGATGCAT-GAATGCATTCGATGTTTGAA-TAAATC
1224363 AG
59 AG
*
1224365 AGTGCATCGATGCATGGAGAGTCCATCGATGCATGGAATGCATTCGATGTTT
1 AGTGCATCGATGCAT--AGAGTGCATCGATGCAT-GAATGCATTCGATGTTT
1224417 CAATTTATTC
Statistics
Matches: 96, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
62 2 0.02
63 1 0.01
64 83 0.86
65 2 0.02
66 6 0.06
67 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (60 bp):
AGTGCATCGATGCATAGAGTGCATCGATGCATGAATGCATTCGATGTTTGAATAAATCAG
Found at i:1224391 original size:19 final size:19
Alignment explanation
Indices: 1224363--1224401 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1224353 TAATTAAATC
*
1224363 AGAGTGCATCGATGCATGG
1 AGAGTCCATCGATGCATGG
1224382 AGAGTCCATCGATGCATGG
1 AGAGTCCATCGATGCATGG
1224401 A
1 A
1224402 ATGCATTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.18, G:0.33, T:0.21
Consensus pattern (19 bp):
AGAGTCCATCGATGCATGG
Found at i:1224451 original size:21 final size:21
Alignment explanation
Indices: 1224427--1224466 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1224417 CAATTTATTC
1224427 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
1224448 ATTGATGCATTGATGCATG
1 ATTGATGCATCGATGCATG
1224467 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.35
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:1227077 original size:24 final size:24
Alignment explanation
Indices: 1227004--1227083 Score: 98
Period size: 24 Copynumber: 3.5 Consensus size: 24
1226994 CATGGTTTTG
*
1227004 TGCATCGATGCACATTCAAA-GAA
1 TGCATCGATGCACATTCAAAGGGA
*
1227027 TGCATCGATG--CA-TC-ATGCGGA
1 TGCATCGATGCACATTCAAAG-GGA
1227048 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTCAAAGGGA
1227072 TGCATCGATGCA
1 TGCATCGATGCA
1227084 TTGTTAAGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
19 1 0.02
20 2 0.04
21 14 0.29
23 12 0.25
24 17 0.35
25 2 0.04
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.23
Consensus pattern (24 bp):
TGCATCGATGCACATTCAAAGGGA
Found at i:1227096 original size:44 final size:43
Alignment explanation
Indices: 1226982--1227103 Score: 138
Period size: 44 Copynumber: 2.8 Consensus size: 43
1226972 ACACCCGACA
* **
1226982 GATGCATCGATGCATGGTTTTGTGCATCGATGCACATTCAAAG
1 GATGCATCGATGCATTGTTAAGTGCATCGATGCACATTCAAAG
* ***
1227025 AATGCATCGATGCATCATGCGGA-TGCATCGATGCACATTCAAAGG
1 GATGCATCGATGCAT--TGTTAAGTGCATCGATGCACATTCAAA-G
*
1227070 GATGCATCGATGCATTGTTAAGTGCATCGGTGCA
1 GATGCATCGATGCATTGTTAAGTGCATCGATGCA
1227104 TTAAGCACAA
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
43 17 0.27
44 31 0.48
45 16 0.25
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (43 bp):
GATGCATCGATGCATTGTTAAGTGCATCGATGCACATTCAAAG
Found at i:1233019 original size:64 final size:64
Alignment explanation
Indices: 1232906--1233115 Score: 212
Period size: 64 Copynumber: 3.2 Consensus size: 64
1232896 TGCACTAAGA
* * *
1232906 GTGCATCGATGCATGAAGTGCATTCGATGTTTGAA--AAAT-AGCCTGGTGCATCGATGCATGGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAG---AGTGCATCGATGCATGGA
1232968 TT
63 TT
* * **
1232970 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAGAGTGCATCGATGCATGGAGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
* * * * *
1233034 GTGCATCGGTGCATGGAATGCATTCGATGTTTCAATTTATTCATTGA-TGTATCGATGCATGGTA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCA--GAGTGCATCGATGCATGG-A
1233098 TT
63 TT
*
1233100 GATGCATCGGTGCATG
1 G-TGCATCGATGCATG
1233116 CCTTTGAAAA
Statistics
Matches: 124, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
64 86 0.69
65 14 0.11
66 8 0.06
67 16 0.13
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
Found at i:1233036 original size:19 final size:19
Alignment explanation
Indices: 1233012--1233062 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1233002 TAATTAAATC
1233012 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1233031 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1233050 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1233063 TTTCAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1233101 original size:21 final size:21
Alignment explanation
Indices: 1233076--1233115 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1233066 CAATTTATTC
*
1233076 ATTGATGTATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
1233097 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
1233116 CCTTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.35
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:1237112 original size:22 final size:22
Alignment explanation
Indices: 1237084--1237127 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1237074 CCTTGTAAGT
1237084 ATGACTACATACATATTGCCCA
1 ATGACTACATACATATTGCCCA
*
1237106 ATGACTACATACATGTTGCCCA
1 ATGACTACATACATATTGCCCA
1237128 CGTGTTATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.27
Consensus pattern (22 bp):
ATGACTACATACATATTGCCCA
Found at i:1237704 original size:29 final size:29
Alignment explanation
Indices: 1237659--1237746 Score: 149
Period size: 29 Copynumber: 3.0 Consensus size: 29
1237649 ATTTTCACTT
*
1237659 AACTAAATTGAGGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
*
1237688 AACTAAATTGATATAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
*
1237717 AACTAAATTGATGTAAGTAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
1237746 A
1 A
1237747 TTAATTTATG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:1239522 original size:22 final size:22
Alignment explanation
Indices: 1239497--1239538 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1239487 ATTTTAATTC
* * *
1239497 TTTTGATTATTAATAAAATTTA
1 TTTTCATTAGTAAAAAAATTTA
1239519 TTTTCATTAGTAAAAAAATT
1 TTTTCATTAGTAAAAAAATT
1239539 AAAATATAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
TTTTCATTAGTAAAAAAATTTA
Found at i:1241204 original size:23 final size:23
Alignment explanation
Indices: 1241160--1241204 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1241150 GACTAAAATA
* * **
1241160 AAATTATATTAAATTAGTACATT
1 AAATTAAAATAAATTAAAACATT
1241183 AAATTAAAATAAATTAAAACAT
1 AAATTAAAATAAATTAAAACAT
1241205 GTTGTTTGGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (23 bp):
AAATTAAAATAAATTAAAACATT
Found at i:1242211 original size:44 final size:44
Alignment explanation
Indices: 1242148--1242237 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
1242138 GTGGAGGCGT
1242148 GGCAACAGCTTCTGGCTGAGGCGGCGGCACGAGATGATAACCTA
1 GGCAACAGCTTCTGGCTGAGGCGGCGGCACGAGATGATAACCTA
*
1242192 GGCAACAGCTTCTGGCTGAGGCGGCGGCGCGAGATGATAACCTA
1 GGCAACAGCTTCTGGCTGAGGCGGCGGCACGAGATGATAACCTA
1242236 GG
1 GG
1242238 GTTATGAAAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.23, C:0.24, G:0.37, T:0.16
Consensus pattern (44 bp):
GGCAACAGCTTCTGGCTGAGGCGGCGGCACGAGATGATAACCTA
Found at i:1242483 original size:3 final size:3
Alignment explanation
Indices: 1242475--1242523 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
1242465 TATTTATATT
*
1242475 TAA TAA TAA TAA T-A TAA -CA TAA TAA T-A TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1242519 TAA TA
1 TAA TA
1242524 TAAGCAAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 7 0.17
3 33 0.82
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1242499 original size:8 final size:8
Alignment explanation
Indices: 1242476--1242523 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
1242466 ATTTATATTT
1242476 AATAATAA
1 AATAATAA
1242484 TAAT-ATAA
1 -AATAATAA
*
1242492 CATAATAA
1 AATAATAA
*
1242500 TATAATAA
1 AATAATAA
1242508 TAATAATAA
1 -AATAATAA
1242517 AATAATA
1 AATAATA
1242524 TAAGCAAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
7 2 0.06
8 22 0.65
9 10 0.29
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (8 bp):
AATAATAA
Found at i:1243362 original size:112 final size:112
Alignment explanation
Indices: 1242844--1243595 Score: 1226
Period size: 112 Copynumber: 6.8 Consensus size: 112
1242834 AGAATCAAAC
* * *
1242844 AAAGGCTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
1242908 ATGAACACTTCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCA
66 ATGAACACTTCTGGCAATGTTGATCCATCAAGTGATGGATTTGAGCA
* *
1242955 AAAGGTTGAACAAGTTCTTCTC-TTATGAACTTCCACTT-CTTTTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
1243018 ATGAACACTTCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCA
66 ATGAACACTTCTGGCAATGTTGATCCATCAAGTGATGGATTTGAGCA
*
1243065 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGCTGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
1243130 ATGAACACTTATGGCAATGTTGATCCTTCAAGTGATGGATTTGAGCA
66 ATGAACACTTCTGGCAATGTTGATCCATCAAGTGATGGATTTGAGCA
* *
1243177 AAAGATTGAACAA---ATTCTCATTA-GAACTTCCTC-TCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
1243237 ATGAACACTTCTGGCAATGCTGATCAATCAAGTGATGGATTTGAGCA
66 ATGAACACTTCTGGCAATGTTGATCCATCAAGTGATGGATTTGAGCA
*
1243284 AAAGATTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1243349 ATGAACACTTCTGGCAATGTTGATCCATCAAGTGATGGATTTGAGCA
66 ATGAACACTTCTGGCAATGTTGATCCATCAAGTGATGGATTTGAGCA
1243396 AAA-GTTGAACAAG-T-TTCTCATTATGAAC-TCC-CTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
1243456 ATGAACACTTCTGGCAATGTTGACCCATCAAGTGATGGATTTGAGCA
66 ATGAACACTTCTGGCAATGTTGATCCATCAAGTGATGGATTTGAGCA
*
1243503 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTTATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
1243568 ATGAACTCTACCTGGC-ATGTTGATCCAT
66 ATGAACACT-TCTGGCAATGTTGATCCAT
1243596 TGAGTAATGG
Statistics
Matches: 600, Mismatches: 27, Indels: 27
0.92 0.04 0.04
Matches are distributed among these distances:
107 160 0.27
108 23 0.04
109 25 0.04
110 129 0.22
111 57 0.09
112 201 0.34
113 5 0.01
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (112 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACACTTCTGGCAATGTTGATCCATCAAGTGATGGATTTGAGCA
Found at i:1243608 original size:219 final size:219
Alignment explanation
Indices: 1242844--1243595 Score: 1228
Period size: 219 Copynumber: 3.4 Consensus size: 219
1242834 AGAATCAAAC
* * *
1242844 AAAGGCTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
1242908 ATGAACACTTCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGTTCT
66 ATGAACACTTCTGGCAATGTTGATCCATCAAGTGATGGATTTGAGCAAAA-GTTGAACAAG-T-T
* *
1242973 TCTC-TTATGAACTTCCACTT-CTTTTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGAAAT
128 TCTCATTATGAAC-TCC-CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGCAAT
1243036 GTTGATCCATCAAGTGATGGATTTGAGCA
191 GTTGATCCATCAAGTGATGGATTTGAGCA
*
1243065 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGCTGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
1243130 ATGAACACTTATGGCAATGTTGATCCTTCAAGTGATGGATTTGAGCAAAAGATTGAACAA-ATTC
66 ATGAACACTTCTGGCAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAG-TTGAACAAGTTTC
* *
1243194 TCATTA-GAACTTCCTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGCAATGCT
130 TCATTATGAACTCCCT-TCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGCAATGTT
*
1243258 GATCAATCAAGTGATGGATTTGAGCA
194 GATCCATCAAGTGATGGATTTGAGCA
*
1243284 AAAGATTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1243349 ATGAACACTTCTGGCAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGTTGAACAAGTTTCT
66 ATGAACACTTCTGGCAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGTTGAACAAGTTTCT
1243414 CATTATGAACTCCCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGCAATGTTGA
131 CATTATGAACTCCCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGCAATGTTGA
*
1243479 CCCATCAAGTGATGGATTTGAGCA
196 TCCATCAAGTGATGGATTTGAGCA
*
1243503 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTTATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
1243568 ATGAACTCTACCTGGC-ATGTTGATCCAT
66 ATGAACACT-TCTGGCAATGTTGATCCAT
1243596 TGAGTAATGG
Statistics
Matches: 497, Mismatches: 26, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
217 2 0.00
218 11 0.02
219 352 0.71
220 16 0.03
221 39 0.08
222 77 0.15
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (219 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACACTTCTGGCAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGTTGAACAAGTTTCT
CATTATGAACTCCCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGCAATGTTGA
TCCATCAAGTGATGGATTTGAGCA
Found at i:1244018 original size:22 final size:22
Alignment explanation
Indices: 1243962--1244019 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
1243952 AATAGAGCCT
* *
1243962 TCATCTTTGAAAAGGGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
1243984 TCATCTTTAAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
1244006 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
1244020 CGTAGATGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:1245309 original size:25 final size:25
Alignment explanation
Indices: 1245275--1245328 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
1245265 ACTGTCACTG
1245275 TTTCACCATTTTCATTCTTCATATC
1 TTTCACCATTTTCATTCTTCATATC
1245300 TTTCACCATTTTCATTCTTCATATC
1 TTTCACCATTTTCATTCTTCATATC
1245325 TTTC
1 TTTC
1245329 TATCTCATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.19, C:0.28, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTCACCATTTTCATTCTTCATATC
Found at i:1246926 original size:114 final size:114
Alignment explanation
Indices: 1246742--1246963 Score: 390
Period size: 114 Copynumber: 1.9 Consensus size: 114
1246732 ATCAAATTCA
* ** * * *
1246742 TCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACTGAACCAGATCAGATAACTCAAAGAATAT
1 TCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAAATAACTCAAAGAACAC
1246807 TTCCAGAAGATGCTATTGGGTCTCTTTATTTCTACTATGAGAAAATTTG
66 TTCCAGAAGATGCTATTGGGTCTCTTTATTTCTACTATGAGAAAATTTG
1246856 TCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAAATAACTCAAAGAACAC
1 TCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAAATAACTCAAAGAACAC
1246921 TTCCAGAAGATGCTATTGGGTCTCTTTATTTCTACTATGAGAA
66 TTCCAGAAGATGCTATTGGGTCTCTTTATTTCTACTATGAGAA
1246964 CGTGGCACTT
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 102 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (114 bp):
TCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAAATAACTCAAAGAACAC
TTCCAGAAGATGCTATTGGGTCTCTTTATTTCTACTATGAGAAAATTTG
Found at i:1251823 original size:14 final size:14
Alignment explanation
Indices: 1251806--1251866 Score: 68
Period size: 14 Copynumber: 4.3 Consensus size: 14
1251796 AAGGCAAACA
*
1251806 TAAAAATACAAATG
1 TAAAAATGCAAATG
* *
1251820 TAAAGATTCCAAATG
1 TAAA-AATGCAAATG
*
1251835 TAAATATGCAAATG
1 TAAAAATGCAAATG
*
1251849 TAAAAATGTAAATG
1 TAAAAATGCAAATG
1251863 TAAA
1 TAAA
1251867 TTATTTAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
14 27 0.69
15 12 0.31
ACGTcount: A:0.56, C:0.07, G:0.11, T:0.26
Consensus pattern (14 bp):
TAAAAATGCAAATG
Found at i:1253070 original size:46 final size:49
Alignment explanation
Indices: 1253003--1253093 Score: 127
Period size: 46 Copynumber: 1.9 Consensus size: 49
1252993 AGGTATAAAT
* *
1253003 CCTAACCTCATGCTTTCTAGTTC-CATGC-TTTGTTT-GGAAAAATTAA
1 CCTAACCTCATGATTTCTAGTTCGCATGCATTTATTTAGGAAAAATTAA
1253049 CCTAA-CTGCATGATTTCTAGTTCGCATGCATTTATTTAGGAAAAA
1 CCTAACCT-CATGATTTCTAGTTCGCATGCATTTATTTAGGAAAAA
1253094 GAAAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
45 2 0.05
46 19 0.49
47 5 0.13
48 6 0.15
49 7 0.18
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (49 bp):
CCTAACCTCATGATTTCTAGTTCGCATGCATTTATTTAGGAAAAATTAA
Found at i:1254773 original size:23 final size:23
Alignment explanation
Indices: 1254729--1254773 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1254719 GACTAAAATA
* * **
1254729 AAATTATATTAAATTAGTACATT
1 AAATTAAAATAAATTAAAACATT
1254752 AAATTAAAATAAATTAAAACAT
1 AAATTAAAATAAATTAAAACAT
1254774 GTTGTTTGGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (23 bp):
AAATTAAAATAAATTAAAACATT
Found at i:1256019 original size:3 final size:3
Alignment explanation
Indices: 1256013--1256058 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
1256003 ATTTATTATT
1256013 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAA TAA TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
1256057 TA
1 TA
1256059 TAAGCAAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 33 0.82
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1256037 original size:19 final size:20
Alignment explanation
Indices: 1256013--1256058 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
1256003 ATTTATTATT
1256013 TAATAATAATAAT-ATAATA
1 TAATAATAATAATAATAATA
1256032 TAATAATAATAATAATAATA
1 TAATAATAATAATAATAATA
1256052 -AATAATA
1 TAATAATA
1256059 TAAGCAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TAATAATAATAATAATAATA
Found at i:1256041 original size:22 final size:22
Alignment explanation
Indices: 1256013--1256058 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1256003 ATTTATTATT
1256013 TAATAATAATAAT-ATAATATAA
1 TAATAATAATAATAATAA-ATAA
1256035 TAATAATAATAATAATAAATAA
1 TAATAATAATAATAATAAATAA
1256057 TA
1 TA
1256059 TAAGCAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
TAATAATAATAATAATAAATAA
Found at i:1265436 original size:22 final size:22
Alignment explanation
Indices: 1265423--1265490 Score: 100
Period size: 22 Copynumber: 3.1 Consensus size: 22
1265413 GCGGTTAGGG
1265423 TTGAGTTTATTAGCATTAAGGC
1 TTGAGTTTATTAGCATTAAGGC
*
1265445 TTGAGTTTGTTAGCATTAAGGC
1 TTGAGTTTATTAGCATTAAGGC
* * *
1265467 TTGAGTTTTTTAGCAGTAATGC
1 TTGAGTTTATTAGCATTAAGGC
1265489 TT
1 TT
1265491 TAATTGAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.44
Consensus pattern (22 bp):
TTGAGTTTATTAGCATTAAGGC
Found at i:1266602 original size:57 final size:57
Alignment explanation
Indices: 1266514--1266624 Score: 188
Period size: 57 Copynumber: 1.9 Consensus size: 57
1266504 CATAGCTCAG
1266514 TATCCATATACACATCTTTACAGTAGACTTGGACCTAATTTTTTTAAGTGGTTTCAT
1 TATCCATATACACATCTTTACAGTAGACTTGGACCTAATTTTTTTAAGTGGTTTCAT
* *
1266571 TATCCATATGCACATCTTTAC-GTTAGACTTGGACCTATTTTTTTTAAGTGGTTT
1 TATCCATATACACATCTTTACAG-TAGACTTGGACCTAATTTTTTTAAGTGGTTT
1266625 TATTTCATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
56 1 0.02
57 50 0.98
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (57 bp):
TATCCATATACACATCTTTACAGTAGACTTGGACCTAATTTTTTTAAGTGGTTTCAT
Found at i:1268306 original size:82 final size:83
Alignment explanation
Indices: 1268149--1268309 Score: 193
Period size: 82 Copynumber: 2.0 Consensus size: 83
1268139 ATACCGCAAT
* * * * *
1268149 AGAGTAGTAATTTAGCGGCGTTTTTTGAACAAACGCCGGTATAGAGTTATTTATTGTGGCGTTTT
1 AGAGTAGTAATTTAGCGACGTTTTTTGAACAAACGCCGCTATAGAGTTATTAATGGTGGCATTTT
1268214 ATCAATAAACGCCGTAAA
66 ATCAATAAACGCCGTAAA
* * *
1268232 AGAGTAGTCATTTAGCGACG-TTTTTGTACAAACGCCGCTATTGAG-TATTAATGGTACGGCATT
1 AGAGTAGTAATTTAGCGACGTTTTTTGAACAAACGCCGCTATAGAGTTATTAATGGT--GGCATT
**
1268295 TT-TTGATAAACGCCG
64 TTATCAATAAACGCCG
1268310 CAATATTATT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
81 8 0.12
82 33 0.50
83 25 0.38
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.34
Consensus pattern (83 bp):
AGAGTAGTAATTTAGCGACGTTTTTTGAACAAACGCCGCTATAGAGTTATTAATGGTGGCATTTT
ATCAATAAACGCCGTAAA
Found at i:1278205 original size:21 final size:21
Alignment explanation
Indices: 1278181--1278257 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
1278171 CAGCAGCAGA
* * *
1278181 AGCAGAGAGAGAAGTAGTTAC
1 AGCACAGAGAGAAGCAGTGAC
* *
1278202 AGCACACAGAG-AGACAGCGAC
1 AGCACAGAGAGAAG-CAGTGAC
*
1278223 AGCACAGAGAGAAGCAGTGGC
1 AGCACAGAGAGAAGCAGTGAC
1278244 AGCACAGAGAGAAG
1 AGCACAGAGAGAAG
1278258 TAATATATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.04
21 42 0.91
22 2 0.04
ACGTcount: A:0.43, C:0.18, G:0.34, T:0.05
Consensus pattern (21 bp):
AGCACAGAGAGAAGCAGTGAC
Found at i:1278230 original size:19 final size:20
Alignment explanation
Indices: 1278160--1278255 Score: 68
Period size: 21 Copynumber: 4.6 Consensus size: 20
1278150 AAGCAAGGGA
*
1278160 AGCAGAGAGAGCAGCAGCAGA-
1 AGCACAGAGAG-AGCAGC-GAC
* * **
1278181 AGCAGAGAGAGAAGTAGTTAC
1 AGCACAGAGAG-AGCAGCGAC
*
1278202 AGCACACAGAGAGACAGCGAC
1 AGCACAGAGAGAG-CAGCGAC
* *
1278223 AGCACAGAGAGAAGCAGTGGC
1 AGCACAGAGAG-AGCAGCGAC
1278244 AGCACAGAGAGA
1 AGCACAGAGAGA
1278256 AGTAATATAT
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
20 4 0.07
21 54 0.90
22 2 0.03
ACGTcount: A:0.43, C:0.19, G:0.34, T:0.04
Consensus pattern (20 bp):
AGCACAGAGAGAGCAGCGAC
Found at i:1278841 original size:43 final size:44
Alignment explanation
Indices: 1278696--1278904 Score: 194
Period size: 43 Copynumber: 4.8 Consensus size: 44
1278686 CATTTTTATC
* * ** **
1278696 ACGCCGCTAAATATCAACATCT-TCTACGGCGTTTG-TAGGAAAA
1 ACGCCGCTAAATATCAACACCTAT-TGCGGCGTTTGTTCTGCCAA
* * * * * *** *
1278739 ACGTCGGTAAAAATCAACATCTACTGCGGCGTTTGTGAAG-AAA
1 ACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTTCTGCCAA
*
1278782 ACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTT-TGCCAA
1 ACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTTCTGCCAA
* *
1278825 ATGCCGTTAAATATCAACACCTATTGCGGCGTTT-TTCTGCCAA
1 ACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTTCTGCCAA
* *
1278868 ACGCCGCTAAATATCAATACCTTTTGCGGCGTTTGTT
1 ACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTT
1278905 GAAACGCCGC
Statistics
Matches: 139, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
42 3 0.02
43 132 0.95
44 4 0.03
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (44 bp):
ACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTTCTGCCAA
Found at i:1283427 original size:20 final size:20
Alignment explanation
Indices: 1283390--1283429 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1283380 TGTTAGTGTG
*
1283390 TATGATGATTGATTGTTGTA
1 TATGATGATTGATAGTTGTA
1283410 TATGATGA-TGCATAGTTGTA
1 TATGATGATTG-ATAGTTGTA
1283430 AGATATTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.28, C:0.03, G:0.25, T:0.45
Consensus pattern (20 bp):
TATGATGATTGATAGTTGTA
Found at i:1284371 original size:18 final size:18
Alignment explanation
Indices: 1284348--1284386 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1284338 TCCCTCGAAA
1284348 TTTAAAATTATTATATAT
1 TTTAAAATTATTATATAT
* * *
1284366 TTTAAAGTTTTTATGTAT
1 TTTAAAATTATTATATAT
1284384 TTT
1 TTT
1284387 TTATTGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTAAAATTATTATATAT
Found at i:1288701 original size:20 final size:19
Alignment explanation
Indices: 1288659--1288695 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1288649 CAATTAAATT
1288659 TATTAAAAATCAGTTTTAA
1 TATTAAAAATCAGTTTTAA
*
1288678 TATTCAAAATC-GTTTTAA
1 TATTAAAAATCAGTTTTAA
1288696 AATATTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (19 bp):
TATTAAAAATCAGTTTTAA
Found at i:1291334 original size:22 final size:22
Alignment explanation
Indices: 1291306--1291353 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1291296 TTATTCACTT
*
1291306 TTTTCTCCCTTCATTGTCGTGA
1 TTTTCTCCCTTCATTGCCGTGA
*
1291328 TTTTCTCCTTTCATTGCCGTGA
1 TTTTCTCCCTTCATTGCCGTGA
1291350 TTTT
1 TTTT
1291354 ACTCGACAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.08, C:0.25, G:0.12, T:0.54
Consensus pattern (22 bp):
TTTTCTCCCTTCATTGCCGTGA
Found at i:1304356 original size:18 final size:19
Alignment explanation
Indices: 1304333--1304370 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1304323 GTAAAGTCCT
1304333 GAAAAACCAG-TGAGGAGA
1 GAAAAACCAGATGAGGAGA
* *
1304351 GAAAAATCAGATTAGGAGA
1 GAAAAACCAGATGAGGAGA
1304370 G
1 G
1304371 GGTCGATCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.50, C:0.08, G:0.32, T:0.11
Consensus pattern (19 bp):
GAAAAACCAGATGAGGAGA
Found at i:1311636 original size:26 final size:26
Alignment explanation
Indices: 1311607--1311658 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1311597 GGATGAAAGT
1311607 AAGGACATTCTCGAAACAGAAATTTG
1 AAGGACATTCTCGAAACAGAAATTTG
1311633 AAGGACATTCTCGAAACAGAAATTTG
1 AAGGACATTCTCGAAACAGAAATTTG
1311659 TGTGTCTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.23
Consensus pattern (26 bp):
AAGGACATTCTCGAAACAGAAATTTG
Found at i:1313868 original size:37 final size:37
Alignment explanation
Indices: 1313826--1313896 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
1313816 TTTTGAAATG
* * *
1313826 AATTTTGTGTCTCTTGAGATAGTTTCCCTTGAAACAA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAA
*
1313863 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAA
1313897 TATAAACATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (37 bp):
AATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAA
Found at i:1313880 original size:102 final size:102
Alignment explanation
Indices: 1313753--1314331 Score: 1009
Period size: 102 Copynumber: 5.7 Consensus size: 102
1313743 GATTGTTTTT
* *
1313753 CTTGAAACAAAA--TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGTAAACATATC
1 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTC
** *
1313816 TTTTGAAATGAATTTTGTGTCTCTTGAGATAGTTTCC
66 CCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCC
*
1313853 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAATATAAACATTGAAAACATTTC
1 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTC
*
1313918 CCTTGAAATGAATTTTGTCTCTCTTGTGATAGTTTCC
66 CCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCC
1313955 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTC
1 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTC
*
1314020 CCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTTC
66 CCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCC
1314057 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTC
1 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTC
1314122 CCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCC
66 CCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCC
* *
1314159 CTTGAAACAAAATTTTGTCTCCATTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACGTTTC
1 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTC
* *
1314224 ACTTGAATTGAATTTTGTCTCTCTTGAGATAGTTTCC
66 CCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCC
* * *
1314261 CTTGAAACAAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACTTTGAAAACGTTTC
1 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTC
1314326 CCTTGA
66 CCTTGA
1314332 GACACAAAAT
Statistics
Matches: 458, Mismatches: 19, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
100 12 0.03
102 446 0.97
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.38
Consensus pattern (102 bp):
CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTC
CCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCC
Found at i:1313989 original size:37 final size:37
Alignment explanation
Indices: 1313914--1314000 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 37
1313904 ATTGAAAACA
** * * *
1313914 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGTGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1313950 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
1313987 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
1314001 TAAACATTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 12 0.27
37 32 0.73
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:1314071 original size:37 final size:37
Alignment explanation
Indices: 1314030--1314102 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
1314020 CCTTGAAATG
* *
1314030 AATTTTGTCTCTCTTGAGATAGTTT-TCCTTGAAACAA
1 AATTTTGTCTCCCTTGAGACAGTTTCT-CTTGAAACAA
1314067 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1314103 TAAACATTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 32 0.97
38 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (37 bp):
AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
Found at i:1314186 original size:37 final size:37
Alignment explanation
Indices: 1314118--1314204 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
1314108 ATTGAAAACA
** *
1314118 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1314154 TTTCCCTTGAAACAAAATTTTGTCTC-CATTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCTC-TTGAGACAG
*
1314191 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
1314205 TAAACATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 13 0.29
37 32 0.71
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
Found at i:1314259 original size:36 final size:36
Alignment explanation
Indices: 1314219--1314303 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 36
1314209 CATTGAAAAC
*** *
1314219 GTTTCACTTGAATTGAATTTTGTCTCTCTTGAGATA
1 GTTTCACTTGAACAAAATTTTGTCTCCCTTGAGATA
*
1314255 GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATA
1 GTTTCACTTG-AACAAAATTTTGTCTCCCTTGAGATA
*
1314292 GTTTCTCTTGAA
1 GTTTCACTTGAA
1314304 ACATAAACTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 11 0.26
37 31 0.74
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.44
Consensus pattern (36 bp):
GTTTCACTTGAACAAAATTTTGTCTCCCTTGAGATA
Found at i:1314281 original size:37 final size:38
Alignment explanation
Indices: 1314234--1314315 Score: 130
Period size: 37 Copynumber: 2.2 Consensus size: 38
1314224 ACTTGAATTG
*
1314234 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA-A
1 AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACATA
*
1314271 AATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATA
1 AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACATA
*
1314309 AACTTTG
1 AATTTTG
1314316 AAAACGTTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 34 0.83
38 7 0.17
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.41
Consensus pattern (38 bp):
AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACATA
Found at i:1316925 original size:31 final size:31
Alignment explanation
Indices: 1316887--1316946 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1316877 GAGTCGAGGG
**
1316887 TTACCTATGTTCTACGGAACATATGGACAAT
1 TTACCTATGTTCTACAAAACATATGGACAAT
*
1316918 TTACCTATGTTCTTCAAAACATATGGACA
1 TTACCTATGTTCTACAAAACATATGGACA
1316947 GTTACATAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (31 bp):
TTACCTATGTTCTACAAAACATATGGACAAT
Found at i:1317151 original size:16 final size:16
Alignment explanation
Indices: 1317130--1317173 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
1317120 TTTGTTTCTT
1317130 TGTGATATGATAAATG
1 TGTGATATGATAAATG
1317146 TGTGATATGATAAATG
1 TGTGATATGATAAATG
*
1317162 TGTTATATGATA
1 TGTGATATGATA
1317174 TACAGAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (16 bp):
TGTGATATGATAAATG
Found at i:1318153 original size:18 final size:19
Alignment explanation
Indices: 1318130--1318167 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1318120 GTAAAGTCCT
1318130 GAAAAACCAG-TGAGGAGA
1 GAAAAACCAGATGAGGAGA
* *
1318148 GAAAAATCAGATTAGGAGA
1 GAAAAACCAGATGAGGAGA
1318167 G
1 G
1318168 GGTCGATCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.50, C:0.08, G:0.32, T:0.11
Consensus pattern (19 bp):
GAAAAACCAGATGAGGAGA
Found at i:1318997 original size:19 final size:17
Alignment explanation
Indices: 1318965--1319002 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
1318955 GATTTGTTTA
1318965 TTCATTTATTATTATTT
1 TTCATTTATTATTATTT
1318982 TTCATTTAATTTATTATTT
1 TTCATTT-A-TTATTATTT
1319001 TT
1 TT
1319003 TTCATTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 1 0.05
19 11 0.58
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (17 bp):
TTCATTTATTATTATTT
Found at i:1319005 original size:21 final size:22
Alignment explanation
Indices: 1318968--1319009 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
1318958 TTGTTTATTC
1318968 ATTTATTATTATTTTTCATTTA
1 ATTTATTATTATTTTTCATTTA
1318990 ATTTATTATT-TTTTTCATTT
1 ATTTATTATTATTTTTCATTT
1319010 TGTTATGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (22 bp):
ATTTATTATTATTTTTCATTTA
Found at i:1319131 original size:12 final size:13
Alignment explanation
Indices: 1319109--1319137 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1319099 CGAATTAAAT
1319109 TTTTGAATTTTAA
1 TTTTGAATTTTAA
1319122 TTTT-AATTTTAA
1 TTTTGAATTTTAA
1319134 TTTT
1 TTTT
1319138 CACAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTTGAATTTTAA
Found at i:1325659 original size:64 final size:65
Alignment explanation
Indices: 1325550--1325681 Score: 230
Period size: 64 Copynumber: 2.0 Consensus size: 65
1325540 GTGAGGTTAA
** *
1325550 ATTATTAGTAGCTACTGATTTTTTTTTATTGAAAATGACTCTCCCATGTCGTTTAGTAGCTTCCG
1 ATTATTAGTAGCTACTGATTTTTTTCCATTGAAAATGAATCTCCCATGTCGTTTAGTAGCTTCCG
1325615 ATTATTAGTAGCTACTGA-TTTTTTCCATTGAAAATGAATCTCCCATGTCGTTTAGTAGCTTCCG
1 ATTATTAGTAGCTACTGATTTTTTTCCATTGAAAATGAATCTCCCATGTCGTTTAGTAGCTTCCG
1325679 ATT
1 ATT
1325682 CTTAACAGAC
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
64 46 0.72
65 18 0.28
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.43
Consensus pattern (65 bp):
ATTATTAGTAGCTACTGATTTTTTTCCATTGAAAATGAATCTCCCATGTCGTTTAGTAGCTTCCG
Found at i:1325734 original size:18 final size:18
Alignment explanation
Indices: 1325711--1325749 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1325701 ATGCTCACGC
1325711 GACGCTACCGGCGAGTGT
1 GACGCTACCGGCGAGTGT
1325729 GACGCTACCGGCGAGTGT
1 GACGCTACCGGCGAGTGT
1325747 GAC
1 GAC
1325750 ACTCGGCGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.28, G:0.38, T:0.15
Consensus pattern (18 bp):
GACGCTACCGGCGAGTGT
Found at i:1332582 original size:2 final size:2
Alignment explanation
Indices: 1332575--1332600 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1332565 AGTCTATTGA
1332575 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
1332601 TCAATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1334798 original size:3 final size:3
Alignment explanation
Indices: 1334790--1334845 Score: 94
Period size: 3 Copynumber: 18.3 Consensus size: 3
1334780 AAAGGCCATT
1334790 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TTGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA -TGA
*
1334836 TGA TGG TGA T
1 TGA TGA TGA T
1334846 TGGCTTTAGG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.30, C:0.00, G:0.34, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:1337545 original size:17 final size:17
Alignment explanation
Indices: 1337511--1337562 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1337501 ACCGAACAAA
* *
1337511 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
1337528 TTTATTAATTTACCGAG
1 TTTATTAATTTACAGAG
*
1337545 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
1337560 TTT
1 TTT
1337563 CTACTGTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:1338561 original size:16 final size:17
Alignment explanation
Indices: 1338540--1338574 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1338530 TACTATTCAC
*
1338540 GTGAATAGT-GAATTTT
1 GTGAATAGTAAAATTTT
1338556 GTGAATAGTAAAATTTT
1 GTGAATAGTAAAATTTT
1338573 GT
1 GT
1338575 CGGCGATACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (17 bp):
GTGAATAGTAAAATTTT
Found at i:1339346 original size:15 final size:15
Alignment explanation
Indices: 1339322--1339353 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1339312 TGGAAGATCC
*
1339322 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
1339337 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
1339352 AA
1 AA
1339354 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:1348344 original size:21 final size:22
Alignment explanation
Indices: 1348309--1348357 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
1348299 AAAGAAAAGG
1348309 AAAATAAAATAAAATTATATGA
1 AAAATAAAATAAAATTATATGA
* * *
1348331 AAAATAATAT-AAATTTTATTA
1 AAAATAAAATAAAATTATATGA
1348352 AAAATA
1 AAAATA
1348358 CATACACATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATAAAATAAAATTATATGA
Found at i:1349782 original size:15 final size:14
Alignment explanation
Indices: 1349756--1349785 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1349746 TTTATTCATC
1349756 AATAATGTATTTTT
1 AATAATGTATTTTT
*
1349770 AATAATGTAATTTT
1 AATAATGTATTTTT
1349784 AA
1 AA
1349786 AAAATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:1350447 original size:3 final size:3
Alignment explanation
Indices: 1350439--1350468 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1350429 TTTTTAATTA
*
1350439 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1350469 TAGTCATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1350770 original size:136 final size:134
Alignment explanation
Indices: 1350599--1350842 Score: 305
Period size: 135 Copynumber: 1.8 Consensus size: 134
1350589 ATCATGTTTG
** * *
1350599 AATATTTATTTTTCAATATTAAGAAAGGGTAGTCTTAAAGCAACGGGATGTCCATTTTCTGATAT
1 AATATTTATTTTTCAATATTAAGAAAGACTAGTCTTAAAGCAACGAGAAGT-CATTTTCTGATAT
* * *
1350664 TTTTAAATAAATAAATATTTTACTTT-TATAAATTATATATATTTTAATTGTTTTTAGATAAATG
65 TTCTAAATAAATAAATATCTTA-TTTATATAAATTA-ATAGATTTTAATTGTTTTTAGATAAATG
1350728 GTTTATT
128 GTTTATT
* * * *
1350735 AATATTT-TTTTTTAATATTAAGAAAAGAACT-GTCTTAAAGCACCTAGAAGTCATTTTTTGATA
1 AATATTTATTTTTCAATATTAAG-AAAG-ACTAGTCTTAAAGCAACGAGAAGTCATTTTCTGATA
* *
1350798 TTTCTAAATATATAAATATCTTATTTATATATATTAATAGATTTT
64 TTTCTAAATAAATAAATATCTTATTTATATAAATTAATAGATTTT
1350843 CTTAAAATTA
Statistics
Matches: 92, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
134 11 0.12
135 53 0.58
136 27 0.29
137 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (134 bp):
AATATTTATTTTTCAATATTAAGAAAGACTAGTCTTAAAGCAACGAGAAGTCATTTTCTGATATT
TCTAAATAAATAAATATCTTATTTATATAAATTAATAGATTTTAATTGTTTTTAGATAAATGGTT
TATT
Found at i:1351365 original size:28 final size:27
Alignment explanation
Indices: 1351333--1351393 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
1351323 TTATAATTCT
*
1351333 TTATTTTCAAAATTTTTATATATACTTA
1 TTATTTTCAAAATATTTATATATA-TTA
**
1351361 TTATTTTCCTAATATTTATATATATTA
1 TTATTTTCAAAATATTTATATATATTA
1351388 TT-TTTT
1 TTATTTT
1351394 ATTAATGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 4 0.13
27 5 0.17
28 21 0.70
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (27 bp):
TTATTTTCAAAATATTTATATATATTA
Found at i:1351399 original size:26 final size:26
Alignment explanation
Indices: 1351347--1351415 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
1351337 TTTCAAAATT
*
1351347 TTTATATATACTTATTATTTTCCTAATA
1 TTTATATATA-TTATT-TTTTACTAATA
* *
1351375 TTTATATATATTATTTTTTATTAATG
1 TTTATATATATTATTTTTTACTAATA
*
1351401 TTT-T-TATTTTATTTT
1 TTTATATATATTATTTT
1351416 CAAGTATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 10 0.27
25 1 0.03
26 11 0.30
27 5 0.14
28 10 0.27
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (26 bp):
TTTATATATATTATTTTTTACTAATA
Found at i:1351407 original size:28 final size:28
Alignment explanation
Indices: 1351343--1351404 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
1351333 TTATTTTCAA
*
1351343 AATTTTTATATATACTTATTATTTTCCT
1 AATTTTTATATATACTTATTATTTTACT
* *
1351371 AATATTTATATATA-TTATT-TTTTATT
1 AATTTTTATATATACTTATTATTTTACT
1351397 AATGTTTT
1 AAT-TTTT
1351405 TATTTTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 8 0.28
27 8 0.28
28 13 0.45
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (28 bp):
AATTTTTATATATACTTATTATTTTACT
Found at i:1355849 original size:8 final size:8
Alignment explanation
Indices: 1355832--1355879 Score: 60
Period size: 8 Copynumber: 5.8 Consensus size: 8
1355822 ATCCATCAAA
1355832 AAAAAGAGG
1 AAAAA-AGG
*
1355841 AAAATAGG
1 AAAAAAGG
*
1355849 AAAAAAGT
1 AAAAAAGG
1355857 AAATAAAGG
1 AAA-AAAGG
1355866 AAAAAAGG
1 AAAAAAGG
1355874 AAAAAA
1 AAAAAA
1355880 ATTGAATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
8 23 0.68
9 11 0.32
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (8 bp):
AAAAAAGG
Found at i:1358607 original size:22 final size:23
Alignment explanation
Indices: 1358582--1358625 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1358572 AATTAAGTTT
1358582 TAATCTTA-AAACAATTTCAAAA
1 TAATCTTACAAACAATTTCAAAA
* **
1358604 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
1358626 CCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCAAAA
Found at i:1367779 original size:18 final size:18
Alignment explanation
Indices: 1367752--1367821 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
1367742 TTAAGGAGTA
*
1367752 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
1367770 GTCCTACGGGACATATACAGTG
1 GTCCTACGGGAC--AT--AGTG
*
1367792 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
*
1367810 GTCTTACGGGAC
1 GTCCTACGGGAC
1367822 GAATACTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 25 0.57
20 4 0.09
22 15 0.34
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
GTCCTACGGGACATAGTG
Found at i:1372645 original size:18 final size:18
Alignment explanation
Indices: 1372618--1372687 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
1372608 TTAAGGAGTA
*
1372618 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
1372636 GTCCTACGGGACATATACAGTG
1 GTCCTACGGGAC--AT--AGTG
* *
1372658 GTCCTTCGGGATATAGTG
1 GTCCTACGGGACATAGTG
1372676 GTCCTACGGGAC
1 GTCCTACGGGAC
1372688 GAATACTGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 25 0.58
20 4 0.09
22 14 0.33
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
GTCCTACGGGACATAGTG
Found at i:1375885 original size:75 final size:75
Alignment explanation
Indices: 1375762--1375937 Score: 253
Period size: 75 Copynumber: 2.3 Consensus size: 75
1375752 ACAAGAAACA
* * *
1375762 AATGATGGAGCATGTTGAAAGCCCATTTCAATTATAATCAAGAATATTGACACATTTTGAACATT
1 AATGATGGAGCATGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTGACACATTTTGAACATT
1375827 TGTATTAGCC
66 TGTATTAGCC
*** *
1375837 AATGATGGAGCATGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTGATGTATTTTGAACGTT
1 AATGATGGAGCATGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTGACACATTTTGAACATT
1375902 TGTATTAGCC
66 TGTATTAGCC
* * * *
1375912 AATGTTGGGGTATGCTGAAAACCCAT
1 AATGATGGAGCATGCTGAAAGCCCAT
1375938 ATCATCTTAT
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 90 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (75 bp):
AATGATGGAGCATGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTGACACATTTTGAACATT
TGTATTAGCC
Found at i:1377713 original size:45 final size:45
Alignment explanation
Indices: 1377649--1377999 Score: 648
Period size: 45 Copynumber: 7.8 Consensus size: 45
1377639 CTATTTCCCA
* *
1377649 CATCTGTAAACCCTTCAGTGCATGATGTTCTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1377694 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1377739 CATATGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1377784 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1377829 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
1377875 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1377920 CATCTGTAAGCCCTTCAGTGCATGAAGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
1377966 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
1378000 CATTTCCATC
Statistics
Matches: 298, Mismatches: 6, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
45 209 0.70
46 89 0.30
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:1377806 original size:90 final size:91
Alignment explanation
Indices: 1377649--1377999 Score: 652
Period size: 91 Copynumber: 3.9 Consensus size: 91
1377639 CTATTTCCCA
* *
1377649 CATCTGTAAACCCTTCAGTGCATGATGTTCTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1377713 GCATGATGTTTTCAAAACCTTCGGGT
66 GCATGATGTTTTCAAAACCTTCGGGT
*
1377739 CATATGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1377803 GCATGATGTTTTCAAAACCTTCGGGT
66 GCATGATGTTTTCAAAACCTTCGGGT
1377829 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1377894 GCATGATGTTTTCAAAACCTTCGGGT
66 GCATGATGTTTTCAAAACCTTCGGGT
*
1377920 CATCTGTAAGCCCTTCAGTGCATGAAGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1377985 GCATGATGTTTTCAA
66 GCATGATGTTTTCAA
1378000 CATTTCCATC
Statistics
Matches: 255, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
90 118 0.46
91 137 0.54
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (91 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
GCATGATGTTTTCAAAACCTTCGGGT
Found at i:1378133 original size:3 final size:3
Alignment explanation
Indices: 1378125--1378203 Score: 115
Period size: 3 Copynumber: 26.0 Consensus size: 3
1378115 CAGTTTTCTT
* *
1378125 TTA TTA TTA TTA TTA TTTA TT- TTA TCA TTA TTA TTA TTA TTA TACA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
1378171 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1378204 AATAATTATA
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
2 2 0.03
3 62 0.90
4 5 0.07
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1380066 original size:24 final size:24
Alignment explanation
Indices: 1380034--1380096 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
1380024 CTTATTTATA
* * *
1380034 TATATTAATAGGTTTTCTTAAAAT
1 TATAGTAATAGATTTCCTTAAAAT
1380058 TATAGTAATAGATTTCCTTAAAAT
1 TATAGTAATAGATTTCCTTAAAAT
1380082 TATAGTAATAGATTT
1 TATAGTAATAGATTT
1380097 GAAATAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.46
Consensus pattern (24 bp):
TATAGTAATAGATTTCCTTAAAAT
Found at i:1380105 original size:24 final size:24
Alignment explanation
Indices: 1380052--1380104 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1380042 TAGGTTTTCT
***
1380052 TAAAATTATAGTAATAGATTTCCT
1 TAAAATTATAGTAATAGATTTAAA
1380076 TAAAATTATAGTAATAGATTTGAAA
1 TAAAATTATAGTAATAGATTT-AAA
1380101 TAAA
1 TAAA
1380105 TAAGATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (24 bp):
TAAAATTATAGTAATAGATTTAAA
Found at i:1380514 original size:16 final size:18
Alignment explanation
Indices: 1380489--1380525 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
1380479 AGTTATTAAT
1380489 ATTTTAAAACTCAAAT-A
1 ATTTTAAAACTCAAATCA
*
1380506 ATTTT-AAACTTAAATCA
1 ATTTTAAAACTCAAATCA
1380523 ATT
1 ATT
1380526 AAAGTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTTTAAAACTCAAATCA
Found at i:1380684 original size:23 final size:23
Alignment explanation
Indices: 1380636--1380684 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1380626 TGTTGTTTAC
* *
1380636 GTTCGTTTACGTTCATTTATTGT
1 GTTCGATTACGTTCATTTATTAT
* *
1380659 GTTCGATTATGTTCATTTGTTAT
1 GTTCGATTACGTTCATTTATTAT
1380682 GTT
1 GTT
1380685 TGTGTGGTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.14, C:0.10, G:0.18, T:0.57
Consensus pattern (23 bp):
GTTCGATTACGTTCATTTATTAT
Found at i:1388621 original size:37 final size:37
Alignment explanation
Indices: 1388552--1388623 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
1388542 CTTTGAGTTA
* *
1388552 TAATTTCATAAACTCGTCTCAAATTAACTTCAAGTGT
1 TAATTTCATAAACTCGACTCAAATAAACTTCAAGTGT
*
1388589 TAATTTCATAAACTCGACTC-AATAAAATTTCAAGT
1 TAATTTCATAAACTCGACTCAAAT-AAACTTCAAGT
1388624 TCATATTGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 3 0.10
37 28 0.90
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (37 bp):
TAATTTCATAAACTCGACTCAAATAAACTTCAAGTGT
Found at i:1413706 original size:2 final size:2
Alignment explanation
Indices: 1413699--1413742 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
1413689 CAACATTTTA
1413699 AT AT AT AT AT AT A- AT AT -T 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
1413739 AT AT
1 AT AT
1413743 TTTGCACCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1415268 original size:20 final size:20
Alignment explanation
Indices: 1415243--1415335 Score: 87
Period size: 21 Copynumber: 4.5 Consensus size: 20
1415233 TTTTCCCAAT
*
1415243 TCGCAATTCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1415263 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1415284 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1415304 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1415325 TCGCAATGCGA
1 TCGCAATGCGA
1415336 TACTTACTAT
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 26 0.46
21 31 0.54
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1415286 original size:21 final size:21
Alignment explanation
Indices: 1415260--1415335 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1415250 TCGAATAAGT
1415260 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
1415281 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
1415301 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
1415322 AAATCGCAATGCGA
1 AAATCGCAACGCGA
1415336 TACTTACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:1415300 original size:41 final size:41
Alignment explanation
Indices: 1415243--1415335 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
1415233 TTTTCCCAAT
*
1415243 TCGCAATTCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1415284 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1415325 TCGCAATGCGA
1 TCGCAATGCGA
1415336 TACTTACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1415348 original size:41 final size:41
Alignment explanation
Indices: 1415262--1415396 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
1415252 GAATAAGTAA
** *
1415262 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
1415303 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * * *
1415344 ATCGCAATGCGATAAT-ACAAAATCGCAACGTGATACTGACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
1415385 TTCGCAACGCGA
1 ATCGCAACGCGA
1415397 TTCTGACTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 5 0.06
41 73 0.91
42 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:1415418 original size:20 final size:20
Alignment explanation
Indices: 1415366--1415418 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1415356 TAATACAAAA
* *
1415366 TCGCAACGTGATACTGACTT
1 TCGCAACGCGATTCTGACTT
1415386 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
1415406 TCGCAACGCGATT
1 TCGCAACGCGATT
1415419 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:1415977 original size:18 final size:18
Alignment explanation
Indices: 1415918--1415997 Score: 87
Period size: 18 Copynumber: 4.5 Consensus size: 18
1415908 TTCGAGAATG
1415918 AAAATCGCAACGCGGAAAT
1 AAAATCGCAACGC-GAAAT
*
1415937 AACTATCGCAA-G-GAAAT
1 AA-AATCGCAACGCGAAAT
1415954 --AATCGCAACGCGAAAT
1 AAAATCGCAACGCGAAAT
*
1415970 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAA-T
1415989 AAAATCGCA
1 AAAATCGCA
1415998 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
14 7 0.13
15 1 0.02
16 5 0.10
17 5 0.10
18 15 0.29
19 12 0.23
20 7 0.13
ACGTcount: A:0.47, C:0.24, G:0.17, T:0.11
Consensus pattern (18 bp):
AAAATCGCAACGCGAAAT
Found at i:1416015 original size:19 final size:19
Alignment explanation
Indices: 1415993--1416176 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
1415983 GAAACCAAAA
*
1415993 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1416012 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1416031 TCGCGTTGCGATTTT-ATT
1 TCGCGTTGCGATTTTCATT
1416049 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1416069 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1416085 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1416102 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1416116 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1416135 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1416155 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1416175 TC
1 TC
1416177 AATCAAAAGA
Statistics
Matches: 138, Mismatches: 13, Indels: 28
0.77 0.07 0.16
Matches are distributed among these distances:
14 20 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 8 0.06
19 64 0.46
20 38 0.28
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1416101 original size:33 final size:33
Alignment explanation
Indices: 1416064--1416151 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
1416054 GTTGCGATTT
* *
1416064 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
1416097 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1416130 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
1416152 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:1416153 original size:20 final size:20
Alignment explanation
Indices: 1416119--1416176 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1416109 GCGATTCTCT
**
1416119 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
1416139 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
1416159 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1416177 AATCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:1418227 original size:42 final size:42
Alignment explanation
Indices: 1418167--1418289 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
1418157 GCCCGACTCG
* * *
1418167 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
1418209 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
1418251 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
1418290 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1418247 original size:21 final size:21
Alignment explanation
Indices: 1418223--1418289 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1418213 TCATTCCTCG
1418223 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1418244 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1418265 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1418286 AGAG
1 AGAG
1418290 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1419630 original size:14 final size:14
Alignment explanation
Indices: 1419611--1419646 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1419601 GATTGTTTAA
1419611 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1419625 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1419639 TGATTTGT
1 TGATTTGT
1419647 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1419825 original size:19 final size:18
Alignment explanation
Indices: 1419783--1419821 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1419773 GCAACGAGAG
1419783 AATCGCAACGCGAAATAA
1 AATCGCAACGCGAAATAA
*
1419801 AATCGCAACGCGAAATTA
1 AATCGCAACGCGAAATAA
1419819 AAT
1 AAT
1419822 TCGCGTTGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.15, T:0.15
Consensus pattern (18 bp):
AATCGCAACGCGAAATAA
Found at i:1419940 original size:65 final size:67
Alignment explanation
Indices: 1419818--1419950 Score: 225
Period size: 65 Copynumber: 2.0 Consensus size: 67
1419808 ACGCGAAATT
* *
1419818 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTTCCCTCGTTGCGATTTTCATTTCGCATTG
1 AAATTAGCGTTGCGATTTTCATTTCACATTGCGATTTCCCTCGTTGCGATTTTCATTTCGCATTG
1419883 CG
66 CG
*
1419885 AAATTAGCGTTGCGA-TTTCATTTCACATTGCGA-TTCTCTCGTTGCGATTTTCATTTCGCATTG
1 AAATTAGCGTTGCGATTTTCATTTCACATTGCGATTTCCCTCGTTGCGATTTTCATTTCGCATTG
1419948 CG
66 CG
1419950 A
1 A
1419951 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
65 32 0.51
66 17 0.27
67 14 0.22
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (67 bp):
AAATTAGCGTTGCGATTTTCATTTCACATTGCGATTTCCCTCGTTGCGATTTTCATTTCGCATTG
CG
Found at i:1419951 original size:33 final size:33
Alignment explanation
Indices: 1419825--1419951 Score: 177
Period size: 34 Copynumber: 3.8 Consensus size: 33
1419815 ATTAAATTCG
*
1419825 CGTTGCGATTTTCATTTCGCATTGCGATTTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGA-TTCTCT
* **
1419859 CGTTGCGATTTTCATTTCGCATTGCGAAAT-TAG
1 CGTTGCGATTTTCATTTCGCATTGCG-ATTCTCT
*
1419892 CGTTGCGA-TTTCATTTCACATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1419924 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1419952 AGTAATTTCC
Statistics
Matches: 81, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
31 2 0.02
32 25 0.31
33 26 0.32
34 27 0.33
35 1 0.01
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1422231 original size:12 final size:12
Alignment explanation
Indices: 1422214--1422238 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1422204 TCTTCGGGGA
1422214 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1422226 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1422238 C
1 C
1422239 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
Done.