Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006398.1 Hibiscus syriacus cultivar Beakdansim tig00015418_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: 206244
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:1571 original size:40 final size:41
Alignment explanation
Indices: 1489--1573 Score: 154
Period size: 41 Copynumber: 2.1 Consensus size: 41
1479 TTCGCGAAGT
*
1489 ACGTTCCTTTATATATGAGAGTTCGCATAGATTTTCAATTC
1 ACGTTCCTTTATATATGAGAGTTCGCATAGATCTTCAATTC
1530 ACGTTCCTTTATATATGAGAGTTCGC-TAGATCTTCAATTC
1 ACGTTCCTTTATATATGAGAGTTCGCATAGATCTTCAATTC
1570 ACGT
1 ACGT
1574 CTCTGAAGAT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 17 0.40
41 26 0.60
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (41 bp):
ACGTTCCTTTATATATGAGAGTTCGCATAGATCTTCAATTC
Found at i:6508 original size:34 final size:33
Alignment explanation
Indices: 6464--6552 Score: 99
Period size: 34 Copynumber: 2.6 Consensus size: 33
6454 AATGAGTTTG
*
6464 AAAA-AGTGGGTTAACGGGGGTTTGAGAAGAAGA
1 AAAAGAGTGGGTTAACGGGGGTGTGA-AAGAAGA
*
6497 AAAAGAGTGGGTTTAACGGGGGTGTGACAGAAGA
1 AAAAGAGTGGG-TTAACGGGGGTGTGAAAGAAGA
* * *
6531 AGAAGAATGGAGTTAATGGGGG
1 AAAAGAGTGG-GTTAACGGGGG
6553 GGGGGGGGGG
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
33 4 0.08
34 29 0.60
35 15 0.31
ACGTcount: A:0.37, C:0.03, G:0.42, T:0.18
Consensus pattern (33 bp):
AAAAGAGTGGGTTAACGGGGGTGTGAAAGAAGA
Found at i:6516 original size:35 final size:34
Alignment explanation
Indices: 6464--6534 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 34
6454 AATGAGTTTG
*
6464 AAAAAGTGGGTTAACGGGGGTTTG-AGAAGAAGA
1 AAAAAGTGGGTTAACGGGGGTGTGAAGAAGAAGA
6497 AAAAGAGTGGGTTTAACGGGGGTGTGACAGAAGAAGA
1 AAAA-AGTGGG-TTAACGGGGGTGTGA-AGAAGAAGA
6534 A
1 A
6535 GAATGGAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
33 4 0.12
34 6 0.18
35 13 0.39
37 10 0.30
ACGTcount: A:0.39, C:0.04, G:0.39, T:0.17
Consensus pattern (34 bp):
AAAAAGTGGGTTAACGGGGGTGTGAAGAAGAAGA
Found at i:9954 original size:23 final size:22
Alignment explanation
Indices: 9920--9967 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
9910 TTATATTTTC
9920 AATTTTGTAAAAAAAATTATATA
1 AATTTTGTAAAAAAAA-TATATA
*
9943 AATTTT-TAAAAAATATATATA
1 AATTTTGTAAAAAAAATATATA
9964 AATT
1 AATT
9968 AATTATAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 10 0.42
22 8 0.33
23 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
AATTTTGTAAAAAAAATATATA
Found at i:19991 original size:59 final size:60
Alignment explanation
Indices: 19918--20053 Score: 159
Period size: 60 Copynumber: 2.3 Consensus size: 60
19908 ATAGTTGAGT
* * * * ** *
19918 GACCATTTTATAACTTTTAATAGTCGAG-GACTCAACAAAGCGACGTCCTATAATTGAAG
1 GACCATTTTGTAACTTTCAATAATCGAGAGACTCAACAAAGCAACACCCTATAATCGAAG
* * *
19977 GACCATTTTGTAACTTTCAATAATCGAGAGACTTAATAAAGCAACACCCTATAATCGATG
1 GACCATTTTGTAACTTTCAATAATCGAGAGACTCAACAAAGCAACACCCTATAATCGAAG
20037 GACCATTTATGT-ACTTT
1 GACCATTT-TGTAACTTT
20054 ACTCTAAAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 25 0.38
60 37 0.57
61 3 0.05
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (60 bp):
GACCATTTTGTAACTTTCAATAATCGAGAGACTCAACAAAGCAACACCCTATAATCGAAG
Found at i:20281 original size:12 final size:12
Alignment explanation
Indices: 20264--20343 Score: 90
Period size: 12 Copynumber: 6.7 Consensus size: 12
20254 TTCACGAACA
20264 AGCTCGTTTATG
1 AGCTCGTTTATG
*
20276 AGCTCGTTTATA
1 AGCTCGTTTATG
*
20288 AGTTCGTTTATG
1 AGCTCGTTTATG
* *
20300 AGCTTGTTTATA
1 AGCTCGTTTATG
*
20312 AGTTCGTTTATG
1 AGCTCGTTTATG
*
20324 AGCTCATTTATCG
1 AGCTCGTTTAT-G
20337 A-CTCGTT
1 AGCTCGTT
20344 CGTTTATATT
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
12 53 0.96
13 2 0.04
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (12 bp):
AGCTCGTTTATG
Found at i:20297 original size:24 final size:24
Alignment explanation
Indices: 20267--20334 Score: 118
Period size: 24 Copynumber: 2.8 Consensus size: 24
20257 ACGAACAAGC
20267 TCGTTTATGAGCTCGTTTATAAGT
1 TCGTTTATGAGCTCGTTTATAAGT
*
20291 TCGTTTATGAGCTTGTTTATAAGT
1 TCGTTTATGAGCTCGTTTATAAGT
*
20315 TCGTTTATGAGCTCATTTAT
1 TCGTTTATGAGCTCGTTTAT
20335 CGACTCGTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.49
Consensus pattern (24 bp):
TCGTTTATGAGCTCGTTTATAAGT
Found at i:21287 original size:2 final size:2
Alignment explanation
Indices: 21280--21307 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21270 GTTTAAGCTA
21280 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
21308 TAAAATTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22820 original size:25 final size:25
Alignment explanation
Indices: 22790--22842 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
22780 TTTACTTGTA
22790 AAGAAAGTTCTAATGAAATTGATTT
1 AAGAAAGTTCTAATGAAATTGATTT
22815 AAGAAAGTTCTAATGAAATTGATTT
1 AAGAAAGTTCTAATGAAATTGATTT
22840 AAG
1 AAG
22843 TGATAGGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (25 bp):
AAGAAAGTTCTAATGAAATTGATTT
Found at i:27177 original size:24 final size:23
Alignment explanation
Indices: 27150--27215 Score: 105
Period size: 24 Copynumber: 2.8 Consensus size: 23
27140 TTACCCTTGT
*
27150 TTATTTCTAGTGTCAGTTTCACCC
1 TTATTTGTAGTGTCAGTTT-ACCC
27174 TTATTTGTAGTGTCAGTGTTACCC
1 TTATTTGTAGTGTCAGT-TTACCC
27198 TTATTTGTAGTGTCAGTT
1 TTATTTGTAGTGTCAGTT
27216 GTTCTTTAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
23 1 0.03
24 37 0.93
25 2 0.05
ACGTcount: A:0.17, C:0.17, G:0.18, T:0.48
Consensus pattern (23 bp):
TTATTTGTAGTGTCAGTTTACCC
Found at i:30421 original size:50 final size:50
Alignment explanation
Indices: 30367--30527 Score: 234
Period size: 50 Copynumber: 3.2 Consensus size: 50
30357 GAATGGGTTT
* * * *
30367 GTGTTCGTTTATTTATTGTTCGCGAACATGTTCCTTTAATGTTCGAGAAT
1 GTGTTCGTTTATTTATTATTCGCGAATATGTTCATTTAATGTTCGAGAAC
* * *
30417 GTGTTTGTTTATTTATTATTCGCGAATATGTTCGTTTAATGTTCGGGAAC
1 GTGTTCGTTTATTTATTATTCGCGAATATGTTCATTTAATGTTCGAGAAC
*
30467 GTGTTCGTTTATTTATTATTCGTGAATATGTTCATTTAATGTTC-ATGAAC
1 GTGTTCGTTTATTTATTATTCGCGAATATGTTCATTTAATGTTCGA-GAAC
30517 GTGTTCGTTTA
1 GTGTTCGTTTA
30528 ATATTCATGA
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
50 100 1.00
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.48
Consensus pattern (50 bp):
GTGTTCGTTTATTTATTATTCGCGAATATGTTCATTTAATGTTCGAGAAC
Found at i:30427 original size:23 final size:23
Alignment explanation
Indices: 30395--30529 Score: 74
Period size: 23 Copynumber: 5.5 Consensus size: 23
30385 TTCGCGAACA
*
30395 TGTTCCTTTAATGTTCGAGAATG
1 TGTTCGTTTAATGTTCGAGAATG
* * * *
30418 TGTTTGTTTATTTATTATTCGCGAATA
1 TGTTCGTTTA---A-TGTTCGAGAATG
* *
30445 TGTTCGTTTAATGTTCGGGAACG
1 TGTTCGTTTAATGTTCGAGAATG
* * *
30468 TGTTCGTTTATTTATTATTCGTGAATA
1 TGTTCGTTTA---A-TGTTCGAGAATG
* *
30495 TGTTCATTTAATGTTC-ATGAACG
1 TGTTCGTTTAATGTTCGA-GAATG
30518 TGTTCGTTTAAT
1 TGTTCGTTTAAT
30530 ATTCATGAAC
Statistics
Matches: 83, Mismatches: 20, Indels: 18
0.69 0.17 0.15
Matches are distributed among these distances:
23 44 0.53
24 2 0.02
26 2 0.02
27 35 0.42
ACGTcount: A:0.21, C:0.10, G:0.19, T:0.49
Consensus pattern (23 bp):
TGTTCGTTTAATGTTCGAGAATG
Found at i:30438 original size:27 final size:27
Alignment explanation
Indices: 30368--30504 Score: 92
Period size: 27 Copynumber: 5.4 Consensus size: 27
30358 AATGGGTTTG
* * *
30368 TGTTCGTTTATTTATTGTTCGCGAACA
1 TGTTCGTTTATTTATTATTCGAGAATA
* * *
30395 TGTTCCTTTA---A-TGTTCGAGAATG
1 TGTTCGTTTATTTATTATTCGAGAATA
* *
30418 TGTTTGTTTATTTATTATTCGCGAATA
1 TGTTCGTTTATTTATTATTCGAGAATA
* * **
30445 TGTTCGTTTA---A-TGTTCGGGAACG
1 TGTTCGTTTATTTATTATTCGAGAATA
*
30468 TGTTCGTTTATTTATTATTCGTGAATA
1 TGTTCGTTTATTTATTATTCGAGAATA
*
30495 TGTTCATTTA
1 TGTTCGTTTA
30505 ATGTTCATGA
Statistics
Matches: 83, Mismatches: 19, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
23 35 0.42
24 2 0.02
26 2 0.02
27 44 0.53
ACGTcount: A:0.20, C:0.11, G:0.19, T:0.50
Consensus pattern (27 bp):
TGTTCGTTTATTTATTATTCGAGAATA
Found at i:30534 original size:23 final size:23
Alignment explanation
Indices: 30445--30566 Score: 91
Period size: 23 Copynumber: 5.1 Consensus size: 23
30435 TTCGCGAATA
**
30445 TGTTCGTTTAATGTTCGGGAACG
1 TGTTCGTTTAATGTTCATGAACG
* * **
30468 TGTTCGTTTATTTATTATTCGTGAATA
1 TGTTCGTTTA---A-TGTTCATGAACG
*
30495 TGTTCATTTAATGTTCATGAACG
1 TGTTCGTTTAATGTTCATGAACG
* *
30518 TGTTCGTTTAATATTCATGAACA
1 TGTTCGTTTAATGTTCATGAACG
* * *
30541 TATTCATTTATATGTTCACGAACG
1 TGTTCGTTTA-ATGTTCATGAACG
30565 TG
1 TG
30567 CTTATTTAGC
Statistics
Matches: 76, Mismatches: 18, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
23 46 0.61
24 12 0.16
26 1 0.01
27 17 0.22
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.45
Consensus pattern (23 bp):
TGTTCGTTTAATGTTCATGAACG
Found at i:30550 original size:46 final size:48
Alignment explanation
Indices: 30367--30566 Score: 145
Period size: 50 Copynumber: 4.1 Consensus size: 48
30357 GAATGGGTTT
* ** * * *
30367 GTGTTCGTTTATTTATTGTTCGCGAACATGTTCCTTTAATGTTCGA-GAAT
1 GTGTTCGTTTA--TATTATTCATGAACATATTCATTTAATGTTC-ACGAAC
* ** * * * **
30417 GTGTTTGTTTATTTATTATTCGCGAATATGTTCGTTTAATGTTCGGGAAC
1 GTGTTCGTTTA--TATTATTCATGAACATATTCATTTAATGTTCACGAAC
* * * *
30467 GTGTTCGTTTATTTATTATTCGTGAATATGTTCATTTAATGTTCATGAAC
1 GTGTTCGTTTA--TATTATTCATGAACATATTCATTTAATGTTCACGAAC
30517 GTGTTCGTTTA-A-TATTCATGAACATATTCATTTATATGTTCACGAAC
1 GTGTTCGTTTATATTATTCATGAACATATTCATTTA-ATGTTCACGAAC
30564 GTG
1 GTG
30567 CTTATTTAGC
Statistics
Matches: 133, Mismatches: 15, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
46 19 0.14
47 15 0.11
50 99 0.74
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (48 bp):
GTGTTCGTTTATATTATTCATGAACATATTCATTTAATGTTCACGAAC
Found at i:31528 original size:25 final size:25
Alignment explanation
Indices: 31494--31545 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
31484 GTATATATTT
*
31494 AAAAACTCTTATTCATTTGACAATG
1 AAAAACTCTTAATCATTTGACAATG
31519 AAAAACTCTTAATCATTTGACAATG
1 AAAAACTCTTAATCATTTGACAATG
31544 AA
1 AA
31546 CGTTTATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (25 bp):
AAAAACTCTTAATCATTTGACAATG
Found at i:34222 original size:74 final size:73
Alignment explanation
Indices: 34142--34350 Score: 255
Period size: 73 Copynumber: 2.8 Consensus size: 73
34132 ATAATATATG
* * *
34142 TATCGATATTTTAACAATTGATCATCTTCATCGACTTTTTCAATATATAAAAGTATCTATCATAA
1 TATCGATATTTTAACATTTGATCATCTT-ATCAACTTTTTCAATATTTAAAAGTATCTATCATAA
34207 TCGCATAAA
65 TCGCATAAA
* * *
34216 TATCGATATTTTAA-ATTTTGATCATTTTATCAACTTTTTCAATATTTAAAAGTATCAATCATTA
1 TATCGATATTTTAACA-TTTGATCATCTTATCAACTTTTTCAATATTTAAAAGTATCTATCATAA
* *
34280 TTGCATTAA
65 TCGCATAAA
* *
34289 TATCGTTTTTTTAAC-TTTCGATCTTATCTT-T-AACTTTTTCAATATTTAAAAGTATCTATCAT
1 TATCGATATTTTAACATTT-GATC--ATCTTATCAACTTTTTCAATATTTAAAAGTATCTATCAT
34351 CATATATCAA
Statistics
Matches: 118, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
72 3 0.03
73 86 0.73
74 25 0.21
75 4 0.03
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (73 bp):
TATCGATATTTTAACATTTGATCATCTTATCAACTTTTTCAATATTTAAAAGTATCTATCATAAT
CGCATAAA
Found at i:34366 original size:73 final size:70
Alignment explanation
Indices: 34129--34382 Score: 210
Period size: 73 Copynumber: 3.5 Consensus size: 70
34119 AGTGTTTAAC
* * * * *
34129 ATCATAA-TATATGTATCGATATTTTAACAATT-GATCATCTTCATCGACTTTTTCAATATATAA
1 ATCATAATTATA-ATATCGATATTTTAA-ATTTCGATCAT-TTTATCAACTTTTTCAATATTTAA
34192 AAGTATCT
63 AAGTATCT
* *
34200 ATCATAATCGCATAAATATCGATATTTTAAATTTTGATCATTTTATCAACTTTTTCAATATTTAA
1 ATCATAAT--TAT-AATATCGATATTTTAAATTTCGATCATTTTATCAACTTTTTCAATATTTAA
*
34265 AAGTATCA
63 AAGTATCT
* * * * *
34273 ATCATTATTGCATTAATATCGTTTTTTTAACTTTCGATC-TTATCT-TTAACTTTTTCAATATTT
1 ATCATAATT--A-TAATATCGATATTTTAAATTTCGATCATT-T-TATCAACTTTTTCAATATTT
34336 AAAAGTATCT
61 AAAAGTATCT
* * *
34346 ATCATCATATATCAAGTATCGATATTTAAAATATCGA
1 ATCATAAT-TAT-AA-TATCGATATTTTAAATTTCGA
34383 AATGCTTTCT
Statistics
Matches: 149, Mismatches: 21, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
71 8 0.05
72 5 0.03
73 110 0.74
74 25 0.17
75 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.44
Consensus pattern (70 bp):
ATCATAATTATAATATCGATATTTTAAATTTCGATCATTTTATCAACTTTTTCAATATTTAAAAG
TATCT
Found at i:34918 original size:187 final size:183
Alignment explanation
Indices: 34523--35100 Score: 653
Period size: 188 Copynumber: 3.1 Consensus size: 183
34513 AAAGCTAAAG
* *
34523 TAACATTTTAGGCTCAATCCATTTTATTAATAAAAATATTAACATTTCATATCGCAACCTAATTT
1 TAACATTTTAGGCTCAATCCATTTTATTAATAAAAATATTAACATTTCA-ATCACAACCTTATTT
* * * * * *
34588 TTTAGTTAATTATGACATTCTTGGACGCAACAGTATTTAATATAGATTTTTATAACATTTTTCGC
65 TTTAGTAAACTATGACATTCTTGGGCGCAACAGTA-TTATTATAGATATTCATAACA-TTTTCGC
* *
34653 --CAACTTATTTTGTTATCGTGAGAAAATCTAAGGTTCCATCAGGTTAAACTCT-A
128 TTTAACTTATTTTGTTATCGTGAGAAAATCTAAGGTTCCATCAGCTTAAACTCTGA
* * *
34706 GTAACATTTTAGGCTCAACCCATTTTATTAATAAAAA-AGTTAACATTTGAGATCACAACCTTCT
1 -TAACATTTTAGGCTCAATCCATTTTATTAATAAAAATA-TTAACATTTCA-ATCACAACCTTAT
* * *
34770 TTCTTAGTAAACTATGACATTCTTGGGCGCAACCGTATGTATTATAGATATTCATAATATTTTCG
63 TTTTTAGTAAACTATGACATTCTTGGGCGCAACAGTAT-TATTATAGATATTCATAACATTTTC-
* *
34835 GCTTTTAACTTATTTTGTTATCGTGAGAAAATCTAAGGTTCCATTAGCTTAAACTATGA
126 GC-TTTAACTTATTTTGTTATCGTGAGAAAATCTAAGGTTCCATCAGCTTAAACTCTGA
* * * * *
34894 TAACATTTTAGGCGCAGTCCATTTTATTATTAAAAATATTAACATTCCAACTCACAACCTATTTT
1 TAACATTTTAGGCTCAATCCATTTTATTAATAAAAATATTAACATTTCAA-TCACAACCT-TATT
* * * * *
34959 TTTTAGTGAACCATGATATTATTGGGCGCAACTA-TATTCATTATAGATATTCATTACATTTTCA
64 TTTTAGTAAACTATGACATTCTTGGGCGCAAC-AGTATT-ATTATAGATATTCATAACATTTTC-
* * * * * ** * *
35023 AGATTTAACGTATTTTGTTATGGTGACAAAATTTAAGGTTTTATCAACTTAAATTCTGA
126 -GCTTTAACTTATTTTGTTATCGTGAGAAAATCTAAGGTTCCATCAGCTTAAACTCTGA
35082 TAACATTTTAGGCTCAATC
1 TAACATTTTAGGCTCAATC
35101 TAAAATATTA
Statistics
Matches: 333, Mismatches: 48, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
183 7 0.02
184 105 0.32
186 1 0.00
187 99 0.30
188 120 0.36
189 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (183 bp):
TAACATTTTAGGCTCAATCCATTTTATTAATAAAAATATTAACATTTCAATCACAACCTTATTTT
TTAGTAAACTATGACATTCTTGGGCGCAACAGTATTATTATAGATATTCATAACATTTTCGCTTT
AACTTATTTTGTTATCGTGAGAAAATCTAAGGTTCCATCAGCTTAAACTCTGA
Found at i:36391 original size:2 final size:2
Alignment explanation
Indices: 36384--36415 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
36374 TAGCAATCAA
36384 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
36416 TGTATTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36465 original size:25 final size:25
Alignment explanation
Indices: 36400--36476 Score: 68
Period size: 25 Copynumber: 3.0 Consensus size: 25
36390 ATATATATAT
* *
36400 ATATATATATATATATTGTATTTAAA
1 ATAT-TATATATTTATTTTATTTAAA
*
36426 TTAATT-TAT-TATTATTTTATTTAAA
1 AT-ATTATATAT-TTATTTTATTTAAA
*
36451 ATATTATATATTTATATTTTTTTAAA
1 ATATTATATATTTAT-TTTATTTAAA
36477 TTTGTATAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
24 4 0.10
25 23 0.56
26 12 0.29
27 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (25 bp):
ATATTATATATTTATTTTATTTAAA
Found at i:40184 original size:17 final size:16
Alignment explanation
Indices: 40162--40197 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
40152 ATTTAAAGAT
*
40162 AAAATATTTTAAAATTA
1 AAAATA-TTCAAAATTA
40179 AAAATATTCAAAATTA
1 AAAATATTCAAAATTA
40195 AAA
1 AAA
40198 CACCATTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATATTCAAAATTA
Found at i:43005 original size:9 final size:8
Alignment explanation
Indices: 42986--43010 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
42976 AATTATAATA
42986 TTTTTTAT
1 TTTTTTAT
42994 TTTTTTAT
1 TTTTTTAT
43002 TTTTTTAT
1 TTTTTTAT
43010 T
1 T
43011 AAAATGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTAT
Found at i:43079 original size:2 final size:2
Alignment explanation
Indices: 43074--43105 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
43064 TTTGTGTGTG
43074 TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
43106 TATCATATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43753 original size:22 final size:23
Alignment explanation
Indices: 43709--43765 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
43699 GTTAAATTAC
*
43709 ATTTAAATTTTTAACTAATTTATA
1 ATTT-AATATTTAACTAATTTATA
*
43733 A-TTATATATTTAA-TACTTTATA
1 ATTTA-ATATTTAACTAATTTATA
43755 ATTTAATATTT
1 ATTTAATATTT
43766 TATAAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 16 0.55
23 12 0.41
24 1 0.03
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTAATATTTAACTAATTTATA
Found at i:43760 original size:15 final size:15
Alignment explanation
Indices: 43734--43776 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
43724 TAATTTATAA
43734 TTATATATTTAATACT
1 TTATA-ATTTAATACT
*
43750 TTATAATTTAATATT
1 TTATAATTTAATACT
*
43765 TTATAAATTAAT
1 TTATAATTTAAT
43777 TTATTGGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATAATTTAATACT
Found at i:47018 original size:9 final size:8
Alignment explanation
Indices: 46989--47015 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
46979 TCAAAAAATC
46989 AAATATTA
1 AAATATTA
46997 AAATATTA
1 AAATATTA
47005 AAATATTA
1 AAATATTA
47013 AAA
1 AAA
47016 ATAAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAATATTA
Found at i:47025 original size:16 final size:16
Alignment explanation
Indices: 46959--47018 Score: 52
Period size: 17 Copynumber: 3.7 Consensus size: 16
46949 ACAATTTTAT
46959 ATATAAAAATATTCAAA
1 ATATAAAAATATT-AAA
* *
46976 AAATCAAAAA-A-TCAA
1 ATAT-AAAAATATTAAA
*
46991 ATATTAAAATATTAAA
1 ATATAAAAATATTAAA
47007 ATATTAAAAATA
1 ATA-TAAAAATA
47019 AAAAATACTA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
14 4 0.12
15 6 0.18
16 7 0.21
17 11 0.33
18 5 0.15
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (16 bp):
ATATAAAAATATTAAA
Found at i:47096 original size:21 final size:21
Alignment explanation
Indices: 47053--47096 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
47043 TGTATATGTA
**
47053 TATTAAAAATGAAAAAGTTAT
1 TATTAAAAATGAAAAAGAAAT
*
47074 TATTAAAAATTAAAAAGAAAT
1 TATTAAAAATGAAAAAGAAAT
47095 TA
1 TA
47097 AATATACCGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (21 bp):
TATTAAAAATGAAAAAGAAAT
Found at i:47608 original size:2 final size:2
Alignment explanation
Indices: 47601--47631 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
47591 CTTAGCTTAT
47601 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47632 TAAGTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47752 original size:16 final size:15
Alignment explanation
Indices: 47731--47769 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
47721 TTATTTTTGG
47731 AATATTTGAATATTTA
1 AATATTT-AATATTTA
*
47747 AATATTTTATATTTA
1 AATATTTAATATTTA
47762 AA-ATTTAA
1 AATATTTAA
47770 AATAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 5 0.24
15 9 0.43
16 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
AATATTTAATATTTA
Found at i:47772 original size:23 final size:24
Alignment explanation
Indices: 47732--47783 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
47722 TATTTTTGGA
*
47732 ATATTTGAATATTTAAAT-ATTTT
1 ATATTTGAAAATTTAAATAATTTT
47755 ATATTT-AAAATTTAAAATAATTTT
1 ATATTTGAAAATTT-AAATAATTTT
47779 -TATTT
1 ATATTT
47784 TTAAATAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 6 0.23
23 15 0.58
24 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
ATATTTGAAAATTTAAATAATTTT
Found at i:48415 original size:15 final size:15
Alignment explanation
Indices: 48383--48448 Score: 75
Period size: 14 Copynumber: 4.5 Consensus size: 15
48373 TTCTAATTTC
48383 ATTTTTATAAATA-T-
1 ATTTTTA-AAATATTA
48397 ATTTTTAAAATATTA
1 ATTTTTAAAATATTA
* *
48412 A-TTTTAAAATTTTT
1 ATTTTTAAAATATTA
48426 ATTTTTAAAATATATA
1 ATTTTTAAAATAT-TA
48442 ATTTTTA
1 ATTTTTA
48449 TTTTGAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
13 5 0.11
14 20 0.45
15 11 0.25
16 8 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTTTAAAATATTA
Found at i:67363 original size:2 final size:2
Alignment explanation
Indices: 67356--67386 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
67346 ATGTCTGTTC
67356 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 A
67387 AATACAGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73756 original size:153 final size:154
Alignment explanation
Indices: 73518--73824 Score: 589
Period size: 153 Copynumber: 2.0 Consensus size: 154
73508 TAGCCTACTA
*
73518 TCTTACCTCCCCCTTACCCTATTACATATGGGAACAAGAGATAACCATTTATGCTATAAACTAAC
1 TCTTACCTCCCCCTTACCCTATTACATATGGGAACAAGAGACAACCATTTATGCTATAAACTAAC
73583 ATAAATAGGCATTCTAATTCATGGAGTGGATAGAAAAACACTTTTTACCGGAATCGTTTTTGCCG
66 ATAAATAGGCATTCTAATTCATGGAGTGGATAGAAAAACACTTTTTACCGGAATCGTTTTTGCCG
73648 ACTCATATGTCACATATATAAGAC
131 ACTCATATGTCACATATATAAGAC
73672 TCTTACCT-CCCCTTACCCTATTACATATGGGAACAAGAGACAACCATTTATGCTATAAACTAAC
1 TCTTACCTCCCCCTTACCCTATTACATATGGGAACAAGAGACAACCATTTATGCTATAAACTAAC
*
73736 ATAAATAGGCATTCTAATTCATGGAGTGGATAGAAAAACACTTTTTACCGGAATCGTTTTTGTCG
66 ATAAATAGGCATTCTAATTCATGGAGTGGATAGAAAAACACTTTTTACCGGAATCGTTTTTGCCG
73801 ACTCATATGTCACATATATAAGAC
131 ACTCATATGTCACATATATAAGAC
73825 GCTTTTTATA
Statistics
Matches: 151, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
153 143 0.95
154 8 0.05
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.31
Consensus pattern (154 bp):
TCTTACCTCCCCCTTACCCTATTACATATGGGAACAAGAGACAACCATTTATGCTATAAACTAAC
ATAAATAGGCATTCTAATTCATGGAGTGGATAGAAAAACACTTTTTACCGGAATCGTTTTTGCCG
ACTCATATGTCACATATATAAGAC
Found at i:76976 original size:57 final size:57
Alignment explanation
Indices: 76776--76975 Score: 181
Period size: 59 Copynumber: 3.5 Consensus size: 57
76766 CCTCTACATA
* * * * *
76776 ATCAATAAATTTGCGTGAAGAAGCCTTCACCATATAA-AAATACCT-CTACATAAAAC
1 ATCAAGAACTTTGCGCGAAGAAGCCTTCTCCATATAACAAATACCTACT-TATAAAAC
* * * * * *
76832 ATCGAGAACTTTGCACGAAGAAGCCTTCTCCACATACCAAATACCTTAGCATATAAAGC
1 ATCAAGAACTTTGCGCGAAGAAGCCTTCTCCATATAACAAATACC-TA-CTTATAAAAC
* * ** * *
76891 ATCGAGAACTATGCTTGAAAAAACCTTCGTCC-TATAACAAATACCTACTTATAAAAC
1 ATCAAGAACTTTGCGCGAAGAAGCCTTC-TCCATATAACAAATACCTACTTATAAAAC
*
76948 ATCAAGAACTTTGCGCGAAGAGGCCTTC
1 ATCAAGAACTTTGCGCGAAGAAGCCTTC
76976 GCTCTATAAT
Statistics
Matches: 112, Mismatches: 27, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
56 29 0.26
57 36 0.32
58 3 0.03
59 40 0.36
60 4 0.04
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (57 bp):
ATCAAGAACTTTGCGCGAAGAAGCCTTCTCCATATAACAAATACCTACTTATAAAAC
Found at i:76983 original size:57 final size:56
Alignment explanation
Indices: 76717--76993 Score: 163
Period size: 57 Copynumber: 4.9 Consensus size: 56
76707 TACATCCACT
* * * * * * *
76717 TAAAGCATCAAAAACTTTGTGCGAAGAAACCTTCGCTTTGTAACGAATACCTC-TA
1 TAAAACATCAAGAACTTTGCGCGAAGAAGCCTTCGCTCTATAACAAATACCTCTTA
* * * * * * *
76772 -CATA-ATCAATAAATTTGCGTGAAGAAGCCTTCAC-CATATAA-AAATACCTCTACA
1 TAAAACATCAAGAACTTTGCGCGAAGAAGCCTTCGCTC-TATAACAAATACCTCT-TA
* * * * * *
76826 TAAAACATCGAGAACTTTGCACGAAGAAGCCTTCTC-CACATACCAAATACCTTAGCATA
1 TAAAACATCAAGAACTTTGCGCGAAGAAGCCTTCGCTC-TATAACAAATACC-T--CTTA
* * * ** * *
76885 TAAAGCATCGAGAACTATGCTTGAAAAAACCTTCG-TCCTATAACAAATACCTACTTA
1 TAAAACATCAAGAACTTTGCGCGAAGAAGCCTTCGCT-CTATAACAAATACCT-CTTA
* **
76942 TAAAACATCAAGAACTTTGCGCGAAGAGGCCTTCGCTCTATAATGAATACCT
1 TAAAACATCAAGAACTTTGCGCGAAGAAGCCTTCGCTCTATAACAAATACCT
76994 TCGTACAAAT
Statistics
Matches: 164, Mismatches: 46, Indels: 22
0.71 0.20 0.09
Matches are distributed among these distances:
52 8 0.05
53 28 0.17
54 2 0.01
55 2 0.01
56 29 0.18
57 50 0.30
58 3 0.02
59 40 0.24
60 2 0.01
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (56 bp):
TAAAACATCAAGAACTTTGCGCGAAGAAGCCTTCGCTCTATAACAAATACCTCTTA
Found at i:82439 original size:33 final size:33
Alignment explanation
Indices: 82402--82482 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
82392 AAAAATAAAT
*
82402 CAACGTATTTGAGTCCTATTGAAATACTAAAAC
1 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
82435 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
1 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
*
82468 CGAA-GCATTTGAGTC
1 C-AACGTATTTGAGTC
82483 TAAGTAGGAC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 43 0.96
34 2 0.04
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (33 bp):
CAACGTATTTGAGTCCTATTGAAACACTAAAAC
Found at i:82541 original size:11 final size:11
Alignment explanation
Indices: 82525--82549 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
82515 GTTTCTTTAA
82525 ACTATAAATAG
1 ACTATAAATAG
82536 ACTATAAATAG
1 ACTATAAATAG
82547 ACT
1 ACT
82550 CAAGCATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.28
Consensus pattern (11 bp):
ACTATAAATAG
Found at i:83042 original size:7 final size:7
Alignment explanation
Indices: 83038--83089 Score: 70
Period size: 8 Copynumber: 7.1 Consensus size: 7
83028 ACATTATTTA
83038 TTATTAT
1 TTATTAT
83045 TTATTATT
1 TTATTA-T
83053 TTATGTAT
1 TTAT-TAT
83061 TTATTATT
1 TTATTA-T
83069 TTATTA-
1 TTATTAT
83075 TTATTAT
1 TTATTAT
83082 TTATTAT
1 TTATTAT
83089 T
1 T
83090 CATTTTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
6 6 0.15
7 16 0.39
8 17 0.41
9 2 0.05
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (7 bp):
TTATTAT
Found at i:83043 original size:3 final size:3
Alignment explanation
Indices: 83030--83089 Score: 61
Period size: 3 Copynumber: 19.0 Consensus size: 3
83020 ATGATAATAC
83030 ATT ATTT ATT ATT ATTT ATT ATT -TT ATGT ATTT ATT ATT -TT ATT ATT
1 ATT A-TT ATT ATT A-TT ATT ATT ATT AT-T A-TT ATT ATT ATT ATT ATT
83077 ATT ATTT ATT ATT
1 ATT A-TT ATT ATT
83090 CATTTTTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
2 4 0.08
3 32 0.64
4 13 0.26
5 1 0.02
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:83063 original size:16 final size:15
Alignment explanation
Indices: 83038--83089 Score: 81
Period size: 16 Copynumber: 3.5 Consensus size: 15
83028 ACATTATTTA
83038 TTATTATTTATTATT
1 TTATTATTTATTATT
83053 TTATGTATTTATTATT
1 TTAT-TATTTATTATT
83069 TTATTA-TTATTA-T
1 TTATTATTTATTATT
83082 TTATTATT
1 TTATTATT
83090 CATTTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.20
14 7 0.20
15 6 0.17
16 15 0.43
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTATTATTTATTATT
Found at i:91127 original size:23 final size:23
Alignment explanation
Indices: 91101--91158 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
91091 ACAAAGAAAA
* *
91101 ACGTGCTATAAAGGCAGAAGAAG
1 ACGTGCCATAAAAGCAGAAGAAG
* * *
91124 ACGTACCATAAAAGCATAAGAAT
1 ACGTGCCATAAAAGCAGAAGAAG
91147 ACGTGCCATAAA
1 ACGTGCCATAAA
91159 CGTAGAATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.16
Consensus pattern (23 bp):
ACGTGCCATAAAAGCAGAAGAAG
Found at i:91458 original size:22 final size:22
Alignment explanation
Indices: 91404--91459 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
91394 ATGAATCATT
* *
91404 TAATAAAATTAATTTAATAGTTA
1 TAATCAAATT-ATTTAATAGTAA
*
91427 TAATTAAATTATTTAAT-GTAA
1 TAATCAAATTATTTAATAGTAA
91448 TAATCATAATTA
1 TAATCA-AATTA
91460 AAATAGAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.28
22 12 0.41
23 9 0.31
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (22 bp):
TAATCAAATTATTTAATAGTAA
Found at i:91504 original size:26 final size:27
Alignment explanation
Indices: 91470--91525 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
91460 AAATAGAAAG
* * *
91470 TAAACTTATTAATTTAATTATTATAAT
1 TAAACTTATTAATCTAATGATCATAAT
91497 TAAA-TTATTAATCTAATGATCATAAT
1 TAAACTTATTAATCTAATGATCATAAT
91523 TAA
1 TAA
91526 TAACTTGTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (27 bp):
TAAACTTATTAATCTAATGATCATAAT
Found at i:92594 original size:46 final size:49
Alignment explanation
Indices: 92495--92595 Score: 138
Period size: 46 Copynumber: 2.1 Consensus size: 49
92485 CGTTTGTTAA
*
92495 TTAGTCGAGATAAAATACTCTAAAAAATAATAAAAACCAAAATAACCATT
1 TTAGTCGAGAAAAAATACTC-AAAAAATAATAAAAACCAAAATAACCATT
*
92545 TTAGTCGAGACAAAAATACTC-AAAAA-AAT-AAAA-TAAAATAACCATT
1 TTAGTCGAGA-AAAAATACTCAAAAAATAATAAAAACCAAAATAACCATT
92591 TTAGT
1 TTAGT
92596 AAACCTTGAC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
46 17 0.35
47 4 0.08
48 3 0.06
49 5 0.10
50 10 0.21
51 9 0.19
ACGTcount: A:0.55, C:0.13, G:0.07, T:0.25
Consensus pattern (49 bp):
TTAGTCGAGAAAAAATACTCAAAAAATAATAAAAACCAAAATAACCATT
Found at i:95849 original size:31 final size:31
Alignment explanation
Indices: 95811--95912 Score: 195
Period size: 31 Copynumber: 3.3 Consensus size: 31
95801 TAGTAAAGTA
95811 AGCCAAAAGCTCTTGTTCCCATTGATATTGG
1 AGCCAAAAGCTCTTGTTCCCATTGATATTGG
95842 AGCCAAAAGCTCTTGTTCCCATTGATATTGG
1 AGCCAAAAGCTCTTGTTCCCATTGATATTGG
*
95873 AGCCAAAAGATCTTGTTCCCATTGATATTGG
1 AGCCAAAAGCTCTTGTTCCCATTGATATTGG
95904 AGCCAAAAG
1 AGCCAAAAG
95913 ATCATATCTG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
31 70 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (31 bp):
AGCCAAAAGCTCTTGTTCCCATTGATATTGG
Found at i:100275 original size:32 final size:32
Alignment explanation
Indices: 100234--100298 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
100224 GATCTCGAAA
*
100234 TGAGGAACCAATTCGTGAGGGTTTTCAGAGTT
1 TGAGGAACCAATTCGTGAGGGTTTGCAGAGTT
100266 TGAGGAACCAATTCGTGAGGGTTTGCAGAGTT
1 TGAGGAACCAATTCGTGAGGGTTTGCAGAGTT
100298 T
1 T
100299 AAGGGGGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.12, G:0.32, T:0.31
Consensus pattern (32 bp):
TGAGGAACCAATTCGTGAGGGTTTGCAGAGTT
Found at i:100314 original size:44 final size:44
Alignment explanation
Indices: 100264--100357 Score: 170
Period size: 44 Copynumber: 2.1 Consensus size: 44
100254 GTTTTCAGAG
*
100264 TTTGAGGAACCAATTCGTGAGGGTTTGCAGAGTTTAAGGGGGAA
1 TTTGAGGAACCAATTCGTGAGGGTTTGCAGAGTTTAAGGCGGAA
*
100308 TTTGAGGAACCAATTCGTGAGGGTTTGCAGAGTTTAAGGCGGAG
1 TTTGAGGAACCAATTCGTGAGGGTTTGCAGAGTTTAAGGCGGAA
100352 TTTGAG
1 TTTGAG
100358 AAAGTGTAGC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.26, C:0.10, G:0.36, T:0.29
Consensus pattern (44 bp):
TTTGAGGAACCAATTCGTGAGGGTTTGCAGAGTTTAAGGCGGAA
Found at i:101834 original size:42 final size:40
Alignment explanation
Indices: 101771--101856 Score: 118
Period size: 42 Copynumber: 2.1 Consensus size: 40
101761 TTCGGTTTCC
* * * *
101771 TTTAATATTAGACCATGATAATAAATTTATTATTAATATTCT
1 TTTAAAATTAAACCATAATAATAAATTTATCATTAAT-TT-T
101813 TTTAAAATTAAACCATAATAATAAATTTATCATTAATTTT
1 TTTAAAATTAAACCATAATAATAAATTTATCATTAATTTT
101853 TTTA
1 TTTA
101857 TCATCTAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 5 0.12
41 2 0.05
42 33 0.82
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (40 bp):
TTTAAAATTAAACCATAATAATAAATTTATCATTAATTTT
Found at i:109127 original size:3 final size:3
Alignment explanation
Indices: 109119--109191 Score: 139
Period size: 3 Copynumber: 24.7 Consensus size: 3
109109 TATTAAGTGG
109119 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
109167 ATA ATA ATA ATA ATA AT- ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
109192 CATCATCATC
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 67 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:109196 original size:3 final size:3
Alignment explanation
Indices: 109190--109224 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
109180 TAATATAATA
109190 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
109225 ACTGCAATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:109361 original size:45 final size:45
Alignment explanation
Indices: 109311--109444 Score: 268
Period size: 45 Copynumber: 3.0 Consensus size: 45
109301 AGCTGCAATG
109311 GTGGTTTTGAAGGAAGAGATGCGAGAACGCATGGACAATCAGATA
1 GTGGTTTTGAAGGAAGAGATGCGAGAACGCATGGACAATCAGATA
109356 GTGGTTTTGAAGGAAGAGATGCGAGAACGCATGGACAATCAGATA
1 GTGGTTTTGAAGGAAGAGATGCGAGAACGCATGGACAATCAGATA
109401 GTGGTTTTGAAGGAAGAGATGCGAGAACGCATGGACAATCAGAT
1 GTGGTTTTGAAGGAAGAGATGCGAGAACGCATGGACAATCAGAT
109445 GCGAGCTACT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 89 1.00
ACGTcount: A:0.35, C:0.11, G:0.34, T:0.20
Consensus pattern (45 bp):
GTGGTTTTGAAGGAAGAGATGCGAGAACGCATGGACAATCAGATA
Found at i:111676 original size:2 final size:2
Alignment explanation
Indices: 111671--111695 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
111661 TTTATCTCAA
111671 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 A
111696 ACAAAATAAT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:111795 original size:24 final size:24
Alignment explanation
Indices: 111763--111811 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
111753 TAGCCTCAAT
111763 CTTTTAATAGATTATTATTCCATG
1 CTTTTAATAGATTATTATTCCATG
111787 CTTTTAATAGATTATTATTCCATG
1 CTTTTAATAGATTATTATTCCATG
111811 C
1 C
111812 ATTAACGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (24 bp):
CTTTTAATAGATTATTATTCCATG
Found at i:120915 original size:4 final size:4
Alignment explanation
Indices: 120903--120942 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
120893 ATGTACATAC
* *
120903 ATAT TTAT ATAT ATAT ATAT ATAT ATAT ATAT ATAC ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
120943 TTAAAACTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:120917 original size:6 final size:6
Alignment explanation
Indices: 120903--120942 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
120893 ATGTACATAC
* *
120903 ATATTT ATATAT ATATAT ATATAT ATATAT ATATAC ATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATAT
120943 TTAAAACTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (6 bp):
ATATAT
Found at i:121117 original size:35 final size:35
Alignment explanation
Indices: 121024--121264 Score: 134
Period size: 35 Copynumber: 6.7 Consensus size: 35
121014 ATTTTAAAAT
* * **
121024 ATATAATATA-TTTTTAAAATCA-TTTTGAAAACTT
1 ATATATTATAGTTTTGAAAAT-ATTTTTGAAAACAC
* *
121058 ATATA-TATAATTTTGAAAACATTTTTGAAAACAC
1 ATATATTATAGTTTTGAAAATATTTTTGAAAACAC
*
121092 ATATATTATAGTTTTGAAAATATTTTTGAAAACATTT
1 ATATATTATAGTTTTGAAAATATTTTTGAAAACA--C
* *
121129 ATATATTATAGTTTTTAAAACGTTTTTTTG-AAA-AC
1 ATATATTATAGTTTTGAAAA--TATTTTTGAAAACAC
* * * * *
121164 TTATATAATATTTTTGAAAACA-TGTTGAAAACATTC
1 ATATATTATAGTTTTGAAAATATTTTTGAAAACA--C
* ** * * ***
121200 GTATATTATATAGTTTAAAAAAAACATTTTGAAAATTT
1 ATATA-T-TATAGTTTTGAAAATA-TTTTTGAAAACAC
121238 ATATATTATATGTTTTTGAAAATATTT
1 ATATATTATA-G-TTTTGAAAATATTT
121265 ATGTATATAT
Statistics
Matches: 158, Mismatches: 32, Indels: 31
0.71 0.14 0.14
Matches are distributed among these distances:
32 4 0.03
33 8 0.05
34 29 0.18
35 42 0.27
36 9 0.06
37 25 0.16
38 26 0.16
39 7 0.04
40 8 0.05
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (35 bp):
ATATATTATAGTTTTGAAAATATTTTTGAAAACAC
Found at i:121217 original size:71 final size:74
Alignment explanation
Indices: 121022--121219 Score: 175
Period size: 71 Copynumber: 2.8 Consensus size: 74
121012 ACATTTTAAA
* * * *
121022 ATATATAATATATTTTTAAAATCATT-TTGAAAAC-TT-ATATA-TATAAT-TTTGAAAAC--AT
1 ATATATAATA-GTTTTGAAAA-CATTGTTGAAAACATTCATATATTATAGTGTTT-AAAACGTTT
121080 TTTTGAAAACAC
63 TTTTGAAAACAC
* * * * *
121092 ATATATTATAGTTTTGAAAATATTTTTGAAAACATTTATATATTATAGTTTTTAAAACGTTTTTT
1 ATATATAATAGTTTTGAAAACATTGTTGAAAACATTCATATATTATAGTGTTTAAAACGTTTTTT
121157 TG-AAA-AC
66 TGAAAACAC
* * *
121164 TTATATAATATTTTTGAAAACA-TGTTGAAAACATTCGTATATTATA-TAGTTTAAAA
1 ATATATAATAGTTTTGAAAACATTGTTGAAAACATTCATATATTATAGT-GTTTAAAA
121220 AAAACATTTT
Statistics
Matches: 106, Mismatches: 14, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
68 3 0.03
69 16 0.15
70 12 0.11
71 33 0.31
72 30 0.28
73 6 0.06
74 6 0.06
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (74 bp):
ATATATAATAGTTTTGAAAACATTGTTGAAAACATTCATATATTATAGTGTTTAAAACGTTTTTT
TGAAAACAC
Found at i:122403 original size:17 final size:19
Alignment explanation
Indices: 122365--122414 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
122355 AAGTTTTATT
*
122365 TTATTTTGTTTTATCGTCA
1 TTATTTTATTTTATCGTCA
*
122384 TTATTTT-TTTTCTCGT-A
1 TTATTTTATTTTATCGTCA
122401 TTATTTTATTTTAT
1 TTATTTTATTTTAT
122415 TGCTTCTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 8 0.29
18 13 0.46
19 7 0.25
ACGTcount: A:0.16, C:0.08, G:0.06, T:0.70
Consensus pattern (19 bp):
TTATTTTATTTTATCGTCA
Found at i:122591 original size:22 final size:22
Alignment explanation
Indices: 122545--122595 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
122535 TTTTTGCAAC
*
122545 TTTTATTTTTATTTTTCATTTT
1 TTTTATTTTTATTTTTCATTCT
122567 TTTTAATTTGTTA-TTTT-ATTC-
1 TTTT-ATTT-TTATTTTTCATTCT
122588 TTTTATTT
1 TTTTATTT
122596 ACTCTTGATC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.15
21 4 0.15
22 7 0.27
23 8 0.31
24 3 0.12
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTTATTTTTATTTTTCATTCT
Found at i:125466 original size:19 final size:19
Alignment explanation
Indices: 125442--125478 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
125432 ATAAACTGTG
125442 AAAATGAATTATGAAATTA
1 AAAATGAATTATGAAATTA
*
125461 AAAATGGATTATGAAATT
1 AAAATGAATTATGAAATT
125479 GAATTCTATT
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:0.54, C:0.00, G:0.14, T:0.32
Consensus pattern (19 bp):
AAAATGAATTATGAAATTA
Found at i:126311 original size:40 final size:40
Alignment explanation
Indices: 126256--126488 Score: 218
Period size: 40 Copynumber: 5.7 Consensus size: 40
126246 ACACGCACTA
*
126256 TAGTGGCGTTTTTATATAAACGCCGATAAATACTGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGATAAATACTGTACTT
* *
126296 TAGTGGTGTTTTTATACAAACGCCGCTAAAGGT-C-GTACTT
1 TAGTGGCGTTTTTATACAAACGCCGATAAA--TACTGTACTT
* * * * * *
126336 TAGTGGCATTTTAAGCACAAGCGCCGATAATTACATGTTCTT
1 TAGTGGCGTTTTTA-TACAAACGCCGATAAATAC-TGTACTT
* * * * *
126378 TAGTGGCGTTTTATACACAAACGCCGCTAATTACACGTACTC
1 TAGTGGCGTTTT-TATACAAACGCCGATAAATAC-TGTACTT
* * * *
126420 TAGTTGCATTTTTATATAAACGCCGAGAAATACTGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGATAAATACTGTACTT
* *
126460 TAGTGGCGTTTTTATATAAACGCCAATAA
1 TAGTGGCGTTTTTATACAAACGCCGATAA
126489 CGGTCGTACT
Statistics
Matches: 155, Mismatches: 31, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
39 1 0.01
40 75 0.48
41 29 0.19
42 49 0.32
43 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (40 bp):
TAGTGGCGTTTTTATACAAACGCCGATAAATACTGTACTT
Found at i:126381 original size:42 final size:42
Alignment explanation
Indices: 126241--126589 Score: 191
Period size: 42 Copynumber: 8.5 Consensus size: 42
126231 ATAACGTCGC
* * * * *
126241 TAATTACACGCACTATAGTGGCGTTTT-TATATAAACGCCGA
1 TAATTACACGTACTTTAGTGGCATTTTATACACAAACGCCGA
* * ** * *
126282 TAAATAC-TGTACTTTAGTGGTGTTTT-TATACAAACGCCGC
1 TAATTACACGTACTTTAGTGGCATTTTATACACAAACGCCGA
** *
126322 TAA--AGGTCGTACTTTAGTGGCATTTTA-AGCACAAGCGCCGA
1 TAATTA-CACGTACTTTAGTGGCATTTTATA-CACAAACGCCGA
* * * *
126363 TAATTACATGTTCTTTAGTGGCGTTTTATACACAAACGCCGC
1 TAATTACACGTACTTTAGTGGCATTTTATACACAAACGCCGA
* * * *
126405 TAATTACACGTACTCTAGTTGCATTTT-TATATAAACGCCGA
1 TAATTACACGTACTTTAGTGGCATTTTATACACAAACGCCGA
* * * * * * *
126446 GAAATAC-TGTACTTTAGTGGCGTTTT-TATATAAACGCCAA
1 TAATTACACGTACTTTAGTGGCATTTTATACACAAACGCCGA
**** ** *
126486 TAA-CGGTCGTACTTTAGTGG-AGTTGCA-AGCACAAACGCCGC
1 TAATTACACGTACTTTAGTGGCA-TTTTATA-CACAAACGCCGA
* ** * * *
126527 TAATTACACGTACTTTTGTGGTGTTTTACACACAAATGCCGC
1 TAATTACACGTACTTTAGTGGCATTTTATACACAAACGCCGA
*
126569 TAATTACACATACTTTAGTGG
1 TAATTACACGTACTTTAGTGG
126590 TGTTTTTAAA
Statistics
Matches: 235, Mismatches: 59, Indels: 27
0.73 0.18 0.08
Matches are distributed among these distances:
38 1 0.00
40 92 0.39
41 45 0.19
42 94 0.40
43 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (42 bp):
TAATTACACGTACTTTAGTGGCATTTTATACACAAACGCCGA
Found at i:126518 original size:164 final size:164
Alignment explanation
Indices: 126233--126589 Score: 491
Period size: 164 Copynumber: 2.2 Consensus size: 164
126223 GGAAAATAAT
* * * *
126233 AACGTCGCTAATTACACGCACTATAGTGGCGTTTTTATATAAACGCCGATAAATACTGTACTTTA
1 AACGCCGCTAATTACACGTACTATAGTGGCATTTTTATATAAACGCCGAGAAATACTGTACTTTA
* ** ** *
126298 GTGGTGTTTTTATACAAACGCCGCTAAAGGTCGTACTTTAGTGGCATTTTAAGCACAAGCGCCGA
66 GTGGCGTTTTTATACAAACGCCAATAAAGGTCGTACTTTAGTGGCATTGCAAGCACAAACGCCGA
* * *
126363 TAATTACATGTTCTTTAGTGGCGTTTTATACACA
131 TAATTACACGTACTTTAGTGGCGTTTTACACACA
* *
126397 AACGCCGCTAATTACACGTACTCTAGTTGCATTTTTATATAAACGCCGAGAAATACTGTACTTTA
1 AACGCCGCTAATTACACGTACTATAGTGGCATTTTTATATAAACGCCGAGAAATACTGTACTTTA
* *
126462 GTGGCGTTTTTATATAAACGCCAATAACGGTCGTACTTTAGTGG-AGTTGCAAGCACAAACGCCG
66 GTGGCGTTTTTATACAAACGCCAATAAAGGTCGTACTTTAGTGGCA-TTGCAAGCACAAACGCCG
* * *
126526 CTAATTACACGTACTTTTGTGGTGTTTTACACACA
130 ATAATTACACGTACTTTAGTGGCGTTTTACACACA
* * *
126561 AATGCCGCTAATTACACATACTTTAGTGG
1 AACGCCGCTAATTACACGTACTATAGTGG
126590 TGTTTTTAAA
Statistics
Matches: 168, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
163 1 0.01
164 167 0.99
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (164 bp):
AACGCCGCTAATTACACGTACTATAGTGGCATTTTTATATAAACGCCGAGAAATACTGTACTTTA
GTGGCGTTTTTATACAAACGCCAATAAAGGTCGTACTTTAGTGGCATTGCAAGCACAAACGCCGA
TAATTACACGTACTTTAGTGGCGTTTTACACACA
Found at i:128098 original size:30 final size:30
Alignment explanation
Indices: 128064--128136 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
128054 CCCGAAGGAC
128064 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
128094 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
128124 CTGTCCATAGGTC
1 CTATCCAGAGGTC
128137 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:128232 original size:63 final size:61
Alignment explanation
Indices: 128119--128247 Score: 188
Period size: 63 Copynumber: 2.1 Consensus size: 61
128109 AAAGATCCTC
* *
128119 GGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
* *
128180 GGTATACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGTA-ACTGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCCGTAGAACATA
128243 GGTAA
1 GGTAA
128248 ACCCTCGACT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
61 5 0.08
62 25 0.41
63 31 0.51
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (61 bp):
GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
Found at i:128242 original size:32 final size:31
Alignment explanation
Indices: 128122--128249 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
128112 GATCCTCGGT
* * * *
128122 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
128153 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
128184 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
128216 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
128247 AAC
1 AAC
128250 CCTCGACTCT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
30 4 0.05
31 51 0.62
32 23 0.28
33 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:128981 original size:22 final size:22
Alignment explanation
Indices: 128937--128978 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
128927 TAAATCAATT
*
128937 TCATATAACTCCTATAATCTTC
1 TCATATAACTCCTATAACCTTC
*
128959 TCATATAACTTC-ATAACCTT
1 TCATATAACTCCTATAACCTT
128979 TCTTATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.40
Consensus pattern (22 bp):
TCATATAACTCCTATAACCTTC
Found at i:129430 original size:21 final size:21
Alignment explanation
Indices: 129406--129450 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
129396 TGTTGTTCGT
* *
129406 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
129427 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
129448 TTG
1 TTG
129451 CCTAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:130900 original size:27 final size:29
Alignment explanation
Indices: 130834--130903 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 29
130824 TAACATTAGT
* *
130834 TATAAAGGAGTTAACACTGGTACTTTCAAAA
1 TATAAAGGAGTTAACACTAGTA-TAT-AAAA
130865 TATAAAGGAGTTAACACTAGT-TAT-AAA
1 TATAAAGGAGTTAACACTAGTATATAAAA
130892 TATAAAGGAGTT
1 TATAAAGGAGTT
130904 CCATTTGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 15 0.41
29 2 0.05
31 20 0.54
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.30
Consensus pattern (29 bp):
TATAAAGGAGTTAACACTAGTATATAAAA
Found at i:132130 original size:42 final size:42
Alignment explanation
Indices: 132070--132225 Score: 154
Period size: 42 Copynumber: 3.7 Consensus size: 42
132060 ATTAATCTTA
* *
132070 GCTATATATCTGACTTTTTGCGGCGTTTGTTCAAAAAACGCC
1 GCTATAGATATGACTTTTTGCGGCGTTTGTTCAAAAAACGCC
* * *
132112 TCTATAGATATGACTTTTTGCGGCGTTTGTTCTAAAAGCGCC
1 GCTATAGATATGACTTTTTGCGGCGTTTGTTCAAAAAACGCC
* * * *
132154 GCTAAAGATA-G-CGGTCTTTTGCGGCATTTGTTCCAAAAATGCC
1 GCTATAGATATGAC--T-TTTTGCGGCGTTTGTTCAAAAAACGCC
* * *
132197 GCTATAGATAGCGACCTATTGCGGCGTTT
1 GCTATAGATA-TGACTTTTTGCGGCGTTT
132226 TTTGTTCTCA
Statistics
Matches: 93, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
40 1 0.01
41 1 0.01
42 46 0.49
43 43 0.46
45 1 0.01
46 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (42 bp):
GCTATAGATATGACTTTTTGCGGCGTTTGTTCAAAAAACGCC
Found at i:132219 original size:43 final size:43
Alignment explanation
Indices: 132085--132225 Score: 167
Period size: 43 Copynumber: 3.3 Consensus size: 43
132075 ATATCTGACT
* * *
132085 TTTTGCGGCGTTTGTTCAAAAAACGCCTCTATAGATA-TGACT
1 TTTTGCGGCGTTTGTTCAAAAAACGCCGCTATAGATAGCGACC
* * * **
132127 TTTTGCGGCGTTTGTTCTAAAAGCGCCGCTAAAGATAGCGGTC
1 TTTTGCGGCGTTTGTTCAAAAAACGCCGCTATAGATAGCGACC
* * *
132170 TTTTGCGGCATTTGTTCCAAAAATGCCGCTATAGATAGCGACC
1 TTTTGCGGCGTTTGTTCAAAAAACGCCGCTATAGATAGCGACC
*
132213 TATTGCGGCGTTT
1 TTTTGCGGCGTTT
132226 TTTGTTCTCA
Statistics
Matches: 81, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
42 33 0.41
43 48 0.59
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (43 bp):
TTTTGCGGCGTTTGTTCAAAAAACGCCGCTATAGATAGCGACC
Found at i:132335 original size:20 final size:20
Alignment explanation
Indices: 132306--132358 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
132296 AGCGGTGCTT
* *
132306 AAAAATGCCGCTATAGATAA
1 AAAAACGCCGCAATAGATAA
* *
132326 TAAAACGCCGCAATAGGTAA
1 AAAAACGCCGCAATAGATAA
*
132346 AAAAACGGCGCAA
1 AAAAACGCCGCAA
132359 ATGCTTTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.13
Consensus pattern (20 bp):
AAAAACGCCGCAATAGATAA
Found at i:137185 original size:21 final size:22
Alignment explanation
Indices: 137161--137211 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
137151 AGATTGTTTC
137161 GATTT-TCTTATTTTAATAAAT
1 GATTTATCTTATTTTAATAAAT
* *
137182 GATTTTTATTTTATTTTAATGAAT
1 GA--TTTATCTTATTTTAATAAAT
137206 GATTTA
1 GATTTA
137212 CAAAATAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 2 0.08
22 4 0.16
23 3 0.12
24 16 0.64
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (22 bp):
GATTTATCTTATTTTAATAAAT
Found at i:142775 original size:20 final size:20
Alignment explanation
Indices: 142711--142780 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
142701 TTATATGTAG
* * *
142711 TATTGTTACTATAAGAACAA
1 TATTGATACTTTAATAACAA
* *
142731 TATCGATACTGTTAAT-GCAA
1 TATTGATACT-TTAATAACAA
*
142751 CATTGATACTTTAATAACAA
1 TATTGATACTTTAATAACAA
*
142771 TATTGGTACT
1 TATTGATACT
142781 ATTTACCCAA
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 5 0.13
20 30 0.79
21 3 0.08
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (20 bp):
TATTGATACTTTAATAACAA
Found at i:143036 original size:35 final size:35
Alignment explanation
Indices: 142997--143068 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
142987 AATTTAATTG
142997 TATCCCTACTAAGGACCCCATAAAAAAGATTACTT
1 TATCCCTACTAAGGACCCCATAAAAAAGATTACTT
* *
143032 TATCCCTACTAAGGATCCCATAAAAAATATTACTT
1 TATCCCTACTAAGGACCCCATAAAAAAGATTACTT
143067 TA
1 TA
143069 ATTAATTCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.29
Consensus pattern (35 bp):
TATCCCTACTAAGGACCCCATAAAAAAGATTACTT
Found at i:148743 original size:37 final size:37
Alignment explanation
Indices: 148667--148743 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
148657 TTTTTATATT
*
148667 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * * *
148704 TTTAATTTTTTTAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
148741 TTT
1 TTT
148744 GTAATATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 13 0.38
37 21 0.62
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:154268 original size:36 final size:36
Alignment explanation
Indices: 154187--154268 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
154177 TCCATGAAGT
* *
154187 TTTGAGTTCAAACAATTATATATGTAGAATGTATGA
1 TTTGAGTTCAAACAACTATATACGTAGAATGTATGA
* ** *
154223 TCT-ATGTTCAAACAACTATATACGTAGGGTGTGTGA
1 TTTGA-GTTCAAACAACTATATACGTAGAATGTATGA
154259 TTTGAGTTCA
1 TTTGAGTTCA
154269 GAAAATTGTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
35 1 0.03
36 35 0.95
37 1 0.03
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (36 bp):
TTTGAGTTCAAACAACTATATACGTAGAATGTATGA
Found at i:156771 original size:2 final size:2
Alignment explanation
Indices: 156764--156789 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
156754 ATACAAAATA
156764 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
156790 TAATATTAAA
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:163331 original size:21 final size:22
Alignment explanation
Indices: 163305--163347 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
163295 GTCTGACTGA
*
163305 CAAAAT-TAAAAAATCGATAAT
1 CAAAATATAAAAAAGCGATAAT
*
163326 CAAAATATAAAAGAGCGATAAT
1 CAAAATATAAAAAAGCGATAAT
163348 TAAATGGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.21
Consensus pattern (22 bp):
CAAAATATAAAAAAGCGATAAT
Found at i:170025 original size:81 final size:78
Alignment explanation
Indices: 169936--170195 Score: 197
Period size: 81 Copynumber: 3.1 Consensus size: 78
169926 ATATGAAAAA
* *
169936 TATTTTTAATATTAAAACAATTATAATTTTGTGTATTTTGTAATTCGTCAAATTATTTTATAACT
1 TATTTTTAATATTAAAACAATTATAATTTT-TGTATTTTTTAATTCATCAAATTATTTTATAA-T
170001 AATTGTTTATGTAAT
64 AATTGTTTATGTAAT
* *
170016 TATTATTTAATTTTTAAAATTAAAA-AAATATAATTTTTGAAATCTAAAATTTTAATT-ATCGAA
1 TATT-TTTAA----T---ATTAAAACAATTATAATTTTTG-TAT-T----TTTTAATTCATC-AA
* * * *
170079 ATTATTTTTTAA-AA--GTATATGAAAAA
51 ATTATTTTATAATAATTGTTTATG-TAAT
* *
170105 TATTTTTAAAATTAAAACAATTATAATTTTATGTATTTTTTAATTCATCAAATTATTTAATAATT
1 TATTTTTAATATTAAAACAATTATAATTTT-TGTATTTTTTAATTCATCAAATTATTTTATAA-T
*
170170 AATTGTTTATTTAAT
64 AATTGTTTATGTAAT
170185 TATTATTTAAT
1 TATT-TTTAAT
170196 TTTTAAAATT
Statistics
Matches: 138, Mismatches: 18, Indels: 47
0.68 0.09 0.23
Matches are distributed among these distances:
77 20 0.14
78 3 0.02
79 2 0.01
80 10 0.07
81 23 0.17
82 13 0.09
83 2 0.01
85 1 0.01
86 2 0.01
87 13 0.09
88 19 0.14
89 6 0.04
90 2 0.01
91 2 0.01
92 20 0.14
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (78 bp):
TATTTTTAATATTAAAACAATTATAATTTTTGTATTTTTTAATTCATCAAATTATTTTATAATAA
TTGTTTATGTAAT
Found at i:170038 original size:88 final size:85
Alignment explanation
Indices: 169937--170221 Score: 286
Period size: 88 Copynumber: 3.3 Consensus size: 85
169927 TATGAAAAAT
* * *
169937 ATTTTTAATATTAAAACAATTATAATTTTGTGTATTTTGTAATTCGTCAAATTATTTTATAACTA
1 ATTTTTAAAATTAAAA-AATTATAATTTT-TGTATTTTTTAATTCATCAAATTATTTTATAA-TA
170002 ATTGTTTATGTAATTATTATTTA
63 ATTGTTTATGTAATTATTATTTA
* * *
170025 ATTTTTAAAATTAAAAAAATATAATTTTTGAAATCTAAAATTTTAATT-ATCGAAATTATTTTTT
1 ATTTTTAAAATTAAAAAATTATAATTTTTG-TAT-T----TTTTAATTCATC-AAATTATTTTAT
* *
170089 AA-AA--GTATATG-AA--A--A-AT-
59 AATAATTGTTTATGTAATTATTATTTA
*
170106 ATTTTTAAAATTAAAACAATTATAATTTTATGTATTTTTTAATTCATCAAATTATTTAATAATTA
1 ATTTTTAAAATTAAAA-AATTATAATTTT-TGTATTTTTTAATTCATCAAATTATTTTATAA-TA
*
170171 ATTGTTTATTTAATTATTATTTA
63 ATTGTTTATGTAATTATTATTTA
170194 ATTTTTAAAATTAAAAAATTATAATTTT
1 ATTTTTAAAATTAAAAAATTATAATTTT
170222 CGAAATCGAA
Statistics
Matches: 161, Mismatches: 15, Indels: 43
0.74 0.07 0.20
Matches are distributed among these distances:
77 20 0.12
78 3 0.02
79 2 0.01
81 22 0.14
82 16 0.10
83 3 0.02
84 1 0.01
85 1 0.01
86 3 0.02
87 28 0.17
88 38 0.24
90 2 0.01
91 2 0.01
92 20 0.12
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (85 bp):
ATTTTTAAAATTAAAAAATTATAATTTTTGTATTTTTTAATTCATCAAATTATTTTATAATAATT
GTTTATGTAATTATTATTTA
Found at i:170097 original size:169 final size:169
Alignment explanation
Indices: 169915--170244 Score: 552
Period size: 169 Copynumber: 2.0 Consensus size: 169
169905 AATTCGTAAC
* *
169915 TTTTTAAAAGTATATGAAAAATATTTTTAATATTAAAACAATTATAATTTTGTGTATTTTGTAAT
1 TTTTTAAAAGTATATGAAAAATATTTTTAAAATTAAAACAATTATAATTTTATGTATTTTGTAAT
* *
169980 TCGTCAAATTATTTTATAACTAATTGTTTATGTAATTATTATTTAATTTTTAAAATTAAAAAAAT
66 TCATCAAATTATTTAATAACTAATTGTTTATGTAATTATTATTTAATTTTTAAAATTAAAAAAAT
* * *
170045 ATAATTTTTGAAATCTAAAATTTTAATTATCGAAATTAT
131 ATAATTTTCGAAATCGAAAAATTTAATTATCGAAATTAT
*
170084 TTTTTAAAAGTATATGAAAAATATTTTTAAAATTAAAACAATTATAATTTTATGTATTTTTTAAT
1 TTTTTAAAAGTATATGAAAAATATTTTTAAAATTAAAACAATTATAATTTTATGTATTTTGTAAT
* * *
170149 TCATCAAATTATTTAATAATTAATTGTTTATTTAATTATTATTTAATTTTTAAAATTAAAAAATT
66 TCATCAAATTATTTAATAACTAATTGTTTATGTAATTATTATTTAATTTTTAAAATTAAAAAAAT
*
170214 ATAATTTTCGAAATCGAAAAATTTATTTATC
131 ATAATTTTCGAAATCGAAAAATTTAATTATC
170245 AAACTATGAA
Statistics
Matches: 149, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
169 149 1.00
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.49
Consensus pattern (169 bp):
TTTTTAAAAGTATATGAAAAATATTTTTAAAATTAAAACAATTATAATTTTATGTATTTTGTAAT
TCATCAAATTATTTAATAACTAATTGTTTATGTAATTATTATTTAATTTTTAAAATTAAAAAAAT
ATAATTTTCGAAATCGAAAAATTTAATTATCGAAATTAT
Found at i:170227 original size:23 final size:23
Alignment explanation
Indices: 170192--170236 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
170182 AATTATTATT
* *
170192 TAATTTTTAAAATTAAAAAATTA
1 TAATTTTCAAAATCAAAAAATTA
* *
170215 TAATTTTCGAAATCGAAAAATT
1 TAATTTTCAAAATCAAAAAATT
170237 TATTTATCAA
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:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (23 bp):
TAATTTTCAAAATCAAAAAATTA
Found at i:173429 original size:29 final size:29
Alignment explanation
Indices: 173383--173441 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
173373 ATTTTCACCT
173383 AACTAAATTGATGGAAGCAATGACATCAA
1 AACTAAATTGATGGAAGCAATGACATCAA
*
173412 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGGAAGCAATGACATCAA
173441 A
1 A
173442 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.49, C:0.14, G:0.15, T:0.22
Consensus pattern (29 bp):
AACTAAATTGATGGAAGCAATGACATCAA
Found at i:178099 original size:29 final size:29
Alignment explanation
Indices: 178057--178115 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
178047 ATTTTCACCT
178057 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
178086 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
178115 A
1 A
178116 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:183391 original size:20 final size:20
Alignment explanation
Indices: 183366--183408 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
183356 AATACCCTTA
183366 TGTTGTAGGATGACAAGAAT
1 TGTTGTAGGATGACAAGAAT
183386 TGTTGTAGGATGACAAGAAT
1 TGTTGTAGGATGACAAGAAT
183406 TGT
1 TGT
183409 CCCTGGAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.33
Consensus pattern (20 bp):
TGTTGTAGGATGACAAGAAT
Found at i:184195 original size:24 final size:24
Alignment explanation
Indices: 184128--184196 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
184118 ATTTTCGACT
* *
184128 TGAATTCTGTTCTG-ATACATTATC
1 TGAATTCTGTTCTGAATTC-TGATC
* * *
184152 TGAATTCTGCTATGATTTCTGATC
1 TGAATTCTGTTCTGAATTCTGATC
*
184176 TGGATTCTGTTCTGAATTCTG
1 TGAATTCTGTTCTGAATTCTG
184197 TTTTGATTTA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
24 33 0.94
25 2 0.06
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.46
Consensus pattern (24 bp):
TGAATTCTGTTCTGAATTCTGATC
Found at i:184197 original size:12 final size:12
Alignment explanation
Indices: 184128--184198 Score: 56
Period size: 12 Copynumber: 5.9 Consensus size: 12
184118 ATTTTCGACT
184128 TGAATTCTGTTC
1 TGAATTCTGTTC
*
184140 TG-ATACAT-TATC
1 TGAATTC-TGT-TC
* *
184152 TGAATTCTGCTA
1 TGAATTCTGTTC
* *
184164 TGATTTCTGATC
1 TGAATTCTGTTC
*
184176 TGGATTCTGTTC
1 TGAATTCTGTTC
184188 TGAATTCTGTT
1 TGAATTCTGTT
184199 TTGATTTATG
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
11 4 0.09
12 37 0.84
13 3 0.07
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:186228 original size:26 final size:26
Alignment explanation
Indices: 186199--186248 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
186189 ACAATGGGCG
186199 ATATACATCGATATGTATCATTAATA
1 ATATACATCGATATGTATCATTAATA
* *
186225 ATATATATTGATATGTATCATTAA
1 ATATACATCGATATGTATCATTAA
186249 ATTTTAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (26 bp):
ATATACATCGATATGTATCATTAATA
Found at i:186504 original size:2 final size:2
Alignment explanation
Indices: 186497--186552 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
186487 TGAATTTTAA
186497 AT AT 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 AT AT
186539 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
186553 GATAACAATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:187535 original size:15 final size:15
Alignment explanation
Indices: 187515--187546 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
187505 TATTATTAAA
187515 TAATTATTAAATTAC
1 TAATTATTAAATTAC
*
187530 TAATTATTAATTTAC
1 TAATTATTAAATTAC
187545 TA
1 TA
187547 GATTTTACAT
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:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATTAAATTAC
Found at i:187733 original size:67 final size:68
Alignment explanation
Indices: 187614--187748 Score: 173
Period size: 67 Copynumber: 2.0 Consensus size: 68
187604 AGTCGAGTCG
* * * * * *
187614 AGTAACAAGTTTTTTTAATGAGCACGAGTCGAGCAAAATTTTGTCGAGCTTAACAAGC-ACGAGT
1 AGTAACAAGTTTTTTTAACGAGCACAAGTCGAGAAAAAATTTATCGAACTTAACAAGCAACGAGT
187678 TGA
66 TGA
* * * *
187681 AGTAACAAGTTTTTTTAACGAGCATAAGTCGAGAAAAAATTTATCTAACTTAACGAGCAATGAGT
1 AGTAACAAGTTTTTTTAACGAGCACAAGTCGAGAAAAAATTTATCGAACTTAACAAGCAACGAGT
187746 TGA
66 TGA
187749 GTCGAGCAAC
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
67 49 0.86
68 8 0.14
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (68 bp):
AGTAACAAGTTTTTTTAACGAGCACAAGTCGAGAAAAAATTTATCGAACTTAACAAGCAACGAGT
TGA
Found at i:189929 original size:43 final size:42
Alignment explanation
Indices: 189813--189943 Score: 126
Period size: 41 Copynumber: 3.1 Consensus size: 42
189803 TTCAATTTTA
* * *
189813 TTTTTATATTTATAATTGAGGCCCCTAATTTTGTGATCAT-AC
1 TTTTTATATTTATAATTGAGGACCCTAATTTTTTAATC-TCAC
* * * * *
189855 -TTTTATCTTTATAATCG-GGACCATTAGTTTTTTCCATCTCAC
1 TTTTTATATTTATAATTGAGGACC-CTAATTTTTT-AATCTCAC
*
189897 TTTTTATATTTATAATTGATGACCCTAATTTTTTAAT-TCAC
1 TTTTTATATTTATAATTGAGGACCCTAATTTTTTAATCTCAC
189938 TTTTTA
1 TTTTTA
189944 CCTTTAAAAT
Statistics
Matches: 71, Mismatches: 13, Indels: 11
0.75 0.14 0.12
Matches are distributed among these distances:
40 4 0.06
41 33 0.46
42 7 0.10
43 23 0.32
44 4 0.06
ACGTcount: A:0.25, C:0.15, G:0.08, T:0.51
Consensus pattern (42 bp):
TTTTTATATTTATAATTGAGGACCCTAATTTTTTAATCTCAC
Found at i:191729 original size:26 final size:26
Alignment explanation
Indices: 191694--191757 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
191684 AAACATTCAA
*
191694 TTAACTTGACATAACTTATATCCAAT
1 TTAACCTGACATAACTTATATCCAAT
*
191720 TTAACCTGACATAATTTATATCCAAT
1 TTAACCTGACATAACTTATATCCAAT
191746 TTAACCTGACAT
1 TTAACCTGACAT
191758 GACGTAATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.38
Consensus pattern (26 bp):
TTAACCTGACATAACTTATATCCAAT
Found at i:192436 original size:14 final size:14
Alignment explanation
Indices: 192397--192447 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
192387 GAGTTCGATA
*
192397 AAATTATCTTATTT
1 AAATTATATTATTT
*
192411 AAATTTTATTATTAT
1 AAATTATATTATT-T
192426 AAATTAT-TTATATT
1 AAATTATATTAT-TT
192440 AACATTAT
1 AA-ATTAT
192448 TAAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (14 bp):
AAATTATATTATTT
Found at i:194349 original size:2 final size:2
Alignment explanation
Indices: 194342--194378 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
194332 TAGTGCCTTC
194342 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
194379 CAAGATAGAA
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:203152 original size:5 final size:5
Alignment explanation
Indices: 203142--203166 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
203132 ATGGGGCAAT
203142 TGTGG TGTGG TGTGG TGTGG TGTGG
1 TGTGG TGTGG TGTGG TGTGG TGTGG
203167 GTTTTCTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.60, T:0.40
Consensus pattern (5 bp):
TGTGG
Done.