Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_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: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 35
Found at i:5652629 original size:33 final size:30
Alignment explanation
Indices: 5652564--5652632 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 30
5652554 ATAAAACTTA
5652564 ATATTATTATTTTTAAAAAATATTATAAATT
1 ATATTATTATTTTTAAAAAATATTAT-AATT
*
5652595 ATATTAATTATTTATTAAAGTAAATGTTAT-ATT
1 ATATT-ATTATTT-TTAAA--AAATATTATAATT
5652628 ATATT
1 ATATT
5652633 TTAAAAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
31 5 0.15
32 7 0.21
33 13 0.39
35 8 0.24
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (30 bp):
ATATTATTATTTTTAAAAAATATTATAATT
Found at i:5652789 original size:8 final size:8
Alignment explanation
Indices: 5652763--5652827 Score: 57
Period size: 8 Copynumber: 8.4 Consensus size: 8
5652753 ATATAATATC
5652763 TTATATTA
1 TTATATTA
5652771 -TAT-TATA
1 TTATAT-TA
5652778 TTATATTA
1 TTATATTA
*
5652786 TTATAATA
1 TTATATTA
5652794 -TA-ATTGA
1 TTATATT-A
*
5652801 TTATTTTA
1 TTATATTA
*
5652809 TTATAATA
1 TTATATTA
5652817 TTATATTA
1 TTATATTA
5652825 TTA
1 TTA
5652828 GAAATATTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
6 3 0.07
7 8 0.18
8 31 0.69
9 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (8 bp):
TTATATTA
Found at i:5652795 original size:23 final size:23
Alignment explanation
Indices: 5652763--5652825 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
5652753 ATATAATATC
*
5652763 TTATATTATATTATATTATATTA
1 TTATAATATATTATATTATATTA
* *
5652786 TTATAATATAATT-GATTATTTTA
1 TTATAATAT-ATTATATTATATTA
5652809 TTAT-A-ATATTATATTAT
1 TTATAATATATTATATTAT
5652826 TAGAAATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 3 0.09
21 7 0.21
22 1 0.03
23 20 0.59
24 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTATAATATATTATATTATATTA
Found at i:5652822 original size:5 final size:5
Alignment explanation
Indices: 5652749--5652825 Score: 55
Period size: 5 Copynumber: 14.4 Consensus size: 5
5652739 TAAAATAAAA
* * * *
5652749 ATATAT ATAAT ATCTT ATATT ATATT ATATT ATATT ATTATA ATATA ATTGATT
1 ATAT-T ATATT ATATT ATATT ATATT ATATT ATATT A-TATT ATATT A-T-ATT
* *
5652803 ATTTT ATTATA ATATT ATATT AT
1 ATATT A-TATT ATATT ATATT AT
5652826 TAGAAATATT
Statistics
Matches: 57, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
5 42 0.74
6 12 0.21
7 3 0.05
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:5653100 original size:42 final size:42
Alignment explanation
Indices: 5653044--5653139 Score: 147
Period size: 42 Copynumber: 2.3 Consensus size: 42
5653034 TTTCTCCAAC
* * *
5653044 CAAACACAGGAAAACATTTTCAGGAAAACTAATTACGTAAAA
1 CAAACACGGGAAAACATTTTCAGAAAAACAAATTACGTAAAA
* *
5653086 CAAACACGGGAAAACATTTTCCGAAAAACAAATTACGTGAAA
1 CAAACACGGGAAAACATTTTCAGAAAAACAAATTACGTAAAA
5653128 CAAACACGGGAA
1 CAAACACGGGAA
5653140 TTCGGGGGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.51, C:0.19, G:0.15, T:0.16
Consensus pattern (42 bp):
CAAACACGGGAAAACATTTTCAGAAAAACAAATTACGTAAAA
Found at i:5658947 original size:21 final size:21
Alignment explanation
Indices: 5658923--5658968 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5658913 AAGTCAATTT
* *
5658923 CTTTTATGTTGTTGTTTATGG
1 CTTTTATGTTGCTGTTGATGG
*
5658944 CTTTGATGTTGCTGTTGATGG
1 CTTTTATGTTGCTGTTGATGG
5658965 -TTTT
1 CTTTT
5658969 CCTGTTCTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.09, C:0.07, G:0.26, T:0.59
Consensus pattern (21 bp):
CTTTTATGTTGCTGTTGATGG
Found at i:5667440 original size:22 final size:22
Alignment explanation
Indices: 5667397--5667440 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5667387 TAAGGTCTTA
* *
5667397 TATTGTTTAAATATGATTTTTT
1 TATTGTTTAAATATAATCTTTT
*
5667419 TATTGTTTAAATGTAATCTTTT
1 TATTGTTTAAATATAATCTTTT
5667441 ACATATACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.61
Consensus pattern (22 bp):
TATTGTTTAAATATAATCTTTT
Found at i:5675568 original size:23 final size:23
Alignment explanation
Indices: 5675542--5675599 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
5675532 CACCACAGCT
*
5675542 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
*
5675565 CGTAGAATTGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
*
5675588 CATAGAAATGCA
1 CGTAGAAATGCA
5675600 TCGTAGTGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:5681507 original size:14 final size:14
Alignment explanation
Indices: 5681456--5681509 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
5681446 TAGAGTCTGG
5681456 TTTTTGTTTTTGTT-
1 TTTTT-TTTTTGTTA
*
5681470 TTTTATTTTT-TTA
1 TTTTTTTTTTGTTA
* *
5681483 -CTTTCTTTTGTTA
1 TTTTTTTTTTGTTA
5681496 TTTTTTTTTTGTTA
1 TTTTTTTTTTGTTA
5681510 CTTTGTGGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
12 8 0.26
13 8 0.26
14 15 0.48
ACGTcount: A:0.07, C:0.04, G:0.07, T:0.81
Consensus pattern (14 bp):
TTTTTTTTTTGTTA
Found at i:5681510 original size:27 final size:25
Alignment explanation
Indices: 5681463--5681513 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
5681453 TGGTTTTTGT
5681463 TTTTGTTTTTTATTTTTTTACTTTC
1 TTTTGTTTTTTATTTTTTTACTTTC
*
5681488 TTTTGTTATTTTTTTTTTGTTACTTT
1 TTTTGTT-TTTTATTTTT-TTACTTT
5681514 GTGGAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.30
26 9 0.39
27 7 0.30
ACGTcount: A:0.08, C:0.06, G:0.06, T:0.80
Consensus pattern (25 bp):
TTTTGTTTTTTATTTTTTTACTTTC
Found at i:5682320 original size:27 final size:27
Alignment explanation
Indices: 5682285--5682340 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
5682275 CCGCCATCAC
*
5682285 CACTTTGAACTTGAAACTCCATAGCAT
1 CACTTTGAACTTGAAACTCCACAGCAT
*
5682312 CACTTTGAACTTGAAAGTCCACAGCAT
1 CACTTTGAACTTGAAACTCCACAGCAT
5682339 CA
1 CA
5682341 AGATCTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (27 bp):
CACTTTGAACTTGAAACTCCACAGCAT
Found at i:5684362 original size:23 final size:22
Alignment explanation
Indices: 5684320--5684364 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
5684310 TGACTAACGA
*
5684320 TTTTTATCAAACAAAGATGTTT
1 TTTTTATCAAACAAAAATGTTT
5684342 TTTTTATCCAAA-ATAAAATGTTT
1 TTTTTAT-CAAACA-AAAATGTTT
5684365 GGGGGTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.47
Consensus pattern (22 bp):
TTTTTATCAAACAAAAATGTTT
Found at i:5686609 original size:475 final size:475
Alignment explanation
Indices: 5685692--5686646 Score: 1683
Period size: 475 Copynumber: 2.0 Consensus size: 475
5685682 TATTTATATT
5685692 AATAATTTAATTTCACATATATTAAAATTTTATAATTTTATACTTGATATAATTCTCTAAAAGAT
1 AATAATTTAATTTCACATATATTAAAATTTTATAATTTTATACTTGATATAATTCTCTAAAAGAT
5685757 TTTATTCTTAATCCTTCTTAATAAAGTAGCTAATTTTATTAAAACTAGAAAATATTCGAAACAAT
66 TTTATTCTTAATCCTTCTTAATAAAGTAGCTAATTTTATTAAAACTAGAAAATATTCGAAACAAT
5685822 AATAAAGTTTGTAAATTAAATACACAATATAATATTTTCTATAAACCACAAACGCACAACAAATT
131 AATAAAGTTTGTAAATTAAATACACAATATAATATTTTCTATAAACCAC-AACGCACAACAAATT
*
5685887 AACCACTTGATATCATATATGAACCATACAAGGAAAATGTTAAAATCCATCTAAAAACCTCGAGC
195 AACCACTTGAGATCA-ATATGAACCATACAAGGAAAATGTTAAAATCCATCTAAAAACCTCGAGC
*
5685952 AAAAACAAATATGAACAAATTTTGTATATATCAACAAACGAACTACAAAATGAGATTAAACTACC
259 AAAAACAAATATGAACAAATTTTGTATATATCAACAAAAGAACTACAAAATGAGATTAAACTACC
*
5686017 GAAACACCACAAAAAACTGTGAATTAGAGTCGAGCATCGTGAGAAAATTATCTACGAACGTAAAT
324 GAAACACCACAAAAAACTGTGAATTAGAGTCGAGCATCGTAAGAAAATTATCTACGAACGTAAAT
5686082 TATGTGTCCGAGTCCTATCCGATACCCAAAGAATGTAAAATTATATATAGTGAATAAGCAACATC
389 TATGTGTCCGAGTCCTATCCGATACCCAAAGAATGTAAAATTATATATAGTGAATAAGCAACATC
5686147 TTTATC-GTCG-GACGATATCA
454 TTTATCAGTCGAGACGATATCA
5686167 AATAATTTAATTTCACATATATTAAAATTTTATAATTTTATACTTGATATAATTCTCTAAAAGAT
1 AATAATTTAATTTCACATATATTAAAATTTTATAATTTTATACTTGATATAATTCTCTAAAAGAT
5686232 TTTATTCTTAATCCTTCTTAAATAAAGTAGCTAATTTTATTAAAACTAGAAAATATTCGAAACAA
66 TTTATTCTTAATCCTTCTT-AATAAAGTAGCTAATTTTATTAAAACTAGAAAATATTCGAAACAA
5686297 TAATAAAGTTTGTAAATTAAATACACAATTATAATATTTTCTTATAAACCAC-ACGCACAAC-AA
130 TAATAAAGTTTGTAAATTAAATACACAA-TATAATATTTTC-TATAAACCACAACGCACAACAAA
5686360 TTAACCACTTGAGATC-ATATGAACCATACAAGGAAAATGTTAAAATCCATCTAAAAAACCTCGA
193 TTAACCACTTGAGATCAATATGAACCATACAAGGAAAATGTTAAAATCCATCT-AAAAACCTCGA
* *
5686424 GCAAAAAAACAAATATGAACAAA-TTTGTCTATATCAACAAAAGAACTACAAAATTAGATTAAAC
257 GC--AAAAACAAATATGAACAAATTTTGTATATATCAACAAAAGAACTACAAAATGAGATTAAAC
* *
5686488 TACCGAAACACCAC-CAAAACTGTGAATTATAGTCGAGCATCGTAAGAAAATTATCTACGAACGT
320 TACCGAAACACCACAAAAAACTGTGAATTAGAGTCGAGCATCGTAAGAAAATTATCTACGAACGT
* *
5686552 -AATTGTGTGTCCGAGTCCTATCCGATACCCAAAGAATGTAAGATTAATATGATAGTGAATAAGC
385 AAATTATGTGTCCGAGTCCTATCCGATACCCAAAGAATGTAAAATT-ATAT-ATAGTGAATAAGC
5686616 AACATCTTTATCAGTCGAGACGATATCA
448 AACATCTTTATCAGTCGAGACGATATCA
5686644 AAT
1 AAT
5686647 GCAATCATAT
Statistics
Matches: 461, Mismatches: 9, Indels: 18
0.94 0.02 0.04
Matches are distributed among these distances:
473 79 0.17
474 64 0.14
475 178 0.39
476 105 0.23
477 25 0.05
478 10 0.02
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (475 bp):
AATAATTTAATTTCACATATATTAAAATTTTATAATTTTATACTTGATATAATTCTCTAAAAGAT
TTTATTCTTAATCCTTCTTAATAAAGTAGCTAATTTTATTAAAACTAGAAAATATTCGAAACAAT
AATAAAGTTTGTAAATTAAATACACAATATAATATTTTCTATAAACCACAACGCACAACAAATTA
ACCACTTGAGATCAATATGAACCATACAAGGAAAATGTTAAAATCCATCTAAAAACCTCGAGCAA
AAACAAATATGAACAAATTTTGTATATATCAACAAAAGAACTACAAAATGAGATTAAACTACCGA
AACACCACAAAAAACTGTGAATTAGAGTCGAGCATCGTAAGAAAATTATCTACGAACGTAAATTA
TGTGTCCGAGTCCTATCCGATACCCAAAGAATGTAAAATTATATATAGTGAATAAGCAACATCTT
TATCAGTCGAGACGATATCA
Found at i:5689863 original size:41 final size:41
Alignment explanation
Indices: 5689768--5689848 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
5689758 TTAAAACTAA
*
5689768 AAAGCAAGAAAATAGCAAAGATGTGATATAATAAAATAAAG
1 AAAGAAAGAAAATAGCAAAGATGTGATATAATAAAATAAAG
5689809 AAAGAAAGAAAATAGCAAAGATGTGATATAATAAAATAAA
1 AAAGAAAGAAAATAGCAAAGATGTGATATAATAAAATAAA
5689849 ATAAAATAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.63, C:0.04, G:0.16, T:0.17
Consensus pattern (41 bp):
AAAGAAAGAAAATAGCAAAGATGTGATATAATAAAATAAAG
Found at i:5690851 original size:34 final size:34
Alignment explanation
Indices: 5690792--5690862 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
5690782 TTTTTTAAAG
*
5690792 TTGTTTTCTCCTTTTTATCAAGAGAGAA-TTATAA
1 TTGTTTTCTCCTTTTGATC-AGAGAGAAGTTATAA
*
5690826 TTGTTTTCTCCTTGGTTGATC-GAGAGAAGTTGTAA
1 TTGTTTTCTCCTT--TTGATCAGAGAGAAGTTATAA
5690861 TT
1 TT
5690863 CCTATTTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
34 20 0.62
35 7 0.22
36 5 0.16
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.46
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTGATCAGAGAGAAGTTATAA
Found at i:5694715 original size:13 final size:13
Alignment explanation
Indices: 5694697--5694723 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5694687 AATATTGGTC
5694697 ACCAAATTGTTGA
1 ACCAAATTGTTGA
5694710 ACCAAATTGTTGA
1 ACCAAATTGTTGA
5694723 A
1 A
5694724 AAAGTAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ACCAAATTGTTGA
Found at i:5704406 original size:17 final size:18
Alignment explanation
Indices: 5704379--5704412 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5704369 AAAATTAATT
*
5704379 TTTTATATATTTTAGATA
1 TTTTATATATTATAGATA
5704397 TTTT-TATATTATAGAT
1 TTTTATATATTATAGAT
5704413 TGAAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (18 bp):
TTTTATATATTATAGATA
Found at i:5707363 original size:2 final size:2
Alignment explanation
Indices: 5707356--5707404 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
5707346 CATCGTTTTC
5707356 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
5707398 AT AT AT A
1 AT AT AT A
5707405 ACCCTTTTGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5722654 original size:63 final size:62
Alignment explanation
Indices: 5722552--5722680 Score: 163
Period size: 63 Copynumber: 2.1 Consensus size: 62
5722542 TTTTTGTTAC
* * * *
5722552 CTATTTAATTTTGAATATTAAAGATAATTATATCCTTTTGAATAATTCAAATTAAAATAATAT
1 CTATTTAAGTTTAAATAGTAAAAATAATTATATCCTTTTGAATAATTCAAATTAAAAT-ATAT
* * *
5722615 CTATTTAAGTTTAAATAGTAAAAATAGTTTATAT-CTTTTGAATATTTTAAATTAAAATATAT
1 CTATTTAAGTTTAAATAGTAAAAATA-ATTATATCCTTTTGAATAATTCAAATTAAAATATAT
5722677 -TATT
1 CTATT
5722681 ATCTGCTTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
61 4 0.07
62 4 0.07
63 44 0.76
64 6 0.10
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (62 bp):
CTATTTAAGTTTAAATAGTAAAAATAATTATATCCTTTTGAATAATTCAAATTAAAATATAT
Found at i:5741518 original size:53 final size:53
Alignment explanation
Indices: 5741443--5741546 Score: 208
Period size: 53 Copynumber: 2.0 Consensus size: 53
5741433 TTCTTGTTAC
5741443 AGCTTCCATCAACTCCTTGATAGGGATAATTGGTTTCGGTAGTAAGTCCTTGT
1 AGCTTCCATCAACTCCTTGATAGGGATAATTGGTTTCGGTAGTAAGTCCTTGT
5741496 AGCTTCCATCAACTCCTTGATAGGGATAATTGGTTTCGGTAGTAAGTCCTT
1 AGCTTCCATCAACTCCTTGATAGGGATAATTGGTTTCGGTAGTAAGTCCTT
5741547 TGTTTGAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (53 bp):
AGCTTCCATCAACTCCTTGATAGGGATAATTGGTTTCGGTAGTAAGTCCTTGT
Found at i:5752744 original size:3 final size:3
Alignment explanation
Indices: 5752736--5752767 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5752726 TGAAGCCACC
5752736 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
5752768 GAACAGTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5761807 original size:33 final size:33
Alignment explanation
Indices: 5761765--5761828 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
5761755 GGCCTCAAAG
5761765 AATAACAATAATTTTTACCACCGAAGCCGCTAA
1 AATAACAATAATTTTTACCACCGAAGCCGCTAA
* *
5761798 AATAACAATAATTTTTATCACCGAGGCCGCT
1 AATAACAATAATTTTTACCACCGAAGCCGCT
5761829 TGCTTCGTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (33 bp):
AATAACAATAATTTTTACCACCGAAGCCGCTAA
Found at i:5762941 original size:2 final size:2
Alignment explanation
Indices: 5762934--5762970 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5762924 TGAATAAATA
5762934 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
5762971 ATGATTAAGT
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:5764356 original size:3 final size:3
Alignment explanation
Indices: 5764350--5764419 Score: 90
Period size: 3 Copynumber: 23.7 Consensus size: 3
5764340 ATAATTTTTT
* * *
5764350 TAA TAA TAA TAA TAA AAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5764398 TAA TAA TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA T-AA TAA TA
5764420 TTCAAATGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
2 4 0.07
3 52 0.90
4 2 0.03
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5764877 original size:112 final size:112
Alignment explanation
Indices: 5764743--5765300 Score: 789
Period size: 112 Copynumber: 5.0 Consensus size: 112
5764733 ATAGAGTCAT
* * *
5764743 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCA
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCA
* * * *
5764808 TTACGAACTTTCTCTGGCAATGATGATCCATCGGGTAATGAATTAAA
66 TTATGAACGTTCTCTGGCAATGCTGATCCATCGGGTGATGAATTAAA
*
5764855 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTC
* ** * **
5764920 ATTATGAACGCT-TCTGGCAATGCTGATCCATCAAGTGATGGATTTGA
65 ATTATGAACGTTCTCTGGCAATGCTGATCCATCGGGTGATGAATTAAA
* *
5764967 GCAAAATGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTTCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TTCTTCTTCAGATGAGTTCTTCTC
* *
5765032 ATTATGAAC-TTCTCTGGCAATGCTAATCCATCGGGTAATGAATTAAA
65 ATTATGAACGTTCTCTGGCAATGCTGATCCATCGGGTGATGAATTAAA
5765079 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTC
* * * **
5765144 ATTATGAACGCT-TCTGGAAATGTTGATCCATCAAGTGATGAATTAAA
65 ATTATGAACGTTCTCTGGCAATGCTGATCCATCGGGTGATGAATTAAA
* *
5765191 GCATAAGGTTCAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTC
* * * * *
5765256 ATTATGAACTTTCTCTGGTAATGGTAATCCATTGGGTGATGAATT
65 ATTATGAACGTTCTCTGGCAATGCTGATCCATCGGGTGATGAATT
5765301 CAAATATTCA
Statistics
Matches: 395, Mismatches: 44, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
111 4 0.01
112 332 0.84
113 59 0.15
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (112 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCA
TTATGAACGTTCTCTGGCAATGCTGATCCATCGGGTGATGAATTAAA
Found at i:5764995 original size:224 final size:224
Alignment explanation
Indices: 5764743--5765300 Score: 911
Period size: 224 Copynumber: 2.5 Consensus size: 224
5764733 ATAGAGTCAT
* *
5764743 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCA
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
* *
5764808 TTACGAACTTTCTCTGGCAATGATGATCCATCGGGTAATGAATTAAAGCAAAAGGTTGAACAAGT
66 TTATGAACTTTCTCTGGCAATGATAATCCATCGGGTAATGAATTAAAGCAAAAGGTTGAACAAGT
* *
5764873 TCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACGCTTCTGGC
131 TCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACGCTTCTGGA
* **
5764938 AATGCTGATCCATCAAGTGATGGATTTGA
196 AATGCTGATCCATCAAGTGATGAATTAAA
* * *
5764967 GCAAAATGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTTCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TTCCTCTTCAGATGAGTTCTTCTC
*
5765032 ATTATGAAC-TTCTCTGGCAATGCTAATCCATCGGGTAATGAATTAAAGCAAAAGGTTGAACAAG
65 ATTATGAACTTTCTCTGGCAATGATAATCCATCGGGTAATGAATTAAAGCAAAAGGTTGAACAAG
5765096 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACGCTTCTGG
130 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACGCTTCTGG
*
5765161 AAATGTTGATCCATCAAGTGATGAATTAAA
195 AAATGCTGATCCATCAAGTGATGAATTAAA
* *
5765191 GCATAAGGTTCAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTC
* * * *
5765256 ATTATGAACTTTCTCTGGTAATGGTAATCCATTGGGTGATGAATT
65 ATTATGAACTTTCTCTGGCAATGATAATCCATCGGGTAATGAATT
5765301 CAAATATTCA
Statistics
Matches: 308, Mismatches: 23, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
223 3 0.01
224 244 0.79
225 61 0.20
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (224 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGCAATGATAATCCATCGGGTAATGAATTAAAGCAAAAGGTTGAACAAGT
TCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACGCTTCTGGA
AATGCTGATCCATCAAGTGATGAATTAAA
Found at i:5766435 original size:20 final size:20
Alignment explanation
Indices: 5766389--5766443 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 20
5766379 TTTACAAAAT
* *
5766389 AAAAGAATAAATTGAATTTC
1 AAAAAAATAAATTGAATCTC
*
5766409 --GAAAATAAATTGAATCTC
1 AAAAAAATAAATTGAATCTC
5766427 AAAAAAATAAATTGAAT
1 AAAAAAATAAATTGAAT
5766444 TTAGAGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 15 0.52
20 14 0.48
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.27
Consensus pattern (20 bp):
AAAAAAATAAATTGAATCTC
Found at i:5766453 original size:20 final size:19
Alignment explanation
Indices: 5766394--5766468 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 19
5766384 AAAATAAAAG
*
5766394 AATAAATTGAATTT-CGAA
1 AATAAATTGAATTTAAGAA
* *
5766412 AATAAATTGAATCTCAAAAA
1 AATAAATTGAAT-TTAAGAA
5766432 AATAAATTGAATTTAGAGAA
1 AATAAATTGAATTTA-AGAA
5766452 AATAAACTTAGAATTTA
1 AATAAA-TT-GAATTTA
5766469 TTAATAAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
18 12 0.26
19 3 0.06
20 23 0.49
21 2 0.04
22 7 0.15
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.31
Consensus pattern (19 bp):
AATAAATTGAATTTAAGAA
Found at i:5766816 original size:18 final size:18
Alignment explanation
Indices: 5766795--5766852 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
5766785 ATCTTGACCC
*
5766795 TCTTTTTTATTTTCTTCT
1 TCTTTTTTATTTTTTTCT
*
5766813 TCTTTTTT-TTCTTTTTTT
1 TCTTTTTTATT-TTTTTCT
5766831 TCTTTATTTCATTTTTTTCT
1 TCTTT-TTT-ATTTTTTTCT
5766851 TC
1 TC
5766853 AAGCATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 2 0.06
18 18 0.55
19 3 0.09
20 8 0.24
21 2 0.06
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (18 bp):
TCTTTTTTATTTTTTTCT
Found at i:5766822 original size:15 final size:15
Alignment explanation
Indices: 5766795--5766831 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
5766785 ATCTTGACCC
5766795 TCTTTTTTATTTTCT
1 TCTTTTTTATTTTCT
5766810 TCTTCTTTT-TTTTCT
1 TCTT-TTTTATTTTCT
5766825 T-TTTTTT
1 TCTTTTTT
5766832 CTTTATTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.19
14 2 0.10
15 11 0.52
16 4 0.19
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.84
Consensus pattern (15 bp):
TCTTTTTTATTTTCT
Found at i:5766826 original size:9 final size:9
Alignment explanation
Indices: 5766797--5766851 Score: 58
Period size: 9 Copynumber: 6.0 Consensus size: 9
5766787 CTTGACCCTC
*
5766797 TTTTTTATT
1 TTTTTTCTT
5766806 TTCTTCTTCTT
1 TT-TT-TTCTT
5766817 TTTTTTCTT
1 TTTTTTCTT
5766826 TTTTTTC-T
1 TTTTTTCTT
* *
5766834 TTATTTCAT
1 TTTTTTCTT
5766843 TTTTTTCTT
1 TTTTTTCTT
5766852 CAAGCATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 7 0.18
9 22 0.56
10 4 0.10
11 6 0.15
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:5774157 original size:15 final size:15
Alignment explanation
Indices: 5774134--5774165 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5774124 TGAAATGAAT
5774134 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
5774149 AATGCATGTATGCAA
1 AATGAATGTATGCAA
5774164 AA
1 AA
5774166 GGTATTGATC
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:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:5779628 original size:3 final size:3
Alignment explanation
Indices: 5779622--5779665 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
5779612 AATTTTTTTA
5779622 AAT AAT AAT AAT AA- AAT AAT AAT AAT AAT AA- AAT -AT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
5779665 A
1 A
5779666 TTCAAATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 6 0.16
3 29 0.78
4 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:5779656 original size:14 final size:14
Alignment explanation
Indices: 5779621--5779649 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5779611 TAATTTTTTT
5779621 AAATAATAATAATA
1 AAATAATAATAATA
5779635 AAATAATAATAATA
1 AAATAATAATAATA
5779649 A
1 A
5779650 TAAAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAATAATAATAATA
Found at i:5779662 original size:14 final size:17
Alignment explanation
Indices: 5779622--5779665 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
5779612 AATTTTTTTA
5779622 AATAATAATAATAAAAT
1 AATAATAATAATAAAAT
5779639 AATAATAATAATAAAAT
1 AATAATAATAATAAAAT
5779656 -ATAAATAATA
1 AAT-AATAATA
5779666 TTCAAATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 2 0.08
17 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AATAATAATAATAAAAT
Found at i:5787005 original size:22 final size:22
Alignment explanation
Indices: 5786979--5787024 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
5786969 GAAAATATTA
5786979 GGTTGTTATTGAATTCAAATGG
1 GGTTGTTATTGAATTCAAATGG
*
5787001 GGTTGTTATTGAATTTAAATGG
1 GGTTGTTATTGAATTCAAATGG
5787023 GG
1 GG
5787025 CTGCAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.02, G:0.30, T:0.41
Consensus pattern (22 bp):
GGTTGTTATTGAATTCAAATGG
Found at i:5788260 original size:15 final size:15
Alignment explanation
Indices: 5788236--5788267 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5788226 TGGCAGATCG
*
5788236 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
5788251 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
5788266 AA
1 AA
5788268 GAAAGATCTC
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:5791490 original size:17 final size:15
Alignment explanation
Indices: 5791450--5791498 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 15
5791440 CAATAAGTAT
5791450 ATGATTATATGATAAA
1 ATGATTA-ATGATAAA
5791466 ATGTATTAATGATAATA
1 ATG-ATTAATGATAA-A
*
5791483 ATAGATTAAAGATAAA
1 AT-GATTAATGATAAA
5791499 GAAGAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 11 0.38
17 17 0.59
18 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (15 bp):
ATGATTAATGATAAA
Found at i:5792552 original size:32 final size:32
Alignment explanation
Indices: 5792516--5792585 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
5792506 AAATGATATG
*
5792516 AGCACATGAATATATGAGATCTTCCAAAGTGA
1 AGCACATGAATATATGAGAGCTTCCAAAGTGA
5792548 AGCACATGAATATATGAGAGCTTCCAAAGTGA
1 AGCACATGAATATATGAGAGCTTCCAAAGTGA
5792580 AGCACA
1 AGCACA
5792586 AGGCGATAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.21
Consensus pattern (32 bp):
AGCACATGAATATATGAGAGCTTCCAAAGTGA
Found at i:5793867 original size:64 final size:63
Alignment explanation
Indices: 5793797--5794007 Score: 230
Period size: 66 Copynumber: 3.3 Consensus size: 63
5793787 TGGACCCTTA
* *
5793797 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGG-TG
**
5793861 GTGCATCGATGCATCAAATGCATTCGATGTTTTTCATAAA-ATCCTCAGTGCATCGATGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATG--TTTCA-AAATATCCAGAGTGCATCGATGCATGGT
*
5793925 AT
63 -G
* ** *
5793927 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ATCCA-GAGTGCATCGATGCATGG--
5793990 TG
62 TG
*
5793992 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
5794008 CTTCTGAAAA
Statistics
Matches: 124, Mismatches: 14, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 47 0.38
65 15 0.12
66 54 0.44
67 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTG
Found at i:5794694 original size:24 final size:24
Alignment explanation
Indices: 5794667--5794721 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
5794657 AACAACAAAT
*
5794667 AAATTCAAAACATCCACAACCATC
1 AAATTCAAAACATCCACAAACATC
* *
5794691 AAATT-TAAACATCCAGAAACATC
1 AAATTCAAAACATCCACAAACATC
*
5794714 AAAATCAA
1 AAATTCAA
5794722 TCCAAGTTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.55, C:0.25, G:0.02, T:0.18
Consensus pattern (24 bp):
AAATTCAAAACATCCACAAACATC
Found at i:5795964 original size:34 final size:35
Alignment explanation
Indices: 5795916--5795989 Score: 141
Period size: 34 Copynumber: 2.1 Consensus size: 35
5795906 TAAGAGGTTG
5795916 GTTTGAACGAGAACGACTCGATGAAGTTCTAGGGT
1 GTTTGAACGAGAACGACTCGATGAAGTTCTAGGGT
5795951 GTTT-AACGAGAACGACTCGATGAAGTTCTAGGGT
1 GTTTGAACGAGAACGACTCGATGAAGTTCTAGGGT
5795985 GTTTG
1 GTTTG
5795990 GGATTAGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 34 0.89
35 4 0.11
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.28
Consensus pattern (35 bp):
GTTTGAACGAGAACGACTCGATGAAGTTCTAGGGT
Found at i:5801699 original size:29 final size:29
Alignment explanation
Indices: 5801656--5801736 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
5801646 TTTTATATGT
5801656 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
5801684 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
5801713 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
5801737 ATATCACATA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 7 0.14
29 37 0.76
30 5 0.10
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.46
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:5802178 original size:64 final size:63
Alignment explanation
Indices: 5802109--5802266 Score: 169
Period size: 64 Copynumber: 2.5 Consensus size: 63
5802099 TAATGAAGGT
**
5802109 ATGCATCGATGCACTACTTGTGCATCGATGCA-TAAAATGCATTCCATG-TTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCCATGTTTTTATT-TTAA-AA
5802172 G
63 G
* * * * *
5802173 ATGCATCGATACA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCCATGTTTTTATTTTAAAAG
*
5802236 AGTGCATCGATGCACTACCTAGTGCATCGAT
1 A-TGCATCGATGCACTA-CTTGTGCATCGAT
5802267 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
63 3 0.04
64 54 0.70
65 20 0.26
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCCATGTTTTTATTTTAAAAG
Found at i:5802490 original size:16 final size:16
Alignment explanation
Indices: 5802469--5802501 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5802459 TTCATCTTAA
5802469 ACCTCCAAATTCTATC
1 ACCTCCAAATTCTATC
5802485 ACCTCCAAATTCTATC
1 ACCTCCAAATTCTATC
5802501 A
1 A
5802502 TTCATATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.30
Consensus pattern (16 bp):
ACCTCCAAATTCTATC
Found at i:5803694 original size:12 final size:12
Alignment explanation
Indices: 5803671--5803704 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
5803661 TGGGGATTGA
5803671 TAAGAA-GAGTT
1 TAAGAATGAGTT
5803682 TAAGAATGAGTT
1 TAAGAATGAGTT
5803694 TAAGAATGAGT
1 TAAGAATGAGT
5803705 ATATTGGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.29
Consensus pattern (12 bp):
TAAGAATGAGTT
Found at i:5807048 original size:21 final size:21
Alignment explanation
Indices: 5807019--5807070 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
5807009 TTACGAAAGT
5807019 CACTGTAGCAGTACATCGATG
1 CACTGTAGCAGTACATCGATG
* * *
5807040 TATTGTAGCAGTGCATCGATG
1 CACTGTAGCAGTACATCGATG
5807061 CACTGTAGCA
1 CACTGTAGCA
5807071 CTGCTCATGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (21 bp):
CACTGTAGCAGTACATCGATG
Found at i:5807472 original size:19 final size:19
Alignment explanation
Indices: 5807448--5807485 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5807438 ATAACCAGAC
5807448 ACACCAGAACTGAGACGCT
1 ACACCAGAACTGAGACGCT
5807467 ACACCAGAACTGAGACGCT
1 ACACCAGAACTGAGACGCT
5807486 CCAGAATTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.32, G:0.21, T:0.11
Consensus pattern (19 bp):
ACACCAGAACTGAGACGCT
Found at i:5807491 original size:16 final size:17
Alignment explanation
Indices: 5807450--5807491 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
5807440 AACCAGACAC
5807450 ACCAGAACTGAGACGCT
1 ACCAGAACTGAGACGCT
5807467 ACACCAGAACTGAGACGCT
1 --ACCAGAACTGAGACGCT
5807486 -CCAGAA
1 ACCAGAA
5807492 TTCCTAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.26
19 17 0.74
ACGTcount: A:0.38, C:0.31, G:0.21, T:0.10
Consensus pattern (17 bp):
ACCAGAACTGAGACGCT
Found at i:5807822 original size:22 final size:22
Alignment explanation
Indices: 5807797--5807846 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
5807787 ATTGGCAGTC
5807797 GGGCTGTTATTGAATTCAAATG
1 GGGCTGTTATTGAATTCAAATG
5807819 GGGCTGTTATTGAATTCAAATG
1 GGGCTGTTATTGAATTCAAATG
5807841 GGGCTG
1 GGGCTG
5807847 CAAAATTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.24, C:0.10, G:0.32, T:0.34
Consensus pattern (22 bp):
GGGCTGTTATTGAATTCAAATG
Found at i:5809591 original size:17 final size:17
Alignment explanation
Indices: 5809569--5809612 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
5809559 ATGTAAAAAT
5809569 AAATATTTAAATTTAAA
1 AAATATTTAAATTTAAA
** **
5809586 AAATATAAAAATTTATT
1 AAATATTTAAATTTAAA
5809603 AAATATTTAA
1 AAATATTTAA
5809613 TCAAGTAGGG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTTAAATTTAAA
Found at i:5814004 original size:52 final size:52
Alignment explanation
Indices: 5813942--5814044 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
5813932 AAATTGGACA
5813942 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
*
5813994 CATAGAAATAGGAGACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
5814045 AATATTATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (52 bp):
CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
Found at i:5818483 original size:52 final size:52
Alignment explanation
Indices: 5818413--5818514 Score: 186
Period size: 52 Copynumber: 2.0 Consensus size: 52
5818403 AAATTGGACA
5818413 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
* *
5818465 CATATAAATAGGAGACTAGCCTAGAGTTAGGGGATTACAACTAATTACAA
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAA
5818515 AAATATCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.23
Consensus pattern (52 bp):
CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
Found at i:5819760 original size:152 final size:152
Alignment explanation
Indices: 5819484--5819787 Score: 599
Period size: 152 Copynumber: 2.0 Consensus size: 152
5819474 AAAAATTATT
5819484 CTTTAAATTTAATTATACAATTTTAAAAAAATAATAGAATAAATTTATCCATGACCCATCGCCGA
1 CTTTAAATTTAATTATACAATTTTAAAAAAATAATAGAATAAATTTATCCATGACCCATCGCCGA
5819549 TAAATATCACATGTAATCAGAAGCTTAACAAAGTGATTAGAATGGAATCCGAGTCCAACTTGGAT
66 TAAATATCACATGTAATCAGAAGCTTAACAAAGTGATTAGAATGGAATCCGAGTCCAACTTGGAT
5819614 TAGCAGATTGACAAACATGATA
131 TAGCAGATTGACAAACATGATA
*
5819636 CTTTAAATTTAATTATACAATTTTAAAAACATAATAGAATAAATTTATCCATGACCCATCGCCGA
1 CTTTAAATTTAATTATACAATTTTAAAAAAATAATAGAATAAATTTATCCATGACCCATCGCCGA
5819701 TAAATATCACATGTAATCAGAAGCTTAACAAAGTGATTAGAATGGAATCCGAGTCCAACTTGGAT
66 TAAATATCACATGTAATCAGAAGCTTAACAAAGTGATTAGAATGGAATCCGAGTCCAACTTGGAT
5819766 TAGCAGATTGACAAACATGATA
131 TAGCAGATTGACAAACATGATA
5819788 TGGGCAGGTC
Statistics
Matches: 151, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
152 151 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (152 bp):
CTTTAAATTTAATTATACAATTTTAAAAAAATAATAGAATAAATTTATCCATGACCCATCGCCGA
TAAATATCACATGTAATCAGAAGCTTAACAAAGTGATTAGAATGGAATCCGAGTCCAACTTGGAT
TAGCAGATTGACAAACATGATA
Found at i:5820262 original size:13 final size:14
Alignment explanation
Indices: 5820246--5820282 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
5820236 AATAAATAGT
5820246 ATATTTTATAA-CA
1 ATATTTTATAATCA
5820259 ATATATTTATAATCA
1 ATAT-TTTATAATCA
5820274 AT-TTTTATA
1 ATATTTTATA
5820283 TTTTAAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 8 0.36
15 4 0.18
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATTTTATAATCA
Found at i:5820316 original size:15 final size:15
Alignment explanation
Indices: 5820240--5820321 Score: 55
Period size: 15 Copynumber: 5.7 Consensus size: 15
5820230 AATAATAATA
*
5820240 AATAGTATATTTTAT
1 AATAATATATTTTAT
*
5820255 AACAATATA-TTTAT
1 AATAATATATTTTAT
*
5820269 AATCA-AT-TTTTAT
1 AATAATATATTTTAT
** * * *
5820282 -ATTTTAAATGTTAA
1 AATAATATATTTTAT
5820296 AATAATATATTTTAT
1 AATAATATATTTTAT
*
5820311 AATAATTTATT
1 AATAATATATT
5820322 GCATTTTTTT
Statistics
Matches: 48, Mismatches: 15, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
12 2 0.04
13 8 0.17
14 12 0.25
15 26 0.54
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
AATAATATATTTTAT
Found at i:5821186 original size:28 final size:29
Alignment explanation
Indices: 5821151--5821237 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 29
5821141 ATCTATCGAA
5821151 ACTGAAATTTGATAAACTACACGTTTAAT
1 ACTGAAATTTGATAAACTACACGTTTAAT
* *
5821180 ACT-AAATTTGTTATCAATCTA-TCG---AA-
1 ACTGAAATTTG--AT-AAACTACACGTTTAAT
5821206 ACTGAAATTTGATAAACTACACGTTTAAT
1 ACTGAAATTTGATAAACTACACGTTTAAT
5821235 ACT
1 ACT
5821238 TAAACTAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 18
0.67 0.06 0.27
Matches are distributed among these distances:
24 5 0.11
25 4 0.09
26 3 0.07
27 9 0.20
28 9 0.20
29 6 0.13
30 4 0.09
31 5 0.11
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (29 bp):
ACTGAAATTTGATAAACTACACGTTTAAT
Found at i:5821215 original size:55 final size:55
Alignment explanation
Indices: 5821131--5821237 Score: 214
Period size: 55 Copynumber: 1.9 Consensus size: 55
5821121 TAAATCATAT
5821131 TTTGTTATCAATCTATCGAAACTGAAATTTGATAAACTACACGTTTAATACTAAA
1 TTTGTTATCAATCTATCGAAACTGAAATTTGATAAACTACACGTTTAATACTAAA
5821186 TTTGTTATCAATCTATCGAAACTGAAATTTGATAAACTACACGTTTAATACT
1 TTTGTTATCAATCTATCGAAACTGAAATTTGATAAACTACACGTTTAATACT
5821238 TAAACTAGTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.37
Consensus pattern (55 bp):
TTTGTTATCAATCTATCGAAACTGAAATTTGATAAACTACACGTTTAATACTAAA
Found at i:5821216 original size:27 final size:27
Alignment explanation
Indices: 5821131--5821216 Score: 81
Period size: 27 Copynumber: 3.1 Consensus size: 27
5821121 TAAATCATAT
5821131 TTTGTTATCAATCTATCGAAACTGAAA
1 TTTGTTATCAATCTATCGAAACTGAAA
* *
5821158 TTTG--AT-AAACTACACGTTTAATACT-AAA
1 TTTGTTATCAATCTA-TCG---AA-ACTGAAA
5821186 TTTGTTATCAATCTATCGAAACTGAAA
1 TTTGTTATCAATCTATCGAAACTGAAA
5821213 TTTG
1 TTTG
5821217 ATAAACTACA
Statistics
Matches: 46, Mismatches: 4, Indels: 18
0.68 0.06 0.26
Matches are distributed among these distances:
24 5 0.11
25 4 0.09
26 3 0.07
27 13 0.28
28 9 0.20
29 3 0.07
30 4 0.09
31 5 0.11
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.38
Consensus pattern (27 bp):
TTTGTTATCAATCTATCGAAACTGAAA
Found at i:5822020 original size:24 final size:24
Alignment explanation
Indices: 5821976--5822021 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
5821966 ACTAATTTTT
*
5821976 ATCTTATATTTTATATCAAGTTTA
1 ATCTTATATTTTAAATCAAGTTTA
5822000 ATCTATATATTTTAAAT-AAGTT
1 ATCT-TATATTTTAAATCAAGTT
5822022 ATATTTATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (24 bp):
ATCTTATATTTTAAATCAAGTTTA
Found at i:5822803 original size:82 final size:83
Alignment explanation
Indices: 5822717--5822871 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 83
5822707 CGTTTTTATC
* * * *
5822717 AAACGCCGCAATAAAGT-GGTAAATTAACGGCGTTTATACCACAAACGCCGTAATATATTA-ACA
1 AAACGCCGCAATAAA-TCGATAAATTAACGGCATTTATACCACAAACGCCGTAATAGAGTACACA
5822780 TATAGTGGCGTTTTAGCCA
65 TATAGTGGCGTTTTAGCCA
* * * *
5822799 AAACGCCGTAATAGATCGATAAATTAGCGGCATTTATACCACAAATGCCGTAATAGAGTACACAT
1 AAACGCCGCAATAAATCGATAAATTAACGGCATTTATACCACAAACGCCGTAATAGAGTACACAT
5822864 ATAGTGGC
66 ATAGTGGC
5822872 ATTTATTCTT
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
81 1 0.02
82 50 0.79
83 12 0.19
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (83 bp):
AAACGCCGCAATAAATCGATAAATTAACGGCATTTATACCACAAACGCCGTAATAGAGTACACAT
ATAGTGGCGTTTTAGCCA
Found at i:5822873 original size:42 final size:41
Alignment explanation
Indices: 5822749--5822917 Score: 141
Period size: 42 Copynumber: 4.1 Consensus size: 41
5822739 ATTAACGGCG
* * *
5822749 TTTATACCACAAACGCCGTAATATATTAACATATAGTGGCG
1 TTTATACCACAAACGCCGTAATAGAGTAACATATAGTGGCA
*
5822790 TTT-TAGCCA-AAACGCCGTAATAGATCGATAA-AT-TAGCGGCA
1 TTTATA-CCACAAACGCCGTAATAGA--G-TAACATATAGTGGCA
*
5822831 TTTATACCACAAATGCCGTAATAGAGTACACATATAGTGGCA
1 TTTATACCACAAACGCCGTAATAGAGTA-ACATATAGTGGCA
* * * * * *
5822873 TTTATTCTTA-AAACGCCGCAATAGTGATAATAAATAGTGGCA
1 TTTATAC-CACAAACGCCGTAATAGAG-TAACATATAGTGGCA
5822915 TTT
1 TTT
5822918 TTAGACAAAC
Statistics
Matches: 104, Mismatches: 13, Indels: 21
0.75 0.09 0.15
Matches are distributed among these distances:
39 2 0.02
40 18 0.17
41 20 0.19
42 58 0.56
43 6 0.06
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29
Consensus pattern (41 bp):
TTTATACCACAAACGCCGTAATAGAGTAACATATAGTGGCA
Found at i:5822902 original size:82 final size:80
Alignment explanation
Indices: 5822717--5822902 Score: 212
Period size: 82 Copynumber: 2.2 Consensus size: 80
5822707 CGTTTTTATC
* * * *
5822717 AAACGCCGCAATAAAGTGGTAAATTAACGGCGTTTATACCACAAACGCCGTAATATATTAACATA
1 AAACGCCGCAAT--AGTGATAAATTAACGGCATTTATACCACAAACGCCGTAATAGAGTAACATA
*
5822782 TAGTGGCGTTTTAGCCA
64 TAGTGGCATTTTAGCCA
* * *
5822799 AAACGCCGTAATAGATCGATAAATTAGCGGCATTTATACCACAAATGCCGTAATAGAGTACACAT
1 AAACGCCGCAATAG-T-GATAAATTAACGGCATTTATACCACAAACGCCGTAATAGAGTA-ACAT
* *
5822864 ATAGTGGCA-TTTATTCTTA
63 ATAGTGGCATTTTA-GC-CA
5822883 AAACGCCGCAATAGTGATAA
1 AAACGCCGCAATAGTGATAA
5822903 TAAATAGTGG
Statistics
Matches: 88, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
80 2 0.02
81 1 0.01
82 57 0.65
83 14 0.16
84 14 0.16
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.26
Consensus pattern (80 bp):
AAACGCCGCAATAGTGATAAATTAACGGCATTTATACCACAAACGCCGTAATAGAGTAACATATA
GTGGCATTTTAGCCA
Found at i:5822952 original size:41 final size:41
Alignment explanation
Indices: 5822883--5823064 Score: 199
Period size: 41 Copynumber: 4.5 Consensus size: 41
5822873 TTTATTCTTA
* * *
5822883 AAACGCCGCAATAGTGATAATAAATAGTGGCATTTTTAGAC
1 AAACGCCGCAATAATGTTAATCAATAGTGGCATTTTTAGAC
* * *
5822924 AAACGCTGCAATAATGTTAATCACTAGTGGCATTTTTAGAA
1 AAACGCCGCAATAATGTTAATCAATAGTGGCATTTTTAGAC
* * * *
5822965 AAACACCGCAATAGTTTTAATCAATAGTGGCGTTTTTTA-AC
1 AAACGCCGCAATAATGTTAATCAATAGTGGC-ATTTTTAGAC
* * ** *
5823006 AAACGCCACAATAATG-TAATCAATAGTGGCGTTTTTTTAT
1 AAACGCCGCAATAATGTTAATCAATAGTGGCATTTTTAGAC
5823046 AAACGCCGCAA-AATGTTAA
1 AAACGCCGCAATAATGTTAA
5823065 ATATATAGTC
Statistics
Matches: 117, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
39 9 0.08
40 28 0.24
41 74 0.63
42 6 0.05
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (41 bp):
AAACGCCGCAATAATGTTAATCAATAGTGGCATTTTTAGAC
Found at i:5823042 original size:82 final size:82
Alignment explanation
Indices: 5822864--5823041 Score: 216
Period size: 82 Copynumber: 2.2 Consensus size: 82
5822854 GAGTACACAT
*** *
5822864 ATAGTGGCATTTATTCTTAAAACGCCGCAATAGTGATAATAAATAGTGGCATTTTTAGACAAACG
1 ATAGTGGCATTT-TTAGAAAAACACCGCAATAGTGATAATAAATAGTGGCATTTTTAGACAAACG
**
5822929 CTGCAATAATGTTAATCA
65 CCACAATAATGTTAATCA
* ** * *
5822947 CTAGTGGCATTTTTAGAAAAACACCGCAATAGTTTTAATCAATAGTGGCGTTTTTTA-ACAAACG
1 ATAGTGGCATTTTTAGAAAAACACCGCAATAGTGATAATAAATAGTGGC-ATTTTTAGACAAACG
5823011 CCACAATAATG-TAATCA
65 CCACAATAATGTTAATCA
*
5823028 ATAGTGGCGTTTTT
1 ATAGTGGCATTTTT
5823042 TTATAAACGC
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
81 18 0.22
82 46 0.57
83 17 0.21
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (82 bp):
ATAGTGGCATTTTTAGAAAAACACCGCAATAGTGATAATAAATAGTGGCATTTTTAGACAAACGC
CACAATAATGTTAATCA
Found at i:5824609 original size:42 final size:42
Alignment explanation
Indices: 5824441--5824610 Score: 141
Period size: 42 Copynumber: 4.1 Consensus size: 42
5824431 GTTTGGTAAC
* *
5824441 AAACGCCGCAGTAGAATAGTTCCTTAGTGGTGTTTTTGAT-AT
1 AAACGCCGCAATAGAATAGTTCCTTAGTGGCGTTTTT-ATAAT
* * * *** *
5824483 AAACGCCGTAATAGAGTTGTAATTTAGTGGC-TTTTTGTAAT
1 AAACGCCGCAATAGAATAGTTCCTTAGTGGCGTTTTTATAAT
* * ** * *
5824524 AAATGTCGCAATAGTGT-GTCCCTTAGTGGCGTTTTTGTAAT
1 AAACGCCGCAATAGAATAGTTCCTTAGTGGCGTTTTTATAAT
* *
5824565 AAACGCCGCAGTAGAATAGTTCCTTTGTGGCGTTTTTA-ATAT
1 AAACGCCGCAATAGAATAGTTCCTTAGTGGCGTTTTTATA-AT
5824607 AAAC
1 AAAC
5824611 ATTGCAAATG
Statistics
Matches: 100, Mismatches: 24, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
40 11 0.11
41 43 0.43
42 46 0.46
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.36
Consensus pattern (42 bp):
AAACGCCGCAATAGAATAGTTCCTTAGTGGCGTTTTTATAAT
Found at i:5831984 original size:19 final size:20
Alignment explanation
Indices: 5831962--5832029 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
5831952 AGCAGCAGCG
5831962 GAAGCAGAGACAG-CAAAGA
1 GAAGCAGAGACAGACAAAGA
* *
5831981 GAAGCAGCGGCAGCACAAAGA
1 GAAGCAGAGACAG-ACAAAGA
* * *
5832002 GAAGCAGCGGCATCACAAAGA
1 GAAGCAGAGACA-GACAAAGA
5832023 GAAGCAG
1 GAAGCAG
5832030 CATATCAGCA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 11 0.26
21 32 0.74
ACGTcount: A:0.46, C:0.21, G:0.32, T:0.01
Consensus pattern (20 bp):
GAAGCAGAGACAGACAAAGA
Found at i:5832001 original size:21 final size:21
Alignment explanation
Indices: 5831975--5832030 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
5831965 GCAGAGACAG
5831975 CAAAGAGAAGCAGCGGCAGCA
1 CAAAGAGAAGCAGCGGCAGCA
*
5831996 CAAAGAGAAGCAGCGGCATCA
1 CAAAGAGAAGCAGCGGCAGCA
5832017 CAAAGAGAAGCAGC
1 CAAAGAGAAGCAGC
5832031 ATATCAGCAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.45, C:0.23, G:0.30, T:0.02
Consensus pattern (21 bp):
CAAAGAGAAGCAGCGGCAGCA
Found at i:5832498 original size:43 final size:43
Alignment explanation
Indices: 5832435--5832772 Score: 279
Period size: 43 Copynumber: 7.9 Consensus size: 43
5832425 TGTTTTTAGC
* *
5832435 AAAAACGCCGCAAAAAATCAATACCTATTGCGGCGTTTGTGAG
1 AAAAACGCCGCAAAATATCAACACCTATTGCGGCGTTTGTGAG
** * * * * * **
5832478 AAAAACGCATCAAAACATCAAAATCTACTACGATGTTTGTG-G
1 AAAAACGCCGCAAAATATCAACACCTATTGCGGCGTTTGTGAG
* * *
5832520 AATAAGCGCCGCAAAACATCAACATCTATTGCGGCGTTTGTG-G
1 AA-AAACGCCGCAAAATATCAACACCTATTGCGGCGTTTGTGAG
* * * *
5832563 AAAAACGCCGTAAAACATCAACACCTACTGTGGCGTTT-TAGAG
1 AAAAACGCCGCAAAATATCAACACCTATTGCGGCGTTTGT-GAG
* * ** * * *
5832606 AAAAACGCCACTAAATATCATTACCTATTACGGCGTTTATCTA-
1 AAAAACGCCGCAAAATATCAACACCTATTGCGGCGTTTGT-GAG
* * * **
5832649 AAAAACGCCGCTAAATATCAACACCTATTGCGGCATTTTTCTG
1 AAAAACGCCGCAAAATATCAACACCTATTGCGGCGTTTGTGAG
* * * * *
5832692 ACAAACGCCGCTAAATATCAACACCTATTGTGGCGTTTGTCAC
1 AAAAACGCCGCAAAATATCAACACCTATTGCGGCGTTTGTGAG
* * *
5832735 ACAAACGCCGCTAAATATCAATACCTATTGCGGCGTTT
1 AAAAACGCCGCAAAATATCAACACCTATTGCGGCGTTT
5832773 TTTGTTTAAA
Statistics
Matches: 241, Mismatches: 49, Indels: 10
0.80 0.16 0.03
Matches are distributed among these distances:
41 1 0.00
42 35 0.15
43 203 0.84
44 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.25
Consensus pattern (43 bp):
AAAAACGCCGCAAAATATCAACACCTATTGCGGCGTTTGTGAG
Found at i:5832760 original size:129 final size:128
Alignment explanation
Indices: 5832526--5832772 Score: 318
Period size: 129 Copynumber: 1.9 Consensus size: 128
5832516 GTGGAATAAG
* *
5832526 CGCCGCAAAACATCAACATCTATTGCGGCGTTTGTGGAAAAACGCCGTAAAACATCAACACCTAC
1 CGCCGCAAAACATCAACACCTATTGCGGCATTTGTGGAAAAACGCCGTAAAACATCAACACCTAC
* * *
5832591 TGTGGCGTTTTAGAGAAAAACGCCACTAAATATCATTACCTATTACGGCGTTTATCTAAAAAA
66 TGTGGCGTTTTACACAAAAACGCCACTAAATATCAATACCTATTACGGCGTTTATCTAAAAAA
* * * * * *
5832654 CGCCGCTAAATATCAACACCTATTGCGGCATTTTTCTGACAAACGCCGCT-AAATATCAACACCT
1 CGCCGCAAAACATCAACACCTATTGCGGCATTTGT-GGAAAAACGCCG-TAAAACATCAACACCT
* * * *
5832718 ATTGTGGCGTTTGT-CACACAAACGCCGCTAAATATCAATACCTATTGCGGCGTTT
64 ACTGTGGCGTTT-TACACAAAAACGCCACTAAATATCAATACCTATTACGGCGTTT
5832773 TTTGTTTAAA
Statistics
Matches: 101, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
128 30 0.30
129 69 0.68
130 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (128 bp):
CGCCGCAAAACATCAACACCTATTGCGGCATTTGTGGAAAAACGCCGTAAAACATCAACACCTAC
TGTGGCGTTTTACACAAAAACGCCACTAAATATCAATACCTATTACGGCGTTTATCTAAAAAA
Found at i:5843845 original size:10 final size:10
Alignment explanation
Indices: 5843830--5843859 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
5843820 TTTTAATTGA
5843830 TATTATTTTT
1 TATTATTTTT
5843840 TATTATTTTT
1 TATTATTTTT
5843850 TATTATTTTT
1 TATTATTTTT
5843860 CACTTATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TATTATTTTT
Found at i:5845365 original size:42 final size:42
Alignment explanation
Indices: 5845209--5845394 Score: 153
Period size: 43 Copynumber: 4.3 Consensus size: 42
5845199 TGACAACATA
* * * *
5845209 TAGCGGCGTTTTTTCAACAAACGCCGCA-ATAGGCT-TTGATGTT
1 TAGCGGCG-TTTTCCTACAAACGCCGCAGA-A-GATGTTGATATT
* * * *
5845252 TAGCGGCGTTTTCTTCT-CAAACGCTGCAGTAGATGTTTATTTT
1 TAGCGGCGTTTTC--CTACAAACGCCGCAGAAGATGTTGATATT
** *
5845295 TCCCGGCGTTTTTCCTACAAACGTCGCAGAAGATGTTGATATT
1 TAGCGGCG-TTTTCCTACAAACGCCGCAGAAGATGTTGATATT
* *
5845338 TAGCGGCGTTTTCCTACAAACGCCGCAGAATATGTCTTGAGATT
1 TAGCGGCGTTTTCCTACAAACGCCGCAGAAGATG--TTGATATT
*
5845382 TAGCGGCATTTTC
1 TAGCGGCGTTTTC
5845395 GTCGAAAACG
Statistics
Matches: 115, Mismatches: 20, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
42 32 0.28
43 58 0.50
44 25 0.22
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (42 bp):
TAGCGGCGTTTTCCTACAAACGCCGCAGAAGATGTTGATATT
Found at i:5845816 original size:21 final size:21
Alignment explanation
Indices: 5845792--5845832 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5845782 ATATATTACT
*
5845792 TCTCTCTGTTCTGCCGCTGCC
1 TCTCTCTGTGCTGCCGCTGCC
*
5845813 TCTCTCTGTGCTGCCTCTGC
1 TCTCTCTGTGCTGCCGCTGC
5845833 TTCCGCTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.41, G:0.20, T:0.39
Consensus pattern (21 bp):
TCTCTCTGTGCTGCCGCTGCC
Found at i:5845845 original size:21 final size:20
Alignment explanation
Indices: 5845821--5845868 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 20
5845811 CCTCTCTCTG
5845821 TGCTGC-CT-CTGCTTCCGC
1 TGCTGCTCTACTGCTTCCGC
5845839 TGCTGCTCTAGCTGCTTCCGC
1 TGCTGCTCTA-CTGCTTCCGC
5845860 TGCTGCTCT
1 TGCTGCTCT
5845869 CTCTCCTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.22
19 2 0.07
21 19 0.70
ACGTcount: A:0.02, C:0.40, G:0.23, T:0.35
Consensus pattern (20 bp):
TGCTGCTCTACTGCTTCCGC
Found at i:5845877 original size:21 final size:21
Alignment explanation
Indices: 5845827--5845878 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
5845817 TCTGTGCTGC
5845827 CTCTGCTTCCGCTGCTGCTCT
1 CTCTGCTTCCGCTGCTGCTCT
**
5845848 AGCTGCTTCCGCTGCTGCTCT
1 CTCTGCTTCCGCTGCTGCTCT
*
5845869 CTCTCCTTCC
1 CTCTGCTTCC
5845879 CTTGCTTCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.02, C:0.44, G:0.17, T:0.37
Consensus pattern (21 bp):
CTCTGCTTCCGCTGCTGCTCT
Found at i:5848611 original size:14 final size:14
Alignment explanation
Indices: 5848592--5848626 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
5848582 TCGTTATATC
5848592 AACTTATATTTGGG
1 AACTTATATTTGGG
5848606 AACTTATATTTGGG
1 AACTTATATTTGGG
5848620 AACTTAT
1 AACTTAT
5848627 GAAGTGGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (14 bp):
AACTTATATTTGGG
Found at i:5849700 original size:42 final size:42
Alignment explanation
Indices: 5849637--5849757 Score: 140
Period size: 42 Copynumber: 2.9 Consensus size: 42
5849627 ACAATGGCGG
* * *
5849637 CGTTTATTACAAAAACGCCCCTAAAACGCCAAACT-TAT-ACGA
1 CGTTTATTACAAAAACACCCCTAAAACACAAAACTAT-TGA-GA
*
5849679 CGTTTATTACAAAAACACCCCTAAAACACAAAACTATTGAGG
1 CGTTTATTACAAAAACACCCCTAAAACACAAAACTATTGAGA
* **
5849721 CGTTTATTA-AAAAACACCACTAAATGACAAAACTATT
1 CGTTTATTACAAAAACACCCCTAAAACACAAAACTATT
5849758 ACGGCATTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
41 25 0.36
42 43 0.61
43 2 0.03
ACGTcount: A:0.45, C:0.24, G:0.08, T:0.23
Consensus pattern (42 bp):
CGTTTATTACAAAAACACCCCTAAAACACAAAACTATTGAGA
Found at i:5849838 original size:41 final size:41
Alignment explanation
Indices: 5849793--5849870 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
5849783 TAAATAACAT
* *
5849793 GGATATAACGGCGTTTGGTCACAAACGCCACTAAAGTATAA
1 GGATATAACGGCGTTTGCTCAAAAACGCCACTAAAGTATAA
** *
5849834 GGATATTGCGGCGTTTTCTCAAAAACGCCACTAAAGT
1 GGATATAACGGCGTTTGCTCAAAAACGCCACTAAAGT
5849871 TTATTGCTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (41 bp):
GGATATAACGGCGTTTGCTCAAAAACGCCACTAAAGTATAA
Found at i:5849901 original size:41 final size:41
Alignment explanation
Indices: 5849811--5849909 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 41
5849801 CGGCGTTTGG
* *
5849811 TCACAAACGCCACTAAAGTATAAGGATATTGCGGCGTTTTC
1 TCACAAACGCCACTAAAGTATAAGGATATTGCGGCATTTTA
* * ** * *
5849852 TCAAAAACGCCACTAAAGTTTATTGCTATTTCGGCATTTTA
1 TCACAAACGCCACTAAAGTATAAGGATATTGCGGCATTTTA
5849893 TCACAAACGCCACTAAA
1 TCACAAACGCCACTAAA
5849910 TTAATCATAT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.28
Consensus pattern (41 bp):
TCACAAACGCCACTAAAGTATAAGGATATTGCGGCATTTTA
Found at i:5850284 original size:18 final size:18
Alignment explanation
Indices: 5850263--5850301 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5850253 CAAATGTTTA
5850263 ATAAAAATACTAATCTAC
1 ATAAAAATACTAATCTAC
* * *
5850281 ATAATAATCCTAGTCTAC
1 ATAAAAATACTAATCTAC
5850299 ATA
1 ATA
5850302 TACTAAATTT
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:0.49, C:0.18, G:0.03, T:0.31
Consensus pattern (18 bp):
ATAAAAATACTAATCTAC
Found at i:5851232 original size:22 final size:22
Alignment explanation
Indices: 5851207--5851251 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
5851197 TTCAGAAGGT
5851207 ATTATTTTCCTATTAGAAAGCA
1 ATTATTTTCCTATTAGAAAGCA
* *
5851229 ATTATTTTTCTATTCGAAAGCA
1 ATTATTTTCCTATTAGAAAGCA
5851251 A
1 A
5851252 AAAAACACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (22 bp):
ATTATTTTCCTATTAGAAAGCA
Found at i:5852106 original size:23 final size:23
Alignment explanation
Indices: 5852080--5852124 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
5852070 CACCACAGCT
* *
5852080 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATACACCGAAGTGCCG
* *
5852103 CGTAGAATTACACCGTAGTGCC
1 CGTAGAAATACACCGAAGTGCC
5852125 ATATAATAAT
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:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCG
Found at i:5852844 original size:21 final size:21
Alignment explanation
Indices: 5852820--5852862 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5852810 TTCATATTCG
* *
5852820 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
5852841 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
5852862 T
1 T
5852863 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:5860735 original size:82 final size:79
Alignment explanation
Indices: 5860649--5860907 Score: 250
Period size: 82 Copynumber: 3.1 Consensus size: 79
5860639 CTTTTTGTAC
* * *
5860649 AAACGCCACTA-AAAAAACCCTATTGCGGCGTTTCTTTGATAAACGCCACTAAATTACTTCTATA
1 AAACGCCACTATAAACAACACTATTGCGGCGTTT-TTT-ATAAACGCCGCTAAATTACTTCTAT-
* *
5860713 TAGCGTCATTTGTTGAAT
63 TA-CGTCGTTTGTTGAAA
* * * * * **
5860731 AAACGCCACTATAAACAACATTATCGCGACGTTTTTATACAAACGCCGCAAAATTAACAAACTAT
1 AAACGCCACTATAAACAACACTATTGCGGCGTTTTT-TATAAACGCCGCTAAATT-AC-TTCTAT
* *
5860796 TACGGCGTTTGTTGAAG
63 TACGTCGTTTGTTGAAA
* *
5860813 AAACGTCACTATAAACAACTCTATTGCGGCGTTTTAGTTATAAACGCCGCTAAATTACTACTCTA
1 AAACGCCACTATAAACAACACTATTGCGGCGTTTT--TTATAAACGCCGCTAAATTACT--TCTA
*
5860878 TTACGTCGTTTGTTTAAAA
62 TTACGTCGTTTG-TTGAAA
5860897 AAACGCCACTA
1 AAACGCCACTA
5860908 AAGTATATTT
Statistics
Matches: 142, Mismatches: 26, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
82 71 0.50
83 52 0.37
84 19 0.13
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Consensus pattern (79 bp):
AAACGCCACTATAAACAACACTATTGCGGCGTTTTTTATAAACGCCGCTAAATTACTTCTATTAC
GTCGTTTGTTGAAA
Found at i:5872644 original size:13 final size:13
Alignment explanation
Indices: 5872614--5872646 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5872604 TCGTTTTCAT
*
5872614 TTTTTTATTTTTA
1 TTTTTTAATTTTA
5872627 -TTTTTAATTTTA
1 TTTTTTAATTTTA
5872639 TTTTTTAA
1 TTTTTTAA
5872647 AATGCTAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTAATTTTA
Found at i:5873277 original size:17 final size:17
Alignment explanation
Indices: 5873251--5873297 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
5873241 ATCTTCTTTA
5873251 TTTTCACTAT-AAATTACT
1 TTTTC-CTATCAAATT-CT
*
5873269 TTTTCCTATCCAATTCT
1 TTTTCCTATCAAATTCT
5873286 TTTTCC-ATCAAA
1 TTTTCCTATCAAA
5873298 ACCCCCCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 5 0.19
17 12 0.46
18 9 0.35
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTCCTATCAAATTCT
Found at i:5882461 original size:72 final size:72
Alignment explanation
Indices: 5882367--5882505 Score: 181
Period size: 72 Copynumber: 1.9 Consensus size: 72
5882357 AGAACAAAGT
* * * * * * *
5882367 AAAATTTTTAGTGAGTTTAACGAGCAACGAATTGAGTTTAGCAACAAGTTTTTTTAACGAGCACG
1 AAAATTTTTAATGAGCTTAACGAACAACAAATCGAGTTGAACAACAA-TTTTTTTAACGAGCACG
5882432 AGTCGAAC
65 AGTCGAAC
* *
5882440 AAAA-TTTTAATGAGCTTAACGAACAACAAATCGGGTTGAACAATAATTTTTTTAACGAGCACGA
1 AAAATTTTTAATGAGCTTAACGAACAACAAATCGAGTTGAACAACAATTTTTTTAACGAGCACGA
5882504 GT
66 GT
5882506 TGAGCACTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
71 20 0.35
72 33 0.58
73 4 0.07
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (72 bp):
AAAATTTTTAATGAGCTTAACGAACAACAAATCGAGTTGAACAACAATTTTTTTAACGAGCACGA
GTCGAAC
Found at i:5882791 original size:170 final size:170
Alignment explanation
Indices: 5882505--5882848 Score: 564
Period size: 170 Copynumber: 2.0 Consensus size: 170
5882495 CGAGCACGAG
* * * *
5882505 TTGAGCACTATCCAACTCACCATCGACTCGCTCAATAAGCACCATATTTCTATATCTGTCAAATT
1 TTGAGCACTATCCAACTCACCATCGACTCGCTCAATAAACACCATAGTTCCATATATGTCAAATT
*
5882570 AAAAAGAATACATATGTTATGGCATGTGGTGCATATTTGTAAAACTTTGTGGTAAGCTGCAAGAA
66 AAAAAGAATACATATGTTATGGCATGTAGTGCATATTTGTAAAACTTTGTGGTAAGCTGCAAGAA
5882635 TTTAAATGGTGACACATAAACCACCATTTTCAA-ATAAAGA
131 TTTAAATGGTGACACATAAACCACCATTTTCAACA-AAAGA
* * * *
5882675 TTGAGCACTATCTAATTCACCATCGACTCGCTCGATAAACACCATAGTTCCATATATGTCAGATT
1 TTGAGCACTATCCAACTCACCATCGACTCGCTCAATAAACACCATAGTTCCATATATGTCAAATT
*
5882740 AAAAAGAATACATATGTTATGGCATGTAGTGCATATTTGTAAAAGTTTGTGGTAAGCTGCAAGAA
66 AAAAAGAATACATATGTTATGGCATGTAGTGCATATTTGTAAAACTTTGTGGTAAGCTGCAAGAA
* *
5882805 TTTAAATGTTGACACATGAACCACCATTTTCAACAAAAGA
131 TTTAAATGGTGACACATAAACCACCATTTTCAACAAAAGA
5882845 TTGA
1 TTGA
5882849 AGCATCTTAT
Statistics
Matches: 161, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
170 160 0.99
171 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (170 bp):
TTGAGCACTATCCAACTCACCATCGACTCGCTCAATAAACACCATAGTTCCATATATGTCAAATT
AAAAAGAATACATATGTTATGGCATGTAGTGCATATTTGTAAAACTTTGTGGTAAGCTGCAAGAA
TTTAAATGGTGACACATAAACCACCATTTTCAACAAAAGA
Found at i:5883646 original size:22 final size:21
Alignment explanation
Indices: 5883612--5883652 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
5883602 ATAATTATTT
5883612 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
5883633 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
5883653 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:5883772 original size:22 final size:21
Alignment explanation
Indices: 5883738--5883778 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
5883728 ATAATTATTT
5883738 AAAAAATTAAATAAAAATATC
1 AAAAAATTAAATAAAAATATC
*
5883759 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
5883779 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATC
Found at i:5883788 original size:126 final size:126
Alignment explanation
Indices: 5883563--5883815 Score: 470
Period size: 126 Copynumber: 2.0 Consensus size: 126
5883553 ATTCAACTGG
* *
5883563 TCGAATCGGTTTGATCGGTCGGAAGAATCGGACGACGTCATAATTATTTAAAAAATTAAATAAAA
1 TCGAATCGGTCTGACCGGTCGGAAGAATCGGACGACGTCATAATTATTTAAAAAATTAAATAAAA
5883628 ATACCAAAAATATTTAATAAAAATAATTTTTTATATCACAAGTCATATTCAAAGCAAGTCA
66 ATACCAAAAATATTTAATAAAAATAATTTTTTATATCACAAGTCATATTCAAAGCAAGTCA
*
5883689 TCGAATCGGTCTGACCGGTCGGAAGAATCGGATGACGTCATAATTATTTAAAAAATTAAATAAAA
1 TCGAATCGGTCTGACCGGTCGGAAGAATCGGACGACGTCATAATTATTTAAAAAATTAAATAAAA
*
5883754 ATATCAAAAATATTTAATAAAAATAATTTTTTATATCACAAGTCATATTCAAAGCAAGTCA
66 ATACCAAAAATATTTAATAAAAATAATTTTTTATATCACAAGTCATATTCAAAGCAAGTCA
5883815 T
1 T
5883816 AACATATATA
Statistics
Matches: 123, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 123 1.00
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (126 bp):
TCGAATCGGTCTGACCGGTCGGAAGAATCGGACGACGTCATAATTATTTAAAAAATTAAATAAAA
ATACCAAAAATATTTAATAAAAATAATTTTTTATATCACAAGTCATATTCAAAGCAAGTCA
Found at i:5893272 original size:29 final size:29
Alignment explanation
Indices: 5893239--5893412 Score: 305
Period size: 29 Copynumber: 5.9 Consensus size: 29
5893229 CAGTGGCAAC
*
5893239 ATAGGTCGCCATGCACGCCTGGCGTCCTT
1 ATAGGTCGCCATGCACGCCCGGCGTCCTT
5893268 ATAGGTCGCCATGCACGCCCGGCGTCCTT
1 ATAGGTCGCCATGCACGCCCGGCGTCCTT
5893297 ATAGGTCGCCATGCACGCCCGGCGTCCTT
1 ATAGGTCGCCATGCACGCCCGGCGTCCTT
5893326 ATAGGTCGCCATGCACGCCCGGCGTCCTT
1 ATAGGTCGCCATGCACGCCCGGCGTCCTT
5893355 ATAGGTCGCCATGCACACGCCCGGCGTCC-T
1 ATAGGTCGCCATG--CACGCCCGGCGTCCTT
5893385 ATAAGGTCGCCATGCACGCCCGGCGTCC
1 AT-AGGTCGCCATGCACGCCCGGCGTCC
5893413 ATCATTATTT
Statistics
Matches: 141, Mismatches: 1, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
29 113 0.80
30 3 0.02
31 25 0.18
ACGTcount: A:0.15, C:0.38, G:0.28, T:0.20
Consensus pattern (29 bp):
ATAGGTCGCCATGCACGCCCGGCGTCCTT
Found at i:5893470 original size:31 final size:31
Alignment explanation
Indices: 5893435--5893499 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
5893425 CCTGGTTCTT
5893435 TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
1 TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
5893466 TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
1 TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
5893497 TGC
1 TGC
5893500 TATGCATGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.03, C:0.29, G:0.32, T:0.35
Consensus pattern (31 bp):
TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
Found at i:5893714 original size:12 final size:12
Alignment explanation
Indices: 5893697--5893721 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5893687 CCGACGACAT
5893697 GGTAGGTGGTAG
1 GGTAGGTGGTAG
5893709 GGTAGGTGGTAG
1 GGTAGGTGGTAG
5893721 G
1 G
5893722 TCGCCATGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.60, T:0.24
Consensus pattern (12 bp):
GGTAGGTGGTAG
Found at i:5893800 original size:35 final size:35
Alignment explanation
Indices: 5893761--5893828 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
5893751 TCCTGCATCG
5893761 CGACCAAGCTTTAACTGTATCACTCATGCATGCAA
1 CGACCAAGCTTTAACTGTATCACTCATGCATGCAA
5893796 CGACCAAGCTTTAACTGTATCACTCATGCATGC
1 CGACCAAGCTTTAACTGTATCACTCATGCATGC
5893829 GTTGCATCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (35 bp):
CGACCAAGCTTTAACTGTATCACTCATGCATGCAA
Found at i:5894282 original size:21 final size:21
Alignment explanation
Indices: 5894257--5894316 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
5894247 AATCTAGTTA
5894257 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* * *
5894278 ATTAGTTGGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
*
5894299 ATATA-TTTATTA-TATAAA
1 AT-TAGTTTGTTAGTATAAA
5894317 AAAAAATTAG
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 4 0.13
21 25 0.81
22 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:5894715 original size:14 final size:14
Alignment explanation
Indices: 5894696--5894722 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5894686 AGTAATTTAT
5894696 TATTTTTTGTTGTC
1 TATTTTTTGTTGTC
5894710 TATTTTTTGTTGT
1 TATTTTTTGTTGT
5894723 TGTGTATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.04, G:0.15, T:0.74
Consensus pattern (14 bp):
TATTTTTTGTTGTC
Found at i:5894722 original size:17 final size:17
Alignment explanation
Indices: 5894693--5894725 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5894683 GTGAGTAATT
5894693 TATTATTTTTTGTTGTC
1 TATTATTTTTTGTTGTC
5894710 TATT-TTTTGTTGTTGT
1 TATTATTTT-TTGTTGT
5894726 GTATGTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.03, G:0.15, T:0.73
Consensus pattern (17 bp):
TATTATTTTTTGTTGTC
Found at i:5894905 original size:11 final size:11
Alignment explanation
Indices: 5894889--5894913 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5894879 AAGGAGTAAA
5894889 AATTAATCTGG
1 AATTAATCTGG
5894900 AATTAATCTGG
1 AATTAATCTGG
5894911 AAT
1 AAT
5894914 GTGTACCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (11 bp):
AATTAATCTGG
Found at i:5896235 original size:2 final size:2
Alignment explanation
Indices: 5896228--5896254 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5896218 GAGAACTCCA
5896228 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 A
5896255 CACACAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5896347 original size:2 final size:2
Alignment explanation
Indices: 5896342--5896374 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
5896332 TCTCCTCTTC
5896342 CT CT CT CT CT CT CT CT CT CT CT CT CT CT ACT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT -CT CT
5896375 TTGGAGTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.03, C:0.48, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:5904771 original size:7 final size:7
Alignment explanation
Indices: 5904759--5904787 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
5904749 TTATACGATG
5904759 AAAATAA
1 AAAATAA
5904766 AAAATAA
1 AAAATAA
5904773 AAAAT-A
1 AAAATAA
5904779 AAAATAA
1 AAAATAA
5904786 AA
1 AA
5904788 CTAAAAGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAATAA
Found at i:5904781 original size:13 final size:14
Alignment explanation
Indices: 5904759--5904787 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5904749 TTATACGATG
5904759 AAAATAAAAAATAA
1 AAAATAAAAAATAA
5904773 AAAAT-AAAAATAA
1 AAAATAAAAAATAA
5904786 AA
1 AA
5904788 CTAAAAGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAATAAAAAATAA
Found at i:5905854 original size:13 final size:13
Alignment explanation
Indices: 5905853--5905895 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
5905843 CCGTTGACCC
5905853 GACCCGACCTGTT
1 GACCCGACCTGTT
**
5905866 GACCCGACCCATT
1 GACCCGACCTGTT
5905879 GACCCGACCTGTT
1 GACCCGACCTGTT
5905892 GACC
1 GACC
5905896 GTAGACCGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.19, C:0.42, G:0.21, T:0.19
Consensus pattern (13 bp):
GACCCGACCTGTT
Found at i:5905871 original size:26 final size:24
Alignment explanation
Indices: 5905848--5905895 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
5905838 CCGACCCGTT
5905848 GACCC-GACCCGACCTGTTGACCC
1 GACCCTGACCCGACCTGTTGACCC
5905871 GACCCATTGACCCGACCTGTTGACC
1 GACCC--TGACCCGACCTGTTGACC
5905896 GTAGACCGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.23
26 17 0.77
ACGTcount: A:0.19, C:0.44, G:0.21, T:0.17
Consensus pattern (24 bp):
GACCCTGACCCGACCTGTTGACCC
Found at i:5905887 original size:18 final size:18
Alignment explanation
Indices: 5905831--5905875 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
5905821 ACCGGTCATA
*
5905831 ACCCAACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
5905849 ACCCGACCCGACCTGTTG
1 ACCCGACCCGACCCGTTG
5905867 ACCCGACCC
1 ACCCGACCC
5905876 ATTGACCCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.20, C:0.51, G:0.18, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:5908464 original size:22 final size:22
Alignment explanation
Indices: 5908412--5908473 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
5908402 GATAAATGAC
* *
5908412 CTGAATTCTGTTCTGATTCTGAT
1 CTGAATTCTGTTATGA-TCTAAT
*
5908435 CTGGATTCTGTTATGATCTAAT
1 CTGAATTCTGTTATGATCTAAT
*
5908457 CTGAATTCTGTTTTGAT
1 CTGAATTCTGTTATGAT
5908474 TTCTGATATC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 20 0.59
23 14 0.41
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48
Consensus pattern (22 bp):
CTGAATTCTGTTATGATCTAAT
Found at i:5910176 original size:154 final size:149
Alignment explanation
Indices: 5909901--5910203 Score: 536
Period size: 154 Copynumber: 2.0 Consensus size: 149
5909891 GGATTACACT
5909901 GATTTAAAATTAATATATCAACATTTTAAATCTGAATTATTATATTTATCCCTTTAGGAGAAAAA
1 GATTTAAAATTAATATATCAACATTTTAAATCTGAATTATTATATTTATCCCTTTAGGAGAAAAA
*
5909966 ATTAAATTTTGTGGTTAAATACAATCATCAGATTAAATATAACTAATTATTAATCCACATACAAT
66 ATTAAATTTTGTGGTTAAATACAATCATCAGATTAAATATAAATAATTATTAATCCACATACAAT
5910031 TTAAAAATCTTTGGAATAG
131 TTAAAAATCTTTGGAATAG
5910050 GATTTAAAATTAATATATCAAGTTACATTTTAAATCTGAATTTATTATATTTATCCCTTTAGGAG
1 GATTTAAAATTAATATATC-A---ACATTTTAAATCTGAA-TTATTATATTTATCCCTTTAGGAG
5910115 AAAAAATTAAATTTTGTGGTTAAATACAATCATCAGAATT-AATATAAATAATTATTAATCCACA
61 AAAAAATTAAATTTTGTGGTTAAATACAATCATCAG-ATTAAATATAAATAATTATTAATCCACA
5910179 TACAATTTAAAAATCTTTGGAATAG
125 TACAATTTAAAAATCTTTGGAATAG
5910204 ATTCTCAAGG
Statistics
Matches: 147, Mismatches: 1, Indels: 7
0.95 0.01 0.05
Matches are distributed among these distances:
149 19 0.13
150 1 0.01
153 16 0.11
154 108 0.73
155 3 0.02
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.39
Consensus pattern (149 bp):
GATTTAAAATTAATATATCAACATTTTAAATCTGAATTATTATATTTATCCCTTTAGGAGAAAAA
ATTAAATTTTGTGGTTAAATACAATCATCAGATTAAATATAAATAATTATTAATCCACATACAAT
TTAAAAATCTTTGGAATAG
Found at i:5917470 original size:24 final size:24
Alignment explanation
Indices: 5917430--5917476 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5917420 TGTTGAAAAC
5917430 TAAACAAATCCACCGAAAGGTGGAT
1 TAAACAAATCCACCGAAA-GTGGAT
*
5917455 TAAAC-AATGCACCGAAAGTGGA
1 TAAACAAATCCACCGAAAGTGGA
5917477 CACAATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 11 0.52
25 5 0.24
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (24 bp):
TAAACAAATCCACCGAAAGTGGAT
Found at i:5933060 original size:36 final size:36
Alignment explanation
Indices: 5933019--5933087 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
5933009 TTTTTATTTT
5933019 TTTAATTTTGTAAAAAAAATATATAAATATTTTGAA
1 TTTAATTTTGTAAAAAAAATATATAAATATTTTGAA
* *
5933055 TTTAATTTTTTAAAGAAAATATATAAATATTTT
1 TTTAATTTTGTAAAAAAAATATATAAATATTTT
5933088 ACAATTTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAAATATATAAATATTTTGAA
Found at i:5937464 original size:23 final size:24
Alignment explanation
Indices: 5937415--5937464 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
5937405 TACCATATTG
* *
5937415 AATTTCCTTTTAAACTTTTTTTAA
1 AATTTCCTTTTAAACTCTTCTTAA
5937439 AATTT-CTTTTAAA-TCTTCTTAGA
1 AATTTCCTTTTAAACTCTTCTTA-A
5937462 AAT
1 AAT
5937465 CTTTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 6 0.26
23 12 0.52
24 5 0.22
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.54
Consensus pattern (24 bp):
AATTTCCTTTTAAACTCTTCTTAA
Found at i:5937966 original size:30 final size:30
Alignment explanation
Indices: 5937908--5937972 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
5937898 GTTTGGATCC
* * *
5937908 AAATTGAATCAAAATTTCATTGTGGTCCCT
1 AAATTGAATCAAAACTTCATTGTAGTCCCG
*
5937938 AAATTTAATCAAAACTTCAATT-TAGTCCCG
1 AAATTGAATCAAAACTTC-ATTGTAGTCCCG
5937968 AAATT
1 AAATT
5937973 AATTTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.35
Consensus pattern (30 bp):
AAATTGAATCAAAACTTCATTGTAGTCCCG
Found at i:5940263 original size:18 final size:18
Alignment explanation
Indices: 5940240--5940281 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
5940230 GGTGATAGAA
5940240 GCTAGGTTGAGACAAGTT
1 GCTAGGTTGAGACAAGTT
5940258 GCTAGGTTGAGACAAGTT
1 GCTAGGTTGAGACAAGTT
*
5940276 ACTAGG
1 GCTAGG
5940282 ATTTCGGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.26
Consensus pattern (18 bp):
GCTAGGTTGAGACAAGTT
Found at i:5943642 original size:12 final size:12
Alignment explanation
Indices: 5943627--5943696 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
5943617 GATACATTAC
5943627 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
5943639 CTGATTTCTGAT
1 CTGAATTCTGTT
**
5943651 CTGGGTTCTGTT
1 CTGAATTCTGTT
* *
5943663 ATG-ATATCTGAT
1 CTGAAT-TCTGTT
5943675 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
5943687 TTGATTTCTG
1 CTGAATTCTG
5943697 ATATCTCCGT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 1 0.02
12 41 0.93
13 2 0.05
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:5943646 original size:48 final size:48
Alignment explanation
Indices: 5943590--5943694 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 48
5943580 AAATATTTTA
* *
5943590 TCTGATTTCCGA-CTTGAATTCTGTTCTGATA-CATTACCTGAATTCTGT
1 TCTGATTTCCGATC-TGAATTCTGTTATGATATC-TGACCTGAATTCTGT
* ** *
5943638 TCTGATTTCTGATCTGGGTTCTGTTATGATATCTGATCTGAATTCTGT
1 TCTGATTTCCGATCTGAATTCTGTTATGATATCTGACCTGAATTCTGT
*
5943686 TTTGATTTC
1 TCTGATTTC
5943695 TGATATCTCC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
48 46 0.96
49 2 0.04
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (48 bp):
TCTGATTTCCGATCTGAATTCTGTTATGATATCTGACCTGAATTCTGT
Found at i:5943659 original size:24 final size:24
Alignment explanation
Indices: 5943627--5943698 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
5943617 GATACATTAC
*
5943627 CTGAATTCTGTTCTGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
** *
5943651 CTGGGTTCTGTTATGATATCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
*
5943675 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
5943699 ATCTCCGTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50
Consensus pattern (24 bp):
CTGAATTCTGTTATGATTTCTGAT
Found at i:5945548 original size:74 final size:74
Alignment explanation
Indices: 5945426--5945572 Score: 251
Period size: 74 Copynumber: 2.0 Consensus size: 74
5945416 AACATGACCT
* * *
5945426 CTGATAGGAAAGTATGGAGACTTAAGACCAGGGTAGCCGAGTATTGT-GGGTCACAATCATAGGT
1 CTGATAGGAAAGTATGGAGACTTAAGACCAGGGTAGCCGAGTAGTGTGGGGGCAC-AGCATAGGT
5945490 GTAGCATTCC
65 GTAGCATTCC
5945500 CTGATAGGAAAGTATGGAGACTTAAGACCAGGGTAGCCGAGTAGTGTGGGGGCACAGCATAGGTG
1 CTGATAGGAAAGTATGGAGACTTAAGACCAGGGTAGCCGAGTAGTGTGGGGGCACAGCATAGGTG
5945565 TAGCATTC
66 TAGCATTC
5945573 ATGTCTTCTT
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
74 63 0.91
75 6 0.09
ACGTcount: A:0.29, C:0.16, G:0.33, T:0.22
Consensus pattern (74 bp):
CTGATAGGAAAGTATGGAGACTTAAGACCAGGGTAGCCGAGTAGTGTGGGGGCACAGCATAGGTG
TAGCATTCC
Found at i:5953773 original size:20 final size:21
Alignment explanation
Indices: 5953726--5953773 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
5953716 ATTAAAATCT
5953726 AGTTAATTAGTTTGTTAGTATA
1 AGTT-ATTAGTTTGTTAGTATA
* *
5953748 AATTATTAG-TTGTTAGTTTA
1 AGTTATTAGTTTGTTAGTATA
5953768 AGTTAT
1 AGTTAT
5953774 ATTATATTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 15 0.65
21 5 0.22
22 3 0.13
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (21 bp):
AGTTATTAGTTTGTTAGTATA
Found at i:5953791 original size:28 final size:29
Alignment explanation
Indices: 5953751--5953812 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
5953741 TAGTATAAAT
*
5953751 TATTAGTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTATTAGTTTAAGTTATATATTA
5953778 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAG-TTATTAGTTTAAGTTATATATTA
5953808 TATTA
1 TATTA
5953813 TATAAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
27 6 0.19
28 12 0.39
29 1 0.03
30 12 0.39
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.56
Consensus pattern (29 bp):
TATTAGTTATTAGTTTAAGTTATATATTA
Found at i:5957363 original size:26 final size:26
Alignment explanation
Indices: 5957337--5957554 Score: 202
Period size: 26 Copynumber: 8.6 Consensus size: 26
5957327 GATGATTTAG
*
5957337 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
5957363 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
5957389 TAATGATTT-AGTAATAATCATTATAAA
1 TAATGATTTGA-TAATAATCATTAT-AA
* * *
5957416 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
5957439 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
*
5957462 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
5957488 TAATGA-TTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
*
5957513 TAATACATTT-AGTAATAATCATTATAA
1 TAAT-GATTTGA-TAATAATCATTATAA
* *
5957540 AAATGATTTAATAAT
1 TAATGATTTGATAAT
5957555 GATTTAAATA
Statistics
Matches: 159, Mismatches: 20, Indels: 26
0.78 0.10 0.13
Matches are distributed among these distances:
21 4 0.03
22 3 0.02
23 12 0.08
24 4 0.03
25 32 0.20
26 66 0.42
27 37 0.23
28 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Done.