Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_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: 6984689
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 29
Found at i:6318655 original size:16 final size:17
Alignment explanation
Indices: 6318636--6318668 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6318626 CATATCTCTT
6318636 ATCTCTT-GTTCATATG
1 ATCTCTTAGTTCATATG
6318652 ATCTCTTACGTTCATAT
1 ATCTCTTA-GTTCATAT
6318669 TCTATATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.48
Consensus pattern (17 bp):
ATCTCTTAGTTCATATG
Found at i:6318824 original size:2 final size:2
Alignment explanation
Indices: 6318817--6318852 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6318807 ATCACTCATC
6318817 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
6318853 TACATACATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6321311 original size:24 final size:22
Alignment explanation
Indices: 6321249--6321312 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 22
6321239 TTCCCTTGAA
6321249 GTGCATCGATGCATCC-T-ACT
1 GTGCATCGATGCATCCTTAACT
* *
6321269 ATGTATCGATGCATCCCTTAACGT
1 GTGCATCGATGCAT-CCTTAAC-T
6321293 GTGCATCGATGCACTCCTTA
1 GTGCATCGATGCA-TCCTTA
6321313 TGCATCGATG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 12 0.34
21 2 0.06
22 1 0.03
23 2 0.06
24 17 0.49
25 1 0.03
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTAACT
Found at i:6325223 original size:16 final size:17
Alignment explanation
Indices: 6325204--6325236 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6325194 CATATCTCTT
6325204 ATCTCTT-GTTCATATG
1 ATCTCTTAGTTCATATG
6325220 ATCTCTTACGTTCATAT
1 ATCTCTTA-GTTCATAT
6325237 TCTATATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.48
Consensus pattern (17 bp):
ATCTCTTAGTTCATATG
Found at i:6332296 original size:115 final size:115
Alignment explanation
Indices: 6332094--6332326 Score: 448
Period size: 115 Copynumber: 2.0 Consensus size: 115
6332084 AGACAACAAC
*
6332094 AAAAAAATTTATAGGGTTTACTTTCCAAATTATTGTCATGTTCATTTACTCATTTATTTTTCATT
1 AAAAAAAATTATAGGGTTTACTTTCCAAATTATTGTCATGTTCATTTACTCATTTATTTTTCATT
6332159 TATTCAGAGTGAGTGTTCCCTAATCTAATTATTAATAATTATTCTAATCA
66 TATTCAGAGTGAGTGTTCCCTAATCTAATTATTAATAATTATTCTAATCA
6332209 AAAAAAAATTATAGGGTTTACTTTCCAAATTATTGTCATGTTCATTTACTCATTTATTTTTCATT
1 AAAAAAAATTATAGGGTTTACTTTCCAAATTATTGTCATGTTCATTTACTCATTTATTTTTCATT
*
6332274 TATTCAGAGTGAGTGTTCCCTAATCTAGTTATTAATAATTATTCTAATCA
66 TATTCAGAGTGAGTGTTCCCTAATCTAATTATTAATAATTATTCTAATCA
6332324 AAA
1 AAA
6332327 GCATCTAAAA
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
115 116 1.00
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (115 bp):
AAAAAAAATTATAGGGTTTACTTTCCAAATTATTGTCATGTTCATTTACTCATTTATTTTTCATT
TATTCAGAGTGAGTGTTCCCTAATCTAATTATTAATAATTATTCTAATCA
Found at i:6337920 original size:16 final size:18
Alignment explanation
Indices: 6337884--6337924 Score: 59
Period size: 16 Copynumber: 2.3 Consensus size: 18
6337874 TTGTATGAAC
6337884 TAATTACTTTATAATTTAT
1 TAATT-CTTTATAATTTAT
6337903 TAATTCTTTAT-A-TTAT
1 TAATTCTTTATAATTTAT
6337919 TAATTC
1 TAATTC
6337925 ACAGTTCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.45
17 1 0.05
18 6 0.27
19 5 0.23
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (18 bp):
TAATTCTTTATAATTTAT
Found at i:6343056 original size:90 final size:90
Alignment explanation
Indices: 6342881--6343058 Score: 266
Period size: 90 Copynumber: 2.0 Consensus size: 90
6342871 TTTTCACAAC
* * *
6342881 TTATAATAATAATAATGTGCACATAGTTACAAATCTTCACTAGTAAAGTAGATTTGTTTCGATTA
1 TTATAATAATAATAATGTGCACATAGTTACAAATCTTCACTAGGAAAGTAGATTCGTTTCAATTA
* *
6342946 ACGGGATTGATTCAATTGATAAGAT
66 ACGAGATTGATTCAAGTGATAAGAT
* *
6342971 TTATAATGATAATAATGTGCACATAGTTGCAAATCTTCACTAGGAAAGTAGATTCGTTTCAATTA
1 TTATAATAATAATAATGTGCACATAGTTACAAATCTTCACTAGGAAAGTAGATTCGTTTCAATTA
* * *
6343036 ACGATATTGGTTTAAGTGATAAG
66 ACGAGATTGATTCAAGTGATAAG
6343059 TAGCTTGATA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 78 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (90 bp):
TTATAATAATAATAATGTGCACATAGTTACAAATCTTCACTAGGAAAGTAGATTCGTTTCAATTA
ACGAGATTGATTCAAGTGATAAGAT
Found at i:6352751 original size:29 final size:31
Alignment explanation
Indices: 6352704--6352766 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
6352694 ATAATTCTGG
*
6352704 TTAGTGACCAAAATGTAAAATTT-G-AAAGT
1 TTAGTGACCAAAATATAAAATTTGGAAAAGT
* *
6352733 TTAGTGACCAAAGTATAAAGTTTGGAAAAGT
1 TTAGTGACCAAAATATAAAATTTGGAAAAGT
6352764 TTA
1 TTA
6352767 AAACCAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 20 0.69
30 1 0.03
31 8 0.28
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.32
Consensus pattern (31 bp):
TTAGTGACCAAAATATAAAATTTGGAAAAGT
Found at i:6358568 original size:17 final size:18
Alignment explanation
Indices: 6358538--6358571 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
6358528 AACCAGTCAC
6358538 GACCCGACCCGTTGACCT
1 GACCCGACCCGTTGACCT
6358556 GACCCGA-CCGTTGACC
1 GACCCGACCCGTTGACC
6358572 GTTGACTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.18, C:0.44, G:0.24, T:0.15
Consensus pattern (18 bp):
GACCCGACCCGTTGACCT
Found at i:6358679 original size:30 final size:29
Alignment explanation
Indices: 6358616--6358683 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
6358606 TTCGATTTTA
* *
6358616 GTGCTATTATGGGAATTAATTCAAAATGG
1 GTGCTATTTTGGGAATTAATTCAAAAGGG
*
6358645 GTGCTATTTTGGTAATTAATTCGAAAAGGG
1 GTGCTATTTTGGGAATTAATTC-AAAAGGG
6358675 GTGCTATTT
1 GTGCTATTT
6358684 CTATAAAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.29, C:0.07, G:0.25, T:0.38
Consensus pattern (29 bp):
GTGCTATTTTGGGAATTAATTCAAAAGGG
Found at i:6365834 original size:17 final size:18
Alignment explanation
Indices: 6365801--6365837 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
6365791 TTTAACCGGT
6365801 CCCGACCCGACCCGTTGA
1 CCCGACCCGACCCGTTGA
6365819 CCCGACCCGA-CCGTTGA
1 CCCGACCCGACCCGTTGA
6365836 CC
1 CC
6365838 GTTGACTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.16, C:0.51, G:0.22, T:0.11
Consensus pattern (18 bp):
CCCGACCCGACCCGTTGA
Found at i:6365945 original size:30 final size:29
Alignment explanation
Indices: 6365881--6365949 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 29
6365871 ATTCGATTTT
* *
6365881 GGTGCTATTATGGGAATTAATTCAAAACG
1 GGTGCTATTTTGGCAATTAATTCAAAACG
*
6365910 GGTGCTATTTTGGCAATTAATTCGAAAAGG
1 GGTGCTATTTTGGCAATTAATTC-AAAACG
6365940 GGTGCTATTT
1 GGTGCTATTT
6365950 CTGTAAAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.35
Consensus pattern (29 bp):
GGTGCTATTTTGGCAATTAATTCAAAACG
Found at i:6374028 original size:2 final size:2
Alignment explanation
Indices: 6374021--6374053 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6374011 TCACTACTTC
6374021 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 A
6374054 CTTTACGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6374315 original size:24 final size:24
Alignment explanation
Indices: 6374259--6374315 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
6374249 TATAGTTTTA
6374259 ATATTAAAATATGATTAGTAATATTT
1 ATATT-AAATAT-ATTAGTAATATTT
*
6374285 ATGTTAAATAT-TTAGTAATTATTT
1 ATATTAAATATATTAGTAA-TATTT
6374309 ATATTAA
1 ATATTAA
6374316 GATTAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.25
24 11 0.39
25 6 0.21
26 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (24 bp):
ATATTAAATATATTAGTAATATTT
Found at i:6378826 original size:2 final size:2
Alignment explanation
Indices: 6378797--6378841 Score: 51
Period size: 2 Copynumber: 23.5 Consensus size: 2
6378787 CTCACGTATG
*
6378797 TA TA TA TCA TA T- TA T- TT TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6378837 TA TA T
1 TA TA T
6378842 TTAATATTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
1 3 0.08
2 33 0.87
3 2 0.05
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:6379216 original size:3 final size:3
Alignment explanation
Indices: 6379208--6379252 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
6379198 AATGTCTTTG
6379208 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6379253 GACGTGCAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6379458 original size:2 final size:2
Alignment explanation
Indices: 6379451--6379475 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6379441 GATTGTATTT
6379451 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
6379476 TTGAATTGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6380562 original size:27 final size:27
Alignment explanation
Indices: 6380532--6380594 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
6380522 TAATCAATTA
* * *
6380532 ATTAATTTTTTTTAATTAAATCTCCTT
1 ATTAAATTCTTTTAATCAAATCTCCTT
6380559 ATTAAATTCTTTTAATCAAATCTCCTT
1 ATTAAATTCTTTTAATCAAATCTCCTT
6380586 ATTAAATTC
1 ATTAAATTC
6380595 CTTCCCAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.52
Consensus pattern (27 bp):
ATTAAATTCTTTTAATCAAATCTCCTT
Found at i:6380564 original size:13 final size:12
Alignment explanation
Indices: 6380546--6380597 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 12
6380536 ATTTTTTTTA
6380546 ATTAAATCTCCTT
1 ATTAAAT-TCCTT
*
6380559 ATTAAATTCTTTT
1 ATTAAATTC-CTT
*
6380572 AATCAAATCTCCTT
1 -ATTAAAT-TCCTT
6380586 ATTAAATTCCTT
1 ATTAAATTCCTT
6380598 CCCAAATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
12 7 0.22
13 15 0.47
14 8 0.25
15 2 0.06
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTAAATTCCTT
Found at i:6382400 original size:18 final size:18
Alignment explanation
Indices: 6382332--6382402 Score: 54
Period size: 22 Copynumber: 3.7 Consensus size: 18
6382322 ATAGTCCTTC
6382332 ATATATTATTTTGTAATTAA
1 ATATATTATTTT-TAA-TAA
* *
6382352 AT-TTTTATTTTTATTAA
1 ATATATTATTTTTAATAA
*
6382369 ATACAAATAATATTTTTAATAA
1 AT----ATATTATTTTTAATAA
6382391 ATATATTATTTT
1 ATATATTATTTT
6382403 GGGTCGGGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
17 5 0.12
18 11 0.28
19 8 0.20
20 2 0.05
22 14 0.35
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (18 bp):
ATATATTATTTTTAATAA
Found at i:6382837 original size:30 final size:29
Alignment explanation
Indices: 6382737--6383004 Score: 143
Period size: 30 Copynumber: 9.3 Consensus size: 29
6382727 TTAAGTTTAG
* * *
6382737 AATAAAGTATATTTATTTAATTTAAAATAA
1 AATAAAATATATTTA-ATAAGTTAAAATAA
* * *
6382767 AATTAAAATA-CTTT--TAAGTTAAGATGAG
1 AA-TAAAATATATTTAATAAGTTAAAAT-AA
* *
6382795 AATAAATTATATTTAATAATTTAAAATAA
1 AATAAAATATATTTAATAAGTTAAAATAA
* * *
6382824 TAATATAATATATTTAATAAATAAAAATAA
1 -AATAAAATATATTTAATAAGTTAAAATAA
6382854 AAT---ATATACTTTCAA-AAGTTAAAAT-A
1 AATAAAATATA-TTT-AATAAGTTAAAATAA
* * * *
6382880 AA-AAAATATTTTTAA-AAGTTTTAATTAG
1 AATAAAATATATTTAATAAG-TTAAAATAA
*
6382908 AA-AGAATATATTTTCAA-AA-TTAAAATAA
1 AATAAAATATA-TTT-AATAAGTTAAAATAA
* * *
6382936 TAATAAAATATATTT-TTAA-TTATATTAAA
1 -AATAAAATATATTTAATAAGTTAAAAT-AA
*
6382965 AATAAAATATATTTAATAAGTTAATATAAA
1 AATAAAATATATTTAATAAGTTAAAAT-AA
6382995 AATAAAATAT
1 AATAAAATAT
6383005 TTTTTTGAAG
Statistics
Matches: 184, Mismatches: 33, Indels: 42
0.71 0.13 0.16
Matches are distributed among these distances:
26 13 0.07
27 34 0.18
28 47 0.26
29 17 0.09
30 67 0.36
31 6 0.03
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (29 bp):
AATAAAATATATTTAATAAGTTAAAATAA
Found at i:6382845 original size:24 final size:24
Alignment explanation
Indices: 6382795--6382860 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
6382785 TTAAGATGAG
* *
6382795 AATAAATTAT-ATTTAATA-ATTT
1 AATAAATAATAATATAATATATTT
6382817 -A-AAATAATAATATAATATATTT
1 AATAAATAATAATATAATATATTT
* *
6382839 AATAAATAAAAATAAAATATAT
1 AATAAATAATAATATAATATAT
6382861 ACTTTCAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 6 0.17
21 8 0.22
22 4 0.11
23 1 0.03
24 17 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AATAAATAATAATATAATATATTT
Found at i:6382883 original size:28 final size:27
Alignment explanation
Indices: 6382847--6382935 Score: 92
Period size: 27 Copynumber: 3.3 Consensus size: 27
6382837 TTAATAAATA
* *
6382847 AAAATAAAATATATACTTTCAAAAGTT
1 AAAATAAAAAATATATTTTCAAAAGTT
*
6382874 AAAATAAAAAA-ATATTTTTAAAAGTTT
1 AAAATAAAAAATATATTTTCAAAAG-TT
* *
6382901 TAATTAGAAAGAATATATTTTCAAAA-TT
1 AAAATA-AAA-AATATATTTTCAAAAGTT
6382929 AAAATAA
1 AAAATAA
6382936 TAATAAAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
26 11 0.22
27 17 0.34
28 9 0.18
29 2 0.04
30 11 0.22
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.35
Consensus pattern (27 bp):
AAAATAAAAAATATATTTTCAAAAGTT
Found at i:6382974 original size:58 final size:60
Alignment explanation
Indices: 6382815--6383029 Score: 172
Period size: 58 Copynumber: 3.7 Consensus size: 60
6382805 ATTTAATAAT
* *
6382815 TTAAAATAATAATATAATATA--TTTAA--TA-AATAAAAATAAAATATATACTTTCAAAAG
1 TTAAAATAATAATAAAATATATTTTTAAGTTATATTAAAAATAAAATATAT--TTTCAAAAG
* * * *
6382872 TTAAAAT-A-AA-AAAATAT-TTTTAAAAGTTTTAATT-AGAA-AGAATATATTTTCAAAA-
1 TTAAAATAATAATAAAATATATTTT-TAAGTTAT-ATTAAAAATAAAATATATTTTCAAAAG
6382927 TTAAAATAATAATAAAATATATTTTTAA-TTATATTAAAAATAAAATATA-TTT-AATAAG
1 TTAAAATAATAATAAAATATATTTTTAAGTTATATTAAAAATAAAATATATTTTCAA-AAG
* * *
6382985 TTAATATAAAAATAAAATATTTTTTTGAAGTTAATATATAAAAAT
1 TTAAAATAATAATAAAATATATTTTT-AAGTT-ATAT-TAAAAAT
6383030 TATTATAAGT
Statistics
Matches: 126, Mismatches: 13, Indels: 33
0.73 0.08 0.19
Matches are distributed among these distances:
54 6 0.05
55 11 0.09
56 17 0.13
57 20 0.16
58 48 0.38
59 9 0.07
60 4 0.03
61 4 0.03
62 7 0.06
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.39
Consensus pattern (60 bp):
TTAAAATAATAATAAAATATATTTTTAAGTTATATTAAAAATAAAATATATTTTCAAAAG
Found at i:6383016 original size:30 final size:29
Alignment explanation
Indices: 6382927--6383027 Score: 107
Period size: 30 Copynumber: 3.4 Consensus size: 29
6382917 ATTTTCAAAA
* * *
6382927 TTAAAATAATAATAAAATATATTTTTAA-
1 TTAATATAAAAATAAAATATTTTTTTAAG
**
6382955 TT-ATATTAAAAATAAAATATATTTAATAAG
1 TTAATA-TAAAAATAAAATAT-TTTTTTAAG
6382985 TTAATATAAAAATAAAATATTTTTTTGAAG
1 TTAATATAAAAATAAAATATTTTTTT-AAG
6383015 TTAATATATAAAA
1 TTAATATA-AAAA
6383028 ATTATTATAA
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
27 2 0.03
28 15 0.25
29 9 0.15
30 27 0.45
31 7 0.12
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (29 bp):
TTAATATAAAAATAAAATATTTTTTTAAG
Found at i:6383201 original size:20 final size:19
Alignment explanation
Indices: 6383154--6383192 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
6383144 AATGACCAAC
*
6383154 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
6383173 AAATCGCAACGCGATCTCT
1 AAATCGCAACGCGATCTCT
6383192 A
1 A
6383193 GTATCGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.23
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:6383239 original size:20 final size:20
Alignment explanation
Indices: 6383216--6383323 Score: 85
Period size: 20 Copynumber: 5.3 Consensus size: 20
6383206 GTTTCCAGAT
*
6383216 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
* * *
6383236 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTATG-ACTA
* *
6383256 TCGCAACGTGATTCTGACTA
1 TCGCAACGCGATTATGACTA
* *
6383276 TCGCAATGCGATAAT-ACATAA
1 TCGCAACGCGATTATGAC-T-A
* *
6383297 TCGCAACGCGATTCTGACTG
1 TCGCAACGCGATTATGACTA
6383317 TCGCAAC
1 TCGCAAC
6383324 ACTGAATTTC
Statistics
Matches: 66, Mismatches: 17, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
19 3 0.05
20 46 0.70
21 15 0.23
22 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:6383260 original size:40 final size:41
Alignment explanation
Indices: 6383216--6383322 Score: 146
Period size: 40 Copynumber: 2.6 Consensus size: 41
6383206 GTTTCCAGAT
* **
6383216 TCGCAACGCGATTTTGACTATCGCAATGCG--AATATGTAAA
1 TCGCAACGCGATTCTGACTATCGCAATGCGATAATACAT-AA
*
6383256 TCGCAACGTGATTCTGACTATCGCAATGCGATAATACATAA
1 TCGCAACGCGATTCTGACTATCGCAATGCGATAATACATAA
*
6383297 TCGCAACGCGATTCTGACTGTCGCAA
1 TCGCAACGCGATTCTGACTATCGCAA
6383323 CACTGAATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
40 28 0.47
41 26 0.44
42 5 0.08
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (41 bp):
TCGCAACGCGATTCTGACTATCGCAATGCGATAATACATAA
Found at i:6383342 original size:41 final size:39
Alignment explanation
Indices: 6383156--6383344 Score: 145
Period size: 40 Copynumber: 4.7 Consensus size: 39
6383146 TGACCAACAA
* *
6383156 ATCGCAATGCG-ATCTCTAAATCGCAACGCGATCTCT-AGT
1 ATCGCAATGCGAATTTC-AAATCGCAACGCGAT-TCTGACT
* * *
6383195 ATCGCAAAT-C-AGTTTCCAGATTCGCAACGCGATTTTGACT
1 ATCGC-AATGCGAATTT-CA-AATCGCAACGCGATTCTGACT
*
6383235 ATCGCAATGCGAATATGT-AAATCGCAACGTGATTCTGACT
1 ATCGCAATGCGAAT-T-TCAAATCGCAACGCGATTCTGACT
* *
6383275 ATCGCAATGCGATAATACATAATCGCAACGCGATTCTGACT
1 ATCGCAATGCGA-ATTTCA-AATCGCAACGCGATTCTGACT
* **
6383316 GTCGCAACACTGAATTTCAAATTCGCAAC
1 ATCGCAATGC-GAATTTCAAA-TCGCAAC
6383345 AGGTTTTAGT
Statistics
Matches: 119, Mismatches: 17, Indels: 26
0.73 0.10 0.16
Matches are distributed among these distances:
39 14 0.12
40 59 0.50
41 42 0.35
42 3 0.03
43 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (39 bp):
ATCGCAATGCGAATTTCAAATCGCAACGCGATTCTGACT
Found at i:6384174 original size:24 final size:24
Alignment explanation
Indices: 6384142--6384195 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
6384132 GTATTCGAAA
6384142 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
6384166 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
6384190 TTTGAT
1 TTTGAT
6384196 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:6384414 original size:14 final size:14
Alignment explanation
Indices: 6384385--6384421 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
6384375 AGAAAAAGAA
6384385 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
6384400 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
6384414 GAAGAAAA
1 GAAGAAAA
6384422 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:6386804 original size:140 final size:140
Alignment explanation
Indices: 6386552--6386821 Score: 486
Period size: 140 Copynumber: 1.9 Consensus size: 140
6386542 AAACGTTGTA
*
6386552 TTATGTGTAAACTTTTAACATTTTTAGTTACACATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTACACATGTATTAGTAACTTGAGTTTGAACATTGCTA
* * *
6386617 TGATCTGTTCAGTTGTTATCACTTATTAGACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTATTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
6386682 TATGTGTATT
131 TATGTGTATT
*
6386692 TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTACACATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
6386757 TGATATGTTCAGTTATTATCACTTATTACACATTCATTTGAATATCGCAATGCGAATTTGACTAT
66 TGATATGTTCAGTTATTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
6386822 CGCAACGCAA
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 124 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTACACATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTATTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:6386817 original size:20 final size:20
Alignment explanation
Indices: 6386792--6386956 Score: 113
Period size: 20 Copynumber: 8.8 Consensus size: 20
6386782 TTACACATTC
* *
6386792 ATTTGAATATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
*
6386812 ATTTGACTATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
* *
6386832 ATTTCATTATCGCAA-GTC-A
1 ATTTGACTATCGCAACG-CGA
*
6386851 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
6386866 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
6386886 ATATGACTATCGCAACG-TA
1 ATTTGACTATCGCAACGCGA
* *
6386905 A----A-AATTGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
6386920 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
6386940 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
6386957 AGAAAATCTC
Statistics
Matches: 114, Mismatches: 17, Indels: 28
0.72 0.11 0.18
Matches are distributed among these distances:
14 16 0.14
15 7 0.06
19 7 0.06
20 84 0.74
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:6386882 original size:54 final size:54
Alignment explanation
Indices: 6386800--6386991 Score: 199
Period size: 54 Copynumber: 3.6 Consensus size: 54
6386790 TCATTTGAAT
* * *
6386800 ATCGCAATGCGAATTTGACTATCGCAACGCAAATTTCATTATCGCAA-GTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAATATCACTATCGCAACGT-AAAA
* *
6386854 ATCGCAACGCGAATTTGACTATCGCAACGCGAATATGACTATCGCAACGTAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAATATCACTATCGCAACGTAAAA
* * *** * *
6386908 ATTGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACG-AGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAATATCACTATCGCAACGTA-AAA
* ** * *
6386962 ATCTCAAAACGTATTAGACTATCGCAACGC
1 ATCGCAACGCGAATTTGACTATCGCAACGC
6386992 GAATTGACTT
Statistics
Matches: 118, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
53 1 0.01
54 115 0.97
55 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCAAATATCACTATCGCAACGTAAAA
Found at i:6387211 original size:14 final size:14
Alignment explanation
Indices: 6387151--6387212 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
6387141 CACAAATAAG
*
6387151 AATTATTTACACATC
1 AATT-TTTACAAATC
**
6387166 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
6387181 AACTTTTACAAATC
1 AATTTTTACAAATC
*
6387195 AATTTTTATAAATC
1 AATTTTTACAAATC
6387209 AATT
1 AATT
6387213 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:6388659 original size:42 final size:42
Alignment explanation
Indices: 6388600--6388693 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
6388590 ATGAATCGTG
* *
6388600 CTCTTGAATGGTGGGA-GGGACCTCTTCAAAGATGACATGGGC
1 CTCTTGAACGGTGGGAGGGGA-CTCTTCAAAGATGACAGGGGC
* ** *
6388642 CTCTTGAACGGTGGGAGGGGACTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTTCAAAGATGACAGGGGC
6388684 CTCTTGAACG
1 CTCTTGAACG
6388694 ATGACAGGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 41 0.91
43 4 0.09
ACGTcount: A:0.21, C:0.18, G:0.37, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTTCAAAGATGACAGGGGC
Found at i:6388696 original size:21 final size:21
Alignment explanation
Indices: 6388615--6388701 Score: 75
Period size: 21 Copynumber: 4.1 Consensus size: 21
6388605 GAATGGTGGG
* * *
6388615 AGGGACCTCTTCAAAGATGAC
1 AGGGGCCTCTTGAACGATGAC
* * **
6388636 ATGGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTGAACGATGAC
* ** *
6388657 AGGGGACTCTTGAGGGATGAT
1 AGGGGCCTCTTGAACGATGAC
6388678 AGGGGCCTCTTGAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
6388699 AGG
1 AGG
6388702 TGAGTTGGGC
Statistics
Matches: 48, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.21
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATGAC
Found at i:6389210 original size:19 final size:20
Alignment explanation
Indices: 6389174--6389211 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
6389164 GAATAGTTTC
*
6389174 TGAAACTTAAAATCGCAACA
1 TGAAACTTAAAATAGCAACA
6389194 TGAAACTT-AAATAGCAAC
1 TGAAACTTAAAATAGCAAC
6389212 GCGAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.21
Consensus pattern (20 bp):
TGAAACTTAAAATAGCAACA
Found at i:6389217 original size:19 final size:20
Alignment explanation
Indices: 6389175--6389217 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
6389165 AATAGTTTCT
* *
6389175 GAAACTTAAAATCGCAACAT
1 GAAACTTAAAATAGCAACAC
*
6389195 GAAACTT-AAATAGCAACGC
1 GAAACTTAAAATAGCAACAC
6389214 GAAA
1 GAAA
6389218 ATGACTATCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (20 bp):
GAAACTTAAAATAGCAACAC
Found at i:6389232 original size:20 final size:20
Alignment explanation
Indices: 6389207--6389252 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
6389197 AACTTAAATA
6389207 GCAACGCGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
*
6389227 GCAACGCGGAAATGACTATC
1 GCAACGCGAAAATGACTATC
6389247 GCAACG
1 GCAACG
6389253 GGATAATCGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.26, G:0.24, T:0.13
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATC
Found at i:6389319 original size:19 final size:19
Alignment explanation
Indices: 6389257--6389319 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
6389247 GCAACGGGAT
*
6389257 AATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAACT-AA
*
6389276 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACTAA
6389295 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
6389314 ATTCGC
1 AATCGC
6389320 GTTGCGATAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.46, C:0.25, G:0.16, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:6389375 original size:33 final size:33
Alignment explanation
Indices: 6389319--6389414 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
6389309 ACTAAATTCG
* *
6389319 CGTTGCGATAGTCATTTTCGCATTGCGATTTTCA
1 CGTTGCGATAGTTA-TTTCGCATTGCGATTATCA
** *
6389353 CGTTGCGATTTTTATTTCGCATTGCGATTATCC
1 CGTTGCGATAGTTATTTCGCATTGCGATTATCA
*
6389386 CGTTGCGATAGTTATTTCCGCGTTGCGAT
1 CGTTGCGATAGTTATTT-CGCATTGCGAT
6389415 AGTCATTTTC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 32 0.60
34 21 0.40
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.42
Consensus pattern (33 bp):
CGTTGCGATAGTTATTTCGCATTGCGATTATCA
Found at i:6389411 original size:20 final size:20
Alignment explanation
Indices: 6389386--6389434 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
6389376 GCGATTATCC
*
6389386 CGTTGCGATAGTTATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
6389406 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
6389426 CGTTGCGAT
1 CGTTGCGAT
6389435 TTAAGTTTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.14, C:0.20, G:0.27, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:6391863 original size:22 final size:22
Alignment explanation
Indices: 6391836--6391886 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
6391826 GATGGAGATA
*
6391836 GATGGATTTCGTCGGAGATGGG
1 GATGGATTTCATCGGAGATGGG
6391858 GATGGATTTCATCGGAGATGGG
1 GATGGATTTCATCGGAGATGGG
*
6391880 GACGGAT
1 GATGGAT
6391887 GTCGCCGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.10, G:0.43, T:0.25
Consensus pattern (22 bp):
GATGGATTTCATCGGAGATGGG
Found at i:6392061 original size:21 final size:21
Alignment explanation
Indices: 6392031--6392105 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
6392021 CGCTTTGAAA
*
6392031 ATCGCATTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
* * * **
6392052 ATCGAGTTGC-A-ATAGTCAGA
1 ATCGCGTTGCGATTTTGT-ATT
*
6392072 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTTTGTATT
6392093 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
6392106 AGTCAAAATC
Statistics
Matches: 39, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
19 3 0.08
20 11 0.28
21 23 0.59
22 2 0.05
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTGTATT
Found at i:6392091 original size:41 final size:41
Alignment explanation
Indices: 6392028--6392164 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
6392018 TGGCGCTTTG
* *
6392028 AAAATCGCATTGCGATTTTGTATTATCGAGTTGCAATAGTC
1 AAAATCGCGTTGCGATTATGTATTATCGAGTTGCAATAGTC
* * *
6392069 AGAATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTC
1 AAAATCGCGTTGCGATTATGTATTATCGAGTTGCAATAGTC
** *
6392110 AAAATCGCGTTGCGATT-TACA-TATTCGTA-TTGCGATAGTC
1 AAAATCGCGTTGCGATTATGTATTA-TCG-AGTTGCAATAGTC
*
6392150 AAAATCGTGTTGCGA
1 AAAATCGCGTTGCGA
6392165 ATCTGGAAAC
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 2 0.02
40 30 0.36
41 52 0.62
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (41 bp):
AAAATCGCGTTGCGATTATGTATTATCGAGTTGCAATAGTC
Found at i:6392123 original size:20 final size:20
Alignment explanation
Indices: 6392052--6392164 Score: 86
Period size: 20 Copynumber: 5.6 Consensus size: 20
6392042 ATTTTGTATT
* * *
6392052 ATCGAGTTGCAATAGTCAGA
1 ATCGCGTTGCGATAGTCAAA
**
6392072 ATCGCGTTGCGATTATGT-ATT
1 ATCGCGTTGCGA-TA-GTCAAA
6392093 ATCGCGTTGCGATAGTCAAA
1 ATCGCGTTGCGATAGTCAAA
* *
6392113 ATCGCGTTGCGAT-TTACATA
1 ATCGCGTTGCGATAGT-CAAA
* **
6392133 TTCGTATTGCGATAGTCAAA
1 ATCGCGTTGCGATAGTCAAA
*
6392153 ATCGTGTTGCGA
1 ATCGCGTTGCGA
6392165 ATCTGGAAAC
Statistics
Matches: 73, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
19 3 0.04
20 52 0.71
21 16 0.22
22 2 0.03
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAAA
Found at i:6402460 original size:21 final size:21
Alignment explanation
Indices: 6402434--6402479 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
6402424 GAGTTCTGGG
* *
6402434 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
6402455 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
6402476 CAAG
1 CAAG
6402480 CGACAGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:6403264 original size:31 final size:31
Alignment explanation
Indices: 6403226--6403381 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
6403216 AGGGTCGAGG
6403226 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
6403257 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
6403288 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
6403319 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
6403350 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
6403381 G
1 G
6403382 GTCCTTCGGG
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:6406573 original size:21 final size:21
Alignment explanation
Indices: 6406547--6406592 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
6406537 GAGTTCTGGG
* *
6406547 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
6406568 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
6406589 CAAG
1 CAAG
6406593 CGACAGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:6407373 original size:31 final size:31
Alignment explanation
Indices: 6407335--6407490 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
6407325 AGGGTCGAGG
6407335 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
6407366 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
6407397 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
6407428 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
6407459 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
6407490 G
1 G
6407491 GTCCTTCGGG
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:6411825 original size:22 final size:22
Alignment explanation
Indices: 6411800--6411845 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
6411790 TTGGAGAAGG
6411800 TTGTAAATCCTTCAAGGAAATA
1 TTGTAAATCCTTCAAGGAAATA
* *
6411822 TTGTAAATTCTTGAAGGAAATA
1 TTGTAAATCCTTCAAGGAAATA
6411844 TT
1 TT
6411846 AGTCTTTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
TTGTAAATCCTTCAAGGAAATA
Found at i:6415283 original size:38 final size:38
Alignment explanation
Indices: 6415232--6415313 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 38
6415222 ACCTCCAACA
* *
6415232 TTAGGAAATTGAATAAGTTGGAATC-TCCAACAATAGTT
1 TTAGGAAATTGAATAAGTT-GAAACATCCAACAATAGCT
* *
6415270 TTAGGAATTTGAATAAGTTGAAACATCCAACACTAGCT
1 TTAGGAAATTGAATAAGTTGAAACATCCAACAATAGCT
6415308 TTAGGA
1 TTAGGA
6415314 TGATTGATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 4 0.10
38 35 0.90
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (38 bp):
TTAGGAAATTGAATAAGTTGAAACATCCAACAATAGCT
Found at i:6415440 original size:19 final size:20
Alignment explanation
Indices: 6415410--6415571 Score: 101
Period size: 19 Copynumber: 8.6 Consensus size: 20
6415400 CACTACTACA
*
6415410 CCAACCTAAAATCT-ATTTT
1 CCAACCTGAAATCTGATTTT
* *
6415429 CTAACCTGAAATATGA-TTT
1 CCAACCTGAAATCTGATTTT
6415448 CCAACCTGAAATCTGA-TTT
1 CCAACCTGAAATCTGATTTT
* * * *
6415467 CTAATCTAAAATTTGA-TTT
1 CCAACCTGAAATCTGATTTT
* * *
6415486 CCAACCTGAAATTTG-GTTC
1 CCAACCTGAAATCTGATTTT
* *
6415505 CCAACCTAAAAT-TTATTTT
1 CCAACCTGAAATCTGATTTT
* * *
6415524 CTAACCT-AGATCTTATTTT
1 CCAACCTGAAATCTGATTTT
* *
6415543 -CAACATGAAATCTAATTTT
1 CCAACCTGAAATCTGATTTT
6415562 -CAACCT-AAAT
1 CCAACCTGAAAT
6415572 TTTGATTTCT
Statistics
Matches: 114, Mismatches: 24, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
18 12 0.11
19 101 0.89
20 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (20 bp):
CCAACCTGAAATCTGATTTT
Found at i:6415461 original size:38 final size:38
Alignment explanation
Indices: 6415410--6415603 Score: 137
Period size: 38 Copynumber: 5.1 Consensus size: 38
6415400 CACTACTACA
* *
6415410 CCAACCTAAAATCT-ATTTTCTAACCTGAAATATGATTT
1 CCAACCTGAAATCTGA-TTTCTAACCTAAAATATGATTT
* *
6415448 CCAACCTGAAATCTGATTTCTAATCTAAAATTTGATTT
1 CCAACCTGAAATCTGATTTCTAACCTAAAATATGATTT
* * * * *
6415486 CCAACCTGAAATTTGGTTCCCAACCTAAAAT-TTATTTT
1 CCAACCTGAAATCTGATTTCTAACCTAAAATATGA-TTT
* * * * * * *
6415524 CTAACCT-AGATCTTATTT-TCAACATGAAATCTAATTT
1 CCAACCTGAAATCTGATTTCT-AACCTAAAATATGATTT
* * *
6415561 TCAACCT-AAATTTTGATTTCTAACCTAAAATATGGTTT
1 CCAACCTGAAA-TCTGATTTCTAACCTAAAATATGATTT
*
6415599 ACAAC
1 CCAAC
6415604 ATAAAATGTG
Statistics
Matches: 119, Mismatches: 31, Indels: 12
0.73 0.19 0.07
Matches are distributed among these distances:
37 26 0.22
38 91 0.76
39 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (38 bp):
CCAACCTGAAATCTGATTTCTAACCTAAAATATGATTT
Found at i:6415579 original size:19 final size:18
Alignment explanation
Indices: 6415411--6415589 Score: 89
Period size: 19 Copynumber: 9.5 Consensus size: 18
6415401 ACTACTACAC
*
6415411 CAACCTAAAATCT-ATTTT
1 CAACCT-AAATTTGATTTT
* *
6415429 CTAACCTGAAATATGATTTC
1 C-AACCT-AAATTTGATTTT
*
6415449 CAACCTGAAATCTGA-TTT
1 CAACCT-AAATTTGATTTT
* *
6415467 CTAATCTAAAATTTGATTTC
1 C-AACCT-AAATTTGATTTT
* **
6415487 CAACCTGAAATTTGGTTCC
1 CAACCT-AAATTTGATTTT
6415506 CAACCTAAAATTT-ATTTT
1 CAACCT-AAATTTGATTTT
*
6415524 CTAACCTAGATCTT-ATTTT
1 C-AACCTAAAT-TTGATTTT
* * *
6415543 CAACATGAAATCTAATTTT
1 CAACCT-AAATTTGATTTT
6415562 CAACCTAAATTTTGA-TTT
1 CAACCTAAA-TTTGATTTT
6415580 CTAACCTAAA
1 C-AACCTAAA
6415590 ATATGGTTTA
Statistics
Matches: 127, Mismatches: 24, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
18 22 0.17
19 97 0.76
20 8 0.06
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (18 bp):
CAACCTAAATTTGATTTT
Found at i:6416048 original size:16 final size:16
Alignment explanation
Indices: 6416007--6416049 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
6415997 CAGACTGCTA
* *
6416007 AAATGAACTAAAATAT
1 AAATAAACTGAAATAT
6416023 AAATAAACTGAAATAT
1 AAATAAACTGAAATAT
6416039 AAATAAACTGA
1 AAATAAACTGA
6416050 TTTTTTAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (16 bp):
AAATAAACTGAAATAT
Found at i:6416103 original size:31 final size:31
Alignment explanation
Indices: 6416067--6416125 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
6416057 AACTTAAAAG
* *
6416067 AGTTTTGCAATACTGAGATTTAAATAATTTA
1 AGTTTTACAATACTGAAATTTAAATAATTTA
6416098 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
6416126 CCATACATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTA
Found at i:6416178 original size:22 final size:21
Alignment explanation
Indices: 6416153--6416194 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6416143 TAATAAATTA
*
6416153 TTTAAAATAAATCAATTCATAT
1 TTTAAAAT-AATCAATCCATAT
6416175 TTTAAAATAATCAATCCATA
1 TTTAAAATAATCAATCCATA
6416195 CTAATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTAAAATAATCAATCCATAT
Found at i:6416202 original size:22 final size:22
Alignment explanation
Indices: 6416155--6416202 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
6416145 ATAAATTATT
* **
6416155 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATCCATATAA
6416177 TAAAAT-AATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
6416199 TAAA
1 TAAA
6416203 TTATTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:6416322 original size:30 final size:30
Alignment explanation
Indices: 6416259--6416327 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
6416249 CCATATTTTA
* *
6416259 AAATAAATCAATCCATACTAATAATTATTT
1 AAATAAATCAATCCATACTAATAAATATAT
6416289 AAATAAATCAATCCATAC-AACTACAATA-AT
1 AAATAAATCAATCCATACTAA-TA-AATATAT
*
6416319 AAATCAATC
1 AAATAAATC
6416328 CATTTTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 2 0.06
30 29 0.85
31 3 0.09
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (30 bp):
AAATAAATCAATCCATACTAATAAATATAT
Found at i:6416343 original size:47 final size:47
Alignment explanation
Indices: 6416289--6416554 Score: 175
Period size: 47 Copynumber: 5.4 Consensus size: 47
6416279 ATAATTATTT
*
6416289 AAATAAATCAATCCATACAACTACAATAATAAATCAATCCATTTTTA
1 AAATAAATCAATCCATACAACTAAAATAATAAATCAATCCATTTTTA
* **
6416336 AAATAAATCAATCCATACTAA-TAAATTATTTAAAATAAATCAATCCATACAACTACA
1 AAATAAATCAATCCATAC-AACTAAA--A--T--AATAAATCAATCCAT----TTTTA
** * * ** *
6416393 ATAATAAATC-ATCCAT--ATTTAAAATCATCAATACAAATAAATTATTA
1 A-AATAAATCAATCCATACAACTAAAATAATAAAT-C-AATCCATTTTTA
* *
6416440 AAAT-AATCAATCCATACAACTACAATAATAAATCAATCCATATTTA
1 AAATAAATCAATCCATACAACTAAAATAATAAATCAATCCATTTTTA
* * *
6416486 AAATAAATCAATCCATACAAATAATTATTTAAAAAAATCAATCCATATTTTA
1 AAATAAATCAATCCATACAACTAA--A-AT-AATAAATCAATCCAT-TTTTA
6416538 AAAT-AATCAATCCATAC
1 AAATAAATCAATCCATAC
6416555 TAATAAATTA
Statistics
Matches: 168, Mismatches: 27, Indels: 44
0.70 0.11 0.18
Matches are distributed among these distances:
45 4 0.02
46 21 0.12
47 41 0.24
48 13 0.08
49 7 0.04
50 2 0.01
51 34 0.20
52 8 0.05
53 16 0.10
54 1 0.01
55 4 0.02
57 9 0.05
58 8 0.05
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (47 bp):
AAATAAATCAATCCATACAACTAAAATAATAAATCAATCCATTTTTA
Found at i:6416344 original size:77 final size:77
Alignment explanation
Indices: 6416158--6416532 Score: 525
Period size: 77 Copynumber: 4.9 Consensus size: 77
6416148 AATTATTTAA
*
6416158 AATAAATCAATTCATATTTTAAAAT-AATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCAT-TTTTAAAATAAATCAATCCATACTAAT-AATTATTT-AAATAAATC-A-
6416222 CATCCATAC-ACTACAAT
61 -ATCCATACAACTACAAT
6416239 AAT-AATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATTTAAATAAATCAATCC
1 AATAAATCAATCCAT-TTTTAAAATAAATCAATCCATACTAATAATTATTTAAATAAATCAATCC
6416303 ATACAACTACAAT
65 ATACAACTACAAT
6416316 AATAAATCAATCCATTTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
1 AATAAATCAATCCATTTTTAAAATAAATCAATCCATACTAAT-AATTATTT-AAATAAATCAATC
6416381 CATACAACTACAAT
64 CATACAACTACAAT
* * * * *
6416395 AATAAATC-ATCCATATTTAAAAT-CATCAATACA-AAT-A-AATTATTAAAAT-AATCAATCCA
1 AATAAATCAATCCATTTTTAAAATAAATCAATCCATACTAATAATTATTTAAATAAATCAATCCA
6416454 TACAACTACAAT
66 TACAACTACAAT
* * *
6416466 AATAAATCAATCCATATTTAAAATAAATCAATCCATACAAATAATTATTTAAAAAAATCAATCCA
1 AATAAATCAATCCATTTTTAAAATAAATCAATCCATACTAATAATTATTTAAATAAATCAATCCA
6416531 TA
66 TA
6416533 TTTTAAAATA
Statistics
Matches: 271, Mismatches: 12, Indels: 26
0.88 0.04 0.08
Matches are distributed among these distances:
71 30 0.11
72 19 0.07
73 15 0.06
74 1 0.00
75 2 0.01
76 20 0.07
77 58 0.21
78 34 0.13
79 44 0.16
80 28 0.10
81 20 0.07
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.31
Consensus pattern (77 bp):
AATAAATCAATCCATTTTTAAAATAAATCAATCCATACTAATAATTATTTAAATAAATCAATCCA
TACAACTACAAT
Found at i:6416479 original size:150 final size:155
Alignment explanation
Indices: 6416158--6416532 Score: 563
Period size: 150 Copynumber: 2.4 Consensus size: 155
6416148 AATTATTTAA
*
6416158 AATAAATCAATTCATATTTTAAAAT-AATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCAT-TTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATC-A-
* *
6416222 CATCCATACACTACAATAATAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTAT
63 -ATCCATACACTACAATAATAATCAATCCATATTTTAAAATAAATCAATACATAATAATAATTAT
*
6416287 TTAAATAAATCAATCCATACAACTACAAT
127 TAAAATAAATCAATCCATACAACTACAAT
6416316 AATAAATCAATCCATTTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
1 AATAAATCAATCCATTTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
*
6416381 CATACAACTACAATAATAAATC-ATCCATA-TTTAAAAT-CATCAATACA-AAT-A-AATTATTA
66 CATAC-ACTACAATAAT-AATCAATCCATATTTTAAAATAAATCAATACATAATAATAATTATTA
6416440 AAAT-AATCAATCCATACAACTACAAT
129 AAATAAATCAATCCATACAACTACAAT
* *
6416466 AATAAATCAATCCATATTTAAAATAAATCAATCCATACAAAT-AATTATTTAAAA-AAATCAATC
1 AATAAATCAATCCATTTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
6416529 CATA
66 CATA
6416533 TTTTAAAATA
Statistics
Matches: 207, Mismatches: 7, Indels: 16
0.90 0.03 0.07
Matches are distributed among these distances:
148 13 0.06
149 12 0.06
150 62 0.30
151 11 0.05
152 1 0.00
153 2 0.01
154 8 0.04
155 16 0.08
156 18 0.09
157 14 0.07
158 50 0.24
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.31
Consensus pattern (155 bp):
AATAAATCAATCCATTTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
CATACACTACAATAATAATCAATCCATATTTTAAAATAAATCAATACATAATAATAATTATTAAA
ATAAATCAATCCATACAACTACAAT
Found at i:6416526 original size:30 final size:30
Alignment explanation
Indices: 6416480--6416586 Score: 99
Period size: 30 Copynumber: 3.8 Consensus size: 30
6416470 AATCAATCCA
6416480 TATTTAAAATAAATCAATCCATACAAATAAT
1 TATTTAAAA-AAATCAATCCATACAAATAAT
6416511 TATTTAAAAAAATCAAT-C---C--AT-A-
1 TATTTAAAAAAATCAATCCATACAAATAAT
* *
6416533 T-TTTAAAATAATCAATCCATACTAATAAAT
1 TATTTAAAAAAATCAATCCATACAAAT-AAT
*
6416563 TATTT-AAATAATCAATCCATACAA
1 TATTTAAAAAAATCAATCCATACAA
6416587 CTACAATAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 21
0.74 0.02 0.24
Matches are distributed among these distances:
21 14 0.22
22 2 0.03
23 1 0.02
24 2 0.03
25 1 0.02
26 1 0.02
27 2 0.03
29 2 0.03
30 27 0.42
31 12 0.19
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (30 bp):
TATTTAAAAAAATCAATCCATACAAATAAT
Found at i:6416528 original size:51 final size:51
Alignment explanation
Indices: 6416437--6416583 Score: 189
Period size: 51 Copynumber: 3.0 Consensus size: 51
6416427 AAATAAATTA
* * *
6416437 TTAAAATAATCAATCCATACAACTACA--A--TAATAAATCAATCCATA-T
1 TTAAAATAATCAATCCATACAAATAAATTATTTAAAAAATCAATCCATATT
6416483 TTAAAATAAATCAATCCATACAAAT-AATTATTTAAAAAAATCAATCCATATT
1 TTAAAAT-AATCAATCCATACAAATAAATTATTT-AAAAAATCAATCCATATT
* *
6416535 TTAAAATAATCAATCCATACTAATAAATTATTTAAATAATCAATCCATA
1 TTAAAATAATCAATCCATACAAATAAATTATTTAAAAAATCAATCCATA
6416584 CAACTACAAT
Statistics
Matches: 88, Mismatches: 5, Indels: 11
0.85 0.05 0.11
Matches are distributed among these distances:
46 8 0.09
47 16 0.18
48 1 0.01
50 1 0.01
51 46 0.52
52 16 0.18
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (51 bp):
TTAAAATAATCAATCCATACAAATAAATTATTTAAAAAATCAATCCATATT
Found at i:6416538 original size:21 final size:21
Alignment explanation
Indices: 6416513--6416553 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
6416503 CAAATAATTA
6416513 TTTAAAAAAATCAATCCATAT
1 TTTAAAAAAATCAATCCATAT
*
6416534 TTTAAAATAATCAATCCATA
1 TTTAAAAAAATCAATCCATA
6416554 CTAATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (21 bp):
TTTAAAAAAATCAATCCATAT
Found at i:6416562 original size:21 final size:21
Alignment explanation
Indices: 6416515--6416561 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
6416505 AATAATTATT
* **
6416515 TAAAAAAATCAATCCATATTT
1 TAAAATAATCAATCCATATAA
6416536 TAAAATAATCAATCCATACTAA
1 TAAAATAATCAATCCATA-TAA
6416558 TAAA
1 TAAA
6416562 TTATTTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAAATAATCAATCCATATAA
Found at i:6416578 original size:128 final size:123
Alignment explanation
Indices: 6416362--6416662 Score: 434
Period size: 128 Copynumber: 2.4 Consensus size: 123
6416352 ACTAATAAAT
*
6416362 TATTTAAAATAAATCAATCCATACAACTACA--A--T-AATAAATC-ATCCATATTTAAAATCAT
1 TATTTAAAATAAATCAATCCATACAAATA-ATTATTTAAATAAATCAATCCATATTTAAAATCAT
6416421 CAATACAAATAAATTATTAAAATAATCAATCCATACAACTACAATAATAAATCAATCCA
65 CAATACAAATAAATTATTAAAATAATCAATCCATACAACTACAATAATAAATCAATCCA
*
6416480 TATTTAAAATAAATCAATCCATACAAATAATTATTTAAAAAAATCAATCCATATTTTAAAATAAT
1 TATTTAAAATAAATCAATCCATACAAATAATTATTTAAATAAATCAATCCATA-TTT--AA-AAT
* * *
6416545 CAATCCATACTAATAAATTATTTAAATAATCAATCCATACAACTACAATAATAAATCAATCCA
62 C-ATCAATACAAATAAATTATTAAAATAATCAATCCATACAACTACAATAATAAATCAATCCA
*
6416608 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAATAAATCAATCCATA
1 TA-TTTAAAATAAATCAATCCATACAAAT-AATTATTTAAATAAATCAATCCATA
6416663 CAACTACAAT
Statistics
Matches: 163, Mismatches: 7, Indels: 14
0.89 0.04 0.08
Matches are distributed among these distances:
117 1 0.01
118 28 0.17
119 1 0.01
121 1 0.01
122 7 0.04
123 7 0.04
124 3 0.02
126 2 0.01
127 4 0.02
128 60 0.37
129 25 0.15
130 24 0.15
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (123 bp):
TATTTAAAATAAATCAATCCATACAAATAATTATTTAAATAAATCAATCCATATTTAAAATCATC
AATACAAATAAATTATTAAAATAATCAATCCATACAACTACAATAATAAATCAATCCA
Found at i:6416595 original size:150 final size:149
Alignment explanation
Indices: 6416298--6416754 Score: 390
Period size: 150 Copynumber: 3.0 Consensus size: 149
6416288 TAAATAAATC
* *
6416298 AATCCATACAACTACAATAATAAATCAATCCATTTTTAAAATAAATCAATCCATACTAATAAATT
1 AATCCATACAACTACAATAATAAATCAATCCATATTTAAAATAAATCAATCCATACAAAT-AATT
*** * * * *
6416363 ATTTAAAATAAATCAATCCATACAACTACAATAATAAAT-CAT-C-CAT--A-T-TTAAAATCAT
65 ATTTAAAA-AAATCAATCCATA-TTTTA-AATAATCAATCCATACTAATAAATTATTTAAATAAT
* * * *
6416421 CAATACAAATAAATTATTAAAATAATC
127 CAAT-C-AATACA--ACTACAATAATA
6416448 AATCCATACAACTACAATAATAAATCAATCCATATTTAAAATAAATCAATCCATACAAATAATTA
1 AATCCATACAACTACAATAATAAATCAATCCATATTTAAAATAAATCAATCCATACAAATAATTA
6416513 TTTAAAAAAATCAATCCATATTTTAAAATAATCAATCCATACTAATAAATTATTTAAATAATCAA
66 TTTAAAAAAATCAATCCATATTTT-AAATAATCAATCCATACTAATAAATTATTTAAATAATCAA
*
6416578 TCCATACAACTACAATAATA
130 TCAATACAACTACAATAATA
* * * **
6416598 AATCAATCCATATTTTAA-AATAAATCAATCCATACTAATAAATTATTTAAATAAATCAATCCAT
1 AATCCATACA-ACTACAATAATAAATCAATCC--A-T-AT---TTA---AAATAAATCAATCCAT
* *
6416662 ACAACTACA--A--T-AATAAATCAATCC--ATTTT-AA-AATCAATCCATACTAATAAATTATT
55 ACAAATA-ATTATTTAAAAAAATCAATCCATATTTTAAATAATCAATCCATACTAATAAATTATT
*
6416718 TAAAATAAATCAATCAACACAACTACAATAATA
119 T-AAAT-AATCAATCAATACAACTACAATAATA
6416751 AATC
1 AATC
6416755 AATCCATATT
Statistics
Matches: 262, Mismatches: 23, Indels: 41
0.80 0.07 0.13
Matches are distributed among these distances:
147 10 0.04
148 17 0.06
149 13 0.05
150 90 0.34
151 30 0.11
152 12 0.05
153 31 0.12
154 19 0.07
156 12 0.05
157 4 0.02
159 1 0.00
160 22 0.08
161 1 0.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.31
Consensus pattern (149 bp):
AATCCATACAACTACAATAATAAATCAATCCATATTTAAAATAAATCAATCCATACAAATAATTA
TTTAAAAAAATCAATCCATATTTTAAATAATCAATCCATACTAATAAATTATTTAAATAATCAAT
CAATACAACTACAATAATA
Found at i:6416640 original size:22 final size:22
Alignment explanation
Indices: 6416568--6416639 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 22
6416558 TAAATTATTT
*
6416568 AAAT-AATCAATCCATACAACTACA
1 AAATAAATCAATCCATATAA-T--A
**
6416592 ATAATAAATCAATCCATATTTTA
1 A-AATAAATCAATCCATATAATA
6416615 AAATAAATCAATCCATACTAATA
1 AAATAAATCAATCCATA-TAATA
6416638 AA
1 AA
6416640 TTATTTAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
22 16 0.40
23 7 0.17
24 1 0.03
25 4 0.10
26 12 0.30
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (22 bp):
AAATAAATCAATCCATATAATA
Found at i:6416672 original size:278 final size:285
Alignment explanation
Indices: 6416242--6416816 Score: 999
Period size: 278 Copynumber: 2.0 Consensus size: 285
6416232 CTACAATAAT
6416242 AATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATTTAAATAAATCAATCCATAC
1 AATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATTTAAATAAATCAATCCATAC
6416307 AACTACAATAATAAATCAATCCATTTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAAT
66 AACTACAATAATAAATCAATCCATTTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAAT
6416372 AAATCAATCCATACAACTACAATAATAAATC-ATCCATATTTAAAATC-ATCAATACAAATAAAT
131 AAATCAATCCATACAACTACAATAATAAATCAATCCAT-TTTAAAATCAATCAATACAAATAAAT
* *
6416435 TA-TTAAAAT-AATCAATCCATACAACTACAATAATAAATCAATCCATA-TTTAAAATAAATCAA
195 TATTTAAAATAAATCAATCAACACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAA
6416497 TCCATACAAAT-AATTATTTAAAA-A
260 TCCATACAAATAAATTATTTAAAATA
6416521 AATCAATCCATATTTTAAAAT-AATCAATCCATACTAATAAATTATTTAAAT-AATCAATCCATA
1 AATCAATCCATATTTTAAAATAAATCAATCCATACTAAT-AATTATTTAAATAAATCAATCCATA
6416584 CAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTT-AA
65 CAACTACAATAATAAATCAATCCAT-TTTTAAAATAAATCAATCCATACTAATAAATTATTTAAA
* *
6416648 ATAAATCAATCCATACAACTACAATAATAAATCAATCCATTTTAAAATCAATCCATACTAATAAA
129 ATAAATCAATCCATACAACTACAATAATAAATCAATCCATTTTAAAATCAATCAATACAAATAAA
6416713 TTATTTAAAATAAATCAATCAACACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCA
194 TTATTTAAAATAAATCAATCAACACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCA
*
6416778 ATCCATACTAATAAATTATTTAAAATA
259 ATCCATACAAATAAATTATTTAAAATA
*
6416805 AATCAATTCATA
1 AATCAATCCATA
6416817 CTAATAAATT
Statistics
Matches: 281, Mismatches: 6, Indels: 13
0.94 0.02 0.04
Matches are distributed among these distances:
278 98 0.35
279 91 0.32
280 7 0.02
281 36 0.13
282 25 0.09
283 12 0.04
284 12 0.04
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (285 bp):
AATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATTTAAATAAATCAATCCATAC
AACTACAATAATAAATCAATCCATTTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAAT
AAATCAATCCATACAACTACAATAATAAATCAATCCATTTTAAAATCAATCAATACAAATAAATT
ATTTAAAATAAATCAATCAACACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAAT
CCATACAAATAAATTATTTAAAATA
Found at i:6416682 original size:79 final size:80
Alignment explanation
Indices: 6416480--6416863 Score: 521
Period size: 79 Copynumber: 4.9 Consensus size: 80
6416470 AATCAATCCA
* *
6416480 TATTTAAAATAAATCAATCCATACAAATA-ATTATTTAAAAAAATCAATCCATATTTTAAAAT-A
1 TATTTAAAATAAATCAATCCATACAACTACA--A--T-AATAAATCAATCCATATTTTAAAATAA
6416543 ATCAATCCATACTAATAAAT
61 ATCAATCCATACTAATAAAT
6416563 TATTT-AAAT-AATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAA
1 TATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAA
6416626 TCCATACTAATAAAT
66 TCCATACTAATAAAT
6416641 TATTT-AAATAAATCAATCCATACAACTACAATAATAAATCAATCC--ATTTT---A-AAATCAA
1 TATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAA
6416699 TCCATACTAATAAAT
66 TCCATACTAATAAAT
* *
6416714 TATTTAAAATAAATCAATCAACACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAA
1 TATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAA
6416779 TCCATACTAATAAAT
66 TCCATACTAATAAAT
* *
6416794 TATTTAAAATAAATCAATTCATACTAA-TA-AATTATATAAAATAAAT---TATTTTAAAATAAA
1 TATTTAAAATAAATCAATCCATAC-AACTACAA-TA-AT-AAATCAATCCATATTTTAAAATAAA
6416854 TCAATCCATA
62 TCAATCCATA
6416864 TTTTTATAAT
Statistics
Matches: 279, Mismatches: 8, Indels: 32
0.87 0.03 0.10
Matches are distributed among these distances:
73 27 0.10
74 39 0.14
76 5 0.02
77 29 0.10
78 31 0.11
79 62 0.22
80 48 0.17
81 21 0.08
82 12 0.04
83 5 0.02
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.33
Consensus pattern (80 bp):
TATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAA
TCCATACTAATAAAT
Found at i:6416793 original size:22 final size:22
Alignment explanation
Indices: 6416747--6416792 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
6416737 CAACTACAAT
**
6416747 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATAATAA
6416769 AATAAATCAATCCATACTAATAA
1 AATAAATCAATCCATA-TAATAA
6416792 A
1 A
6416793 TTATTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.30
Consensus pattern (22 bp):
AATAAATCAATCCATATAATAA
Found at i:6416803 original size:32 final size:32
Alignment explanation
Indices: 6416764--6416839 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
6416754 CAATCCATAT
6416764 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
6416796 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
6416828 TATAAAATAAAT
1 TTTAAAATAAAT
6416840 TATTTTAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:6416822 original size:18 final size:18
Alignment explanation
Indices: 6416769--6416825 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
6416759 CATATTTTAA
*
6416769 AATAAATCAATCCATACT
1 AATAAATCAATTCATACT
* *
6416787 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
6416801 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
6416819 AATAAAT
1 AATAAAT
6416826 TATATAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 7 0.23
15 5 0.17
17 4 0.13
18 14 0.47
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAAATCAATTCATACT
Found at i:6416850 original size:15 final size:15
Alignment explanation
Indices: 6416787--6416962 Score: 130
Period size: 14 Copynumber: 11.5 Consensus size: 15
6416777 AATCCATACT
6416787 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
* * *
6416801 AATAAATCAATTCATACT
1 AATAAAT-TATT-TTA-A
*
6416819 AATAAATTA-TATAA
1 AATAAATTATTTTAA
6416833 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
6416848 AATAAATCAATCCATATTT-T
1 AATAAAT---T--AT-TTTAA
* *
6416868 TATAATTTTATTTTAA
1 AATAA-ATTATTTTAA
* *
6416884 AGT-AATTATTTTAT
1 AATAAATTATTTTAA
*
6416898 AATAAATTATTTTAT
1 AATAAATTATTTTAA
6416913 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
6416927 AATAAATTATTTT-A
1 AATAAATTATTTTAA
6416941 AATAAATTATTTTAA
1 AATAAATTATTTTAA
6416956 AATAAAT
1 AATAAAT
6416963 AACCTTATTA
Statistics
Matches: 130, Mismatches: 16, Indels: 31
0.73 0.09 0.18
Matches are distributed among these distances:
14 53 0.41
15 50 0.38
16 5 0.04
17 3 0.02
18 9 0.07
20 6 0.05
21 4 0.03
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:6416925 original size:29 final size:29
Alignment explanation
Indices: 6416875--6416962 Score: 135
Period size: 29 Copynumber: 3.0 Consensus size: 29
6416865 TTTTATAATT
*
6416875 TTATTTTAAAGT-AATTATTTTATAATAAA
1 TTATTTTAAA-TAAATTATTTTAAAATAAA
6416904 TTATTTTATAATAAATTA-TTTAAAATAAA
1 TTATTTTA-AATAAATTATTTTAAAATAAA
6416933 TTATTTTAAATAAATTATTTTAAAATAAA
1 TTATTTTAAATAAATTATTTTAAAATAAA
6416962 T
1 T
6416963 AACCTTATTA
Statistics
Matches: 55, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
28 9 0.16
29 39 0.71
30 7 0.13
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (29 bp):
TTATTTTAAATAAATTATTTTAAAATAAA
Found at i:6420809 original size:5 final size:5
Alignment explanation
Indices: 6420799--6420827 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
6420789 ATTATACATG
6420799 TCATA TCATA TCATA TCATA TCATA TCAT
1 TCATA TCATA TCATA TCATA TCATA TCAT
6420828 GATCTTAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (5 bp):
TCATA
Found at i:6421154 original size:35 final size:36
Alignment explanation
Indices: 6421011--6421202 Score: 179
Period size: 36 Copynumber: 5.2 Consensus size: 36
6421001 ATCACACTTT
* * *
6421011 TAATCATTATTTGCAAGCACATGAATATAATGCATA
1 TAATCATTATTAGCAAGCACATGTATATCATGCATA
* ** * ** * *
6421047 TAATCGTTAGCAACAAGTGCATGTATATAATGCATG
1 TAATCATTATTAGCAAGCACATGTATATCATGCATA
* * *
6421083 TAATCATCAATAGCAAGTGTATACTCATGTATATCATGCATA
1 TAATCATTATTAGCAA--G----CACATGTATATCATGCATA
*
6421125 TAATCATTATTAGC-AGCGCATGTATATCATGCATA
1 TAATCATTATTAGCAAGCACATGTATATCATGCATA
*
6421160 TAATCATTATTAGCAAGCACATGTACATCATGCATA
1 TAATCATTATTAGCAAGCACATGTATATCATGCATA
6421196 TAATCAT
1 TAATCAT
6421203 CAATAATAAG
Statistics
Matches: 126, Mismatches: 23, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
35 32 0.25
36 64 0.51
38 1 0.01
39 1 0.01
41 1 0.01
42 27 0.21
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (36 bp):
TAATCATTATTAGCAAGCACATGTATATCATGCATA
Found at i:6422008 original size:19 final size:19
Alignment explanation
Indices: 6421976--6422360 Score: 271
Period size: 19 Copynumber: 20.4 Consensus size: 19
6421966 AACTTGCCCT
*
6421976 TAAAGATCTGGTTCCCAACC
1 TAAA-ATCTGGTTTCCAACC
*
6421996 TAAAATCTAG-TTCTCAACC
1 TAAAATCTGGTTTC-CAACC
* *
6422015 TGAAACCTGGTTTCCAACC
1 TAAAATCTGGTTTCCAACC
* *
6422034 TAAAAT-TGGCTTCTAACC
1 TAAAATCTGGTTTCCAACC
* * * *
6422052 TAAAATTTGATTTCCAGCA
1 TAAAATCTGGTTTCCAACC
* * *
6422071 TGAAATCTAGTTTCCAAAC
1 TAAAATCTGGTTTCCAACC
* *
6422090 TGAAATCGGGTTTCCAACC
1 TAAAATCTGGTTTCCAACC
* **
6422109 T-AAATCT-ATTTTTAACC
1 TAAAATCTGGTTTCCAACC
* ** *
6422126 TGAAATCTTATTTCTAACC
1 TAAAATCTGGTTTCCAACC
* *
6422145 TAAAATAC-AGTTTCCAATC
1 TAAAAT-CTGGTTTCCAACC
6422164 TAAAATCTGGTTTCCAACC
1 TAAAATCTGGTTTCCAACC
** *
6422183 TAAAATCTATTTTCTAACC
1 TAAAATCTGGTTTCCAACC
* * * *
6422202 TGAAGTCTGATTTTCAACC
1 TAAAATCTGGTTTCCAACC
* *
6422221 TAAAATATGATTTCCAACC
1 TAAAATCTGGTTTCCAACC
* *
6422240 TGAAATCTGGTTTCTAACC
1 TAAAATCTGGTTTCCAACC
* *
6422259 TAAAATCTGGTTTCTAACA
1 TAAAATCTGGTTTCCAACC
*
6422278 TAAAATATGGTTTCCAACC
1 TAAAATCTGGTTTCCAACC
* ** **
6422297 TGAAAT-TCAATTTTTAACC
1 TAAAATCT-GGTTTCCAACC
**
6422316 TGGAATCTGGTTTCCAACC
1 TAAAATCTGGTTTCCAACC
*
6422335 TGAAATCT-GTTTCCAACC
1 TAAAATCTGGTTTCCAACC
6422353 TAAAATCT
1 TAAAATCT
6422361 CTAAACTGAA
Statistics
Matches: 286, Mismatches: 70, Indels: 20
0.76 0.19 0.05
Matches are distributed among these distances:
17 8 0.03
18 48 0.17
19 221 0.77
20 9 0.03
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.34
Consensus pattern (19 bp):
TAAAATCTGGTTTCCAACC
Found at i:6422034 original size:38 final size:37
Alignment explanation
Indices: 6421981--6422360 Score: 302
Period size: 38 Copynumber: 10.1 Consensus size: 37
6421971 GCCCTTAAAG
*
6421981 ATCTGGTTCCCAACCTAAAATCTAGTTCTCAACCTGAA
1 ATCTGGTTTCCAACCTAAAATCTAGTT-TCAACCTGAA
* * * *
6422019 ACCTGGTTTCCAACCTAAAAT-TGGCTTCTAACCTAAA
1 ATCTGGTTTCCAACCTAAAATCTAGTTTC-AACCTGAA
* * * * * *
6422056 ATTTGATTTCCAGCATGAAATCTAGTTTCCAAACTGAA
1 ATCTGGTTTCCAACCTAAAATCTAGTTT-CAACCTGAA
* * *
6422094 ATCGGGTTTCCAACCT-AAATCTATTTTTAACCTGAA
1 ATCTGGTTTCCAACCTAAAATCTAGTTTCAACCTGAA
** * * *
6422130 ATCTTATTTCTAACCTAAAATAC-AGTTTCCAATCTAAA
1 ATCTGGTTTCCAACCTAAAAT-CTAGTTT-CAACCTGAA
*
6422168 ATCTGGTTTCCAACCTAAAATCTATTTTCTAACCTGAA
1 ATCTGGTTTCCAACCTAAAATCTAGTTTC-AACCTGAA
* * * *
6422206 GTCTGATTTTCAACCTAAAATAT-GATTTCCAACCTGAA
1 ATCTGGTTTCCAACCTAAAATCTAG-TTT-CAACCTGAA
* * * *
6422244 ATCTGGTTTCTAACCTAAAATCTGGTTTCTAACATAAA
1 ATCTGGTTTCCAACCTAAAATCTAGTTTC-AACCTGAA
* * * * * *
6422282 ATATGGTTTCCAACCTGAAATTCAATTTTTAACCTGGA
1 ATCTGGTTTCCAACCT-AAAATCTAGTTTCAACCTGAA
* *
6422320 ATCTGGTTTCCAACCTGAAATCT-GTTTCCAACCTAAA
1 ATCTGGTTTCCAACCTAAAATCTAGTTT-CAACCTGAA
6422357 ATCT
1 ATCT
6422361 CTAAACTGAA
Statistics
Matches: 261, Mismatches: 67, Indels: 29
0.73 0.19 0.08
Matches are distributed among these distances:
36 24 0.09
37 60 0.23
38 166 0.64
39 11 0.04
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.34
Consensus pattern (37 bp):
ATCTGGTTTCCAACCTAAAATCTAGTTTCAACCTGAA
Found at i:6422421 original size:19 final size:19
Alignment explanation
Indices: 6422399--6422447 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
6422389 GTTTTCTGAT
*
6422399 CTGAAATCTGATTTCCAAC
1 CTGAAATATGATTTCCAAC
*
6422418 CTGAAATATGATTTTCAA-
1 CTGAAATATGATTTCCAAC
6422436 CTAGAAATATGA
1 CT-GAAATATGA
6422448 ACGCATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 2 0.07
19 25 0.93
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (19 bp):
CTGAAATATGATTTCCAAC
Found at i:6429913 original size:87 final size:87
Alignment explanation
Indices: 6429734--6429937 Score: 228
Period size: 87 Copynumber: 2.3 Consensus size: 87
6429724 TGAGCTTTTT
* * * * * *
6429734 CTCTTAATGAATTTATAGCTCAAGTTTTGGGTGGTCCTAATGAGAATGACTTGATGAATTCATCA
1 CTCTTAATGAATTCATAGCCCAAGATTTGGGTGGTCCTAATGAAAAGGACTTGATGAATTCAACA
6429799 ACTTGAAAGGATGAGCTTTACA
66 ACTTGAAAGGATGAGCTTTACA
* * * *
6429821 ATCTTAATGAATTCATAGCCCAGGATTTGGGTGGTCCTAGTGAAAAGGACTTGATGGATTCAACA
1 CTCTTAATGAATTCATAGCCCAAGATTTGGGTGGTCCTAATGAAAAGGACTTGATGAATTCAACA
* * * * * *
6429886 ACTTGAGATGTTGAGTTTTGCG
66 ACTTGAAAGGATGAGCTTTACA
* * **
6429908 CTCTTAATGAGTCCATAATCCAAGATTTGG
1 CTCTTAATGAATTCATAGCCCAAGATTTGG
6429938 ATAGTCTTTG
Statistics
Matches: 95, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
87 95 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (87 bp):
CTCTTAATGAATTCATAGCCCAAGATTTGGGTGGTCCTAATGAAAAGGACTTGATGAATTCAACA
ACTTGAAAGGATGAGCTTTACA
Found at i:6430383 original size:27 final size:27
Alignment explanation
Indices: 6430352--6430416 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
6430342 GAATTTAGAA
*
6430352 GTGACTTCACTTGACCCAAGTTT-AGG
1 GTGACTTCACCTGACCCAAGTTTAAGG
* *
6430378 GATGACCTCACCTGACCCGAGTTTAAGG
1 G-TGACTTCACCTGACCCAAGTTTAAGG
6430406 GTGACTTCACC
1 GTGACTTCACC
6430417 CAGCCTGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.03
27 28 0.85
28 4 0.12
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (27 bp):
GTGACTTCACCTGACCCAAGTTTAAGG
Found at i:6430740 original size:22 final size:20
Alignment explanation
Indices: 6430700--6430747 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
6430690 ATAAACTAGG
*
6430700 GATGCATTGTCTGATGCATC
1 GATGCATTGTCAGATGCATC
*
6430720 GATGCATTAGTGCAGATGCATG
1 GATGCATT-GT-CAGATGCATC
6430742 GATGCA
1 GATGCA
6430748 CTACAGGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 2 0.08
22 14 0.58
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (20 bp):
GATGCATTGTCAGATGCATC
Found at i:6430760 original size:21 final size:21
Alignment explanation
Indices: 6430734--6430791 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
6430724 CATTAGTGCA
6430734 GATGCATGGATGCACTACAGG
1 GATGCATGGATGCACTACAGG
*
6430755 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTACAGG
6430776 GATGCATGGATGCACT
1 GATGCATGGATGCACT
6430792 TTGACACCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (21 bp):
GATGCATGGATGCACTACAGG
Found at i:6430906 original size:30 final size:30
Alignment explanation
Indices: 6430872--6430931 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
6430862 AACTTTGAAT
*
6430872 AAATTTAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
6430902 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
6430932 CTTAAATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:6442042 original size:25 final size:25
Alignment explanation
Indices: 6441999--6442048 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
6441989 TTTCAGATTA
6441999 ATGAATTTAGGTTAATTTTAGGTAT
1 ATGAATTTAGGTTAATTTTAGGTAT
* *
6442024 ATGAATTTAGTTTAATTTTATGTAT
1 ATGAATTTAGGTTAATTTTAGGTAT
6442049 GATTTTTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (25 bp):
ATGAATTTAGGTTAATTTTAGGTAT
Found at i:6444880 original size:2 final size:2
Alignment explanation
Indices: 6444873--6444899 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6444863 TTGTAATGTC
6444873 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
6444900 GTTGTAACTA
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:6451176 original size:12 final size:12
Alignment explanation
Indices: 6451156--6451222 Score: 55
Period size: 12 Copynumber: 5.6 Consensus size: 12
6451146 TATACATTAC
*
6451156 CTGAATTCTGTT
1 CTGATTTCTGTT
*
6451168 CTGATTTCTGAT
1 CTGATTTCTGTT
6451180 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
* * *
6451192 TTGATATCTGAT
1 CTGATTTCTGTT
*
6451204 CTGAATTCTGTT
1 CTGATTTCTGTT
*
6451216 TTGATTT
1 CTGATTT
6451223 ATGATATCTT
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
11 2 0.05
12 37 0.90
13 2 0.05
ACGTcount: A:0.16, C:0.13, G:0.18, T:0.52
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:6451187 original size:24 final size:24
Alignment explanation
Indices: 6451156--6451227 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
6451146 TATACATTAC
*
6451156 CTGAATTCTGTTCTGATTTCTGAT
1 CTGAATTCTGTTTTGATTTCTGAT
* *
6451180 CTGGATTCTGTTTTGATATCTGAT
1 CTGAATTCTGTTTTGATTTCTGAT
*
6451204 CTGAATTCTGTTTTGATTTATGAT
1 CTGAATTCTGTTTTGATTTCTGAT
6451228 ATCTTCGTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.51
Consensus pattern (24 bp):
CTGAATTCTGTTTTGATTTCTGAT
Found at i:6455964 original size:24 final size:24
Alignment explanation
Indices: 6455937--6455990 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
6455927 TTACCTGAAT
* * *
6455937 TCTGTTCTGGATTCTGTTTTGATA
1 TCTGATCTGAATTCTATTTTGATA
*
6455961 TCTGATCTGAATTCTATTTTGATT
1 TCTGATCTGAATTCTATTTTGATA
6455985 TCTGAT
1 TCTGAT
6455991 ATCTTCGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.54
Consensus pattern (24 bp):
TCTGATCTGAATTCTATTTTGATA
Found at i:6460724 original size:24 final size:23
Alignment explanation
Indices: 6460671--6460742 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 23
6460661 ATACATTACC
* * *
6460671 TGAATTCTGTTCTGATTTTGATC
1 TGAATTCTGTTATGATTCTGATA
*
6460694 TGGATTCTGTTATGATATCTGATA
1 TGAATTCTGTTATGAT-TCTGATA
* *
6460718 TGAATTCTGTTTTTATTTCTGATA
1 TGAATTCTGTTATGA-TTCTGATA
6460742 T
1 T
6460743 CTCCATTTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
23 14 0.35
24 25 0.62
25 1 0.03
ACGTcount: A:0.21, C:0.10, G:0.17, T:0.53
Consensus pattern (23 bp):
TGAATTCTGTTATGATTCTGATA
Found at i:6467572 original size:24 final size:24
Alignment explanation
Indices: 6467537--6467606 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
6467527 GTTGGGGTAG
* *
6467537 TTGACCCTGTTTAACCCGACCCAT
1 TTGACCCGGTTTGACCCGACCCAT
*
6467561 TTGACCCGGTTTGACCCGATCCAT
1 TTGACCCGGTTTGACCCGACCCAT
* *
6467585 TTGACCTGGTTTGACCCAACCC
1 TTGACCCGGTTTGACCCGACCC
6467607 GTTGACCGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.19, C:0.36, G:0.17, T:0.29
Consensus pattern (24 bp):
TTGACCCGGTTTGACCCGACCCAT
Found at i:6469744 original size:18 final size:18
Alignment explanation
Indices: 6469721--6469767 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
6469711 GCTATATAAG
6469721 TGTGACTATTCCAAGACT
1 TGTGACTATTCCAAGACT
6469739 TGTGACTATTCCAAGACT
1 TGTGACTATTCCAAGACT
6469757 TGTGACTATTC
1 TGTGACTATTC
6469768 TAGACATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (18 bp):
TGTGACTATTCCAAGACT
Found at i:6474096 original size:20 final size:20
Alignment explanation
Indices: 6474058--6474096 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6474048 TGTAAAAATA
* * *
6474058 AATTTATAATATTATAATTT
1 AATTTAAAATATAAAAATTT
6474078 AATTTAAAATATAAAAATT
1 AATTTAAAATATAAAAATT
6474097 AAAGAGTTAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATTTAAAATATAAAAATTT
Found at i:6478015 original size:23 final size:23
Alignment explanation
Indices: 6477981--6478041 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
6477971 TTTTAATAAT
* *
6477981 AAAAAATCTTTAATATTCA-ATCC
1 AAAAAATATTTAATATT-ATATCA
* *
6478004 AAAAAATATTTAA-AATATATTA
1 AAAAAATATTTAATATTATATCA
6478026 AAAAAATATTTAATAT
1 AAAAAATATTTAATAT
6478042 ATGTTAAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 1 0.03
22 17 0.55
23 13 0.42
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAAAATATTTAATATTATATCA
Found at i:6478023 original size:11 final size:11
Alignment explanation
Indices: 6478004--6478038 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
6477994 TATTCAATCC
6478004 AAAAAATATTT
1 AAAAAATATTT
* *
6478015 AAAATATATTA
1 AAAAAATATTT
6478026 AAAAAATATTT
1 AAAAAATATTT
6478037 AA
1 AA
6478039 TATATGTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AAAAAATATTT
Found at i:6478029 original size:22 final size:22
Alignment explanation
Indices: 6478004--6478050 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
6477994 TATTCAATCC
6478004 AAAAAATATTTAAAATATATTA
1 AAAAAATATTTAAAATATATTA
* *
6478026 AAAAAATATTTAATATATGTTA
1 AAAAAATATTTAAAATATATTA
6478048 AAA
1 AAA
6478051 GACATTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAAAATATTTAAAATATATTA
Found at i:6479279 original size:21 final size:23
Alignment explanation
Indices: 6479244--6479291 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
6479234 ATTTTTCAAC
*
6479244 TTCCCTCCAAATAAAATTTAA-A
1 TTCCCTCCAAATAAAATTGAATA
*
6479266 TTCCCT-CTAATAAAATTGAATA
1 TTCCCTCCAAATAAAATTGAATA
6479288 TTCC
1 TTCC
6479292 TTATTCATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.40, C:0.23, G:0.02, T:0.35
Consensus pattern (23 bp):
TTCCCTCCAAATAAAATTGAATA
Found at i:6481394 original size:19 final size:18
Alignment explanation
Indices: 6481355--6481399 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
6481345 ACTTTTGATA
* *
6481355 TTTATTATAAAGTTTATT
1 TTTATTTTAAAGTTAATT
6481373 TTTATTTTAAAGTCTAATT
1 TTTATTTTAAAGT-TAATT
6481392 TTTATTTT
1 TTTATTTT
6481400 TGAAATCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (18 bp):
TTTATTTTAAAGTTAATT
Found at i:6481450 original size:35 final size:35
Alignment explanation
Indices: 6481404--6481474 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
6481394 TATTTTTGAA
*
6481404 ATCATATAGTGCAAGGATGATGAATAACCAAATAC
1 ATCATATAGTGCAAGGATGATGAAGAACCAAATAC
6481439 ATCATATAGTGCAAGGATGATGAAGAACCAAATAC
1 ATCATATAGTGCAAGGATGATGAAGAACCAAATAC
6481474 A
1 A
6481475 AAAGTAATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.46, C:0.14, G:0.18, T:0.21
Consensus pattern (35 bp):
ATCATATAGTGCAAGGATGATGAAGAACCAAATAC
Found at i:6481652 original size:18 final size:19
Alignment explanation
Indices: 6481617--6481661 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
6481607 TATGATTTCA
*
6481617 AAAATAAAAATTAGACTTT
1 AAAATAAAAATTAAACTTT
6481636 AAAATAAAAA-TAAACTTT
1 AAAATAAAAATTAAACTTT
*
6481654 ATAATAAA
1 AAAATAAA
6481662 TATCAAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATAAAAATTAAACTTT
Found at i:6484238 original size:20 final size:19
Alignment explanation
Indices: 6484210--6484257 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
6484200 CATAATTATT
*
6484210 AAAAA-TTAGAAAAATATAG
1 AAAAATTTAGAAAAAT-TAA
*
6484229 AAAAATTTAGATAAATTAA
1 AAAAATTTAGAAAAATTAA
6484248 AAATAATTTA
1 AAA-AATTTA
6484258 AATAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (19 bp):
AAAAATTTAGAAAAATTAA
Found at i:6484262 original size:20 final size:20
Alignment explanation
Indices: 6484232--6484269 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6484222 AATATAGAAA
*
6484232 AATTTAGATAAATTAAAAAT
1 AATTTAAATAAATTAAAAAT
*
6484252 AATTTAAATAATTTAAAA
1 AATTTAAATAAATTAAAA
6484270 TAGTAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
AATTTAAATAAATTAAAAAT
Found at i:6485429 original size:23 final size:22
Alignment explanation
Indices: 6485369--6485438 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 22
6485359 AGAATATGTC
* * *
6485369 TTTTAACATATATTAAATAATT
1 TTTTAATATATATTAAAGATTT
*
6485391 TTTTAATATATTTTAAAGATTT
1 TTTTAATATATATTAAAGATTT
6485413 TTTTAAT-TGAATATTAAAGATTT
1 TTTTAATAT--ATATTAAAGATTT
6485436 TTT
1 TTT
6485439 ATTATTAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 1 0.02
22 25 0.61
23 15 0.37
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTTAATATATATTAAAGATTT
Found at i:6487060 original size:2 final size:2
Alignment explanation
Indices: 6487053--6487088 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6487043 TTTAACCTCT
6487053 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6487089 ATTTTGTACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6492398 original size:48 final size:48
Alignment explanation
Indices: 6492327--6492420 Score: 134
Period size: 48 Copynumber: 2.0 Consensus size: 48
6492317 TTAAACGGAG
*
6492327 ATATCAGAAATCAAAACATAATTCAGAACAGATATCAGAACAGAATCC
1 ATATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCC
* ** * *
6492375 ATATCAGAAATCAGAACAGAATTCAGGTCATATATCATAACAGAAT
1 ATATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAAT
6492421 TTAAGTCGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (48 bp):
ATATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCC
Found at i:6492400 original size:12 final size:12
Alignment explanation
Indices: 6492331--6492400 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
6492321 ACGGAGATAT
* *
6492331 CAGAAATCAAAA
1 CAGAATTCAGAA
*
6492343 CATAATTCAGAA
1 CAGAATTCAGAA
6492355 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * *
6492367 CAGAATCCATAT
1 CAGAATTCAGAA
*
6492379 CAGAAATCAGAA
1 CAGAATTCAGAA
6492391 CAGAATTCAG
1 CAGAATTCAG
6492401 GTCATATATC
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.51, C:0.19, G:0.13, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:6492411 original size:24 final size:24
Alignment explanation
Indices: 6492329--6492421 Score: 96
Period size: 24 Copynumber: 3.9 Consensus size: 24
6492319 AAACGGAGAT
* * *
6492329 ATCAGAAATCAAAACATAATTCAG
1 ATCAGATATCAGAACAGAATTCAG
* * *
6492353 AACAGATATCAGAACAGAATCCAT
1 ATCAGATATCAGAACAGAATTCAG
*
6492377 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGATATCAGAACAGAATTCAG
* * *
6492401 GTCATATATCATAACAGAATT
1 ATCAGATATCAGAACAGAATT
6492422 TAAGTCGGAA
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22
Consensus pattern (24 bp):
ATCAGATATCAGAACAGAATTCAG
Found at i:6492435 original size:24 final size:24
Alignment explanation
Indices: 6492330--6492437 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
6492320 AACGGAGATA
* *
6492330 TCAGAAATCAAAACATAATTC-AG
1 TCAGAAATCAGAACAGAATTCAAG
* * *
6492353 AACAGATATCAGAACAGAATCCATA-
1 -TCAGAAATCAGAACAGAATTCA-AG
*
6492378 TCAGAAATCAGAACAGAATTCAGG
1 TCAGAAATCAGAACAGAATTCAAG
* * * *
6492402 TCATATATCATAACAGAATTTAAG
1 TCAGAAATCAGAACAGAATTCAAG
*
6492426 TCGGAAATCAGA
1 TCAGAAATCAGA
6492438 TAAAATATTT
Statistics
Matches: 63, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
24 62 0.98
26 1 0.02
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:6494832 original size:13 final size:13
Alignment explanation
Indices: 6494814--6494838 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6494804 GGTCAACGTC
6494814 AGTCAACGGGTCT
1 AGTCAACGGGTCT
6494827 AGTCAACGGGTC
1 AGTCAACGGGTC
6494839 GGGTCGGGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.20
Consensus pattern (13 bp):
AGTCAACGGGTCT
Found at i:6497022 original size:24 final size:24
Alignment explanation
Indices: 6496917--6497022 Score: 72
Period size: 24 Copynumber: 4.4 Consensus size: 24
6496907 AATGGAGATA
* * *
6496917 TCAGAAATCAAAACATAATTCAGAA
1 TCAGAAATCATAACAGAATTCA-AG
* * *
6496942 T-AGATATCAGAACAGAATCCATA-
1 TCAGAAATCATAACAGAATTCA-AG
* *
6496965 TAAAAAATCATAACAGAATTCAAG
1 TCAGAAATCATAACAGAATTCAAG
* * * *
6496989 TCATATATCATAATAGAATTTAAG
1 TCAGAAATCATAACAGAATTCAAG
6497013 TCAGAAATCA
1 TCAGAAATCA
6497023 GATAAAATAT
Statistics
Matches: 63, Mismatches: 16, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
23 2 0.03
24 60 0.95
25 1 0.02
ACGTcount: A:0.52, C:0.14, G:0.09, T:0.25
Consensus pattern (24 bp):
TCAGAAATCATAACAGAATTCAAG
Found at i:6501576 original size:24 final size:24
Alignment explanation
Indices: 6501549--6501636 Score: 106
Period size: 24 Copynumber: 3.7 Consensus size: 24
6501539 GATATCAGAA
* *
6501549 ATCAAAACAGAATTCAGAACATAT
1 ATCAGAACAGAATTCAGATCATAT
* * *
6501573 ATCATAACAGAATCCAGATCATAA
1 ATCAGAACAGAATTCAGATCATAT
*
6501597 ATCAGAACAAAATTCATG-TCATAT
1 ATCAGAACAGAATTCA-GATCATAT
6501621 ATCAGAACAGAATTCA
1 ATCAGAACAGAATTCA
6501637 AGTCAGAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
24 53 0.98
25 1 0.02
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.23
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGATCATAT
Found at i:6501611 original size:48 final size:47
Alignment explanation
Indices: 6501542--6501650 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 47
6501532 AAACGGAGAT
* * *
6501542 ATCAGAAATCAAAACAGAATTCA-GAACATATATCATAACAGAATCCA
1 ATCAGAAATCAGAACAAAATTCATG-ACATATATCAGAACAGAATCCA
* * *
6501589 GATCATAAATCAGAACAAAATTCATGTCATATATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAAAATTCATGACATATATCAGAACAGAATCCA
6501637 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
6501651 TAAAATATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 1 0.02
48 50 0.96
49 1 0.02
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.21
Consensus pattern (47 bp):
ATCAGAAATCAGAACAAAATTCATGACATATATCAGAACAGAATCCA
Found at i:6501641 original size:24 final size:25
Alignment explanation
Indices: 6501542--6501650 Score: 100
Period size: 24 Copynumber: 4.5 Consensus size: 25
6501532 AAACGGAGAT
* *
6501542 ATCAGAAATCAAAACAGAATTC-AG
1 ATCATAAATCAGAACAGAATTCAAG
* * * *
6501566 AACATATATCATAACAGAA-TCCAG
1 ATCATAAATCAGAACAGAATTCAAG
* *
6501590 ATCATAAATCAGAACAAAATTCATG
1 ATCATAAATCAGAACAGAATTCAAG
*
6501615 -TCATATATCAGAACAGAATTCAAG
1 ATCATAAATCAGAACAGAATTCAAG
*
6501639 -TCAGAAATCAGA
1 ATCATAAATCAGA
6501651 TAAAATATTT
Statistics
Matches: 68, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
23 2 0.03
24 63 0.93
25 3 0.04
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.21
Consensus pattern (25 bp):
ATCATAAATCAGAACAGAATTCAAG
Found at i:6504142 original size:12 final size:13
Alignment explanation
Indices: 6504112--6504166 Score: 76
Period size: 13 Copynumber: 4.3 Consensus size: 13
6504102 GCTGGTCAAC
*
6504112 GGTCAACAAGTCG
1 GGTCAACAGGTCG
*
6504125 GGTCAACGGGTC-
1 GGTCAACAGGTCG
6504137 GGTCAACAGGTCG
1 GGTCAACAGGTCG
*
6504150 GGTCAACAAGTCG
1 GGTCAACAGGTCG
6504163 GGTC
1 GGTC
6504167 GGGTTGGAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
12 11 0.30
13 26 0.70
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.16
Consensus pattern (13 bp):
GGTCAACAGGTCG
Found at i:6504162 original size:25 final size:25
Alignment explanation
Indices: 6504111--6504163 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
6504101 CGCTGGTCAA
**
6504111 CGGTCAACAAGTCGGGTCAACGGGT
1 CGGTCAACAAGTCGGGTCAACAAGT
*
6504136 CGGTCAACAGGTCGGGTCAACAAGT
1 CGGTCAACAAGTCGGGTCAACAAGT
6504161 CGG
1 CGG
6504164 GTCGGGTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.36, T:0.15
Consensus pattern (25 bp):
CGGTCAACAAGTCGGGTCAACAAGT
Found at i:6510415 original size:23 final size:23
Alignment explanation
Indices: 6510384--6510452 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
6510374 CACCACAGCT
*
6510384 CATATAATTGCACCTAAGTGCCA
1 CATAGAATTGCACCTAAGTGCCA
* ** *
6510407 CGTAGAATTGCACCGGAGTGCCG
1 CATAGAATTGCACCTAAGTGCCA
*
6510430 CATAGAATTGCACCTTAGTGCCA
1 CATAGAATTGCACCTAAGTGCCA
6510453 TATAATAATG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (23 bp):
CATAGAATTGCACCTAAGTGCCA
Done.