Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, 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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 6 of 105
Found at i:818642 original size:18 final size:18
Alignment explanation
Indices: 818596--818644 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
818586 TATATTTTCG
*
818596 ATATAAATTATAAATTATA
1 ATATAAA-TATAAAATATA
* **
818615 ATTTTTATATAAAATATA
1 ATATAAATATAAAATATA
818633 ATATAAATATAA
1 ATATAAATATAA
818645 TATTTTATAT
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAAATATAAAATATA
Found at i:819041 original size:25 final size:25
Alignment explanation
Indices: 818990--819042 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
818980 AATGAACCTG
* * *
818990 AAGAAAGGCTGCTTAACAGGTTTAC
1 AAGAAAGGCAGCTTAACAGCTTAAC
*
819015 AAGAAAGGCAGCTTAACTGCTTAAC
1 AAGAAAGGCAGCTTAACAGCTTAAC
819040 AAG
1 AAG
819043 TAGCTTTCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.21
Consensus pattern (25 bp):
AAGAAAGGCAGCTTAACAGCTTAAC
Found at i:824787 original size:16 final size:16
Alignment explanation
Indices: 824763--824797 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
824753 ATTAAATAAT
*
824763 TTATTTTATATTTTGA
1 TTATATTATATTTTGA
824779 TTATATTATATTTTGA
1 TTATATTATATTTTGA
824795 TTA
1 TTA
824798 AAATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (16 bp):
TTATATTATATTTTGA
Found at i:825342 original size:44 final size:44
Alignment explanation
Indices: 825294--825382 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
825284 AAAATTAATT
825294 CGTATCAATTAAAAAAAGATTCATTCGATATTTTTATTGATATC
1 CGTATCAATTAAAAAAAGATTCATTCGATATTTTTATTGATATC
* * *
825338 CGTATCAATTAAGAAAGGATTCATTCTATATTTTTATTGATATC
1 CGTATCAATTAAAAAAAGATTCATTCGATATTTTTATTGATATC
825382 C
1 C
825383 TTTCATTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (44 bp):
CGTATCAATTAAAAAAAGATTCATTCGATATTTTTATTGATATC
Found at i:827184 original size:2 final size:2
Alignment explanation
Indices: 827177--827210 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
827167 ATTGCTTAGC
827177 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
827211 TCATTACAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:829095 original size:26 final size:27
Alignment explanation
Indices: 829065--829120 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
829055 ATTGTATTGA
**
829065 ACATAAATACTACA-GTTGTAAGGACC
1 ACATAAATACTACATGTACTAAGGACC
*
829091 ACATAAATTCTACATGTACTAAGGACC
1 ACATAAATACTACATGTACTAAGGACC
829118 ACA
1 ACA
829121 ACATAATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.23
Consensus pattern (27 bp):
ACATAAATACTACATGTACTAAGGACC
Found at i:834195 original size:2 final size:2
Alignment explanation
Indices: 834182--834225 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
834172 TGGTTGTAAC
* * * *
834182 AT AT AT AC AT AT AT AT AT AT AA AT AT AT AT AT GT AC 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
834224 AT
1 AT
834226 TGAGGACATG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:834201 original size:14 final size:14
Alignment explanation
Indices: 834182--834225 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
834172 TGGTTGTAAC
834182 ATATATACATATAT
1 ATATATACATATAT
*
834196 ATATATAAATATAT
1 ATATATACATATAT
*
834210 ATATGTACATATAT
1 ATATATACATATAT
834224 AT
1 AT
834226 TGAGGACATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (14 bp):
ATATATACATATAT
Found at i:842320 original size:2 final size:2
Alignment explanation
Indices: 842315--842355 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
842305 ACACACACAC
842315 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
842356 GTGATCTGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:849249 original size:14 final size:14
Alignment explanation
Indices: 849227--849256 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
849217 TGGTTGTAAC
849227 ATATATACATATAT
1 ATATATACATATAT
*
849241 ATATGTACATATAT
1 ATATATACATATAT
849255 AT
1 AT
849257 TGAGTACATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (14 bp):
ATATATACATATAT
Found at i:856905 original size:2 final size:2
Alignment explanation
Indices: 856900--856928 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
856890 ACACACACAC
856900 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
856929 GTGATCTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:859956 original size:2 final size:2
Alignment explanation
Indices: 859949--859981 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
859939 AGTGAGAAGA
859949 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
859982 AAGTGTTAAT
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:862573 original size:7 final size:7
Alignment explanation
Indices: 862561--862636 Score: 59
Period size: 8 Copynumber: 10.7 Consensus size: 7
862551 TGATTACAAA
862561 TATTTTT
1 TATTTTT
862568 TA-TTTT
1 TATTTTT
862574 TA-TTTT
1 TATTTTT
862580 TATTTTT
1 TATTTTT
862587 TGATTTTT
1 T-ATTTTT
*
862595 TGTTATTT
1 TATT-TTT
862603 TATTTTAT
1 TATTTT-T
* *
862611 CATTTTA
1 TATTTTT
862618 TA-TTTT
1 TATTTTT
*
862624 AAGTTTTT
1 TA-TTTTT
862632 TATTT
1 TATTT
862637 CATTTTTATT
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
6 16 0.29
7 15 0.27
8 24 0.44
ACGTcount: A:0.18, C:0.01, G:0.04, T:0.76
Consensus pattern (7 bp):
TATTTTT
Found at i:862575 original size:6 final size:6
Alignment explanation
Indices: 862564--862653 Score: 53
Period size: 6 Copynumber: 14.3 Consensus size: 6
862554 TTACAAATAT
*
862564 TTTTTA TTTTTA TTTTTA TTTTT- TGATTTT- TTGTTA -TTTTA TTTTATCA
1 TTTTTA TTTTTA TTTTTA TTTTTA T--TTTTA TTTTTA TTTTTA TTTT-T-A
* *
862613 TTTTATA TTTTAA GTTTTT- TATTTCA TTTTTA TTATTTA TT
1 TTTT-TA TTTTTA -TTTTTA T-TTTTA TTTTTA TT-TTTA TT
862654 ATATTTTGTT
Statistics
Matches: 68, Mismatches: 6, Indels: 19
0.73 0.06 0.20
Matches are distributed among these distances:
5 9 0.13
6 30 0.44
7 22 0.32
8 7 0.10
ACGTcount: A:0.19, C:0.02, G:0.03, T:0.76
Consensus pattern (6 bp):
TTTTTA
Found at i:862659 original size:18 final size:19
Alignment explanation
Indices: 862615--862660 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
862605 TTTTATCATT
*
862615 TTATATTTTAAGTTTTTTA
1 TTATATTTTAAGTTATTTA
*
862634 TT-TCATTTTTA-TTATTTA
1 TTAT-ATTTTAAGTTATTTA
862652 TTATATTTT
1 TTATATTTT
862661 GTTGATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (19 bp):
TTATATTTTAAGTTATTTA
Found at i:863150 original size:2 final size:2
Alignment explanation
Indices: 863145--863171 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
863135 CGCGCGTGTG
863145 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
863172 TCTTTGACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:863409 original size:12 final size:12
Alignment explanation
Indices: 863392--863418 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
863382 TTACTGATGC
863392 ACATAAAGGCTT
1 ACATAAAGGCTT
863404 ACATAAAGGCTT
1 ACATAAAGGCTT
863416 ACA
1 ACA
863419 AAAATTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (12 bp):
ACATAAAGGCTT
Found at i:865459 original size:13 final size:13
Alignment explanation
Indices: 865441--865469 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
865431 AACATATTTT
865441 TTTATTTTTTTAA
1 TTTATTTTTTTAA
865454 TTTATTTTTTTAA
1 TTTATTTTTTTAA
865467 TTT
1 TTT
865470 TTTAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATTTTTTTAA
Found at i:865461 original size:21 final size:21
Alignment explanation
Indices: 865435--865474 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
865425 ATATATAACA
*
865435 TATTTTTTTATTTTTTTAATT
1 TATTTTTTTAATTTTTTAATT
865456 TATTTTTTTAATTTTTTAA
1 TATTTTTTTAATTTTTTAA
865475 ATATACATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (21 bp):
TATTTTTTTAATTTTTTAATT
Found at i:881485 original size:4 final size:4
Alignment explanation
Indices: 881476--881504 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
881466 TCCAAAATAC
881476 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
881505 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:882962 original size:10 final size:10
Alignment explanation
Indices: 882947--882972 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
882937 ATAATTATTT
882947 TATATTTAAA
1 TATATTTAAA
882957 TATATTTAAA
1 TATATTTAAA
882967 TATATT
1 TATATT
882973 AAAAATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TATATTTAAA
Found at i:887267 original size:14 final size:14
Alignment explanation
Indices: 887248--887292 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
887238 TAAATATATA
887248 TTAAAAATTTAAAT
1 TTAAAAATTTAAAT
887262 TT-AAAATTTAAAAT
1 TTAAAAATTT-AAAT
*
887276 TTAAAAAAATTAAAT
1 TT-AAAAATTTAAAT
887291 TT
1 TT
887293 TATATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 7 0.26
14 8 0.30
15 6 0.22
16 6 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAAAAATTTAAAT
Found at i:887270 original size:7 final size:7
Alignment explanation
Indices: 887251--887281 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
887241 ATATATATTA
887251 AAAATTT
1 AAAATTT
887258 -AAATTT
1 AAAATTT
887264 AAAATTT
1 AAAATTT
887271 AAAATTT
1 AAAATTT
887278 AAAA
1 AAAA
887282 AAATTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAAATTT
Found at i:887376 original size:17 final size:16
Alignment explanation
Indices: 887354--887385 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
887344 ATAATTATTT
887354 TATATTTAAATATTTAA
1 TATATTTAAAT-TTTAA
887371 TATATTTAAATTTTA
1 TATATTTAAATTTTA
887386 TATTAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATATTTAAATTTTAA
Found at i:887417 original size:32 final size:30
Alignment explanation
Indices: 887350--887417 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
887340 TAAAATAATT
* *
887350 ATTTTATATTTAAATATTTAATATATTTAA
1 ATTTTATATTAAAATATTTAAAATATTTAA
887380 ATTTTATATTAAAATAATTATAAAA-ATTTTAA
1 ATTTTATATTAAAAT-ATT-TAAAATA-TTTAA
*
887412 CTTTTA
1 ATTTTA
887418 AAATTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 14 0.44
31 4 0.12
32 14 0.44
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (30 bp):
ATTTTATATTAAAATATTTAAAATATTTAA
Found at i:888655 original size:16 final size:15
Alignment explanation
Indices: 888605--888655 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 15
888595 AATGTTATTT
*
888605 ATTATTTAAATTCAA
1 ATTATTTATATTCAA
* *
888620 ATTA-TCATATTCGA
1 ATTATTTATATTCAA
*
888634 ACTATTTTATATTCAA
1 ATTA-TTTATATTCAA
888650 ATTATT
1 ATTATT
888656 AAGTTTTAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
14 10 0.37
15 6 0.22
16 11 0.41
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (15 bp):
ATTATTTATATTCAA
Found at i:888688 original size:21 final size:20
Alignment explanation
Indices: 888637--888688 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
888627 TATTCGAACT
*
888637 ATTTTATATTCAAATTATTA
1 ATTTTAAATTCAAATTATTA
888657 AGTTTTAAAATT-AAATTAATTTA
1 A-TTTT-AAATTCAAATT-A-TTA
888680 ATTTTAAAT
1 ATTTTAAAT
888689 CATTTGAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 1 0.04
21 13 0.48
22 9 0.33
23 4 0.15
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTTTAAATTCAAATTATTA
Found at i:889838 original size:3 final size:3
Alignment explanation
Indices: 889830--889869 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
889820 TAATTTAACA
* *
889830 ATT ATT ATT ATT ATC ATT GTT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
889870 GTCTATATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:897087 original size:16 final size:15
Alignment explanation
Indices: 897063--897114 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
897053 TTTTAATATA
897063 AATATAAAATTAAAT
1 AATATAAAATTAAAT
* * *
897078 AATTTAAAAATATAT
1 AATATAAAATTAAAT
897093 GAATATAAAATTAAAT
1 -AATATAAAATTAAAT
897109 AA-ATAA
1 AATATAA
897115 TTAAAAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 4 0.13
15 14 0.47
16 12 0.40
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (15 bp):
AATATAAAATTAAAT
Found at i:898892 original size:19 final size:20
Alignment explanation
Indices: 898863--898900 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
898853 AAAAGCGTTG
*
898863 CTTTATAAAAGCTGGAAAGT
1 CTTTATAAAAGATGGAAAGT
898883 CTTT-TAAAAGATGGAAAG
1 CTTTATAAAAGATGGAAAG
898901 AATAATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (20 bp):
CTTTATAAAAGATGGAAAGT
Found at i:902798 original size:21 final size:21
Alignment explanation
Indices: 902772--902819 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
902762 TAAGCCTCAG
902772 AATTAAATCTGAA-AAAAATCC
1 AATTAAAT-TGAAGAAAAATCC
*
902793 AATT-AATTGAAGAAAAATTC
1 AATTAAATTGAAGAAAAATCC
902813 AATTAAA
1 AATTAAA
902820 CCTGTATTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.17
20 14 0.58
21 6 0.25
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.27
Consensus pattern (21 bp):
AATTAAATTGAAGAAAAATCC
Found at i:907044 original size:21 final size:23
Alignment explanation
Indices: 907010--907057 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
907000 TCTTGTTTTT
*
907010 CTTCTCTTCATCTTCATCTTCCA
1 CTTCTCTTCATCTTCATCCTCCA
907033 CTTCT-TTC-TCTTCATCCTCCA
1 CTTCTCTTCATCTTCATCCTCCA
907054 CTTC
1 CTTC
907058 ATCATCGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 16 0.67
22 3 0.12
23 5 0.21
ACGTcount: A:0.10, C:0.42, G:0.00, T:0.48
Consensus pattern (23 bp):
CTTCTCTTCATCTTCATCCTCCA
Found at i:913269 original size:29 final size:29
Alignment explanation
Indices: 913183--913269 Score: 67
Period size: 27 Copynumber: 3.1 Consensus size: 29
913173 TATAAAAATA
* * *
913183 TATAAAAAATATTTATATATATATTTTATAT
1 TATATAAAATA-TTATATAAATATATTA-AT
* * *
913214 TA-ATAAAA-ATTAT-GACATA-ATT-TT
1 TATATAAAATATTATATAAATATATTAAT
913238 TATATAAAATATTATATAAATATATTAAT
1 TATATAAAATATTATATAAATATATTAAT
913267 TAT
1 TAT
913270 TCATTTTTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
24 3 0.07
25 6 0.14
26 7 0.16
27 8 0.19
28 7 0.16
29 5 0.12
30 5 0.12
31 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (29 bp):
TATATAAAATATTATATAAATATATTAAT
Found at i:916025 original size:18 final size:20
Alignment explanation
Indices: 916002--916043 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
915992 TTTAATTATC
916002 ATATAAATAATTT-TT-TAA
1 ATATAAATAATTTATTATAA
*
916020 ATATAAATATTTTATTATAA
1 ATATAAATAATTTATTATAA
916040 ATAT
1 ATAT
916044 TTTTTTTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.57
19 2 0.10
20 7 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATAAATAATTTATTATAA
Found at i:918006 original size:7 final size:7
Alignment explanation
Indices: 917962--918021 Score: 58
Period size: 7 Copynumber: 9.3 Consensus size: 7
917952 ATAGAACAAA
917962 AATATAT
1 AATATAT
* *
917969 AATTTAA
1 AATATAT
*
917976 AAT-TTT
1 AATATAT
917982 AATA-AT
1 AATATAT
917988 AAT-TAT
1 AATATAT
917994 -ATATAT
1 AATATAT
918000 AATATAT
1 AATATAT
918007 AATATA-
1 AATATAT
918013 AATATAT
1 AATATAT
918020 AA
1 AA
918022 ATTTTATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
5 2 0.05
6 19 0.44
7 22 0.51
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AATATAT
Found at i:918012 original size:18 final size:18
Alignment explanation
Indices: 917981--918018 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
917971 TTTAAAATTT
*
917981 TAATAATAATTATATATA
1 TAATAATAATTATAAATA
917999 TAATATATAA-TATAAATA
1 TAATA-ATAATTATAAATA
918017 TA
1 TA
918019 TAAATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAATAATTATAAATA
Found at i:925094 original size:101 final size:101
Alignment explanation
Indices: 924919--925120 Score: 332
Period size: 101 Copynumber: 2.0 Consensus size: 101
924909 TAATGAAAAC
* *
924919 TTTCTGTTAGGCTGCCTTTTGTCTGATTCTATTGGACTCAATTCAGTGCAGTTTAAGGTTTGCTG
1 TTTCTGTTAGGCTGCCTTTTGTCTGATTCTATAGGACTCAATTCAGTGCAGTTTAAGGTTTGCTA
* *
924984 CTAAATAATAGATATAATTTAGCCTAAGATATTTTT
66 CTAAATAATAGATATAATCTAGCCTAAGATAATTTT
* * *
925020 TTTCTGTTAGGGTGCCTTTTGTGTGATTCTATAGGATTCAATTCAGTGCAGTTTAAGGTTTGCTA
1 TTTCTGTTAGGCTGCCTTTTGTCTGATTCTATAGGACTCAATTCAGTGCAGTTTAAGGTTTGCTA
*
925085 CTAAATAATAGATATAATCTAGCCTACGATAATTTT
66 CTAAATAATAGATATAATCTAGCCTAAGATAATTTT
925121 CTCCCAGATA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 93 1.00
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (101 bp):
TTTCTGTTAGGCTGCCTTTTGTCTGATTCTATAGGACTCAATTCAGTGCAGTTTAAGGTTTGCTA
CTAAATAATAGATATAATCTAGCCTAAGATAATTTT
Found at i:927925 original size:10 final size:10
Alignment explanation
Indices: 927894--927950 Score: 60
Period size: 10 Copynumber: 5.2 Consensus size: 10
927884 TAACTAACCC
927894 CTAGAACAAA
1 CTAGAACAAA
*
927904 CAAGAACAAA
1 CTAGAACAAA
927914 CTAGAACAAA
1 CTAGAACAAA
927924 CTTTAGAAGAACAAA
1 C--T---AGAACAAA
927939 CTAGAACAAA
1 CTAGAACAAA
927949 CT
1 CT
927951 TTAGAAGAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
10 29 0.73
12 1 0.03
13 1 0.03
15 9 0.22
ACGTcount: A:0.58, C:0.19, G:0.11, T:0.12
Consensus pattern (10 bp):
CTAGAACAAA
Found at i:927936 original size:15 final size:15
Alignment explanation
Indices: 927916--927965 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
927906 AGAACAAACT
927916 AGAACAAACTTTAGA
1 AGAACAAACTTTAGA
927931 AGAACAAAC--T---
1 AGAACAAACTTTAGA
927941 AGAACAAACTTTAGA
1 AGAACAAACTTTAGA
927956 AGAACAAACT
1 AGAACAAACT
927966 AGTACAAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
10 9 0.30
12 1 0.03
13 1 0.03
15 19 0.63
ACGTcount: A:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (15 bp):
AGAACAAACTTTAGA
Found at i:927981 original size:25 final size:25
Alignment explanation
Indices: 927905--927974 Score: 131
Period size: 25 Copynumber: 2.8 Consensus size: 25
927895 TAGAACAAAC
927905 AAGAACAAACTAGAACAAACTTTAG
1 AAGAACAAACTAGAACAAACTTTAG
927930 AAGAACAAACTAGAACAAACTTTAG
1 AAGAACAAACTAGAACAAACTTTAG
*
927955 AAGAACAAACTAGTACAAAC
1 AAGAACAAACTAGAACAAAC
927975 CTCAGAACAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.57, C:0.17, G:0.11, T:0.14
Consensus pattern (25 bp):
AAGAACAAACTAGAACAAACTTTAG
Found at i:930345 original size:35 final size:36
Alignment explanation
Indices: 930306--930375 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
930296 ATTATTGAAA
*
930306 TTAAAAA-TTTATGATTTATTAACAAATCATATAAC
1 TTAAAAATTTTACGATTTATTAACAAATCATATAAC
*
930341 TTAAAAATTTTACGATTTATTAACAGATCATATAA
1 TTAAAAATTTTACGATTTATTAACAAATCATATAA
930376 TTATCGACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 7 0.22
36 25 0.78
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (36 bp):
TTAAAAATTTTACGATTTATTAACAAATCATATAAC
Found at i:931955 original size:22 final size:21
Alignment explanation
Indices: 931927--932017 Score: 94
Period size: 22 Copynumber: 4.2 Consensus size: 21
931917 AATTTTACTT
931927 ATAAATAATATTATACTAATAA
1 ATAAATAATATTATA-TAATAA
931949 ATAAATAATATTATATTAATAA
1 ATAAATAATATTATA-TAATAA
* *
931971 ACAATATAATATTAATATAATAT
1 ATAA-ATAATATT-ATATAATAA
* * *
931994 TTTAATAA-ATAATATAATAA
1 ATAAATAATATTATATAATAA
932014 ATAA
1 ATAA
932018 TAAATAGATT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 10 0.18
21 2 0.04
22 28 0.49
23 14 0.25
24 3 0.05
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAAATAATATTATATAATAA
Found at i:932057 original size:16 final size:16
Alignment explanation
Indices: 931980--932124 Score: 65
Period size: 16 Copynumber: 9.1 Consensus size: 16
931970 AACAATATAA
931980 TATTAATATAATATTT
1 TATTAATATAATATTT
* *
931996 TAATAA-ATAATATAAT
1 TATTAATATAATAT-TT
* * *
932012 AAATAATA-AATAGATT
1 TATTAATATAATA-TTT
*
932028 TATT--TA-AGTATTT
1 TATTAATATAATATTT
932041 TATTAATATAATATTT
1 TATTAATATAATATTT
* *
932057 TAATACTA-AATATTAT
1 TATTAATATAATATT-T
*
932073 TGTTAAAATATAATTATTT
1 TATT--AATATAA-TATTT
932092 T-TTAATATTAATAATTT
1 TATTAATA-TAAT-ATTT
932109 TGA-TAATA-AATATTT
1 T-ATTAATATAATATTT
932124 T
1 T
932125 CAATATACTT
Statistics
Matches: 99, Mismatches: 15, Indels: 31
0.68 0.10 0.21
Matches are distributed among these distances:
13 6 0.06
14 5 0.05
15 20 0.20
16 41 0.41
17 9 0.09
18 10 0.10
19 4 0.04
20 4 0.04
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.50
Consensus pattern (16 bp):
TATTAATATAATATTT
Found at i:934144 original size:2 final size:2
Alignment explanation
Indices: 934137--934169 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
934127 ACCATGTATG
934137 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
934170 GGCTTACTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:934897 original size:16 final size:16
Alignment explanation
Indices: 934884--934917 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
934874 TTTAAATACT
934884 ATATAAATATAATATA
1 ATATAAATATAATATA
934900 ATATAAATATAATATA
1 ATATAAATATAATATA
934916 AT
1 AT
934918 GATATAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAATATAATATA
Found at i:934899 original size:5 final size:5
Alignment explanation
Indices: 934884--934917 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
934874 TTTAAATACT
934884 ATATAA ATATA ATATA ATATAA ATATA ATATA AT
1 ATAT-A ATATA ATATA ATAT-A ATATA ATATA AT
934918 GATATAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 18 0.67
6 9 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:934924 original size:13 final size:11
Alignment explanation
Indices: 934884--934926 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
934874 TTTAAATACT
934884 ATATAA-ATATA
1 ATATAATATA-A
934895 ATATAATATAA
1 ATATAATATAA
934906 ATATAATATAA
1 ATATAATATAA
934917 TGATATAATA
1 --ATATAATA
934927 CGAAAAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 18 0.62
12 3 0.10
13 8 0.28
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
ATATAATATAA
Found at i:937995 original size:20 final size:19
Alignment explanation
Indices: 937962--938004 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
937952 CATATTTATT
937962 TTTTGTATATGCATCCATTG
1 TTTTGTATATGCATCC-TTG
*
937982 TTTTGTACTA-GCATTCTTG
1 TTTTGTA-TATGCATCCTTG
938001 TTTT
1 TTTT
938005 CTTTACAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 12 0.57
21 2 0.10
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.56
Consensus pattern (19 bp):
TTTTGTATATGCATCCTTG
Found at i:941653 original size:25 final size:27
Alignment explanation
Indices: 941617--941680 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
941607 TTTTATCTTG
*
941617 TATAT-TTAA-ATA-ATTATTTTATAAA
1 TATATATTAATATATATT-TTTAATAAA
941642 TATATATTAATATATATTTTTCAATAAA
1 TATATATTAATATATATTTTT-AATAAA
*
941670 AATATATTAAT
1 TATATATTAAT
941681 TCTAATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 5 0.15
26 4 0.12
27 6 0.18
28 18 0.55
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
TATATATTAATATATATTTTTAATAAA
Found at i:942859 original size:31 final size:31
Alignment explanation
Indices: 942810--942875 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
942800 AGATTGATAG
* * * * *
942810 AATTTAATATGAAGATTAATAATATCTAAGA
1 AATTCAATATCAAAATTAATAATATATAAAA
942841 AATTCAATATCAAAATTAATAATATATAAAA
1 AATTCAATATCAAAATTAATAATATATAAAA
942872 AATT
1 AATT
942876 ATTAAAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (31 bp):
AATTCAATATCAAAATTAATAATATATAAAA
Found at i:949022 original size:12 final size:12
Alignment explanation
Indices: 949005--949029 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
948995 ATTTTTATGC
949005 TAAAATAATTTT
1 TAAAATAATTTT
949017 TAAAATAATTTT
1 TAAAATAATTTT
949029 T
1 T
949030 TGAATCTCTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATAATTTT
Found at i:949404 original size:24 final size:24
Alignment explanation
Indices: 949372--949429 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
949362 TGATAATTTG
* **
949372 AAATTTAATATCATGATATTATAT
1 AAATATAATATCAAAATATTATAT
*
949396 AAATATAATATGAAAATATTATAT
1 AAATATAATATCAAAATATTATAT
*
949420 AAAAATAATA
1 AAATATAATA
949430 CAATTTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (24 bp):
AAATATAATATCAAAATATTATAT
Found at i:949980 original size:9 final size:10
Alignment explanation
Indices: 949966--950018 Score: 56
Period size: 9 Copynumber: 5.4 Consensus size: 10
949956 GAAATTGATT
949966 TTAATAA-AA
1 TTAATAATAA
949975 TTAATAATAA
1 TTAATAATAA
949985 -TAATAATAA
1 TTAATAATAA
* * *
949994 TTATTATTAT
1 TTAATAATAA
950004 TATAATAATAA
1 T-TAATAATAA
950015 TTAA
1 TTAA
950019 AAAAATTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
9 16 0.46
10 12 0.34
11 7 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TTAATAATAA
Found at i:950026 original size:21 final size:21
Alignment explanation
Indices: 949984--950027 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
949974 ATTAATAATA
** **
949984 ATAATAATAATTATTATTATT
1 ATAATAATAATTAAAAAAATT
950005 ATAATAATAATTAAAAAAATT
1 ATAATAATAATTAAAAAAATT
950026 AT
1 AT
950028 TGTAGTTGTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAATAATAATTAAAAAAATT
Found at i:954692 original size:12 final size:12
Alignment explanation
Indices: 954677--954720 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
954667 ATTTTTAATA
954677 TAAATATAAAAT
1 TAAATATAAAAT
*
954689 TAAATATATATAAA
1 TAAATATA-A-AAT
*
954703 TAAATATAACAT
1 TAAATATAAAAT
954715 TAAATA
1 TAAATA
954721 AACACTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 15 0.56
13 2 0.07
14 10 0.37
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (12 bp):
TAAATATAAAAT
Found at i:954976 original size:25 final size:21
Alignment explanation
Indices: 954924--954968 Score: 76
Period size: 19 Copynumber: 2.2 Consensus size: 21
954914 TTCGAAATTA
954924 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
954945 ATAAAATATTA--TTTTAAAT
1 ATAAAATATTATTTTTTAAAT
954964 ATAAA
1 ATAAA
954969 TGTAAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 13 0.54
21 11 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATAAAATATTATTTTTTAAAT
Found at i:955017 original size:16 final size:16
Alignment explanation
Indices: 954964--955021 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 16
954954 TATTTTAAAT
*
954964 ATAAATGTAAAATTAA
1 ATAAATATAAAATTAA
* *
954980 ATATATCTAATATATATAA
1 ATAAATATAA-A-AT-TAA
954999 ATAAATATAAAATTAA
1 ATAAATATAAAATTAA
955015 ATAAATA
1 ATAAATA
955022 ATTAAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 18 0.51
17 3 0.09
18 3 0.09
19 11 0.31
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (16 bp):
ATAAATATAAAATTAA
Found at i:964588 original size:18 final size:20
Alignment explanation
Indices: 964565--964606 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
964555 TTTAATTATC
964565 ATATAAATAATTT-TT-TAA
1 ATATAAATAATTTATTATAA
*
964583 ATATAAATATTTTATTATAA
1 ATATAAATAATTTATTATAA
964603 ATAT
1 ATAT
964607 TTTTTTTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.57
19 2 0.10
20 7 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATAAATAATTTATTATAA
Found at i:966593 original size:5 final size:5
Alignment explanation
Indices: 966585--966643 Score: 52
Period size: 5 Copynumber: 12.2 Consensus size: 5
966575 TATATATAAT
* * * *
966585 ATATA ATATA A-ATT ATATT ATATA ATTTTT ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA A-TATA ATATA ATATA ATATA ATATA
966635 A-AT- ATATA A
1 ATATA ATATA A
966644 AATTTATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
3 1 0.02
4 7 0.16
5 33 0.75
6 3 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (5 bp):
ATATA
Found at i:966638 original size:16 final size:16
Alignment explanation
Indices: 966565--966640 Score: 52
Period size: 16 Copynumber: 4.8 Consensus size: 16
966555 TTTAAAATTT
*
966565 TAATAATAATTAT-ATA
1 TAAT-ATAAATATAATA
966581 TAATATATAATATAA-A
1 TAATATA-AATATAATA
* *
966597 TTATAT-TATATAAT-
1 TAATATAAATATAATA
**
966611 TTTTATATAATATAATA
1 TAATATA-AATATAATA
966628 TAATATAAATATA
1 TAATATAAATATA
966641 TAAAATTTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
14 11 0.23
15 3 0.06
16 27 0.57
17 6 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAATATAAATATAATA
Found at i:966667 original size:41 final size:40
Alignment explanation
Indices: 966585--966667 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 40
966575 TATATATAAT
** *
966585 ATATAATATAAATTATATTATATAATTTTTATATAATATA
1 ATATAATATAAATTATAAAATATAATTTTTATATAACATA
* *
966625 ATATAATATAAATATATAAAATTTATTTTTTAT-TCAACATA
1 ATATAATATAAAT-TATAAAATATAATTTTTATAT-AACATA
966666 AT
1 AT
966668 TACACAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
40 14 0.39
41 22 0.61
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (40 bp):
ATATAATATAAATTATAAAATATAATTTTTATATAACATA
Found at i:966951 original size:18 final size:20
Alignment explanation
Indices: 966911--966952 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
966901 AATAAAATAT
*
966911 TATTTTTTTAAAATATAAAA
1 TATTATTTTAAAATATAAAA
966931 TATTATTTT-AAATAT-AAA
1 TATTATTTTAAAATATAAAA
966949 TATT
1 TATT
966953 TAAAAATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 6 0.29
20 8 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTATTTTAAAATATAAAA
Found at i:966987 original size:30 final size:28
Alignment explanation
Indices: 966921--966988 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 28
966911 TATTTTTTTA
*
966921 AAATATAAAATATTATTTTAAATATAAAT
1 AAATA-AAAATATCATTTTAAATATAAAT
** *
966950 ATTTAAAAATATCATTATATAAATATATAT
1 AAATAAAAATATCATT-T-TAAATATAAAT
966980 AAATAAAAA
1 AAATAAAAA
966989 ATTAAATAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 10 0.32
29 4 0.13
30 17 0.55
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (28 bp):
AAATAAAAATATCATTTTAAATATAAAT
Found at i:974179 original size:101 final size:101
Alignment explanation
Indices: 974004--974205 Score: 332
Period size: 101 Copynumber: 2.0 Consensus size: 101
973994 TAATGAAAAC
* *
974004 TTTCTGTTAGGCTGCCTTTTGTCTGATTCTATTGGACTCAATTCAGTGCAGTTTAAGGTTTGCTG
1 TTTCTGTTAGGCTGCCTTTTGTCTGATTCTATGGGACTCAATTCAGTGCAGTTTAAGGTTTGCTA
*
974069 CTAAATAATAGATATAATTTAGCCTAAGATATTTTT
66 CTAAATAATAGATATAATTTAGCCTAAGATAATTTT
* * *
974105 TTTCTGTTAGGGTGCCTTTTGTGTGATTCTATGGGATTCAATTCAGTGCAGTTTAAGGTTTGCTA
1 TTTCTGTTAGGCTGCCTTTTGTCTGATTCTATGGGACTCAATTCAGTGCAGTTTAAGGTTTGCTA
* *
974170 TTAAATAATAGATATAATTTAGCCTACGATAATTTT
66 CTAAATAATAGATATAATTTAGCCTAAGATAATTTT
974206 CTCCCAGATA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 93 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (101 bp):
TTTCTGTTAGGCTGCCTTTTGTCTGATTCTATGGGACTCAATTCAGTGCAGTTTAAGGTTTGCTA
CTAAATAATAGATATAATTTAGCCTAAGATAATTTT
Found at i:976804 original size:14 final size:14
Alignment explanation
Indices: 976785--976812 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
976775 CAAATAGCAT
976785 TGCCTGGAGCCTCG
1 TGCCTGGAGCCTCG
976799 TGCCTGGAGCCTCG
1 TGCCTGGAGCCTCG
976813 AATTATCTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.36, G:0.36, T:0.21
Consensus pattern (14 bp):
TGCCTGGAGCCTCG
Found at i:976979 original size:10 final size:10
Alignment explanation
Indices: 976964--977116 Score: 67
Period size: 10 Copynumber: 14.1 Consensus size: 10
976954 TAACTAACCC
976964 CTAGAACAAA
1 CTAGAACAAA
976974 CTAGAACAAA
1 CTAGAACAAA
976984 CTTTAGAAGAACAAA
1 C--T---AGAACAAA
* *
976999 CTGGTACAAA
1 CTAGAACAAA
**
977009 TCTCAGAAC-CC
1 -CT-AGAACAAA
977020 CTAGAACAAA
1 CTAGAACAAA
*
977030 CAAGAACAAA
1 CTAGAACAAA
977040 CTAGAACAAA
1 CTAGAACAAA
977050 CTTTGGAAGAACAAA
1 C--T---AGAACAAA
*
977065 CTAGTACAAA
1 CTAGAACAAA
**
977075 CCTCAGAAC-CC
1 -CT-AGAACAAA
977086 CTAGAACAAA
1 CTAGAACAAA
**
977096 AAAGAACAAA
1 CTAGAACAAA
*
977106 CTAGTACAAA
1 CTAGAACAAA
977116 C
1 C
977117 CTCAGAACAT
Statistics
Matches: 106, Mismatches: 21, Indels: 32
0.67 0.13 0.20
Matches are distributed among these distances:
9 10 0.09
10 63 0.59
11 4 0.04
12 9 0.08
13 2 0.02
15 18 0.17
ACGTcount: A:0.52, C:0.23, G:0.12, T:0.13
Consensus pattern (10 bp):
CTAGAACAAA
Found at i:976998 original size:25 final size:23
Alignment explanation
Indices: 976966--977075 Score: 86
Period size: 25 Copynumber: 4.8 Consensus size: 23
976956 ACTAACCCCT
976966 AGAACAAACTAGAACAAACTTTAGA
1 AGAACAAACTAGAACAAACTTT--A
* * * *
976991 AGAACAAACTGGTACAAA-TCTC
1 AGAACAAACTAGAACAAACTTTA
**
977013 AGAAC-CCCTAGAACAAAC---A
1 AGAACAAACTAGAACAAACTTTA
977032 AGAACAAACTAGAACAAACTTTGGA
1 AGAACAAACTAGAACAAACTTT--A
*
977057 AGAACAAACTAGTACAAAC
1 AGAACAAACTAGAACAAAC
977076 CTCAGAACCC
Statistics
Matches: 66, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
19 5 0.08
20 11 0.17
21 8 0.12
22 5 0.08
24 2 0.03
25 35 0.53
ACGTcount: A:0.53, C:0.21, G:0.13, T:0.14
Consensus pattern (23 bp):
AGAACAAACTAGAACAAACTTTA
Found at i:977046 original size:66 final size:66
Alignment explanation
Indices: 976966--977116 Score: 257
Period size: 66 Copynumber: 2.3 Consensus size: 66
976956 ACTAACCCCT
* * *
976966 AGAACAAACTAGAACAAACTTTAGAAGAACAAACTGGTACAAATCTCAGAACCCCTAGAACAAAC
1 AGAACAAACTAGAACAAACTTTAGAAGAACAAACTAGTACAAACCTCAGAACCCCTAGAACAAAA
977031 A
66 A
*
977032 AGAACAAACTAGAACAAACTTTGGAAGAACAAACTAGTACAAACCTCAGAACCCCTAGAACAAAA
1 AGAACAAACTAGAACAAACTTTAGAAGAACAAACTAGTACAAACCTCAGAACCCCTAGAACAAAA
977097 A
66 A
*
977098 AGAACAAACTAGTACAAAC
1 AGAACAAACTAGAACAAAC
977117 CTCAGAACAT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 80 1.00
ACGTcount: A:0.53, C:0.23, G:0.12, T:0.13
Consensus pattern (66 bp):
AGAACAAACTAGAACAAACTTTAGAAGAACAAACTAGTACAAACCTCAGAACCCCTAGAACAAAA
A
Found at i:979490 original size:34 final size:34
Alignment explanation
Indices: 979451--979515 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
979441 ATTGAAATTA
*
979451 AAAATTTATGATTTATTAACAAATCATATAACTT
1 AAAATTTACGATTTATTAACAAATCATATAACTT
*
979485 AAAATTTACGATTTATTAACAGATCATATAA
1 AAAATTTACGATTTATTAACAAATCATATAA
979516 TTATCGACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (34 bp):
AAAATTTACGATTTATTAACAAATCATATAACTT
Found at i:981088 original size:22 final size:22
Alignment explanation
Indices: 981060--981117 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
981050 AATTTTACTT
981060 ATAAATAATATTATACTAACAA
1 ATAAATAATATTATACTAACAA
* * *
981082 ATAAATAATTTTATATTAATAA
1 ATAAATAATATTATACTAACAA
981104 ATAATATAATATTA
1 ATAA-ATAATATTA
981118 ATATAATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 23 0.74
23 8 0.26
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAAATAATATTATACTAACAA
Found at i:981102 original size:18 final size:18
Alignment explanation
Indices: 981081--981125 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
981071 TATACTAACA
* *
981081 AATAAATAATTTTATATT
1 AATAAATAATATAATATT
981099 AATAAATAATATAATATT
1 AATAAATAATATAATATT
981117 AATATAATA
1 AATA-AATA
981126 TATTAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATAAATAATATAATATT
Found at i:981278 original size:26 final size:24
Alignment explanation
Indices: 981235--981299 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 24
981225 TTTTTTAATA
*
981235 TTAATAATTTTGATAATAAATA-TT
1 TTAAT-ATTTTAATAATAAATACTT
981259 TTCAATATACTTTAATAATAAATACTT
1 TT-AATAT--TTTAATAATAAATACTT
981286 TTAATATTTTAATA
1 TTAATATTTTAATA
981300 GTTATATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
24 11 0.31
25 3 0.08
26 18 0.50
27 4 0.11
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.49
Consensus pattern (24 bp):
TTAATATTTTAATAATAAATACTT
Found at i:983072 original size:4 final size:4
Alignment explanation
Indices: 983063--983120 Score: 102
Period size: 4 Copynumber: 15.0 Consensus size: 4
983053 TGAATCTATA
983063 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
983111 A--T ATGT ATGT
1 ATGT ATGT ATGT
983121 GTATATATAT
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
4 50 0.96
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:984047 original size:16 final size:16
Alignment explanation
Indices: 984034--984067 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
984024 TTTAAATACT
*
984034 ATATTAATATAATATA
1 ATATAAATATAATATA
984050 ATATAAATATAATATA
1 ATATAAATATAATATA
984066 AT
1 AT
984068 GATATAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATAAATATAATATA
Found at i:984048 original size:5 final size:5
Alignment explanation
Indices: 984038--984067 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
984028 AATACTATAT
984038 TAATA TAATA TAATA TAAATA TAATA TAAT
1 TAATA TAATA TAATA T-AATA TAATA TAAT
984068 GATATAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:984074 original size:13 final size:11
Alignment explanation
Indices: 984038--984076 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
984028 AATACTATAT
984038 TAATAT-AATA
1 TAATATAAATA
984048 TAATATAAATA
1 TAATATAAATA
984059 TAATATAATGATA
1 TAATATAA--ATA
984072 TAATA
1 TAATA
984077 CGAAAAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 6 0.23
11 12 0.46
13 8 0.31
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
TAATATAAATA
Found at i:987146 original size:20 final size:19
Alignment explanation
Indices: 987113--987155 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
987103 CATATTTATT
987113 TTTTGTATATGCATCCATTG
1 TTTTGTATATGCATCC-TTG
*
987133 TTTTGTACTA-GCATTCTTG
1 TTTTGTA-TATGCATCCTTG
987152 TTTT
1 TTTT
987156 CTTTACAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 12 0.57
21 2 0.10
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.56
Consensus pattern (19 bp):
TTTTGTATATGCATCCTTG
Found at i:991526 original size:30 final size:31
Alignment explanation
Indices: 991485--991548 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
991475 ATAAATTACG
*
991485 ATATATAATTTTTATA-TAAAATATAATATAA
1 ATATATAATTTTAATATTAAAA-ATAATATAA
**
991516 ATATAT-ATTTTAATATTTTAAATAATATAA
1 ATATATAATTTTAATATTAAAAATAATATAA
991546 ATA
1 ATA
991549 CACGAAGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 20 0.69
31 9 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
ATATATAATTTTAATATTAAAAATAATATAA
Found at i:991940 original size:31 final size:31
Alignment explanation
Indices: 991891--991956 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
991881 AGATTGATAG
* * * * *
991891 AATTTAATATGAAGATTAATAATATCTAAGA
1 AATTCAATATCAAAATTAATAATATATAAAA
991922 AATTCAATATCAAAATTAATAATATATAAAA
1 AATTCAATATCAAAATTAATAATATATAAAA
991953 AATT
1 AATT
991957 ATTAAAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (31 bp):
AATTCAATATCAAAATTAATAATATATAAAA
Found at i:996560 original size:2 final size:2
Alignment explanation
Indices: 996555--996589 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
996545 TCTCTCTCTC
*
996555 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
996590 TCATGGCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:998513 original size:24 final size:24
Alignment explanation
Indices: 998481--998539 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
998471 TGATAATTTG
* **
998481 AAATTTAATATCATGATATTATAT
1 AAATATAATATCAAAATATTATAT
*
998505 AAATATAATATGAAAATATTATAT
1 AAATATAATATCAAAATATTATAT
*
998529 AAAAATAATAT
1 AAATATAATAT
998540 AATTTAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (24 bp):
AAATATAATATCAAAATATTATAT
Found at i:998521 original size:13 final size:12
Alignment explanation
Indices: 998496--998541 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
998486 TAATATCATG
*
998496 ATATTATAT-AA
1 ATATAATATAAA
998507 ATATAATATGAAA
1 ATATAATAT-AAA
*
998520 ATATTATATAAA
1 ATATAATATAAA
998532 A-ATAATATAA
1 ATATAATATAA
998542 TTTAAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.53
12 4 0.13
13 10 0.33
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:998566 original size:27 final size:29
Alignment explanation
Indices: 998506--998567 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
998496 ATATTATATA
998506 AATATAATATGAAAATATTATATAAAAAT
1 AATATAATATGAAAATATTATATAAAAAT
* * *
998535 AATATAAT-TTAAAATTTTA-ATAATAAT
1 AATATAATATGAAAATATTATATAAAAAT
*
998562 TATATA
1 AATATA
998568 TAAATTTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 12 0.41
28 9 0.31
29 8 0.28
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
AATATAATATGAAAATATTATATAAAAAT
Found at i:1003815 original size:12 final size:12
Alignment explanation
Indices: 1003800--1003843 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
1003790 ATTTTTAATA
1003800 TAAATATAAAAT
1 TAAATATAAAAT
*
1003812 TAAATATATATAAA
1 TAAATATA-A-AAT
*
1003826 TAAATATAACAT
1 TAAATATAAAAT
1003838 TAAATA
1 TAAATA
1003844 AACACTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 15 0.56
13 2 0.07
14 10 0.37
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (12 bp):
TAAATATAAAAT
Found at i:1003868 original size:2 final size:2
Alignment explanation
Indices: 1003863--1003889 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1003853 AAAAAGAAGT
1003863 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1003890 CAGGTTGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1004091 original size:19 final size:20
Alignment explanation
Indices: 1004057--1004098 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
1004047 CGAAATTAAT
1004057 AAATATTATTTTTTAAATATA
1 AAATATTA-TTTTTAAATATA
1004078 AAATATTA-TTTTAAATATA
1 AAATATTATTTTTAAATATA
1004097 AA
1 AA
1004099 TGTAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 13 0.62
21 8 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AAATATTATTTTTAAATATA
Found at i:1010704 original size:2 final size:2
Alignment explanation
Indices: 1010697--1010726 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1010687 AAGCTGCAAC
1010697 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
1010727 GGACATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1019434 original size:3 final size:3
Alignment explanation
Indices: 1019428--1019467 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1019418 GTATTTTTTT
1019428 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1019468 ATCCCAATAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1020248 original size:18 final size:17
Alignment explanation
Indices: 1020205--1020248 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1020195 AATATGTTTA
*
1020205 AATATTTATTTAAAAAT
1 AATATTTAATTAAAAAT
1020222 AATATTTTAATTAAAAAT
1 AATA-TTTAATTAAAAAT
1020240 AATTATTTA
1 AA-TATTTA
1020249 TTATTTTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 18 0.75
19 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATATTTAATTAAAAAT
Found at i:1020481 original size:15 final size:14
Alignment explanation
Indices: 1020441--1020483 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
1020431 TAGATTCAAC
*
1020441 TTTTTATATATTAT
1 TTTTTATTTATTAT
*
1020455 TTTATTAGTTATTAT
1 TTT-TTATTTATTAT
1020470 TTATTTATTTATTA
1 TT-TTTATTTATTA
1020484 AATCTAATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 3 0.12
15 20 0.83
16 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (14 bp):
TTTTTATTTATTAT
Found at i:1020953 original size:143 final size:141
Alignment explanation
Indices: 1020598--1020976 Score: 376
Period size: 143 Copynumber: 2.7 Consensus size: 141
1020588 TATCTAACCA
* * * *
1020598 TCATCTTTTTATAGCTTTTATCAAAATAAAATTCTTCTAAATTCTTCATCCAATTCTTAATCTTG
1 TCATTTTTTTATAGCTTTTATCAAAATAAATTTATTCTAAATTCTTCATCCAATTCTCAAT-TTG
* * *
1020663 CCATCTTTTTGCTTAAATAAAAATAA-----ATTTGTCATCTTGATTGGTGTTGGACAGTTGAAG
65 CCATCTTTTTGCTTTAATAAAAATAATTTTTTTTTGTCATCTTGATTGGTGTCGGACAGTTGAAG
*
1020723 CACCCTCTAGAC
130 CACCCTCTACAC
* * * * *
1020735 TCATCTTTTCTATAGCTTTTACCAACATAAGTTTATTCTAAATTCTTCATCTAATTC-CTAATGT
1 TCAT-TTTTTTATAGCTTTTATCAAAATAAATTTATTCTAAATTCTTCATCCAATTCTC-AAT-T
* * * * * *
1020799 GGCCATATTTTTGCTTTAGTAAAAATAAGTTTTTTTTTTTTATCTTGATTGGTGTCGGGC-GATT
63 TGCCATCTTTTTGCTTTAATAAAAATAA-TTTTTTTTTGTCATCTTGATTGGTGTCGGACAG-TT
* ** * *
1020863 GAAGTACTTTTTTCAC
126 GAAGCACCCTCTACAC
* * *
1020879 TCATTTTTTTATACCTTTTATCAAAATAATTTTATTTTAAATTCTTCATCCAATTCTCAATTTAG
1 TCATTTTTTTATAGCTTTTATCAAAATAAATTTATTCTAAATTCTTCATCCAATTCTCAATTT-G
* *
1020944 TCATCTTTTTGCTTTACTAAAAATACATTTTTT
65 CCATCTTTTTGCTTTAATAAAAATA-ATTTTTT
1020977 ATCTCGATTG
Statistics
Matches: 194, Mismatches: 36, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
137 4 0.02
138 72 0.37
142 1 0.01
143 78 0.40
144 39 0.20
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (141 bp):
TCATTTTTTTATAGCTTTTATCAAAATAAATTTATTCTAAATTCTTCATCCAATTCTCAATTTGC
CATCTTTTTGCTTTAATAAAAATAATTTTTTTTTGTCATCTTGATTGGTGTCGGACAGTTGAAGC
ACCCTCTACAC
Found at i:1021164 original size:55 final size:55
Alignment explanation
Indices: 1021099--1021203 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 55
1021089 ATATACTATT
* * * * *
1021099 TTATTTTTTAT-TAGTTTACATTGATTTGTTACATTGTTTTAATTTAATATTCACC
1 TTATTATTTATAT-GTTTACATTAATCTATTACATTATTTTAATTTAATATTCACC
* *
1021154 TTATTATTTATATGTTTGCATTAATCTATTATATTATTTTAATTTAATAT
1 TTATTATTTATATGTTTACATTAATCTATTACATTATTTTAATTTAATAT
1021204 GTTGTTTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
55 41 0.98
56 1 0.02
ACGTcount: A:0.29, C:0.07, G:0.06, T:0.59
Consensus pattern (55 bp):
TTATTATTTATATGTTTACATTAATCTATTACATTATTTTAATTTAATATTCACC
Found at i:1021237 original size:53 final size:56
Alignment explanation
Indices: 1021099--1021303 Score: 206
Period size: 53 Copynumber: 3.7 Consensus size: 56
1021089 ATATACTATT
* * * * *
1021099 TTAT-TTTTTATTAGTTTACATTGATTTGTTACATTGTTTTAATTTAATATTCA-CC
1 TTATGTTTTTATTTGTTTACATTGATTTATTACATTATTTTAATTTAATA-TGATGC
* * * * * * *
1021154 TTAT-TATTTATATGTTTGCATTAATCTATTATATTATTTTAATTTAATATGTTG-
1 TTATGTTTTTATTTGTTTACATTGATTTATTACATTATTTTAATTTAATATGATGC
* * *
1021208 TT-T-TTTTTATTTGTTTATATTGGTTTATTAGATTATTTTAATTTAATATGATGC
1 TTATGTTTTTATTTGTTTACATTGATTTATTACATTATTTTAATTTAATATGATGC
*
1021262 TTATGTTTTTATTTGTTTGCATTGATTTATTACATTACTTTT
1 TTATGTTTTTATTTGTTTACATTGATTTATTACATTA-TTTT
1021304 TTCATAATAG
Statistics
Matches: 120, Mismatches: 25, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
53 42 0.35
54 5 0.04
55 41 0.34
56 28 0.23
57 4 0.03
ACGTcount: A:0.25, C:0.05, G:0.09, T:0.61
Consensus pattern (56 bp):
TTATGTTTTTATTTGTTTACATTGATTTATTACATTATTTTAATTTAATATGATGC
Found at i:1021265 original size:108 final size:110
Alignment explanation
Indices: 1021102--1021303 Score: 257
Period size: 108 Copynumber: 1.9 Consensus size: 110
1021092 TACTATTTTA
* *
1021102 TTTTTTATTAGTTTACATTGATTTGTTACATTGTTTTAATTTAATATTCACCTTAT-TATTTATA
1 TTTTTTATTAGTTTACATTGATTTATTACATTATTTTAATTTAATATTCACCTTATGTATTTATA
*
1021166 TGTTTGCATTAATCTATTATATTA-TTTTAATTTAATATGTTGTT
66 TGTTTGCATTAATCTATTACATTACTTTTAATTTAATATGTTGTT
* * * * * * *
1021210 TTTTTTATTTGTTTATATTGGTTTATTAGATTATTTTAATTTAATA-TGATGCTTATGTTTTTAT
1 TTTTTTATTAGTTTACATTGATTTATTACATTATTTTAATTTAATATTCA-CCTTATGTATTTAT
* * *
1021274 TTGTTTGCATTGATTTATTACATTACTTTT
65 ATGTTTGCATTAATCTATTACATTACTTTT
1021304 TTCATAATAG
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
107 2 0.03
108 45 0.58
109 27 0.35
110 4 0.05
ACGTcount: A:0.25, C:0.05, G:0.09, T:0.61
Consensus pattern (110 bp):
TTTTTTATTAGTTTACATTGATTTATTACATTATTTTAATTTAATATTCACCTTATGTATTTATA
TGTTTGCATTAATCTATTACATTACTTTTAATTTAATATGTTGTT
Found at i:1023717 original size:23 final size:24
Alignment explanation
Indices: 1023668--1023715 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1023658 GGATTATTGT
*
1023668 ATTTTTTTTAATGTGGTACTTAAA
1 ATTTTTTTTAATGTGATACTTAAA
1023692 ATTTTTTTTAAT-TAGATACTTAAA
1 ATTTTTTTTAATGT-GATACTTAAA
1023716 TTATATTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTTTTTTAATGTGATACTTAAA
Found at i:1023889 original size:17 final size:17
Alignment explanation
Indices: 1023864--1023897 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1023854 TAAAAGAAAT
*
1023864 TTTTTAAAAATTTTAAA
1 TTTTAAAAAATTTTAAA
1023881 TTTTAAAAAATTTTAAA
1 TTTTAAAAAATTTTAAA
1023898 AAATTCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTAAAAAATTTTAAA
Found at i:1023891 original size:10 final size:10
Alignment explanation
Indices: 1023878--1024076 Score: 69
Period size: 11 Copynumber: 20.2 Consensus size: 10
1023868 TAAAAATTTT
1023878 AAATTTTAAA
1 AAATTTTAAA
1023888 AAATTTTAAA
1 AAATTTTAAA
*
1023898 AAATTCTAAA
1 AAATTTTAAA
*
1023908 AAGTTTTTAAA
1 AA-ATTTTAAA
* *
1023919 AACTTCTAAA
1 AAATTTTAAA
**
1023929 ATCTTTTTAAA
1 A-AATTTTAAA
1023940 AAA--TT-AA
1 AAATTTTAAA
* *
1023947 ATA-TTCAAA
1 AAATTTTAAA
* *
1023956 AACTATTCAAA
1 AAAT-TTTAAA
*
1023967 AAA--AT-AA
1 AAATTTTAAA
*
1023974 AAA-TTCAAA
1 AAATTTTAAA
1023983 AAATTTTTAAA
1 AAA-TTTTAAA
*
1023994 AAATTTTTAGA
1 AAA-TTTTAAA
*
1024005 AACTTTT--A
1 AAATTTTAAA
*
1024013 AAATTTTCAA
1 AAATTTTAAA
* *
1024023 AAGTTTCAAA
1 AAATTTTAAA
*
1024033 GAATTCTTAAA
1 AAATT-TTAAA
* *
1024044 AAAATCT-AA
1 AAATTTTAAA
1024053 AAATTTCTAAA
1 AAATTT-TAAA
1024064 AAATTTATAAA
1 AAATTT-TAAA
1024075 AA
1 AA
1024077 TTCTAAAAGA
Statistics
Matches: 139, Mismatches: 35, Indels: 29
0.68 0.17 0.14
Matches are distributed among these distances:
7 9 0.06
8 10 0.07
9 14 0.10
10 45 0.32
11 61 0.44
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (10 bp):
AAATTTTAAA
Found at i:1023915 original size:21 final size:20
Alignment explanation
Indices: 1023878--1023944 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 20
1023868 TAAAAATTTT
* *
1023878 AAATTTTAAAAAATTTTAAA
1 AAATTCTAAAAATTTTTAAA
1023898 AAATTCTAAAAAGTTTTTAAA
1 AAATTCTAAAAA-TTTTTAAA
* *
1023919 AACTTCTAAAATCTTTTTAAA
1 AAATTCTAAAA-ATTTTTAAA
1023940 AAATT
1 AAATT
1023945 AAATATTCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
20 11 0.28
21 29 0.73
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.40
Consensus pattern (20 bp):
AAATTCTAAAAATTTTTAAA
Found at i:1023967 original size:27 final size:27
Alignment explanation
Indices: 1023937--1023998 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
1023927 AAATCTTTTT
* *
1023937 AAAAAATTAAATATTCAAAAACTATTC
1 AAAAAATTAAAAATTCAAAAAATATTC
* * *
1023964 AAAAAAATAAAAATTCAAAAAATTTTT
1 AAAAAATTAAAAATTCAAAAAATATTC
1023991 AAAAAATT
1 AAAAAATT
1023999 TTTAGAAACT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (27 bp):
AAAAAATTAAAAATTCAAAAAATATTC
Found at i:1023995 original size:28 final size:27
Alignment explanation
Indices: 1023915--1023996 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 27
1023905 AAAAAGTTTT
* * *
1023915 TAAAAACTTCTAAAATCTTTTTAAAAAAT
1 TAAAAA-TTCAAAAAT-TTTTAAAAAAAA
* * * *
1023944 TAAATATTCAAAAACTATTCAAAAAAA
1 TAAAAATTCAAAAATTTTTAAAAAAAA
1023971 TAAAAATTCAAAAAATTTTTAAAAAA
1 TAAAAATTC-AAAAATTTTTAAAAAA
1023997 TTTTTAGAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
27 17 0.40
28 20 0.48
29 5 0.12
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.32
Consensus pattern (27 bp):
TAAAAATTCAAAAATTTTTAAAAAAAA
Found at i:1024257 original size:12 final size:12
Alignment explanation
Indices: 1024240--1024265 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1024230 TAAAAAATTC
1024240 AAAAAATTCAAA
1 AAAAAATTCAAA
1024252 AAAAAATTCAAA
1 AAAAAATTCAAA
1024264 AA
1 AA
1024266 TAGAAAAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAAATTCAAA
Found at i:1024341 original size:7 final size:8
Alignment explanation
Indices: 1024312--1024340 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1024302 TGAAAATTCC
1024312 TAAAAATA
1 TAAAAATA
1024320 TAAAAATA
1 TAAAAATA
1024328 TAAAAA-A
1 TAAAAATA
1024335 TAAAAA
1 TAAAAA
1024341 AAACATTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
TAAAAATA
Found at i:1024385 original size:18 final size:19
Alignment explanation
Indices: 1024362--1024401 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1024352 AAATTCTTTT
*
1024362 AAATTTTT-TAAAATTAAA
1 AAATTTTTAAAAAATTAAA
1024380 AAATTTTTAAAAAATTAAA
1 AAATTTTTAAAAAATTAAA
1024399 AAA
1 AAA
1024402 ATTCAACTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTTTTAAAAAATTAAA
Found at i:1025000 original size:12 final size:12
Alignment explanation
Indices: 1024985--1025014 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1024975 AATTTTATAG
1024985 AATTTTTTTAAA
1 AATTTTTTTAAA
1024997 AATTTTTTTAAA
1 AATTTTTTTAAA
*
1025009 ACTTTT
1 AATTTT
1025015 AGAATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (12 bp):
AATTTTTTTAAA
Found at i:1025001 original size:42 final size:41
Alignment explanation
Indices: 1024937--1025042 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 41
1024927 CTTTTATAAA
* *
1024937 TTATAAATTTTATTTTAGAATTTTTTTAAAAAAATTAGAATT
1 TTATAAATTTT-TTTAAAAATTTTTTTAAAAAAATTAGAATT
***
1024979 TTATAGAATTTTTTTAAAAATTTTTTTAAAACTTTTAGAATT
1 TTATA-AATTTTTTTAAAAATTTTTTTAAAAAAATTAGAATT
*
1025021 TT-TAAA-ATTTTTAGAAAATTTT
1 TTATAAATTTTTTTA-AAAATTTT
1025043 AAATTTTTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
39 6 0.11
40 10 0.18
41 2 0.04
42 32 0.57
43 6 0.11
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.54
Consensus pattern (41 bp):
TTATAAATTTTTTTAAAAATTTTTTTAAAAAAATTAGAATT
Found at i:1025002 original size:10 final size:10
Alignment explanation
Indices: 1024989--1025071 Score: 59
Period size: 10 Copynumber: 8.6 Consensus size: 10
1024979 TTATAGAATT
1024989 TTTTTAAAAA
1 TTTTTAAAAA
*
1024999 TTTTTTTAAAA
1 -TTTTTAAAAA
* *
1025010 CTTTT-AGAA
1 TTTTTAAAAA
1025019 TTTTT-AAAA
1 TTTTTAAAAA
1025028 TTTTTAGAAAA
1 TTTTTA-AAAA
1025039 -TTTT--AAA
1 TTTTTAAAAA
***
1025046 TTTTTTTGAA
1 TTTTTAAAAA
1025056 TTTTTAAAAA
1 TTTTTAAAAA
1025066 TTTTTA
1 TTTTTA
1025072 CTTTTTAGAA
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
7 3 0.05
8 4 0.07
9 15 0.26
10 23 0.40
11 13 0.22
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.57
Consensus pattern (10 bp):
TTTTTAAAAA
Found at i:1025014 original size:9 final size:9
Alignment explanation
Indices: 1025001--1025071 Score: 70
Period size: 9 Copynumber: 7.7 Consensus size: 9
1024991 TTTAAAAATT
1025001 TTTTTAAAA
1 TTTTTAAAA
* *
1025010 CTTTTAGAA
1 TTTTTAAAA
1025019 TTTTTAAAA
1 TTTTTAAAA
1025028 TTTTTAGAAA
1 TTTTTA-AAA
* *
1025038 ATTTTAAAT
1 TTTTTAAAA
**
1025047 TTTTTTGAA
1 TTTTTAAAA
1025056 TTTTTAAAAA
1 TTTTT-AAAA
1025066 TTTTTA
1 TTTTTA
1025072 CTTTTTAGAA
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
9 33 0.69
10 15 0.31
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:1025024 original size:18 final size:18
Alignment explanation
Indices: 1025001--1025071 Score: 88
Period size: 19 Copynumber: 3.8 Consensus size: 18
1024991 TTTAAAAATT
*
1025001 TTTTTAAAACTTTTAGAA
1 TTTTTAAAATTTTTAGAA
1025019 TTTTTAAAATTTTTAGAAA
1 TTTTTAAAATTTTTAG-AA
* * *
1025038 ATTTTAAATTTTTTTGAA
1 TTTTTAAAATTTTTAGAA
1025056 TTTTTAAAAATTTTTA
1 TTTTT-AAAATTTTTA
1025072 CTTTTTAGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 21 0.48
19 23 0.52
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (18 bp):
TTTTTAAAATTTTTAGAA
Found at i:1025076 original size:17 final size:17
Alignment explanation
Indices: 1025056--1025094 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1025046 TTTTTTTGAA
1025056 TTTTTAAAAATTTTTAC
1 TTTTTAAAAATTTTTAC
* *
1025073 TTTTTAGAATTTTTTAC
1 TTTTTAAAAATTTTTAC
1025090 TTTTT
1 TTTTT
1025095 TTTTAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTTTAAAAATTTTTAC
Found at i:1025085 original size:9 final size:9
Alignment explanation
Indices: 1025001--1025086 Score: 61
Period size: 9 Copynumber: 9.6 Consensus size: 9
1024991 TTTAAAAATT
*
1025001 TTTTTAAAA
1 TTTTTAGAA
*
1025010 CTTTTAGAA
1 TTTTTAGAA
*
1025019 TTTTTAAAA
1 TTTTTAGAA
1025028 TTTTTAGAAA
1 TTTTTAG-AA
*
1025038 ATTTTA-AA
1 TTTTTAGAA
*
1025046 TTTTTTTGAA
1 -TTTTTAGAA
*
1025056 TTTTTAAAAA
1 TTTTT-AGAA
*
1025066 TTTTT--AC
1 TTTTTAGAA
1025073 TTTTTAGAA
1 TTTTTAGAA
1025082 TTTTT
1 TTTTT
1025087 TACTTTTTTT
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
7 6 0.10
8 2 0.03
9 35 0.59
10 16 0.27
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (9 bp):
TTTTTAGAA
Found at i:1025087 original size:28 final size:28
Alignment explanation
Indices: 1025000--1025088 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 28
1024990 TTTTAAAAAT
* *
1025000 TTTTTTAAAACTTTTAGAATTTTTA-AA
1 TTTTTTAAAAATTTTAAAATTTTTAGAA
* * *
1025027 ATTTTTAGAAAATTTTAAATTTTTTTGAA
1 TTTTTTA-AAAATTTTAAAATTTTTAGAA
* *
1025056 -TTTTTAAAAATTTT-TACTTTTTAGAA
1 TTTTTTAAAAATTTTAAAATTTTTAGAA
1025082 TTTTTTA
1 TTTTTTA
1025089 CTTTTTTTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
26 9 0.18
27 20 0.39
28 20 0.39
29 2 0.04
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (28 bp):
TTTTTTAAAAATTTTAAAATTTTTAGAA
Found at i:1025088 original size:10 final size:10
Alignment explanation
Indices: 1024971--1025070 Score: 55
Period size: 10 Copynumber: 10.1 Consensus size: 10
1024961 TTTAAAAAAA
1024971 TTAGAATTTT
1 TTAGAATTTT
*
1024981 ATAGAATTTTT
1 TTAGAA-TTTT
*
1024992 TTAAAAATTTTT
1 TT-AGAA-TTTT
**
1025004 TTA-AAACTT
1 TTAGAATTTT
1025013 TTAGAA-TTT
1 TTAGAATTTT
*
1025022 TTA-AAATTT
1 TTAGAATTTT
**
1025031 TTAGAAAATT
1 TTAGAATTTT
1025041 TTA-AATTTT
1 TTAGAATTTT
*
1025050 TTTGAATTTT
1 TTAGAATTTT
* *
1025060 TAAAAATTTT
1 TTAGAATTTT
1025070 T
1 T
1025071 ACTTTTTAGA
Statistics
Matches: 71, Mismatches: 13, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
8 2 0.03
9 22 0.31
10 31 0.44
11 6 0.08
12 10 0.14
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (10 bp):
TTAGAATTTT
Found at i:1025192 original size:2 final size:2
Alignment explanation
Indices: 1025185--1025210 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1025175 ACAGAAAAAG
1025185 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
1025211 TGTGGTGTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1025325 original size:21 final size:21
Alignment explanation
Indices: 1025299--1025356 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
1025289 AAAATTAGAA
1025299 TTTTTAGAATTCTTTTA-AAAT
1 TTTTTAGAATT-TTTTACAAAT
*
1025320 TTTTTA-AAATTTTTACAAAT
1 TTTTTAGAATTTTTTACAAAT
*
1025340 TATTTTTGAATTTTTTA
1 T-TTTTAGAATTTTTTA
1025357 TTTTTCTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 5 0.16
20 8 0.26
21 10 0.32
22 8 0.26
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (21 bp):
TTTTTAGAATTTTTTACAAAT
Found at i:1025326 original size:10 final size:10
Alignment explanation
Indices: 1025299--1025438 Score: 69
Period size: 11 Copynumber: 14.0 Consensus size: 10
1025289 AAAATTAGAA
*
1025299 TTTTTAGAAT
1 TTTTTAAAAT
1025309 TCTTTTAAAAT
1 T-TTTTAAAAT
1025320 TTTTTAAAA-
1 TTTTTAAAAT
1025329 TTTTTACAAAT
1 TTTTTA-AAAT
**
1025340 TATTTTTGAAT
1 T-TTTTAAAAT
1025351 TTTTT---AT
1 TTTTTAAAAT
1025358 TTTTCT-AAA-
1 TTTT-TAAAAT
*
1025367 TTTTTATAA-
1 TTTTTAAAAT
*
1025376 TTTATAAAAT
1 TTTTTAAAAT
1025386 TTTTTAAAAAT
1 TTTTT-AAAAT
* * *
1025397 ATTTCAAAACA
1 TTTTTAAAA-T
*
1025408 TTTTAAAAAT
1 TTTTTAAAAT
* *
1025418 ATTTTTATATT
1 -TTTTTAAAAT
1025429 TTTTTAAAAT
1 TTTTTAAAAT
1025439 ATTCTTTTAA
Statistics
Matches: 100, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
7 6 0.06
8 2 0.02
9 19 0.19
10 33 0.33
11 36 0.36
12 4 0.04
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (10 bp):
TTTTTAAAAT
Found at i:1025432 original size:21 final size:21
Alignment explanation
Indices: 1025381--1025441 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1025371 TATAATTTAT
1025381 AAAATTTTTTAAAAATATTTC
1 AAAATTTTTTAAAAATATTTC
** *
1025402 AAAACATTTTAAAAATATTTT
1 AAAATTTTTTAAAAATATTTC
* * *
1025423 TATATTTTTTTAAAATATT
1 AAAATTTTTTAAAAATATT
1025442 CTTTTAATAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (21 bp):
AAAATTTTTTAAAAATATTTC
Found at i:1028716 original size:24 final size:24
Alignment explanation
Indices: 1028684--1028739 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1028674 AATTTTTTAT
*
1028684 TAATTTTTTTAATTATAATTACAA
1 TAATTTTTTTAATCATAATTACAA
*
1028708 TAATTTTTTTAATCGTAATTACAA
1 TAATTTTTTTAATCATAATTACAA
*
1028732 TAAATTTT
1 TAATTTTT
1028740 ATTACTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (24 bp):
TAATTTTTTTAATCATAATTACAA
Found at i:1037901 original size:45 final size:45
Alignment explanation
Indices: 1037829--1037917 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
1037819 AGACCTGACT
1037829 AATGGGTAATAGTAGTTAGTAAAGACATGATTCATACAGCCCTACC
1 AATGGGTAATAGTAGTTAGTAAAGACATGATT-ATACAGCCCTACC
*
1037875 AATGGGTTATAGTA-TTAGTAAAGACATGATTATACAGCCCTAC
1 AATGGGTAATAGTAGTTAGTAAAGACATGATTATACAGCCCTAC
1037918 TAACGGATTA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
44 12 0.29
45 17 0.40
46 13 0.31
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (45 bp):
AATGGGTAATAGTAGTTAGTAAAGACATGATTATACAGCCCTACC
Found at i:1037929 original size:44 final size:46
Alignment explanation
Indices: 1037837--1037936 Score: 150
Period size: 44 Copynumber: 2.2 Consensus size: 46
1037827 CTAATGGGTA
* *
1037837 ATAGTAGTTAGTAAAGACATGATTCATACAGCCCTACCAATGGGTT
1 ATAGTAGTTAGTAAAGACATGATTCATACAGCCCTACCAACGGATT
*
1037883 ATAGTA-TTAGTAAAGACATGATT-ATACAGCCCTACTAACGGATT
1 ATAGTAGTTAGTAAAGACATGATTCATACAGCCCTACCAACGGATT
*
1037927 ATAATAGTTA
1 ATAGTAGTTA
1037937 ACGAAGCTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
44 23 0.47
45 20 0.41
46 6 0.12
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (46 bp):
ATAGTAGTTAGTAAAGACATGATTCATACAGCCCTACCAACGGATT
Found at i:1044328 original size:2 final size:2
Alignment explanation
Indices: 1044321--1044362 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1044311 CTGCCATTTT
1044321 GA GA GA GA -A GA GA GA GA GA GA GA -A GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1044361 GA
1 GA
1044363 TTAATTGATC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Done.