Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold231
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: 1009718
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 6 of 7
Found at i:859355 original size:10 final size:9
Alignment explanation
Indices: 859340--859453 Score: 64
Period size: 8 Copynumber: 13.2 Consensus size: 9
859330 AAATTAATTA
859340 AAATAATAT
1 AAATAATAT
859349 AATATAATAT
1 AA-ATAATAT
*
859359 -AAT-ATAA
1 AAATAATAT
859366 AAATAA-AT
1 AAATAATAT
**
859374 ATTTAATAT
1 AAATAATAT
859383 AAAT-ATAT
1 AAATAATAT
* *
859391 AAATATTTT
1 AAATAATAT
859400 AAA-ATATAT
1 AAATA-ATAT
859409 AAA-AATAT
1 AAATAATAT
859417 AAATAAT-T
1 AAATAATAT
** *
859425 AATATTTTAA
1 AA-ATAATAT
*
859435 AAATTATAT
1 AAATAATAT
859444 AAAT-ATAT
1 AAATAATAT
859452 AA
1 AA
859454 TATTTTAATT
Statistics
Matches: 81, Mismatches: 15, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
7 3 0.04
8 35 0.43
9 34 0.42
10 9 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
AAATAATAT
Found at i:859374 original size:27 final size:27
Alignment explanation
Indices: 859316--859393 Score: 71
Period size: 27 Copynumber: 3.0 Consensus size: 27
859306 GTATCAGATG
*
859316 AAATACAATATAA-AAAAT-TAAT-T-A
1 AAATA-AATATAATATAATATAATATAA
859340 AAAT-AATATAATATAATATAATATAA
1 AAATAAATATAATATAATATAATATAA
859366 AAATAAATATTTAATATAA-AT-ATATAA
1 AAATAAATA--TAATATAATATAATATAA
859393 A
1 A
859394 TATTTTAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
22 7 0.15
23 4 0.09
24 8 0.17
25 1 0.02
26 5 0.11
27 11 0.24
28 2 0.04
29 8 0.17
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (27 bp):
AAATAAATATAATATAATATAATATAA
Found at i:859434 original size:33 final size:36
Alignment explanation
Indices: 859378--859453 Score: 113
Period size: 34 Copynumber: 2.2 Consensus size: 36
859368 ATAAATATTT
859378 AATATAAATATATAAATATTTT-AAAA-TATATAAA
1 AATATAAATATATAAATATTTTAAAAATTATATAAA
*
859412 AATATAAATA-ATTAATATTTTAAAAATTATATAAA
1 AATATAAATATATAAATATTTTAAAAATTATATAAA
*
859447 TATATAA
1 AATATAA
859454 TATTTTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 10 0.26
34 14 0.37
35 14 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (36 bp):
AATATAAATATATAAATATTTTAAAAATTATATAAA
Found at i:859454 original size:27 final size:30
Alignment explanation
Indices: 859337--859461 Score: 102
Period size: 27 Copynumber: 4.1 Consensus size: 30
859327 AAAAAATTAA
*
859337 TTAAAATAATATAATATAATATAATATAA-A-A
1 TTAAAAT-ATATAATATAA-AT-ATATAATATT
* *
859368 AT-AAATATTTAATATAAATATATAAATATT
1 TTAAAATATATAATATAAATATAT-AATATT
859398 TTAAAATATATAAAAATATAAATA-ATTAATATT
1 TTAAAATATAT---AATATAAATATA-TAATATT
859431 TTAAAA-AT-T-ATATAAATATATAATATT
1 TTAAAATATATAATATAAATATATAATATT
859458 TTAA
1 TTAA
859462 TTTTAATTTT
Statistics
Matches: 80, Mismatches: 5, Indels: 22
0.75 0.05 0.21
Matches are distributed among these distances:
27 24 0.30
28 5 0.06
29 11 0.14
30 5 0.06
31 9 0.11
32 2 0.03
33 13 0.16
34 11 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
TTAAAATATATAATATAAATATATAATATT
Found at i:859464 original size:6 final size:6
Alignment explanation
Indices: 859455--859480 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
859445 AATATATAAT
859455 ATTTTA ATTTTA ATTTTA ATTTTA AT
1 ATTTTA ATTTTA ATTTTA ATTTTA AT
859481 ATAATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
ATTTTA
Found at i:860205 original size:15 final size:15
Alignment explanation
Indices: 860187--860217 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
860177 TATAAGATCC
860187 AATAAAATAAAATAT
1 AATAAAATAAAATAT
860202 AATAAAATAAAATAT
1 AATAAAATAAAATAT
860217 A
1 A
860218 TTATGTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAAAATAAAATAT
Found at i:860566 original size:13 final size:13
Alignment explanation
Indices: 860548--860572 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
860538 TTTTTTTATT
860548 TATTTATATTTAA
1 TATTTATATTTAA
860561 TATTTATATTTA
1 TATTTATATTTA
860573 TATCATAGTT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTATATTTAA
Found at i:860951 original size:17 final size:17
Alignment explanation
Indices: 860929--860998 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
860919 TCATACCTTT
*
860929 AATTTATATTTAAATAA
1 AATTTAAATTTAAATAA
* *
860946 AATTTAAATATAAAT-T
1 AATTTAAATTTAAATAA
860962 AATCTTAAATTTTAAATAAA
1 AAT-TTAAA-TTTAAAT-AA
860982 AATTT--ATTTAAA-AA
1 AATTTAAATTTAAATAA
860996 AAT
1 AAT
860999 AAAAATAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
14 5 0.11
16 9 0.20
17 19 0.43
18 6 0.14
19 2 0.05
20 3 0.07
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTTAAATTTAAATAA
Found at i:860992 original size:23 final size:24
Alignment explanation
Indices: 860943--861009 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 24
860933 TATATTTAAA
*
860943 TAAAATTTAAATATAAATTAATCT
1 TAAAATTTAAATAAAAATTAATCT
* *
860967 TAAATTTTAAATAAAAATTTAT-T
1 TAAAATTTAAATAAAAATTAATCT
*
860990 TAAAA---AAATAAAAATAAATC
1 TAAAATTTAAATAAAAATTAATC
861010 ATGGATTTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
20 12 0.33
23 5 0.14
24 19 0.53
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (24 bp):
TAAAATTTAAATAAAAATTAATCT
Found at i:861240 original size:2 final size:2
Alignment explanation
Indices: 861233--861272 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
861223 GTTGACATTA
*
861233 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
861273 CAGATCATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:861598 original size:14 final size:14
Alignment explanation
Indices: 861579--861627 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
861569 GACGTATTAA
861579 AAATATAATATAAT
1 AAATATAATATAAT
861593 AAATATAATATAA-
1 AAATATAATATAAT
*
861606 AATATTTAAATATAAT
1 AA-ATAT-AATATAAT
*
861622 TAATAT
1 AAATAT
861628 GAAATATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 2 0.07
14 16 0.55
15 10 0.34
16 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATATAATATAAT
Found at i:861625 original size:24 final size:24
Alignment explanation
Indices: 861590--861637 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
861580 AATATAATAT
861590 AATAAATATAATATAAAATATTTA
1 AATAAATATAATATAAAATATTTA
*
861614 AATATAAT-TAATATGAAATATTTA
1 AATA-AATATAATATAAAATATTTA
861638 TTATATATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
AATAAATATAATATAAAATATTTA
Found at i:861912 original size:3 final size:3
Alignment explanation
Indices: 861904--861938 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
861894 ATCAAGAAAG
*
861904 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
861939 ACCCAAACTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:862251 original size:5 final size:5
Alignment explanation
Indices: 862241--862272 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
862231 TTTCTACAGT
862241 AATAA AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AATAA AA
862273 ATACAGTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:863001 original size:4 final size:4
Alignment explanation
Indices: 862992--863018 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
862982 CCTCAGCATG
862992 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
863019 CTTTGATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:864110 original size:11 final size:11
Alignment explanation
Indices: 864091--864126 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
864081 ATATTCATCC
864091 TTTTAATTTTT
1 TTTTAATTTTT
*
864102 TTTTTATTTTT
1 TTTTAATTTTT
*
864113 TTTCAATTTTT
1 TTTTAATTTTT
864124 TTT
1 TTT
864127 AAAAAGAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTAATTTTT
Found at i:864623 original size:10 final size:10
Alignment explanation
Indices: 864607--864640 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
864597 AAAAAATAGT
864607 AATAAAATTC
1 AATAAAATTC
*
864617 GATAAAATTC
1 AATAAAATTC
*
864627 AATAAAATTA
1 AATAAAATTC
864637 AATA
1 AATA
864641 TTAAATTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (10 bp):
AATAAAATTC
Found at i:865624 original size:2 final size:2
Alignment explanation
Indices: 865617--865659 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
865607 ATTTTAAGAG
*
865617 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
865659 T
1 T
865660 GCAATTCTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:867252 original size:21 final size:21
Alignment explanation
Indices: 867196--867252 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
867186 AAAGTGAAAT
867196 GTTATTATAACATTAATACTAAA
1 GTTATTATAACA-T-ATACTAAA
** * *
867219 AATA-TATTACATATACTTAA
1 GTTATTATAACATATACTAAA
867239 GTTATTATAACATA
1 GTTATTATAACATA
867253 AATGGTGGGA
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
20 9 0.35
21 9 0.35
22 6 0.23
23 2 0.08
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (21 bp):
GTTATTATAACATATACTAAA
Found at i:868203 original size:12 final size:12
Alignment explanation
Indices: 868186--868212 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
868176 TATATGTATC
868186 GTATTATATTTA
1 GTATTATATTTA
868198 GTATTATATTTA
1 GTATTATATTTA
868210 GTA
1 GTA
868213 GAGAATTACT
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:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (12 bp):
GTATTATATTTA
Found at i:868737 original size:25 final size:25
Alignment explanation
Indices: 868709--868761 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
868699 ATTGAATACG
868709 ATAATAAAAATATGAAATA-AATA-AA
1 ATAATAAAAATA--AAATACAATATAA
*
868734 ATAATTAAAATAAAATACAATATAA
1 ATAATAAAAATAAAATACAATATAA
868759 ATA
1 ATA
868762 TATATATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 5 0.20
24 4 0.16
25 16 0.64
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (25 bp):
ATAATAAAAATAAAATACAATATAA
Found at i:868809 original size:31 final size:31
Alignment explanation
Indices: 868752--868821 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
868742 AATAAAATAC
868752 AATATAAATATATATATTAAAATTTATA-T-
1 AATATAAATATATATATTAAAATTTATATTA
868781 AATATAAATTATTATCATATT-AAATTTATATTA
1 AATATAAA-TA-TAT-ATATTAAAATTTATATTA
868814 AATATAAA
1 AATATAAA
868822 CTATCTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
29 8 0.22
30 2 0.06
31 12 0.33
32 6 0.17
33 8 0.22
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (31 bp):
AATATAAATATATATATTAAAATTTATATTA
Found at i:870289 original size:2 final size:2
Alignment explanation
Indices: 870282--870308 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
870272 TATGTAAAAT
870282 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
870309 GAAGTTGAAA
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:870872 original size:35 final size:37
Alignment explanation
Indices: 870796--870873 Score: 106
Period size: 35 Copynumber: 2.2 Consensus size: 37
870786 TTCTGCTCCG
* * *
870796 TTATAATAACTTTAAATATATATTTTTACTATTAATG
1 TTATAATAACTTTAAATATATATTATTACCATTAATA
*
870833 TTATAGTAAC-TTAAATATATA-TATTACCATTAATA
1 TTATAATAACTTTAAATATATATTATTACCATTAATA
870868 TTATAA
1 TTATAA
870874 ATAGCTGTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
35 16 0.44
36 11 0.31
37 9 0.25
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (37 bp):
TTATAATAACTTTAAATATATATTATTACCATTAATA
Found at i:876123 original size:23 final size:23
Alignment explanation
Indices: 876093--876138 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
876083 TCTCGAGGCA
876093 AAGGTCGATACTAATGCTGTAAG
1 AAGGTCGATACTAATGCTGTAAG
* *
876116 AAGGTCGATATTAATTCTGTAAG
1 AAGGTCGATACTAATGCTGTAAG
876139 CGAGTTAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (23 bp):
AAGGTCGATACTAATGCTGTAAG
Found at i:876185 original size:9 final size:9
Alignment explanation
Indices: 876163--876221 Score: 55
Period size: 10 Copynumber: 6.1 Consensus size: 9
876153 TGATAATATT
876163 AAATATTAAA
1 AAATATT-AA
876173 AAATATTAA
1 AAATATTAA
876182 AAATAATATAA
1 AAAT-AT-TAA
* *
876193 ATATAATAA
1 AAATATTAA
876202 AAATATATAA
1 AAATAT-TAA
*
876212 ATATATTAA
1 AAATATTAA
876221 A
1 A
876222 TTTTATATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
9 17 0.41
10 18 0.44
11 6 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAATATTAA
Found at i:876203 original size:19 final size:19
Alignment explanation
Indices: 876179--876268 Score: 75
Period size: 20 Copynumber: 4.9 Consensus size: 19
876169 TAAAAAATAT
876179 TAAAAATAATATAAATATAA
1 TAAAAAT-ATATAAATATAA
876199 TAAAAATATATAAATAT-A
1 TAAAAATATATAAATATAA
* *
876217 T-TAAAT-T-T-TATATAA
1 TAAAAATATATAAATATAA
* * *
876232 TATAAAT-TATTAATATAT
1 TAAAAATATATAAATATAA
876250 TAAAAATTATATAAATATA
1 TAAAAA-TATATAAATATA
876269 TTACATTTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
14 4 0.07
15 3 0.05
16 7 0.12
17 5 0.09
18 12 0.21
19 11 0.19
20 16 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAAATATATAAATATAA
Found at i:876230 original size:20 final size:20
Alignment explanation
Indices: 876158--876271 Score: 90
Period size: 19 Copynumber: 6.3 Consensus size: 20
876148 AAATATGATA
876158 ATATTAAATATTA-A-AAA-
1 ATATTAAATATTATATAAAT
* *
876175 ATATTAAAAATAATATAAAT
1 ATATTAAATATTATATAAAT
* *
876195 ATAATAAA-AATATATAAAT
1 ATATTAAATATTATATAAAT
*
876214 ATATTAAAT-TT-TATATA-
1 ATATTAAATATTATATAAAT
876231 ATA-T-AA-ATTAT-T-AAT
1 ATATTAAATATTATATAAAT
*
876246 ATATTAAAAATTATATAAAT
1 ATATTAAATATTATATAAAT
876266 ATATTA
1 ATATTA
876272 CATTTTAAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
14 1 0.01
15 8 0.11
16 3 0.04
17 16 0.21
18 11 0.14
19 21 0.28
20 16 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATTAAATATTATATAAAT
Found at i:876247 original size:18 final size:18
Alignment explanation
Indices: 876192--876259 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
876182 AAATAATATA
*
876192 AATATAATAAAAATATATA
1 AATATAATAAAAAT-TATT
*
876211 AATAT-AT-TAAATT-TT
1 AATATAATAAAAATTATT
*
876226 -ATATAATATAAATTATT
1 AATATAATAAAAATTATT
*
876243 AATATATTAAAAATTAT
1 AATATAATAAAAATTAT
876260 ATAAATATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
14 4 0.10
15 3 0.07
16 7 0.17
17 6 0.15
18 16 0.39
19 5 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATATAATAAAAATTATT
Found at i:876250 original size:32 final size:33
Alignment explanation
Indices: 876193--876268 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 33
876183 AATAATATAA
* **
876193 ATATAATAAAAATATATAAATATATTAAATTTT
1 ATATAATATAAATATATAAATATATTAAAAATT
*
876226 ATATAATATAAAT-TATTAATATATTAAAAATT
1 ATATAATATAAATATATAAATATATTAAAAATT
876258 ATATAAATATA
1 ATAT-AATATA
876269 TTACATTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
32 20 0.53
33 18 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
ATATAATATAAATATATAAATATATTAAAAATT
Found at i:876279 original size:27 final size:26
Alignment explanation
Indices: 876199--876283 Score: 88
Period size: 27 Copynumber: 3.3 Consensus size: 26
876189 ATAAATATAA
876199 TAAAAA-TATATAAATATATTAAATTT
1 TAAAAATTATATAAATATATT-AATTT
* *
876225 T--ATATAATATAAAT-TATTAATATAT
1 TAAAAATTATATAAATATATTAAT-T-T
876250 TAAAAATTATATAAATATATTACATTT
1 TAAAAATTATATAAATATATTA-ATTT
876277 TAAAAAT
1 TAAAAAT
876284 AATAAAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
23 3 0.06
24 7 0.15
25 10 0.21
26 1 0.02
27 19 0.40
28 6 0.12
29 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (26 bp):
TAAAAATTATATAAATATATTAATTT
Found at i:876289 original size:52 final size:51
Alignment explanation
Indices: 876192--876289 Score: 144
Period size: 52 Copynumber: 1.9 Consensus size: 51
876182 AAATAATATA
*
876192 AATATAATAAAAATATATAAATATATTAAATTTTATATAATATAAATTATT
1 AATATAATAAAAATATATAAATATATTAAATTTTATAAAATATAAATTATT
* *
876243 AATATATTAAAAATTATATAAATATATTACATTTTA-AAAATAATAAA
1 AATATAATAAAAA-TATATAAATATATTAAATTTTATAAAAT-ATAAA
876290 AAATAATTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
51 16 0.38
52 26 0.62
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (51 bp):
AATATAATAAAAATATATAAATATATTAAATTTTATAAAATATAAATTATT
Found at i:877206 original size:34 final size:34
Alignment explanation
Indices: 877114--877295 Score: 260
Period size: 34 Copynumber: 5.4 Consensus size: 34
877104 AAGAAAAAAC
* * *
877114 TGTTGATTAAAT-GGTGATTTGGTAGTTTATCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
877147 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
877180 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
877214 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
877248 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
877282 TGTTGATTAAATGG
1 TGTTGATTAAATGG
877296 TGGTTTTTAC
Statistics
Matches: 133, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 40 0.30
34 93 0.70
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:877654 original size:19 final size:19
Alignment explanation
Indices: 877598--877660 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
877588 TGGTTGTCGA
**
877598 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
877617 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
877636 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
877655 GTTACT
1 GGTACT
877661 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:881820 original size:34 final size:34
Alignment explanation
Indices: 881726--881909 Score: 273
Period size: 34 Copynumber: 5.5 Consensus size: 34
881716 AAGTGGGAGA
* *
881726 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
881759 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
881792 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
881826 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
881860 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
881894 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
881910 TGGTTTTTAC
Statistics
Matches: 136, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 43 0.32
34 93 0.68
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:882994 original size:45 final size:45
Alignment explanation
Indices: 882930--883019 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
882920 CTATTACAAT
882930 GATGTTCTTATCTCACCCTCCAAATGGAACTACTAAATCTTATCC
1 GATGTTCTTATCTCACCCTCCAAATGGAACTACTAAATCTTATCC
*
882975 GATGTTCTTATCTCGCCCTCCAAATGGAACTACTAAATCTTATCC
1 GATGTTCTTATCTCACCCTCCAAATGGAACTACTAAATCTTATCC
883020 TGGAACTACC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33
Consensus pattern (45 bp):
GATGTTCTTATCTCACCCTCCAAATGGAACTACTAAATCTTATCC
Found at i:883628 original size:99 final size:98
Alignment explanation
Indices: 883455--883646 Score: 303
Period size: 99 Copynumber: 1.9 Consensus size: 98
883445 ATTTACTCAC
* *
883455 TTCTTGGTGCATTTTTTTGCCTTGTGTAACAAATCTTGCCTAAATCAGTATGCTCTTCCTATATC
1 TTCTTGGTGCACTTTTTTGCCTTGTGTAACAAATCTTGCCTAAATCAATATGCTCTTCCTATATC
883520 TTAGAAAACTTGTAAGCTACTAGATTTGCCCAT
66 TTAGAAAACTTGTAAGCTACTAGATTTGCCCAT
* * *
883553 TTCTTGGTGCACTTTTTTGCCTTGTGTAGACAAGTCTTGGCTAAATCAATCTGCTCTTCCTATAT
1 TTCTTGGTGCACTTTTTTGCCTTGTGTA-ACAAATCTTGCCTAAATCAATATGCTCTTCCTATAT
* * *
883618 CTTAGCAAACTTGTAAGTTGCTAGATTTG
65 CTTAGAAAACTTGTAAGCTACTAGATTTG
883647 GTCCTATGTA
Statistics
Matches: 85, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
98 27 0.32
99 58 0.68
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (98 bp):
TTCTTGGTGCACTTTTTTGCCTTGTGTAACAAATCTTGCCTAAATCAATATGCTCTTCCTATATC
TTAGAAAACTTGTAAGCTACTAGATTTGCCCAT
Found at i:886432 original size:16 final size:16
Alignment explanation
Indices: 886397--886439 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
886387 AAAATGAAAG
* *
886397 AAAGAAAGAAAATTGAA
1 AAAGAAA-AATATGGAA
886414 AAAGAAAAATATGGAA
1 AAAGAAAAATATGGAA
*
886430 AAAAAAAAAT
1 AAAGAAAAAT
886440 TAGTTCTTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (16 bp):
AAAGAAAAATATGGAA
Found at i:888167 original size:14 final size:14
Alignment explanation
Indices: 888148--888174 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
888138 AAAGTGTTCC
888148 CGAATATTGATGCT
1 CGAATATTGATGCT
888162 CGAATATTGATGC
1 CGAATATTGATGC
888175 ATTGATTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (14 bp):
CGAATATTGATGCT
Found at i:889992 original size:20 final size:20
Alignment explanation
Indices: 889967--890014 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
889957 AAAAATATTT
*
889967 TAATTTAAATTTAATTATAA
1 TAATTTAAAATTAATTATAA
* *
889987 TAATTTAAAATTATTTTTAA
1 TAATTTAAAATTAATTATAA
*
890007 TATTTTAA
1 TAATTTAA
890015 TATATTTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAATTTAAAATTAATTATAA
Found at i:898935 original size:16 final size:16
Alignment explanation
Indices: 898894--898944 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
898884 TAACTTGATA
898894 AAACTTAAAAAAATTT
1 AAACTTAAAAAAATTT
898910 AAA-TTCAAAATAAA-TT
1 AAACTT-AAAA-AAATTT
898926 AAACTT--AAAAATTT
1 AAACTTAAAAAAATTT
898940 AAACT
1 AAACT
898945 CGAATTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 3 0.10
14 9 0.29
15 2 0.06
16 12 0.39
17 5 0.16
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (16 bp):
AAACTTAAAAAAATTT
Found at i:899879 original size:28 final size:29
Alignment explanation
Indices: 899848--899903 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
899838 TAAATTTGAA
*
899848 AATAAT-TTTATTTTTCTCTT-AAGTTTTG
1 AATAATATTTATTTCTC-CTTAAAGTTTTG
899876 AATAATACTTTATTTCTCCTTAAAGTTT
1 AATAATA-TTTATTTCTCCTTAAAGTTT
899904 GATACAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 6 0.25
29 3 0.12
30 15 0.62
ACGTcount: A:0.29, C:0.11, G:0.05, T:0.55
Consensus pattern (29 bp):
AATAATATTTATTTCTCCTTAAAGTTTTG
Found at i:900719 original size:25 final size:27
Alignment explanation
Indices: 900691--900757 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 27
900681 TATTATTTTG
900691 TAATTAAAAATATTT-TAAATAA-AAA
1 TAATTAAAAATATTTATAAATAATAAA
* *
900716 TAA-TAAAAA-ATTTATAATTAATAAT
1 TAATTAAAAATATTTATAAATAATAAA
*
900741 TAATAAAAAATATTTAT
1 TAATTAAAAATATTTAT
900758 CTTTTTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
23 4 0.11
24 12 0.34
25 8 0.23
26 5 0.14
27 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
TAATTAAAAATATTTATAAATAATAAA
Found at i:900793 original size:15 final size:16
Alignment explanation
Indices: 900773--900803 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
900763 TATTTAAAAT
900773 TAACTTAAAAA-ATAA
1 TAACTTAAAAAGATAA
900788 TAACTTAAAAAGATAA
1 TAACTTAAAAAGATAA
900804 ATATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (16 bp):
TAACTTAAAAAGATAA
Found at i:900886 original size:28 final size:29
Alignment explanation
Indices: 900795--900899 Score: 92
Period size: 28 Copynumber: 3.6 Consensus size: 29
900785 TAATAACTTA
* *
900795 AAAAGATAAATAT-TTTTTAATCAAATTTT
1 AAAAGATAAATATATTTTT-ATAAAAATTT
* *
900824 AAAGATATAAATAAATATTTTT-TAAATA-TT
1 AAA-AGATAAAT--ATATTTTTATAAAAATTT
*
900854 AAAAAATAAATATATTTTTATAAAAATTT
1 AAAAGATAAATATATTTTTATAAAAATTT
*
900883 AAAA-ATAAATATCTTTT
1 AAAAGATAAATATATTTT
900900 ATTTTTTATA
Statistics
Matches: 63, Mismatches: 7, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
27 8 0.13
28 17 0.27
29 16 0.25
30 12 0.19
31 3 0.05
32 2 0.03
33 5 0.08
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (29 bp):
AAAAGATAAATATATTTTTATAAAAATTT
Found at i:901170 original size:2 final size:2
Alignment explanation
Indices: 901163--901195 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
901153 TTTGTGCATG
901163 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
901196 AACAATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:901316 original size:13 final size:14
Alignment explanation
Indices: 901291--901318 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
901281 TTGTTTTGTG
901291 AAAAATAATTTTTA
1 AAAAATAATTTTTA
901305 AAAAATAATTTTTA
1 AAAAATAATTTTTA
901319 TATTTAGTCA
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAAATAATTTTTA
Found at i:902128 original size:18 final size:18
Alignment explanation
Indices: 902101--902136 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
902091 GTAATAATTT
* *
902101 AATTATAAAATTATAATA
1 AATTAAAAAATTAAAATA
902119 AATTAAAAAATTAAAATA
1 AATTAAAAAATTAAAATA
902137 TAAATTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATTAAAAAATTAAAATA
Found at i:902145 original size:13 final size:13
Alignment explanation
Indices: 902129--902153 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
902119 AATTAAAAAA
902129 TTAAAATATAAAT
1 TTAAAATATAAAT
902142 TTAAAATATAAA
1 TTAAAATATAAA
902154 AATAATAAAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAAAATATAAAT
Found at i:902283 original size:29 final size:27
Alignment explanation
Indices: 902218--902288 Score: 65
Period size: 29 Copynumber: 2.5 Consensus size: 27
902208 TTTTATAAAT
* *
902218 TTTTTAATTTAAATTAAAAAATTATTA
1 TTTTTAATTAAAATTAAAAAATTATAA
902245 TTTTAATAATTAAAATTATGATAAAA-TATAA
1 TTTT--TAATTAAAATTA--A-AAAATTATAA
902276 TTTTTAA-TAAAAT
1 TTTTTAATTAAAAT
902289 AATATTTTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
27 4 0.11
28 6 0.16
29 14 0.38
31 9 0.24
32 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (27 bp):
TTTTTAATTAAAATTAAAAAATTATAA
Found at i:902854 original size:13 final size:14
Alignment explanation
Indices: 902829--902869 Score: 59
Period size: 12 Copynumber: 3.1 Consensus size: 14
902819 ATTAATTTTT
*
902829 TATTTTTAATAAAA
1 TATTTTTTATAAAA
902843 TATTTTTT-T-AAA
1 TATTTTTTATAAAA
902855 TATTTTTTATAAAA
1 TATTTTTTATAAAA
902869 T
1 T
902870 TTAAGTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 11 0.46
13 2 0.08
14 11 0.46
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTTTTTATAAAA
Found at i:904584 original size:20 final size:18
Alignment explanation
Indices: 904561--904602 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
904551 TCAAAAAAAT
*
904561 TAATTTTTTATTTTTATTAA
1 TAATTTATT-TTTTTA-TAA
904581 TAA-TTATTTTTTTATAA
1 TAATTTATTTTTTTATAA
904598 TAATT
1 TAATT
904603 ATAAATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 6 0.30
18 7 0.35
19 4 0.20
20 3 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TAATTTATTTTTTTATAA
Found at i:904591 original size:17 final size:17
Alignment explanation
Indices: 904571--904604 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
904561 TAATTTTTTA
904571 TTTTTATTAATAATTATT
1 TTTTTA-TAATAATTATT
904589 TTTTTATAATAATTAT
1 TTTTTATAATAATTAT
904605 AAATATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTATAATAATTATT
Found at i:906452 original size:2 final size:2
Alignment explanation
Indices: 906445--906488 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
906435 AAACTAGTAT
906445 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
906487 AG
1 AG
906489 TTGGTCTGCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:911947 original size:49 final size:50
Alignment explanation
Indices: 911882--911982 Score: 195
Period size: 49 Copynumber: 2.0 Consensus size: 50
911872 TATTGTGGGA
911882 TGCAGTTCGTATTAACCTTGAGAAATGACATGCCAAGTTCTCTGGGAATT
1 TGCAGTTCGTATTAACCTTGAGAAATGACATGCCAAGTTCTCTGGGAATT
911932 TGCA-TTCGTATTAACCTTGAGAAATGACATGCCAAGTTCTCTGGGAATT
1 TGCAGTTCGTATTAACCTTGAGAAATGACATGCCAAGTTCTCTGGGAATT
911981 TG
1 TG
911983 TTCCACATAG
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 47 0.92
50 4 0.08
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.33
Consensus pattern (50 bp):
TGCAGTTCGTATTAACCTTGAGAAATGACATGCCAAGTTCTCTGGGAATT
Found at i:913136 original size:33 final size:33
Alignment explanation
Indices: 913093--913165 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
913083 TATCTAAAAG
*
913093 AAGCAATCAAGTTCTGCATTTTGTCAGCTTTCTC
1 AAGC-ATCAAGTTCTGCATTTTGTCAGCTTGCTC
913127 AAGCATCAAGTTCTGCATTTTGTCAGCTTGCTC
1 AAGCATCAAGTTCTGCATTTTGTCAGCTTGCTC
913160 AAGCAT
1 AAGCAT
913166 TTTTTAGATT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 34 0.89
34 4 0.11
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (33 bp):
AAGCATCAAGTTCTGCATTTTGTCAGCTTGCTC
Found at i:913737 original size:47 final size:47
Alignment explanation
Indices: 913672--913765 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 47
913662 TAAACTAACC
*
913672 TATAAAATAAAATAAAACTTTTATTTGTTAGAATATCAAACTAAATA
1 TATAAAATAAAATAAAACTTTTATTCGTTAGAATATCAAACTAAATA
* * *
913719 TATAAAGTAAAACT-AAACTTTTGTTCGTTAGAATATCAAAGTAAATA
1 TATAAAATAAAA-TAAAACTTTTATTCGTTAGAATATCAAACTAAATA
913766 GTAAATAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
47 41 0.98
48 1 0.02
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.35
Consensus pattern (47 bp):
TATAAAATAAAATAAAACTTTTATTCGTTAGAATATCAAACTAAATA
Found at i:914382 original size:22 final size:22
Alignment explanation
Indices: 914357--914398 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
914347 TATCTAAAAA
914357 ATATTTTTAT-ATTAATATTTAT
1 ATATTTTTATAATTAA-ATTTAT
914379 ATATTTTTATAATTAAATTT
1 ATATTTTTATAATTAAATTT
914399 TAAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATATTTTTATAATTAAATTTAT
Found at i:914929 original size:16 final size:16
Alignment explanation
Indices: 914897--914928 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
914887 TTAAAAATAT
914897 ATTTAAAATAATAAAA
1 ATTTAAAATAATAAAA
914913 ATTTAAAAT-ATAAAA
1 ATTTAAAATAATAAAA
914928 A
1 A
914929 AAAAGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTTAAAATAATAAAA
Found at i:915797 original size:28 final size:28
Alignment explanation
Indices: 915736--915798 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
915726 GAATATGATT
915736 TAATTT-AAGATTCTTACAATTTGGTCC
1 TAATTTAAAGATTCTTACAATTTGGTCC
915763 -AATTTTAAAGATTCTTGA-AATTTGGTCC
1 TAA-TTTAAAGATTCTT-ACAATTTGGTCC
915791 TAATTTAA
1 TAATTTAA
915799 GAATTATTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
26 2 0.06
27 3 0.09
28 24 0.75
29 3 0.09
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (28 bp):
TAATTTAAAGATTCTTACAATTTGGTCC
Found at i:915808 original size:28 final size:29
Alignment explanation
Indices: 915736--915808 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 29
915726 GAATATGATT
915736 TAATTTAAG-ATTCTT-ACAATTTGGTCC
1 TAATTTAAGAATTCTTGACAATTTGGTCC
915763 -AATTTTAA-AGATTCTTGA-AATTTGGTCC
1 TAA-TTTAAGA-ATTCTTGACAATTTGGTCC
*
915791 TAATTTAAGAATTATTGA
1 TAATTTAAGAATTCTTGA
915809 TTCTTCAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
26 2 0.05
27 5 0.13
28 28 0.72
29 4 0.10
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (29 bp):
TAATTTAAGAATTCTTGACAATTTGGTCC
Found at i:916388 original size:20 final size:20
Alignment explanation
Indices: 916360--916401 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
916350 TGAGTTGAAC
*
916360 AATTTATTTAA-ATCTTAAAA
1 AATTCATTTAATAT-TTAAAA
916380 AATTCATTTAATATTTAAAA
1 AATTCATTTAATATTTAAAA
916400 AA
1 AA
916402 ACTTGAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (20 bp):
AATTCATTTAATATTTAAAA
Found at i:917179 original size:2 final size:2
Alignment explanation
Indices: 917172--917217 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
917162 CGTTCTACTA
* *
917172 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
917214 AT AT
1 AT AT
917218 TTAAATCAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:917517 original size:21 final size:21
Alignment explanation
Indices: 917493--917532 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
917483 TTAGATGAAA
* *
917493 ATTTTTTATTTATATAATTTC
1 ATTTTTTAATTAAATAATTTC
917514 ATTTTTTAATTAAATAATT
1 ATTTTTTAATTAAATAATT
917533 GCATAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTTAATTAAATAATTTC
Found at i:917880 original size:9 final size:9
Alignment explanation
Indices: 917866--917901 Score: 56
Period size: 10 Copynumber: 4.0 Consensus size: 9
917856 GAGCCATTGA
917866 TAAAAAAAT
1 TAAAAAAAT
917875 TAAAAAAAAT
1 T-AAAAAAAT
917885 T-AAAAAAT
1 TAAAAAAAT
917893 TAAAAAAAT
1 TAAAAAAAT
917902 GTGGTCAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.32
9 8 0.32
10 9 0.36
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:920003 original size:12 final size:12
Alignment explanation
Indices: 919973--920006 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
919963 TTAATTATTT
919973 TTTAATATTATA
1 TTTAATATTATA
*
919985 TTT-ATATTATG
1 TTTAATATTATA
919996 TTTAATATTAT
1 TTTAATATTAT
920007 CAAGTCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (12 bp):
TTTAATATTATA
Found at i:922666 original size:4 final size:4
Alignment explanation
Indices: 922657--922686 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
922647 ACATGAGCAA
922657 TTAT TTAT TTAT TTAT TTAT TTAT TT-T TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
922687 CTTTTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:923833 original size:26 final size:26
Alignment explanation
Indices: 923804--923908 Score: 74
Period size: 27 Copynumber: 4.0 Consensus size: 26
923794 AAAAATTTAT
923804 TTTATTATTTAAA-ATATATTAAAATA
1 TTTATTATTTAAATATA-ATTAAAATA
* * *
923830 TTTAATTTTTTATAT-TAATATTAACAT-
1 TTT-ATTATTTAAATAT-A-ATTAAAATA
* *
923857 TTTA-TATTTAAATATAAATAAAAAA
1 TTTATTATTTAAATATAATTAAAATA
* *
923882 TTTTATTAATTAAATATAATTTAAATA
1 -TTTATTATTTAAATATAATTAAAATA
923909 CAATCAAGTT
Statistics
Matches: 60, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
24 5 0.08
25 8 0.13
26 9 0.15
27 29 0.48
28 9 0.15
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTATTATTTAAATATAATTAAAATA
Found at i:923833 original size:31 final size:32
Alignment explanation
Indices: 923787--923847 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 32
923777 CAAGTGTGTT
923787 TATATTCAAAAATTT-ATTTTATTAT-TTAAAA
1 TATATTCAAAAATTTAATTTT-TTATATTAAAA
923818 TATATT-AAAATATTTAATTTTTTATATTAA
1 TATATTCAAAA-ATTTAATTTTTTATATTAA
923848 TATTAACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 4 0.15
31 14 0.52
32 9 0.33
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (32 bp):
TATATTCAAAAATTTAATTTTTTATATTAAAA
Found at i:923853 original size:19 final size:20
Alignment explanation
Indices: 923826--923864 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
923816 AATATATTAA
**
923826 AATATTTAATTTTTTATATT
1 AATATTTAACATTTTATATT
923846 AATA-TTAACATTTTATATT
1 AATATTTAACATTTTATATT
923865 TAAATATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
AATATTTAACATTTTATATT
Found at i:925174 original size:3 final size:3
Alignment explanation
Indices: 925168--925255 Score: 149
Period size: 3 Copynumber: 29.3 Consensus size: 3
925158 GAAACTACTT
* *
925168 TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
925216 TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
925256 GGTGCTAAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:925606 original size:7 final size:7
Alignment explanation
Indices: 925594--925627 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
925584 AAATAAAAAA
925594 AAAGAAC
1 AAAGAAC
925601 AAAGAAC
1 AAAGAAC
925608 AAAGAAC
1 AAAGAAC
925615 AAAGAAC
1 AAAGAAC
925622 AAAGAA
1 AAAGAA
925628 TCTTTATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.74, C:0.12, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAGAAC
Found at i:928901 original size:15 final size:14
Alignment explanation
Indices: 928881--928935 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
928871 TTTATTTATT
928881 TATTTTTATTCATAA
1 TATTTTT-TTCATAA
*
928896 TATTTTTTTAATAAA
1 TATTTTTTTCAT-AA
*
928911 GTGTTTTTTTTCATAA
1 -T-ATTTTTTTCATAA
928927 TATTTTTTT
1 TATTTTTTT
928936 TAGTATGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
14 11 0.33
15 10 0.30
16 3 0.09
17 9 0.27
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (14 bp):
TATTTTTTTCATAA
Found at i:928905 original size:17 final size:17
Alignment explanation
Indices: 928883--928935 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
928873 TATTTATTTA
928883 TTTTTATTCATAATATT
1 TTTTTATTCATAATATT
928900 TTTTTA---ATAA-AGTGT
1 TTTTTATTCATAATA-T-T
928915 TTTTT-TTCATAATATT
1 TTTTTATTCATAATATT
928931 TTTTT
1 TTTTT
928936 TAGTATGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 13
0.70 0.00 0.30
Matches are distributed among these distances:
13 1 0.03
14 5 0.17
15 6 0.20
16 6 0.20
17 11 0.37
18 1 0.03
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (17 bp):
TTTTTATTCATAATATT
Found at i:928936 original size:15 final size:15
Alignment explanation
Indices: 928881--928936 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
928871 TTTATTTATT
*
928881 TATTTTTATTCATAA
1 TATTTTTTTTCATAA
*
928896 TA-TTTTTTTAATAAA
1 TATTTTTTTTCAT-AA
*
928911 GTGTTTTTTTTCATAA
1 -TATTTTTTTTCATAA
928927 TATTTTTTTT
1 TATTTTTTTT
928937 AGTATGTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
14 8 0.24
15 13 0.39
16 3 0.09
17 9 0.27
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.66
Consensus pattern (15 bp):
TATTTTTTTTCATAA
Found at i:934130 original size:29 final size:25
Alignment explanation
Indices: 934074--934132 Score: 64
Period size: 29 Copynumber: 2.2 Consensus size: 25
934064 TCAAGTTTTG
*
934074 TATAATTTATTTTTAAATTATTTAA
1 TATAATTTATTTTTAAATTATATAA
*
934099 TATATATTTATATTTATATAATTATATCA
1 TATA-ATTTAT-TTT-TA-AATTATATAA
934128 TATAA
1 TATAA
934133 ATATAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 4 0.14
26 6 0.21
27 3 0.11
28 3 0.11
29 12 0.43
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TATAATTTATTTTTAAATTATATAA
Found at i:935591 original size:18 final size:17
Alignment explanation
Indices: 935568--935602 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
935558 GAGATATTAA
935568 TAATAAAAATTAAAATAC
1 TAAT-AAAATTAAAATAC
*
935586 TAATAAATTTAAAATAC
1 TAATAAAATTAAAATAC
935603 ATTAGTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
TAATAAAATTAAAATAC
Found at i:936273 original size:17 final size:15
Alignment explanation
Indices: 936250--936295 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 15
936240 TTAATTTATT
936250 TATTTTTAAAATATAA
1 TATTTTTAAAATAT-A
*
936266 TAATTTTTAAAAAATA
1 T-ATTTTTAAAATATA
*
936282 TATTTTTAATATAT
1 TATTTTTAAAATAT
936296 TTAAATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 11 0.42
16 3 0.12
17 12 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTTTAAAATATA
Found at i:939249 original size:17 final size:17
Alignment explanation
Indices: 939215--939266 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
939205 AGTCAGATAA
* *
939215 TTTAGTTAAATGTATATT
1 TTTA-TTAAATATTTATT
939233 TTTATTAAATATTTA-T
1 TTTATTAAATATTTATT
* *
939249 TATATTTAATATTTATT
1 TTTATTAAATATTTATT
939266 T
1 T
939267 AGTATTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 14 0.48
17 11 0.38
18 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (17 bp):
TTTATTAAATATTTATT
Found at i:940625 original size:25 final size:25
Alignment explanation
Indices: 940570--940625 Score: 105
Period size: 24 Copynumber: 2.3 Consensus size: 25
940560 TAAAAGTCTA
940570 TTGTTTTGCCAATAATTTTCTTTTT
1 TTGTTTTGCCAATAATTTTCTTTTT
940595 TT-TTTTGCCAATAATTTTCTTTTT
1 TTGTTTTGCCAATAATTTTCTTTTT
940619 TTGTTTT
1 TTGTTTT
940626 TGTTTAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 24 0.80
25 6 0.20
ACGTcount: A:0.14, C:0.11, G:0.07, T:0.68
Consensus pattern (25 bp):
TTGTTTTGCCAATAATTTTCTTTTT
Found at i:941444 original size:23 final size:23
Alignment explanation
Indices: 941418--941464 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
941408 CCTTAATCAA
941418 TATCATTTCACACGAATTAACAT
1 TATCATTTCACACGAATTAACAT
*
941441 TATCATTTGACACGAATTAACAT
1 TATCATTTCACACGAATTAACAT
941464 T
1 T
941465 CCCCTTTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.36
Consensus pattern (23 bp):
TATCATTTCACACGAATTAACAT
Found at i:943528 original size:23 final size:23
Alignment explanation
Indices: 943502--943556 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
943492 GAACATGGTG
*
943502 GTAATGGTAAGACGGCATTATCA
1 GTAATGGCAAGACGGCATTATCA
*
943525 GTAATGGCAAGATGGCATTATCA
1 GTAATGGCAAGACGGCATTATCA
943548 GTAATGGCA
1 GTAATGGCA
943557 TGTCTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.27, T:0.25
Consensus pattern (23 bp):
GTAATGGCAAGACGGCATTATCA
Found at i:948386 original size:4 final size:4
Alignment explanation
Indices: 948377--948401 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
948367 TAAAAAAATA
948377 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
948402 TCTTCAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:950461 original size:20 final size:18
Alignment explanation
Indices: 950415--950452 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
950405 TTCTCTCTTA
*
950415 TTTTCTTGTTACTTTTTT
1 TTTTCTTATTACTTTTTT
950433 TTTTCTTATTACTTTTTT
1 TTTTCTTATTACTTTTTT
950451 TT
1 TT
950453 CTTTCTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTCTTATTACTTTTTT
Found at i:953382 original size:2 final size:2
Alignment explanation
Indices: 953375--953403 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
953365 TTACATGTTA
953375 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
953404 ACAATGTGGA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:955817 original size:25 final size:27
Alignment explanation
Indices: 955773--955824 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
955763 GCAATTAATC
*
955773 TTTATTTTTATAAAATAAAAAATCTAT
1 TTTATTTTTATAAAATAAAAAAACTAT
*
955800 TTTA-TTTT-TAAATTAAAAAAACTAT
1 TTTATTTTTATAAAATAAAAAAACTAT
955825 AAAAATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 15 0.65
26 4 0.17
27 4 0.17
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (27 bp):
TTTATTTTTATAAAATAAAAAAACTAT
Found at i:956125 original size:17 final size:17
Alignment explanation
Indices: 956105--956184 Score: 60
Period size: 17 Copynumber: 4.8 Consensus size: 17
956095 TATTACAGAG
*
956105 ATTCATGAATTATTGAT
1 ATTCATGAATTATTGAA
956122 ATTCAT-ATATTA-TGAA
1 ATTCATGA-ATTATTGAA
* *
956138 GATTCATAAATTA-TAAA
1 -ATTCATGAATTATTGAA
*
956155 CATTCATGTATTA-TGAA
1 -ATTCATGAATTATTGAA
*
956172 ATTCATGCATTAT
1 ATTCATGAATTAT
956185 AGACATTCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
16 15 0.29
17 36 0.69
18 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (17 bp):
ATTCATGAATTATTGAA
Found at i:956141 original size:34 final size:34
Alignment explanation
Indices: 956103--956218 Score: 126
Period size: 34 Copynumber: 3.4 Consensus size: 34
956093 TGTATTACAG
* *
956103 AGATTCATGAATTATTGATATTCATATATTATGA
1 AGATTCATGAATTATAGACATTCATATATTATGA
* * *
956137 AGATTCATAAATTATAAACATTCATGTATTATGA
1 AGATTCATGAATTATAGACATTCATATATTATGA
* * * ** *
956171 A-ATTCATGCATTATAGACATTCTTGTAGCATAA
1 AGATTCATGAATTATAGACATTCATATATTATGA
956204 AGATTCATGAATTAT
1 AGATTCATGAATTAT
956219 GAATATTAAT
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
33 26 0.38
34 42 0.62
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (34 bp):
AGATTCATGAATTATAGACATTCATATATTATGA
Found at i:956288 original size:17 final size:17
Alignment explanation
Indices: 956261--956293 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
956251 ATTACGAGAA
956261 AGTTATATTAACATATTT
1 AGTTATATTAA-ATATTT
956279 AGTT-TATTAAATATT
1 AGTTATATTAAATATT
956294 ATATTAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (17 bp):
AGTTATATTAAATATTT
Found at i:956799 original size:15 final size:14
Alignment explanation
Indices: 956774--956813 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
956764 TATAACATAC
956774 TAATTATAAAAATT
1 TAATTATAAAAATT
956788 TAATTAATAAAAATT
1 TAATT-ATAAAAATT
956803 TAATT-TAAAAA
1 TAATTATAAAAA
956814 AAAGGTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.24
14 5 0.20
15 14 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATTATAAAAATT
Found at i:962255 original size:22 final size:23
Alignment explanation
Indices: 962229--962272 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
962219 ATGTCTAATT
962229 AAAATAAAAAATTAA-TAAAATA
1 AAAATAAAAAATTAATTAAAATA
**
962251 AAAATAATTAATTAATTAAAAT
1 AAAATAAAAAATTAATTAAAAT
962273 TAATTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
AAAATAAAAAATTAATTAAAATA
Found at i:962281 original size:18 final size:18
Alignment explanation
Indices: 962224--962281 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
962214 TATTTATGTC
962224 TAATTAAA-ATAAAA-AAT
1 TAATTAAATA-AAAATAAT
*
962241 TAATAAAATAAAAATAAT
1 TAATTAAATAAAAATAAT
* *
962259 TAATTAATTAAAATTAAT
1 TAATTAAATAAAAATAAT
962277 TAATT
1 TAATT
962282 TTACACTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 11 0.31
18 24 0.69
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATTAAATAAAAATAAT
Found at i:962689 original size:2 final size:2
Alignment explanation
Indices: 962682--962724 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
962672 CAAAGGTAAG
962682 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
962724 T
1 T
962725 TACTAGATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:963214 original size:28 final size:27
Alignment explanation
Indices: 963159--963215 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
963149 ATATTTATCG
* *
963159 TTCATAATATTTATTCAATATTTGATT
1 TTCATAATATTTATTCAAAATTTAATT
963186 TTCATTAATATTTATT-AAAATTTAAATT
1 TTCA-TAATATTTATTCAAAATTT-AATT
963214 TT
1 TT
963216 TTGATTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (27 bp):
TTCATAATATTTATTCAAAATTTAATT
Found at i:964688 original size:2 final size:2
Alignment explanation
Indices: 964681--964731 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
964671 GAAAACTGAA
964681 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
964723 AT AT AT AT A
1 AT AT AT AT A
964732 AAGGAGATGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:966761 original size:166 final size:164
Alignment explanation
Indices: 966551--966887 Score: 622
Period size: 166 Copynumber: 2.0 Consensus size: 164
966541 GAATGAAAAT
966551 AAAATATTGATAAATAATTATGACATCAATAAATTTTATTATTATTTCTTTTA-ACAAAAAACAA
1 AAAATATTGATAAATAATTATGACATCAATAAATTTTATTATTATTTCTTTTATA-AAAAAACAA
966615 TAATTAATAACTTTTAAACAATTAAAAGCTTGATAAGAGGTTATATAAAATAAAACCTCGGAAAA
65 TAATTAATAACTTTTAAACAATTAAAAGCTTGATAAGAGGTTATATAAAATAAAACCTCGGAAAA
*
966680 AAGGGAAAGTTACATCTACAATTAATTTAATATGC
130 AAAGGAAAGTTACATCTACAATTAATTTAATATGC
*
966715 AAAATATTGATAAATGATTATGAATCATCAATAAATTTTATTATTATTTCTTTTATAAAAAAACA
1 AAAATATTGATAAATAATTATG-A-CATCAATAAATTTTATTATTATTTCTTTTATAAAAAAACA
966780 ATAATTAATAACTTTTAAACAATTAAAAGCTTGATAAGAGGTTATATAAAATAAAACCTCGGAAA
64 ATAATTAATAACTTTTAAACAATTAAAAGCTTGATAAGAGGTTATATAAAATAAAACCTCGGAAA
966845 AAAAGGAAAGTTACATCTACAATTAATTTAATATGC
129 AAAAGGAAAGTTACATCTACAATTAATTTAATATGC
966881 AAAATAT
1 AAAATAT
966888 AGCAACTAAA
Statistics
Matches: 168, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
164 21 0.12
165 1 0.01
166 145 0.86
167 1 0.01
ACGTcount: A:0.49, C:0.09, G:0.08, T:0.34
Consensus pattern (164 bp):
AAAATATTGATAAATAATTATGACATCAATAAATTTTATTATTATTTCTTTTATAAAAAAACAAT
AATTAATAACTTTTAAACAATTAAAAGCTTGATAAGAGGTTATATAAAATAAAACCTCGGAAAAA
AAGGAAAGTTACATCTACAATTAATTTAATATGC
Found at i:967612 original size:17 final size:17
Alignment explanation
Indices: 967594--967627 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
967584 AATTTTTTAA
967594 TTTATAATTAAATAAAAT
1 TTTAT-ATTAAATAAAAT
*
967612 TTTATTTTAAATAAAA
1 TTTATATTAAATAAAA
967628 ATAAATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTATATTAAATAAAAT
Found at i:967614 original size:23 final size:23
Alignment explanation
Indices: 967572--967620 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
967562 TATATTTTCG
* **
967572 TTATATTTAAATAATTTTTTAAT
1 TTATAATTAAATAAAATTTTAAT
*
967595 TTATAATTAAATAAAATTTTATT
1 TTATAATTAAATAAAATTTTAAT
967618 TTA
1 TTA
967621 AATAAAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTATAATTAAATAAAATTTTAAT
Found at i:967635 original size:17 final size:17
Alignment explanation
Indices: 967601--967659 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 17
967591 TAATTTATAA
* **
967601 TTAAATAAAATTTTATT
1 TTAAATAAAAATAAATT
967618 TTAAATAAAAATAAA-T
1 TTAAATAAAAATAAATT
**
967634 TTATGTAAAAATAAATT
1 TTAAATAAAAATAAATT
*
967651 ATAAA-AAAA
1 TTAAATAAAA
967660 TTGTCAGTGG
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
16 18 0.55
17 15 0.45
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
TTAAATAAAAATAAATT
Found at i:968207 original size:2 final size:2
Alignment explanation
Indices: 968200--968234 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
968190 GCAATTTCTT
*
968200 TA TA TA TA TA CA 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 T
968235 CCCCCATGCG
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:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:969029 original size:79 final size:78
Alignment explanation
Indices: 968880--969027 Score: 246
Period size: 79 Copynumber: 1.9 Consensus size: 78
968870 TTTAATATGC
968880 TACAATCATATAGGTAACTTAATAAAGTATAAATATTTGGATATTGTAAAAAAAATATATACTTT
1 TACAATCATATAGGTAACTTAATAAAGTATAAATATTTGGATATTG-AAAAAAAATATATACTTT
*
968945 TAAAAAATTACTTT
65 AAAAAAATTACTTT
* *
968959 TACAGTCATATATGTAACTTAATAAAGTATAAATATTTGGATATTG-AAAAAAA-ATATACTTTA
1 TACAATCATATAGGTAACTTAATAAAGTATAAATATTTGGATATTGAAAAAAAATATATACTTTA
969022 AAAAAA
66 AAAAAA
969028 AACTATTTTG
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
76 15 0.23
77 7 0.11
79 44 0.67
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (78 bp):
TACAATCATATAGGTAACTTAATAAAGTATAAATATTTGGATATTGAAAAAAAATATATACTTTA
AAAAAATTACTTT
Found at i:969975 original size:21 final size:21
Alignment explanation
Indices: 969951--969997 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
969941 TTCTAATAAG
*
969951 ATTTTAA-AAATATTTGATATA
1 ATTTTAACAAAT-TTTAATATA
*
969972 ATTTTAACAACTTTTAATATA
1 ATTTTAACAAATTTTAATATA
969993 ATTTT
1 ATTTT
969998 GGTAGCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTTTAACAAATTTTAATATA
Found at i:970064 original size:20 final size:20
Alignment explanation
Indices: 970041--970094 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
970031 CACAATTTTA
**
970041 TAACTTTTTTTATAATTTGG
1 TAACTTTTAATATAATTTGG
*
970061 TAACTTTTAATATAATTTGA
1 TAACTTTTAATATAATTTGG
* *
970081 TAAATTTTGATATA
1 TAACTTTTAATATA
970095 CTTTTGATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (20 bp):
TAACTTTTAATATAATTTGG
Found at i:970268 original size:21 final size:19
Alignment explanation
Indices: 970244--970308 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 19
970234 TATAATTTTG
970244 ATTTTAGTAATTTTTTATATA
1 ATTTT-GTAA-TTTTTATATA
**
970265 ATTTTGGTAACCTTTA-ATA
1 ATTTT-GTAATTTTTATATA
*
970284 ATTTTGATAACTTTTAATATA
1 ATTTTG-TAA-TTTTTATATA
970305 ATTT
1 ATTT
970309 GATAATATTC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.03
19 11 0.31
20 7 0.20
21 16 0.46
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.55
Consensus pattern (19 bp):
ATTTTGTAATTTTTATATA
Found at i:970286 original size:19 final size:19
Alignment explanation
Indices: 970257--970313 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
970247 TTAGTAATTT
*
970257 TTTATATAATTTTGGTAACC
1 TTTA-ATAATTTTGATAACC
*
970277 TTTAATAATTTTGATAACT
1 TTTAATAATTTTGATAACC
*
970296 TTTAATATAATTTGATAA
1 TTTAATA-ATTTTGATAA
970314 TATTCGATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (19 bp):
TTTAATAATTTTGATAACC
Found at i:970399 original size:24 final size:22
Alignment explanation
Indices: 970358--970433 Score: 91
Period size: 24 Copynumber: 3.4 Consensus size: 22
970348 ATAACTTTTG
970358 ATATTATTTTAGTAAACTTTGAA
1 ATATT-TTTTAGTAAACTTTGAA
970381 ATAGTTTTTCTAGTAAACTTTGAA
1 ATA-TTTTT-TAGTAAACTTTGAA
* *
970405 ATA-ATTTTAATAAACTTTGAA
1 ATATTTTTTAGTAAACTTTGAA
*
970426 ATAATTTT
1 ATATTTTT
970434 AATAACCTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
21 16 0.34
22 6 0.13
23 6 0.13
24 19 0.40
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (22 bp):
ATATTTTTTAGTAAACTTTGAA
Found at i:970435 original size:21 final size:21
Alignment explanation
Indices: 970339--970438 Score: 103
Period size: 21 Copynumber: 4.6 Consensus size: 21
970329 TTGTAAAATT
* *
970339 ATAATTTTTAT-AACTTTTGAT
1 ATAATTTTAATAAAC-TTTGAA
* *
970360 ATTATTTTAGTAAACTTTGAA
1 ATAATTTTAATAAACTTTGAA
* *
970381 ATAGTTTTTCTAGTAAACTTTGAA
1 ATA--ATTT-TAATAAACTTTGAA
970405 ATAATTTTAATAAACTTTGAA
1 ATAATTTTAATAAACTTTGAA
970426 ATAATTTTAATAA
1 ATAATTTTAATAA
970439 CCTTCAATAT
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
21 41 0.61
22 6 0.09
23 3 0.04
24 17 0.25
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (21 bp):
ATAATTTTAATAAACTTTGAA
Found at i:970535 original size:21 final size:21
Alignment explanation
Indices: 970399--970731 Score: 118
Period size: 21 Copynumber: 16.1 Consensus size: 21
970389 TCTAGTAAAC
*
970399 TTTGAAATAATTTTAATAA-A
1 TTTGATATAATTTTAATAATA
* **
970419 CTTTGAAATAATTTTAATAACC
1 -TTTGATATAATTTTAATAATA
** **
970441 TTCAATATAATTTCGATAAT-
1 TTTGATATAATTTTAATAATA
** * *
970461 TTAAAATATATTTTTAATTAGT-
1 TT-TGATATAATTTTAA-TAATA
* * *
970483 TTTGATATAATTTTGATGATC
1 TTTGATATAATTTTAATAATA
* * *
970504 TTCAGA-GTAATTTTGATAATA
1 TT-TGATATAATTTTAATAATA
*
970525 TTTGATATAATTTTAGTAACT-
1 TTTGATATAATTTTAATAA-TA
* * * * *
970546 TTTTAAATAATTATAA-ATTTT
1 TTTGATATAATTTTAATA-ATA
* *
970567 TTTGTTATAATTTTAATAGCT-
1 TTTGATATAATTTTAATA-ATA
* * * *
970588 TTTGACATGATTTTGATAGTA
1 TTTGATATAATTTTAATAATA
* *
970609 TTCGATATAATTTTAATAACA
1 TTTGATATAATTTTAATAATA
* *
970630 TGT-A-ATAATTTTAATACCTA
1 TTTGATATAATTTTAATA-ATA
* * * *
970650 --TAACATAATTTTTATAATT
1 TTTGATATAATTTTAATAATA
*
970669 TTTAATATAATTTTAATAATA
1 TTTGATATAATTTTAATAATA
* *
970690 TTT-TTATAA-TTTAATAATT
1 TTTGATATAATTTTAATAATA
*
970709 TTTAATATAATTTTAATAA-A
1 TTTGATATAATTTTAATAATA
970729 TTT
1 TTT
970732 TTATAATAAA
Statistics
Matches: 232, Mismatches: 62, Indels: 37
0.70 0.19 0.11
Matches are distributed among these distances:
18 1 0.00
19 26 0.11
20 35 0.15
21 160 0.69
22 10 0.04
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.50
Consensus pattern (21 bp):
TTTGATATAATTTTAATAATA
Found at i:970644 original size:9 final size:9
Alignment explanation
Indices: 970615--970738 Score: 61
Period size: 10 Copynumber: 12.6 Consensus size: 9
970605 AGTATTCGAT
970615 ATAATTTTA
1 ATAATTTTA
* *
970624 ATAACATGTA
1 ATAA-TTTTA
970634 ATAATTTTA
1 ATAATTTTA
* * *
970643 ATACCTATAA
1 ATA-ATTTTA
*
970653 CATAATTTTT
1 -ATAATTTTA
970663 ATAATTTTTAA
1 ATAA-TTTT-A
970674 TATAATTTTA
1 -ATAATTTTA
*
970684 ATAATATTTTT
1 AT-A-ATTTTA
970695 ATAA-TTTA
1 ATAATTTTA
970703 ATAATTTTTAA
1 ATAA-TTTT-A
970714 TATAATTTTA
1 -ATAATTTTA
*
970724 ATAAATTTTT
1 AT-AATTTTA
970734 ATAAT
1 ATAAT
970739 AAAATTTAAA
Statistics
Matches: 87, Mismatches: 15, Indels: 26
0.68 0.12 0.20
Matches are distributed among these distances:
8 7 0.08
9 22 0.25
10 31 0.36
11 19 0.22
12 8 0.09
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (9 bp):
ATAATTTTA
Found at i:970679 original size:12 final size:12
Alignment explanation
Indices: 970662--970734 Score: 71
Period size: 11 Copynumber: 5.9 Consensus size: 12
970652 ACATAATTTT
970662 TATAATTTTTAA
1 TATAATTTTTAA
970674 TATAA-TTTTAA
1 TATAATTTTTAA
*
970685 TAATATTTTTATAA
1 T-ATAATTTT-TAA
970699 TTTAATAATTTTTAA
1 --T-ATAATTTTTAA
970714 TATAA-TTTTAA
1 TATAATTTTTAA
970725 TA-AATTTTTA
1 TATAATTTTTA
970735 TAATAAAATT
Statistics
Matches: 53, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
10 2 0.04
11 20 0.38
12 12 0.23
13 4 0.08
14 3 0.06
15 3 0.06
16 9 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATAATTTTTAA
Found at i:970684 original size:11 final size:11
Alignment explanation
Indices: 970654--970754 Score: 76
Period size: 10 Copynumber: 9.6 Consensus size: 11
970644 TACCTATAAC
970654 ATAATTTT--T
1 ATAATTTTAAT
970663 ATAATTTTTAAT
1 ATAA-TTTTAAT
970675 ATAATTTTAAT
1 ATAATTTTAAT
970686 A-ATATTTT--T
1 ATA-ATTTTAAT
970695 ATAA-TTTAAT
1 ATAATTTTAAT
*
970705 A-ATTTTTAAT
1 ATAATTTTAAT
970715 ATAATTTTAAT
1 ATAATTTTAAT
*
970726 A-AATTTTTAT
1 ATAATTTTAAT
*
970736 AATAAAATTTAA-
1 -AT-AATTTTAAT
970748 ATAATTT
1 ATAATTT
970755 AGTTACATAA
Statistics
Matches: 74, Mismatches: 6, Indels: 23
0.72 0.06 0.22
Matches are distributed among these distances:
8 3 0.04
9 8 0.11
10 27 0.36
11 25 0.34
12 5 0.07
13 6 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATAATTTTAAT
Found at i:970718 original size:40 final size:39
Alignment explanation
Indices: 970654--970738 Score: 143
Period size: 40 Copynumber: 2.1 Consensus size: 39
970644 TACCTATAAC
*
970654 ATAATTTTTATAATTTTTAATATAATTTTAATAATATTTTT
1 ATAA-TTTAATAATTTTTAATATAATTTTAATAA-ATTTTT
970695 ATAATTTAATAATTTTTAATATAATTTTAATAAATTTTT
1 ATAATTTAATAATTTTTAATATAATTTTAATAAATTTTT
970734 ATAAT
1 ATAAT
970739 AAAATTTAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
39 11 0.26
40 28 0.65
41 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (39 bp):
ATAATTTAATAATTTTTAATATAATTTTAATAAATTTTT
Found at i:970744 original size:24 final size:22
Alignment explanation
Indices: 970656--970751 Score: 87
Period size: 24 Copynumber: 4.5 Consensus size: 22
970646 CCTATAACAT
* *
970656 AATTTTTAT-AATTTTTAATAT
1 AATTTTAATAAATTTTTAATAA
970677 AATTTTAATAATATTTTT-AT--
1 AATTTTAATAA-ATTTTTAATAA
*
970697 AA-TTTAAT-AATTTTTAATAT
1 AATTTTAATAAATTTTTAATAA
970717 AATTTTAATAAATTTTTATAATAA
1 AATTTTAATAAA-TTTT-TAATAA
*
970741 AATTTAAATAA
1 AATTTTAATAA
970752 TTTAGTTACA
Statistics
Matches: 63, Mismatches: 3, Indels: 15
0.78 0.04 0.19
Matches are distributed among these distances:
17 6 0.10
18 3 0.05
19 6 0.10
20 4 0.06
21 14 0.22
22 5 0.08
23 10 0.16
24 15 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTTTAATAAATTTTTAATAA
Found at i:973797 original size:2 final size:2
Alignment explanation
Indices: 973790--973832 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
973780 CTCCTTTATT
973790 TA TA TA 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 TA TA TA
973832 T
1 T
973833 GTCTATGCAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:974245 original size:17 final size:17
Alignment explanation
Indices: 974223--974256 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
974213 AATAATCTCT
*
974223 TATTAAATATTAATTTA
1 TATTAAAAATTAATTTA
*
974240 TATTAAAAATTTATTTA
1 TATTAAAAATTAATTTA
974257 AATATAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTAAAAATTAATTTA
Found at i:978498 original size:2 final size:2
Alignment explanation
Indices: 978491--978520 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
978481 TGTTTCCTTC
*
978491 AT AT AT AT AA 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
978521 TCTGAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:979126 original size:20 final size:21
Alignment explanation
Indices: 979097--979137 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
979087 ATAAAATCTA
*
979097 AATAATTTAG-TTAAGTTTAC
1 AATAAATTAGATTAAGTTTAC
*
979117 AATAAATTAGATTAATTTTAC
1 AATAAATTAGATTAAGTTTAC
979138 TTAAACTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (21 bp):
AATAAATTAGATTAAGTTTAC
Found at i:982830 original size:25 final size:26
Alignment explanation
Indices: 982802--982869 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 26
982792 CATTTTGAAT
*
982802 TTTAAATAAATTAAAATATTTAAT-A
1 TTTAAATAAATTAAAAAATTTAATCA
** *
982827 TTTATTTAATATAAAAAAATTTAATCA
1 TTTAAATAA-ATTAAAAAATTTAATCA
*
982854 -TTAAATATATTAAAAA
1 TTTAAATAAATTAAAAA
982870 TAATAATATT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
25 14 0.42
26 18 0.55
27 1 0.03
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (26 bp):
TTTAAATAAATTAAAAAATTTAATCA
Found at i:983231 original size:13 final size:13
Alignment explanation
Indices: 983210--983242 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
983200 TGCTTGTGAG
*
983210 ATTTTTTATTATT
1 ATTTATTATTATT
983223 ATTTATTATTATT
1 ATTTATTATTATT
983236 A-TTATTA
1 ATTTATTA
983243 ATGTATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
ATTTATTATTATT
Found at i:992513 original size:28 final size:28
Alignment explanation
Indices: 992473--992527 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
992463 ATAATAAATG
992473 ACAATTTCCATACAGTCCATTTTAACTA
1 ACAATTTCCATACAGTCCATTTTAACTA
*
992501 ACAATTTCTATACAGTCCATTTTAACT
1 ACAATTTCCATACAGTCCATTTTAACT
992528 CACTAGATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.38
Consensus pattern (28 bp):
ACAATTTCCATACAGTCCATTTTAACTA
Done.