Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold206
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: 2736418
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 22040 characters in sequence are not A, C, G, or T
File 5 of 20
Found at i:681936 original size:19 final size:20
Alignment explanation
Indices: 681891--681936 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
681881 AATTAATTTA
681891 AAAT-TTTA-TTTTACTATT
1 AAATATTTATTTTTACTATT
*
681909 AAAGA-TTATTTTTA-TATT
1 AAATATTTATTTTTACTATT
681927 AAATATTTAT
1 AAATATTTAT
681937 AATTAAATTT
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:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
AAATATTTATTTTTACTATT
Found at i:682292 original size:5 final size:5
Alignment explanation
Indices: 682253--682284 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
682243 TAAATAATAA
*
682253 TTAAT TTAAT TTAAT TTAAT TTAAT TTGAT TT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TT
682285 TTAATTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (5 bp):
TTAAT
Found at i:683866 original size:29 final size:30
Alignment explanation
Indices: 683800--683867 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
683790 TTATTTTTAT
*
683800 ATTAATAATATTTTATATTAATTAAATTTAA
1 ATTAA-AATATTTTATATTAATTAAATTAAA
*
683831 ATAAAAATATTTT-TATT-ATTAAATTAATA
1 ATTAAAATATTTTATATTAATTAAATTAA-A
683860 ATTAAAAT
1 ATTAAAAT
683868 TGAGCTACGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 9 0.27
29 12 0.36
30 8 0.24
31 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
ATTAAAATATTTTATATTAATTAAATTAAA
Found at i:683866 original size:30 final size:30
Alignment explanation
Indices: 683795--683866 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
683785 AAAATTTATT
*
683795 TTTATATTAATAATATTTTATATTAATTAAA
1 TTTA-ATTAAAAATATTTTATATTAATTAAA
*
683826 TTTAAATAAAAATATTTT-TATT-ATTAAA
1 TTTAATTAAAAATATTTTATATTAATTAAA
683854 TTAATAATTAAAA
1 TT--TAATTAAAA
683867 TTGAGCTACG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 8 0.22
29 4 0.11
30 20 0.56
31 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
TTTAATTAAAAATATTTTATATTAATTAAA
Found at i:684163 original size:31 final size:28
Alignment explanation
Indices: 684125--684201 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 28
684115 TATTTTAATA
684125 ATTTATATTATATATTTTAAGTTATTTGTAT
1 ATTTATA-T-TATATTTTAA-TTATTTGTAT
*
684156 ATTTATATTATATTTTAATTATTTTTAT
1 ATTTATATTATATTTTAATTATTTGTAT
*
684184 A-ATAT-TTATATTGTTAAT
1 ATTTATATTATATT-TTAAT
684202 CTAGATTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
26 7 0.16
27 8 0.19
28 10 0.23
29 10 0.23
30 1 0.02
31 7 0.16
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (28 bp):
ATTTATATTATATTTTAATTATTTGTAT
Found at i:685433 original size:21 final size:22
Alignment explanation
Indices: 685407--685450 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
685397 AAAATATATT
*
685407 AAAATAATATTTT-TTAAATAA
1 AAAATAATATTTTAATAAATAA
*
685428 AAAATATTATTTTAATAAATAA
1 AAAATAATATTTTAATAAATAA
685450 A
1 A
685451 TAATGATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATAATATTTTAATAAATAA
Found at i:685435 original size:18 final size:18
Alignment explanation
Indices: 685406--685452 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 18
685396 TAAAATATAT
685406 TAAAATAATATT-TTTTAAA
1 TAAAA-AATATTATTTT-AA
685425 TAAAAAATATTATTTTAA
1 TAAAAAATATTATTTTAA
685443 TAAATAAATA
1 TAAA-AAATA
685453 ATGATTCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAAAATATTATTTTAA
Found at i:685451 original size:19 final size:19
Alignment explanation
Indices: 685408--685452 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
685398 AAATATATTA
685408 AAAT-AATATTTTTTAAAT
1 AAATAAATATTTTTTAAAT
685426 AAA-AAATATTATTTT-AAT
1 AAATAAATATT-TTTTAAAT
685444 AAATAAATA
1 AAATAAATA
685453 ATGATTCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATAAATATTTTTTAAAT
Found at i:685771 original size:18 final size:18
Alignment explanation
Indices: 685729--685781 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 18
685719 TTTGACATAT
*
685729 TCATATTTTTTTTATCTATA
1 TCATA-TTTTTATAT-TATA
685749 T--TATTTTTATATTATA
1 TCATATTTTTATATTATA
685765 TCATA-TTTTA-ATTATA
1 TCATATTTTTATATTATA
685781 T
1 T
685782 TTTATATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
16 12 0.40
17 13 0.43
18 4 0.13
20 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (18 bp):
TCATATTTTTATATTATA
Found at i:685893 original size:13 final size:14
Alignment explanation
Indices: 685871--685902 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
685861 GTTTAAAAAA
685871 TAAA-TTTTAT-AT
1 TAAATTTTTATAAT
685883 TAAATTTTTATAAT
1 TAAATTTTTATAAT
685897 TAAATT
1 TAAATT
685903 AAAATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.22
13 6 0.33
14 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAAATTTTTATAAT
Found at i:686508 original size:22 final size:25
Alignment explanation
Indices: 686462--686512 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 25
686452 ATAATTCAAC
686462 AAATTTAATTTTTAAAATAATTATAT
1 AAATTTAA-TTTTAAAATAATTATAT
686488 AAATTTAA-TTT-AAAT-ATTATAT
1 AAATTTAATTTTAAAATAATTATAT
686510 AAA
1 AAA
686513 ATACAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.40
23 4 0.16
24 3 0.12
26 8 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AAATTTAATTTTAAAATAATTATAT
Found at i:693020 original size:6 final size:6
Alignment explanation
Indices: 693009--693038 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
692999 GTTATATGAT
693009 ACTGAC ACTGAC ACTGAC ACTGAC ACTGAC
1 ACTGAC ACTGAC ACTGAC ACTGAC ACTGAC
693039 TGACTCTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17
Consensus pattern (6 bp):
ACTGAC
Found at i:693258 original size:2 final size:2
Alignment explanation
Indices: 693233--693281 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
693223 AAATTATTGG
* * * *
693233 TA TA TA TG TA TG TA T- TA TA CA TA TA TA TC 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
693274 TA TA TA TA
1 TA TA TA TA
693282 GAATTTGAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:693410 original size:19 final size:20
Alignment explanation
Indices: 693388--693429 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
693378 ATTGATAATG
693388 TTTAAAT-A-TATTTATTATA
1 TTTAAATAATTATTT-TTATA
693407 TTT-AATAATTATTTTTATA
1 TTTAAATAATTATTTTTATA
693426 TTTA
1 TTTA
693430 TTTCATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
18 3 0.15
19 12 0.60
20 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTAAATAATTATTTTTATA
Found at i:695364 original size:20 final size:18
Alignment explanation
Indices: 695339--695382 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 18
695329 TATGATCTTT
695339 AAAAAAATTTTAAATACATA
1 AAAAAAATTTTAAA-A-ATA
695359 AAAAAAATTTTAAAAATA
1 AAAAAAATTTTAAAAATA
695377 AAAAAA
1 AAAAAA
695383 TTCATGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 9 0.38
19 1 0.04
20 14 0.58
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAAAAATTTTAAAAATA
Found at i:697380 original size:26 final size:24
Alignment explanation
Indices: 697333--697380 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
697323 AAATTAATCT
*
697333 AATATTTTTTAAAAATTAAATAAA
1 AATATTTTTTAAAAAATAAATAAA
*
697357 AATATTATATTTAAAAAATGAATA
1 AATATT-T-TTTAAAAAATAAATA
697381 TACAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 1 0.05
26 13 0.65
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
AATATTTTTTAAAAAATAAATAAA
Found at i:697533 original size:21 final size:20
Alignment explanation
Indices: 697495--697533 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
697485 ATTATATTTA
* *
697495 TATTTATATATTACATAATT
1 TATTTATATATAAAATAATT
697515 TATTTAGTATATAAAATAA
1 TATTTA-TATATAAAATAA
697534 AAATATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (20 bp):
TATTTATATATAAAATAATT
Found at i:697943 original size:22 final size:22
Alignment explanation
Indices: 697915--697956 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
697905 ATTTAAATAT
697915 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
697937 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
697957 AATAAAAATA
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):
TATTTTTATAATTAAATTTATA
Found at i:698001 original size:2 final size:2
Alignment explanation
Indices: 697994--698023 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
697984 AGTAAAATTA
697994 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
698024 TGTAGCCTTT
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:698110 original size:2 final size:2
Alignment explanation
Indices: 698098--698185 Score: 76
Period size: 2 Copynumber: 45.5 Consensus size: 2
698088 TTCAACAATC
* * *
698098 AT AT A- AT AT AT AT AT AT AG AT AT AT GT -T AA 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
* * * *
698138 AT AT AT AT AT AT AT AT -T A- AA AA AT GAT AA AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
698179 AT AT AT A
1 AT AT AT A
698186 AACACTTAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
1 4 0.06
2 65 0.92
3 2 0.03
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:698141 original size:31 final size:30
Alignment explanation
Indices: 698098--698184 Score: 104
Period size: 31 Copynumber: 2.9 Consensus size: 30
698088 TTCAACAATC
* *
698098 ATATA-ATATATATATATAGATATATGTTAA
1 ATATATATATATATATATATATATAT-TAAA
698128 ATATATATATATATATATATATATATTAAA
1 ATATATATATATATATATATATATATTAAA
* * *
698158 AAATGATAAATATATATTTATATATAT
1 ATAT-ATATATATATATATATATATAT
698185 AAACACTTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
30 11 0.22
31 39 0.78
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (30 bp):
ATATATATATATATATATATATATATTAAA
Found at i:698170 original size:29 final size:29
Alignment explanation
Indices: 698102--698187 Score: 93
Period size: 29 Copynumber: 2.9 Consensus size: 29
698092 ACAATCATAT
* * *
698102 AATATATATATATAGATATATGTTAAATA
1 AATATAAATATATATATATATATTAAATA
* *
698131 TATATATATATATATATATATATTAAA-A
1 AATATAAATATATATATATATATTAAATA
*
698159 AATGATAAATATATATTTATATATATAAA
1 AAT-ATAAATATATATATATATAT-TAAA
698188 CACTTAATCT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
28 3 0.06
29 42 0.86
30 4 0.08
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (29 bp):
AATATAAATATATATATATATATTAAATA
Found at i:703538 original size:2 final size:2
Alignment explanation
Indices: 703531--703562 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
703521 AGCCCCCGGT
703531 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
703563 CAAACATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:710567 original size:3 final size:3
Alignment explanation
Indices: 710552--710595 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
710542 AAGAACTATG
*
710552 ATA ATA CTA ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA A
710596 AGAAGATTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:711884 original size:17 final size:17
Alignment explanation
Indices: 711864--711908 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
711854 GATATAATTT
*
711864 ATTTAAATATATAAAAA
1 ATTTAAAAATATAAAAA
*
711881 ATTTAAAAATTTAAAAA
1 ATTTAAAAATATAAAAA
711898 A-TTAAAAATAT
1 ATTTAAAAATAT
711909 TTATATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATTTAAAAATATAAAAA
Found at i:711889 original size:9 final size:9
Alignment explanation
Indices: 711875--711911 Score: 51
Period size: 8 Copynumber: 4.2 Consensus size: 9
711865 TTTAAATATA
711875 TAAAAAATT
1 TAAAAAATT
711884 T-AAAAATT
1 TAAAAAATT
711892 TAAAAAA-T
1 TAAAAAATT
711900 TAAAAATATT
1 TAAAAA-ATT
711910 TA
1 TA
711912 TATTAAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 15 0.60
9 7 0.28
10 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TAAAAAATT
Found at i:713212 original size:17 final size:16
Alignment explanation
Indices: 713189--713265 Score: 75
Period size: 16 Copynumber: 4.8 Consensus size: 16
713179 AATCATATTA
*
713189 AACAAAATTTATTGTG
1 AACAAAATTTATTTTG
*
713205 AACAAAAATTATTTTG
1 AACAAAATTTATTTTG
*
713221 AACATAATTTATTTTG
1 AACAAAATTTATTTTG
* * *
713237 AATATGAA-TTACTTTG
1 AACA-AAATTTATTTTG
*
713253 AACATAATTTATT
1 AACAAAATTTATT
713266 CTAAATAAGA
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
15 2 0.04
16 45 0.92
17 2 0.04
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (16 bp):
AACAAAATTTATTTTG
Found at i:713212 original size:33 final size:32
Alignment explanation
Indices: 713164--713238 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
713154 TTAATATGAG
*
713164 TTATTTTGAATAAAAAATCATATTAAACAAAAT
1 TTATTTTGAA-CAAAAATCATATTAAACAAAAT
* * * * *
713197 TTATTGTGAACAAAAATTATTTTGAACATAAT
1 TTATTTTGAACAAAAATCATATTAAACAAAAT
713229 TTATTTTGAA
1 TTATTTTGAA
713239 TATGAATTAC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
32 26 0.74
33 9 0.26
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (32 bp):
TTATTTTGAACAAAAATCATATTAAACAAAAT
Found at i:713247 original size:32 final size:32
Alignment explanation
Indices: 713211--713283 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 32
713201 TGTGAACAAA
* * *
713211 AATTATTTTGAACATAATTTATTTTGAATATG
1 AATTATTTTGAACATAATTTATTCTAAATAAG
*
713243 AATTACTTTGAACATAATTTATTCTAAATAAG
1 AATTATTTTGAACATAATTTATTCTAAATAAG
713275 AATTATTTT
1 AATTATTTT
713284 AAATAAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (32 bp):
AATTATTTTGAACATAATTTATTCTAAATAAG
Found at i:713298 original size:15 final size:15
Alignment explanation
Indices: 713261--713308 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
713251 TGAACATAAT
*
713261 TTATTCTAAATAAGAA
1 TTATTTTAAATAA-AA
713277 TTATTTTAAATAAAA
1 TTATTTTAAATAAAA
*
713292 TTGTTTTAAATAAAA
1 TTATTTTAAATAAAA
713307 TT
1 TT
713309 TATTCTAAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 18 0.60
16 12 0.40
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (15 bp):
TTATTTTAAATAAAA
Found at i:713459 original size:14 final size:13
Alignment explanation
Indices: 713440--713477 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
713430 TAAAATAATA
*
713440 TAATTATTTGTTTT
1 TAATTATTT-TTAT
713454 TAATTATTTTTAT
1 TAATTATTTTTAT
713467 T-ATTATTTTTA
1 TAATTATTTTTA
713478 AAAGTACAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.43
13 4 0.17
14 9 0.39
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (13 bp):
TAATTATTTTTAT
Found at i:720490 original size:3 final size:3
Alignment explanation
Indices: 720482--720533 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
720472 GCAACCTTCT
720482 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
720529 TTA TT
1 TTA TT
720534 TTTTTAAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:720538 original size:8 final size:8
Alignment explanation
Indices: 720485--720539 Score: 65
Period size: 9 Copynumber: 6.4 Consensus size: 8
720475 ACCTTCTTTA
720485 TTATTATT
1 TTATTATT
720493 ATTATTATT
1 -TTATTATT
720502 ATTATTATT
1 -TTATTATT
720511 ATTATTATT
1 -TTATTATT
720520 ATTATTATT
1 -TTATTATT
*
720529 TTATTTTT
1 TTATTATT
720537 TTA
1 TTA
720540 AAAAAAAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
8 10 0.22
9 35 0.78
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
TTATTATT
Found at i:724170 original size:13 final size:14
Alignment explanation
Indices: 724147--724180 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
724137 TTATAAAAAT
724147 TTATATAATATAAA
1 TTATATAATATAAA
*
724161 TTAT-TAATATATA
1 TTATATAATATAAA
724174 TTATATA
1 TTATATA
724181 TAATAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTATATAATATAAA
Found at i:724351 original size:28 final size:30
Alignment explanation
Indices: 724316--724376 Score: 92
Period size: 28 Copynumber: 2.1 Consensus size: 30
724306 TATAAGTTGG
724316 ATTTAAATTTT-TTTAAATTTAA-TA-TTAA
1 ATTTAAATTTTATTT-AATTTAATTATTTAA
724344 ATTTAAATTTTATTTAATTTAATTATTTAA
1 ATTTAAATTTTATTTAATTTAATTATTTAA
724374 ATT
1 ATT
724377 ATTATTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 18 0.60
29 5 0.17
30 7 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
ATTTAAATTTTATTTAATTTAATTATTTAA
Found at i:724389 original size:13 final size:12
Alignment explanation
Indices: 724344--724386 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
724334 TTAATATTAA
724344 ATTTAAATT-TT
1 ATTTAAATTATT
*
724355 ATTTAATTTAATT
1 ATTTAAATT-ATT
724368 ATTTAAATTATT
1 ATTTAAATTATT
724380 ATTTAAA
1 ATTTAAA
724387 ATTTATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 8 0.29
12 10 0.36
13 10 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTTAAATTATT
Found at i:724389 original size:22 final size:23
Alignment explanation
Indices: 724344--724402 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
724334 TTAATATTAA
724344 ATTTAAATT-TTATTTAATTTAATT
1 ATTTAAATTATTATTTAA--TAATT
724368 ATTTAAATTATTATTTAA-AATT
1 ATTTAAATTATTATTTAATAATT
*
724390 -TATTAAAATATTA
1 AT-TTAAATTATTA
724403 AAAAAATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 1 0.03
22 14 0.44
24 9 0.28
25 8 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTAAATTATTATTTAATAATT
Found at i:724392 original size:14 final size:13
Alignment explanation
Indices: 724344--724394 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
724334 TTAATATTAA
724344 ATTTAAA-TT-TT
1 ATTTAAATTTATT
724355 ATTT-AATTTAATT
1 ATTTAAATTT-ATT
724368 ATTTAAA-TTATT
1 ATTTAAATTTATT
724380 ATTTAAAATTTATT
1 ATTT-AAATTTATT
724394 A
1 A
724395 AAATATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
10 2 0.06
11 6 0.18
12 7 0.21
13 11 0.32
14 8 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTAAATTTATT
Found at i:724516 original size:2 final size:2
Alignment explanation
Indices: 724511--724554 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
724501 AAATATACAA
724511 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
724553 AT
1 AT
724555 GCATGAGTGG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:724516 original size:10 final size:10
Alignment explanation
Indices: 724493--724554 Score: 70
Period size: 10 Copynumber: 6.2 Consensus size: 10
724483 AATAAACCTA
*
724493 ATATATAAAA
1 ATATATAAAT
*
724503 ATATACAAAT
1 ATATATAAAT
*
724513 ATATATATAT
1 ATATATAAAT
*
724523 ATATATATAT
1 ATATATAAAT
*
724533 ATATATATAT
1 ATATATAAAT
*
724543 ATATATATAT
1 ATATATAAAT
724553 AT
1 AT
724555 GCATGAGTGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 48 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (10 bp):
ATATATAAAT
Found at i:729140 original size:2 final size:2
Alignment explanation
Indices: 729133--729169 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
729123 AATTTCTAAG
729133 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 T
729170 CTACACATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:729457 original size:14 final size:14
Alignment explanation
Indices: 729438--729466 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
729428 AACGTCGTTG
729438 ATTTAAAACGAGAA
1 ATTTAAAACGAGAA
729452 ATTTAAAACGAGAA
1 ATTTAAAACGAGAA
729466 A
1 A
729467 AAAATAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.21
Consensus pattern (14 bp):
ATTTAAAACGAGAA
Found at i:731629 original size:18 final size:18
Alignment explanation
Indices: 731606--731667 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
731596 TTATGTTTAA
*
731606 AAATTTTTATATTTATAT
1 AAATTTTAATATTTATAT
731624 AAATTTTAATATATTA-AT
1 AAATTTTAATAT-TTATAT
731642 -AATTTT--TA-TTATAT
1 AAATTTTAATATTTATAT
731656 AAATTTTAATAT
1 AAATTTTAATAT
731668 ATTTTTATTG
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 3 0.08
14 2 0.05
15 8 0.22
17 8 0.22
18 13 0.35
19 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATTTTAATATTTATAT
Found at i:731662 original size:14 final size:14
Alignment explanation
Indices: 731618--731669 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
731608 ATTTTTATAT
731618 TTATATAAATTTTAA
1 TTATATAAATTTT-A
*
731633 TATATTAATAATTTTTA
1 T-TA-T-ATAAATTTTA
731650 TTATATAAATTTTA
1 TTATATAAATTTTA
*
731664 ATATAT
1 TTATAT
731670 TTTTATTGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 14 0.45
15 2 0.06
16 4 0.13
17 3 0.10
18 8 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTATATAAATTTTA
Found at i:732153 original size:4 final size:4
Alignment explanation
Indices: 732144--732177 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
732134 TTTTGCTGCC
732144 TTAA TTAA TTAA -TAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
732178 CTATCTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:732314 original size:16 final size:16
Alignment explanation
Indices: 732295--732347 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
732285 TTTAATATTT
*
732295 ATATAGAATATATATC
1 ATATTGAATATATATC
* *
732311 ATATTTAATATATATT
1 ATATTGAATATATATC
* *
732327 AGATTGAAAATATATC
1 ATATTGAATATATATC
732343 ATATT
1 ATATT
732348 TGATATTTAT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (16 bp):
ATATTGAATATATATC
Found at i:732672 original size:3 final size:3
Alignment explanation
Indices: 732664--732693 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
732654 GTTACATGGG
732664 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
732694 AAGATATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:733164 original size:20 final size:20
Alignment explanation
Indices: 733127--733164 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
733117 GTCATGGATG
*
733127 AAAATTTAATAATGTTTTAA
1 AAAATTTAATAATATTTTAA
*
733147 AAAATTTAATAGTATTTT
1 AAAATTTAATAATATTTT
733165 GAATATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
AAAATTTAATAATATTTTAA
Found at i:739316 original size:25 final size:25
Alignment explanation
Indices: 739288--739339 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
739278 TATTTTATTA
739288 TTTAAAATAATATTAAAAATTAAAT
1 TTTAAAATAATATTAAAAATTAAAT
* * * *
739313 TTTATATTAATATTTATAATTAAAT
1 TTTAAAATAATATTAAAAATTAAAT
739338 TT
1 TT
739340 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTAAAATAATATTAAAAATTAAAT
Found at i:739734 original size:21 final size:20
Alignment explanation
Indices: 739704--739743 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
739694 TTTATTTTTT
*
739704 AAAATTTTTTATATATTTAA
1 AAAATTTTTTAAATATTTAA
739724 AAAATTATTTTAAATATTTA
1 AAAATT-TTTTAAATATTTA
739744 TATTCGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAAATTTTTTAAATATTTAA
Found at i:739984 original size:22 final size:22
Alignment explanation
Indices: 739959--740000 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
739949 AATAAAAAAT
739959 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
739981 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
740001 AATAAAAAAT
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):
TATTTTTATAATTAAATTTATA
Found at i:741047 original size:21 final size:22
Alignment explanation
Indices: 741014--741082 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 22
741004 ATAAATTTTA
741014 AAATATATTTATATAA-TATATT
1 AAATATATTTATA-AATTATATT
741036 AAATAT-TTTATAAATTATATTT
1 AAATATATTTATAAATTATA-TT
741058 ATATATCATATTTA-AAATTAT-TT
1 A-A-AT-ATATTTATAAATTATATT
741081 AA
1 AA
741083 TTTTAATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
20 2 0.05
21 10 0.24
22 10 0.24
23 4 0.10
24 2 0.05
25 9 0.22
26 4 0.10
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATATATTTATAAATTATATT
Found at i:741320 original size:22 final size:22
Alignment explanation
Indices: 741294--741335 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
741284 GAACTCTATT
741294 TATAAAAATATATAAATATTAA
1 TATAAAAATATATAAATATTAA
* *
741316 TATAAAAATATTTTAATATT
1 TATAAAAATATATAAATATT
741336 TTAATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TATAAAAATATATAAATATTAA
Found at i:742808 original size:2 final size:2
Alignment explanation
Indices: 742801--742847 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
742791 TCCCATTCTC
*
742801 AT AT AT AT AT AT AC 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
742843 AT AT A
1 AT AT A
742848 CACACACACA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:743118 original size:24 final size:25
Alignment explanation
Indices: 743076--743124 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
743066 TTCGAAATAA
*
743076 AAGATATCTATTTATAATTATTTTT
1 AAGATATCTATTTAAAATTATTTTT
*
743101 AAGATAT-TTTTTAAAATTATTTTT
1 AAGATATCTATTTAAAATTATTTTT
743125 TTAAAAGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (25 bp):
AAGATATCTATTTAAAATTATTTTT
Found at i:744195 original size:27 final size:27
Alignment explanation
Indices: 744160--744214 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
744150 GATCTAATCT
*
744160 AATTCATAA-ATAAATATATATCATTTA
1 AATTAATAATATAAATATATAT-ATTTA
*
744187 AATTAATAATTTTAAATATATATATTTA
1 AATTAATAA-TATAAATATATATATTTA
744215 TCATTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.33
28 5 0.21
29 11 0.46
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (27 bp):
AATTAATAATATAAATATATATATTTA
Found at i:744214 original size:14 final size:15
Alignment explanation
Indices: 744170--744214 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
744160 AATTCATAAA
*
744170 TAAATATATATCATT
1 TAAATATATATAATT
744185 TAAAT-TA-ATAATTT
1 TAAATATATATAA-TT
744199 TAAATATATAT-ATT
1 TAAATATATATAATT
744213 TA
1 TA
744215 TCATTTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
13 3 0.12
14 13 0.50
15 8 0.31
16 2 0.08
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TAAATATATATAATT
Found at i:744766 original size:20 final size:22
Alignment explanation
Indices: 744738--744799 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 22
744728 CTACTCAAAC
744738 ATAAATAAAAT-T-ATATAAAA
1 ATAAATAAAATATAATATAAAA
*
744758 ATAATTAAAATATAATAT-AAA
1 ATAAATAAAATATAATATAAAA
744779 ATAAA-AATAATATAAATATAA
1 ATAAATAA-AATAT-AATATAA
744800 TTATTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
20 12 0.34
21 13 0.37
22 9 0.26
23 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAAATAAAATATAATATAAAA
Found at i:744772 original size:11 final size:12
Alignment explanation
Indices: 744738--744799 Score: 57
Period size: 11 Copynumber: 5.8 Consensus size: 12
744728 CTACTCAAAC
744738 ATAA-ATAAAAT
1 ATAATATAAAAT
744749 -T-ATATAAAA-
1 ATAATATAAAAT
744758 ATAAT-TAAAAT
1 ATAATATAAAAT
744769 ATAATATAAAAT
1 ATAATATAAAAT
* *
744781 A-AAAATAATAT
1 ATAATATAAAAT
744792 A-AATATAA
1 ATAATATAA
744800 TTATTTTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
9 1 0.02
10 13 0.30
11 22 0.51
12 7 0.16
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:744772 original size:27 final size:27
Alignment explanation
Indices: 744742--744799 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
744732 TCAAACATAA
* *
744742 ATAAAATTATATAAAAATAAT-TAAAAT
1 ATAAAATAAAATAAAAATAATAT-AAAT
*
744769 ATAATATAAAATAAAAATAATATAAAT
1 ATAAAATAAAATAAAAATAATATAAAT
744796 ATAA
1 ATAA
744800 TTATTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (27 bp):
ATAAAATAAAATAAAAATAATATAAAT
Found at i:744777 original size:16 final size:15
Alignment explanation
Indices: 744758--744796 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
744748 TTATATAAAA
*
744758 ATAATTAAAATATAAT
1 ATAAATAAAA-ATAAT
744774 ATAAAATAAAAATAAT
1 AT-AAATAAAAATAAT
744790 ATAAATA
1 ATAAATA
744797 TAATTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 9 0.43
17 7 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAAATAAAAATAAT
Found at i:744895 original size:30 final size:30
Alignment explanation
Indices: 744854--744910 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
744844 TTAAAATTTA
744854 TATAATTATAAAATAT-T-TTTAATATGAT
1 TATAATTATAAAATATGTATTTAATATGAT
744882 TATAATATAATAAAATATGTATTTAATAT
1 TATAAT-T-ATAAAATATGTATTTAATAT
744911 AAATATATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 6 0.24
29 1 0.04
30 9 0.36
31 1 0.04
32 8 0.32
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (30 bp):
TATAATTATAAAATATGTATTTAATATGAT
Found at i:745150 original size:21 final size:21
Alignment explanation
Indices: 745125--745164 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
745115 TAAATAAAAC
*
745125 TTGAAAAGTTAAAAAAATAGA
1 TTGAAAACTTAAAAAAATAGA
*
745146 TTGAAAACTTTAAAAAATA
1 TTGAAAACTTAAAAAAATA
745165 TTTTACTTTG
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:0.60, C:0.03, G:0.10, T:0.28
Consensus pattern (21 bp):
TTGAAAACTTAAAAAAATAGA
Found at i:747735 original size:19 final size:19
Alignment explanation
Indices: 747698--747737 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
747688 ACTCTAATCA
*
747698 TATTTTTTAAAATTTATTT
1 TATTTTTTAAAATTAATTT
747717 TATTATTTTAAAA-TAATTT
1 TATT-TTTTAAAATTAATTT
747736 TA
1 TA
747738 AAAAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTTTAAAATTAATTT
Found at i:747747 original size:34 final size:34
Alignment explanation
Indices: 747705--747809 Score: 99
Period size: 34 Copynumber: 3.0 Consensus size: 34
747695 TCATATTTTT
* *
747705 TAAAATTTATTTTATTATTTTAAAATAATTTTAAA
1 TAAAATTTATTTTATTATTAT-AAATAAATTTAAA
* * *
747740 -AAAATTTATTTAATAATTATAATTAAATTTAAA
1 TAAAATTTATTTTATTATTATAAATAAATTTAAA
747773 TAAAA-TTATTTT-TTATTAAATAAATAATAATTTAAA
1 TAAAATTTATTTTATTATT--ATAAAT-A-AATTTAAA
747809 T
1 T
747810 TTATTCCAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
32 4 0.07
33 17 0.30
34 26 0.46
35 1 0.02
36 9 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (34 bp):
TAAAATTTATTTTATTATTATAAATAAATTTAAA
Found at i:748543 original size:29 final size:30
Alignment explanation
Indices: 748484--748543 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
748474 TGAATACTTG
* * *
748484 TTTATATTATAAAATTATTTTTTATTTAAA
1 TTTATATTATAAAATTAATATTTATTAAAA
748514 TTTA-ATTATAAATATTAATATTTA-TAAAA
1 TTTATATTATAAA-ATTAATATTTATTAAAA
748543 T
1 T
748544 AAATATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TTTATATTATAAAATTAATATTTATTAAAA
Found at i:748550 original size:15 final size:16
Alignment explanation
Indices: 748519--748553 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
748509 TTAAATTTAA
*
748519 TTATAAATATTAATAT
1 TTATAAATATAAATAT
748535 TTATAAA-ATAAATAT
1 TTATAAATATAAATAT
748550 TTAT
1 TTAT
748554 TTTTAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTATAAATATAAATAT
Found at i:748844 original size:17 final size:18
Alignment explanation
Indices: 748808--748846 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
748798 ATCACCTAAC
**
748808 AAAATTAAAATATTTTAA
1 AAAATTAAAATATTAAAA
748826 AAAATTAAAA-ATTAAAA
1 AAAATTAAAATATTAAAA
748843 AAAA
1 AAAA
748847 ATTTAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATTAAAATATTAAAA
Found at i:749025 original size:5 final size:5
Alignment explanation
Indices: 749015--749085 Score: 60
Period size: 5 Copynumber: 14.4 Consensus size: 5
749005 TGATTATACG
749015 AATAT AATAT -ATAT -ATAT AATAT ATGATAT AATAT AATAT AA-AT ATATAT
1 AATAT AATAT AATAT AATAT AATAT A--ATAT AATAT AATAT AATAT A-ATAT
** *
749065 CTTAA AATAT -ATAT AATAT AA
1 AATAT AATAT AATAT AATAT AA
749086 ATTATTAACA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
4 15 0.28
5 32 0.59
6 2 0.04
7 5 0.09
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (5 bp):
AATAT
Found at i:749028 original size:2 final size:2
Alignment explanation
Indices: 749016--749084 Score: 53
Period size: 2 Copynumber: 37.5 Consensus size: 2
749006 GATTATACGA
749016 AT AT A- AT AT AT AT AT AT A- AT AT AT GAT AT A- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
* * *
749055 AA AT AT AT AT CT -T A- AA AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
749085 AATTATTAAC
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
1 7 0.13
2 46 0.84
3 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (2 bp):
AT
Found at i:749048 original size:25 final size:24
Alignment explanation
Indices: 749016--749084 Score: 83
Period size: 23 Copynumber: 3.0 Consensus size: 24
749006 GATTATACGA
749016 ATATAATATATATATATAATATAT
1 ATATAATATATATATATAATATAT
749040 GATATAATATA-ATATA-AATATAT
1 -ATATAATATATATATATAATATAT
*
749063 ATCTTAA-A-ATATATATAATATA
1 AT-ATAATATATATATATAATATA
749085 AATTATTAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
21 1 0.03
22 8 0.20
23 16 0.40
24 5 0.12
25 10 0.25
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (24 bp):
ATATAATATATATATATAATATAT
Found at i:749075 original size:30 final size:30
Alignment explanation
Indices: 749015--749087 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
749005 TGATTATACG
* **
749015 AATATAATATATATATATAATATATGATAT
1 AATATAATATAAATATATAATATAAAATAT
*
749045 AATATAATATAAATATAT-ATCTTAAAATAT
1 AATATAATATAAATATATAAT-ATAAAATAT
749075 -ATATAATATAAAT
1 AATATAATATAAAT
749088 TATTAACATA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 15 0.39
30 23 0.61
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (30 bp):
AATATAATATAAATATATAATATAAAATAT
Found at i:749391 original size:17 final size:17
Alignment explanation
Indices: 749353--749399 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
749343 ATATGGTAAA
749353 AAAT-TAAAATATAATAT
1 AAATATAAAA-ATAATAT
* *
749370 TAATATAAAAATTATAT
1 AAATATAAAAATAATAT
*
749387 AAATATTAAAATA
1 AAATATAAAAATA
749400 TGTTAAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATAAAAATAATAT
Found at i:750524 original size:19 final size:20
Alignment explanation
Indices: 750508--750547 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
750498 TATCATATTT
750508 TATATTAA-TTTTTATATCA
1 TATATTAATTTTTTATATCA
*
750527 TATTTTAATTTTTTATATCA
1 TATATTAATTTTTTATATCA
750547 T
1 T
750548 TCGTGTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
TATATTAATTTTTTATATCA
Found at i:750727 original size:28 final size:26
Alignment explanation
Indices: 750694--750746 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
750684 TAAAATATTT
* *
750694 ATTTAAATTTAATTATAAAATATATAA
1 ATTTTAATTTAAATAT-AAATATATAA
*
750721 ATTTTAATTTAAATATTAATATATAA
1 ATTTTAATTTAAATATAAATATATAA
750747 TAAAATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTTTAATTTAAATATAAATATATAA
Found at i:754184 original size:19 final size:17
Alignment explanation
Indices: 754133--754192 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 17
754123 TGGGCCATAT
754133 TTTAAATTTTTTTAAAA
1 TTTAAATTTTTTTAAAA
**
754150 TTTTTATTTATGTTTAAAA
1 TTTAAATTT-T-TTTAAAA
754169 TTTAAATTATTATTTAAATA
1 TTTAAATT-TT-TTTAAA-A
754189 TTTA
1 TTTA
754193 TAAAAATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
17 7 0.21
18 1 0.03
19 20 0.59
20 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTAAATTTTTTTAAAA
Found at i:754235 original size:21 final size:21
Alignment explanation
Indices: 754209--754248 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
754199 TTAAATAAAT
754209 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
*
754230 TATTTTCTAATTAAATTTA
1 TATTTTATAATTAAATTTA
754249 AATAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:754667 original size:19 final size:19
Alignment explanation
Indices: 754635--754676 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
754625 TTAAAATTAA
*
754635 ATTTAAATAAAAAATATACT
1 ATTTAAATAAAAAA-ATAAT
*
754655 ATTT-AATATAAAAATAAT
1 ATTTAAATAAAAAAATAAT
754673 ATTT
1 ATTT
754677 TTAAATAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 8 0.40
20 4 0.20
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTTAAATAAAAAAATAAT
Found at i:757026 original size:27 final size:27
Alignment explanation
Indices: 756996--757087 Score: 75
Period size: 26 Copynumber: 3.4 Consensus size: 27
756986 TTGGGCTACG
*
756996 TTTATAATAAATATGATAATTTATATA
1 TTTATAATAAATATTATAATTTATATA
* * * *
757023 TTTATATTTTATTATTATTATTT-TATA
1 TTTATA-ATAAATATTATAATTTATATA
*
757050 -TTATAATTAAAT-TTAAAATATTATATA
1 TTTATAA-TAAATATTATAAT-TTATATA
757077 TTTAT-ATAAAT
1 TTTATAATAAAT
757088 TTTAATACAT
Statistics
Matches: 50, Mismatches: 10, Indels: 11
0.70 0.14 0.15
Matches are distributed among these distances:
25 5 0.10
26 15 0.30
27 15 0.30
28 15 0.30
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (27 bp):
TTTATAATAAATATTATAATTTATATA
Found at i:757051 original size:13 final size:14
Alignment explanation
Indices: 757014--757054 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
757004 AAATATGATA
757014 ATTTATATATT-TAT
1 ATTT-TATATTATAT
757028 ATTTTATTATTAT-T
1 ATTTTA-TATTATAT
757042 ATTTTATATTATA
1 ATTTTATATTATA
757055 ATTAAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 8 0.33
14 15 0.62
15 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTTTATATTATAT
Found at i:757168 original size:13 final size:13
Alignment explanation
Indices: 757147--757176 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
757137 TATATTCATA
*
757147 TTATTTTTTATTT
1 TTATATTTTATTT
757160 TTATATTTTATTT
1 TTATATTTTATTT
757173 TTAT
1 TTAT
757177 CATATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATATTTTATTT
Found at i:757183 original size:16 final size:17
Alignment explanation
Indices: 757162--757199 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
757152 TTTTATTTTT
757162 ATATTTT-ATTTTTATC
1 ATATTTTAATTTTTATC
*
757178 ATATTTTAATTTTTTTC
1 ATATTTTAATTTTTATC
757195 ATATT
1 ATATT
757200 GAGTCCATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (17 bp):
ATATTTTAATTTTTATC
Found at i:758757 original size:18 final size:20
Alignment explanation
Indices: 758736--758779 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
758726 ATGAATATAA
758736 TTTAAATATTT-A-AATTTT
1 TTTAAATATTTAACAATTTT
*
758754 TTTATATATTTAACAATTTT
1 TTTAAATATTTAACAATTTT
758774 TTTAAA
1 TTTAAA
758780 AAATGCACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 10 0.45
19 1 0.05
20 11 0.50
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAAATATTTAACAATTTT
Found at i:759654 original size:16 final size:16
Alignment explanation
Indices: 759633--759669 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
759623 TTTAACGTGA
*
759633 ATATTACATATAATAT
1 ATATTAAATATAATAT
759649 ATATTAAATATAATAT
1 ATATTAAATATAATAT
*
759665 TTATT
1 ATATT
759670 TAATTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATTAAATATAATAT
Found at i:759697 original size:17 final size:17
Alignment explanation
Indices: 759670--759711 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
759660 AATATTTATT
*
759670 TAATTTTTAAAAAATT-
1 TAATATTTAAAAAATTA
759686 TATATATTTAAAAAATTA
1 TA-ATATTTAAAAAATTA
759704 TAATATTT
1 TAATATTT
759712 TTATATGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 2 0.09
17 19 0.83
18 2 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATATTTAAAAAATTA
Found at i:760097 original size:17 final size:17
Alignment explanation
Indices: 760075--760113 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
760065 TAAATTTTAA
760075 TATATTTATTTATATAT
1 TATATTTATTTATATAT
* *
760092 TATATTTATTTGTATTT
1 TATATTTATTTATATAT
760109 TATAT
1 TATAT
760114 ATATATACGC
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:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TATATTTATTTATATAT
Found at i:760326 original size:18 final size:17
Alignment explanation
Indices: 760291--760341 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
760281 TGATAAAATT
760291 TTATAAAAATT-AAA-AA
1 TTAT-AAAATTAAAATAA
* *
760307 TTTTAATATGTAAAATAA
1 TTATAAAAT-TAAAATAA
760325 TTATAAAATTAAAATAA
1 TTATAAAATTAAAATAA
760342 AGACTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 4 0.14
16 4 0.14
17 11 0.39
18 9 0.32
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
TTATAAAATTAAAATAA
Found at i:760542 original size:27 final size:28
Alignment explanation
Indices: 760469--760549 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 28
760459 TATAATTTTA
*
760469 TAAATAAATAAAAATATATATT-TATTAAT
1 TAAATAAA-AAAAATA-ATATTAAATTAAT
760498 TAAATAATAAAATGAATAATATTAAATTAAT
1 TAAATAA-AAAA--AATAATATTAAATTAAT
* *
760529 T-CATAAAAAAAATATTATTAA
1 TAAATAAAAAAAATAATATTAA
760550 GTTTGACAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
27 10 0.22
29 14 0.31
30 10 0.22
31 11 0.24
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (28 bp):
TAAATAAAAAAAATAATATTAAATTAAT
Found at i:770944 original size:15 final size:14
Alignment explanation
Indices: 770920--770959 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
770910 ACTTTAAAAG
*
770920 TAAATTTAATAATA
1 TAAATATAATAATA
*
770934 TTAAATATAATTATA
1 -TAAATATAATAATA
770949 TAAATATAATA
1 TAAATATAATA
770960 TAAAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAATATAATAATA
Found at i:771371 original size:24 final size:23
Alignment explanation
Indices: 771330--771399 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 23
771320 CTCTGGATCT
*
771330 AATAATAT-TAAAAATAATAATAA
1 AATAATATAAAAAAATAAT-ATAA
*
771353 CATAATATAAAAAAATAAT-TAA
1 AATAATATAAAAAAATAATATAA
*
771375 AATAAAATATAAAAAATAATATAA
1 AATAATATA-AAAAAATAATATAA
771399 A
1 A
771400 TACGATATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 10 0.25
23 17 0.43
24 13 0.32
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.27
Consensus pattern (23 bp):
AATAATATAAAAAAATAATATAA
Found at i:771397 original size:12 final size:12
Alignment explanation
Indices: 771330--771399 Score: 74
Period size: 12 Copynumber: 5.9 Consensus size: 12
771320 CTCTGGATCT
*
771330 AATAATATTAAA
1 AATAATATAAAA
*
771342 AATAATA-ATAA
1 AATAATATAAAA
*
771353 CATAATATAAAAA
1 AATAATAT-AAAA
771366 AATAAT-TAAAA
1 AATAATATAAAA
771377 TAA-AATATAAAA
1 -AATAATATAAAA
771389 AATAATATAAA
1 AATAATATAAA
771400 TACGATATGA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
11 17 0.35
12 23 0.48
13 8 0.17
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.27
Consensus pattern (12 bp):
AATAATATAAAA
Found at i:774727 original size:2 final size:2
Alignment explanation
Indices: 774720--774752 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
774710 ACTATCAGGA
774720 CT CT 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 CT CT C
774753 ACGCTCGCTC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:775365 original size:11 final size:11
Alignment explanation
Indices: 775341--775392 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
775331 TAAATATATT
* *
775341 TAATACAAATA
1 TAATATAAAAA
775352 TAATATAAAAA
1 TAATATAAAAA
775363 TAAT-TAAAATA
1 TAATATAAAA-A
775374 TAATATAATAAA
1 TAATATAA-AAA
*
775386 AAATATA
1 TAATATA
775393 TATTAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 5 0.14
11 18 0.51
12 10 0.29
13 2 0.06
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (11 bp):
TAATATAAAAA
Found at i:775383 original size:27 final size:28
Alignment explanation
Indices: 775348--775421 Score: 89
Period size: 27 Copynumber: 2.6 Consensus size: 28
775338 ATTTAATACA
775348 AATATAATATAAAAATAATTAAAATA-T
1 AATATAATATAAAAATAATTAAAATATT
* *
775375 AATATAATAAAAAATATATATTAATATATT
1 AATATAATATAAAA-ATA-ATTAAAATATT
*
775405 AATAT-TTATAAAAATAA
1 AATATAATATAAAAATAA
775422 ATTATCAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 14 0.35
28 6 0.15
29 14 0.35
30 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
AATATAATATAAAAATAATTAAAATATT
Found at i:775399 original size:17 final size:17
Alignment explanation
Indices: 775332--775400 Score: 52
Period size: 17 Copynumber: 3.9 Consensus size: 17
775322 TTACACCTTT
775332 AAATATAT-TTAATACAA
1 AAATATATATTAATA-AA
* **
775349 ATATAATATAAAAATAATTA
1 AAAT-ATATATTAATAA--A
775369 AAATATA-ATATAATAAA
1 AAATATATAT-TAATAAA
775386 AAATATATATTAATA
1 AAATATATATTAATA
775401 TATTAATATT
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
17 16 0.40
18 8 0.20
19 12 0.30
20 4 0.10
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATATATATTAATAAA
Found at i:775716 original size:24 final size:26
Alignment explanation
Indices: 775657--775716 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 26
775647 ATAAAAATAT
*
775657 AATATTTTATTTACTTTTTAATTATTA
1 AATATATT-TTTACTTTTTAATTATTA
*
775684 TATATATTTTTA-TTTTT-ATTATTTA
1 AATATATTTTTACTTTTTAATTA-TTA
775709 AATA-ATTT
1 AATATATTT
775717 AATAAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 8 0.28
25 11 0.38
26 4 0.14
27 6 0.21
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (26 bp):
AATATATTTTTACTTTTTAATTATTA
Found at i:775738 original size:23 final size:25
Alignment explanation
Indices: 775702--775749 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
775692 TTTATTTTTA
775702 TTATTTAAATAATTTAAT-AAATAT
1 TTATTTAAATAATTTAATGAAATAT
775726 TTATTTAAA-AATTTAATGAAATAT
1 TTATTTAAATAATTTAATGAAATAT
775750 ATAATTTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
TTATTTAAATAATTTAATGAAATAT
Found at i:776258 original size:18 final size:20
Alignment explanation
Indices: 776235--776280 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
776225 AATATTAAAA
*
776235 AAATTTAAG-TTAAAT-ATC
1 AAATTTAAGCATAAATAATC
776253 AAATTTAAGCATAAATAATC
1 AAATTTAAGCATAAATAATC
*
776273 TAATTTAA
1 AAATTTAA
776281 AGTCAAGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.38
19 5 0.21
20 10 0.42
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (20 bp):
AAATTTAAGCATAAATAATC
Found at i:776535 original size:29 final size:30
Alignment explanation
Indices: 776467--776536 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 30
776457 AATCTTTATG
* *
776467 AAAAATACAC-TTACCTTTTAACATTTAAA
1 AAAAATACACTTTACCTCTTAACAGTTAAA
** * *
776496 AATTATCCACTTTTCCTCTTAA-AGTTAAA
1 AAAAATACACTTTACCTCTTAACAGTTAAA
776525 AAAAATACACTT
1 AAAAATACACTT
776537 ACTTTTCTAA
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
29 22 0.71
30 9 0.29
ACGTcount: A:0.44, C:0.19, G:0.01, T:0.36
Consensus pattern (30 bp):
AAAAATACACTTTACCTCTTAACAGTTAAA
Found at i:776757 original size:37 final size:39
Alignment explanation
Indices: 776691--776771 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 39
776681 TTACTATTAA
* *
776691 ATTAAATTATTATTAAGTTATGTTTTAATTCAAGTGTAT
1 ATTAAATTATTATTAACTTATGTTTTAATTCAAGTATAT
* *
776730 ATTAAA-TATT-TTAAACTTAT-TTTTAATTTAATTATAT
1 ATTAAATTATTATT-AACTTATGTTTTAATTCAAGTATAT
776767 ATTAA
1 ATTAA
776772 GTTTAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 21 0.57
38 10 0.27
39 6 0.16
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (39 bp):
ATTAAATTATTATTAACTTATGTTTTAATTCAAGTATAT
Found at i:779200 original size:3 final size:3
Alignment explanation
Indices: 779192--779275 Score: 57
Period size: 3 Copynumber: 28.0 Consensus size: 3
779182 AATTAAAAAT
* * * * *
779192 ATA ATA ATA ATA ATA ATT ATT ATT ATT ATT ATA ATA A-A TATCA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -AT-A ATA
* *
779238 ATA ATA ATA ATTA A-A ATT ATA A-A ATA ATA ATT ATA ATA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
779276 TTATATTTTA
Statistics
Matches: 69, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
2 5 0.07
3 58 0.84
4 5 0.07
5 1 0.01
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:779920 original size:2 final size:2
Alignment explanation
Indices: 779902--779948 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
779892 TTCTCTGCTT
* * *
779902 TC TC TG TC TC TC CC TC TC TC TA 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
779944 TC TC T
1 TC TC T
779949 ATATATATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.02, C:0.47, G:0.02, T:0.49
Consensus pattern (2 bp):
TC
Found at i:780934 original size:22 final size:23
Alignment explanation
Indices: 780892--780935 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
780882 TGAAATTAAC
*
780892 ATAAATAATTTATTTTATTAATA
1 ATAAATAATTTATTATATTAATA
780915 ATAAA-AATTTAATTAT-TTAAT
1 ATAAATAATTT-ATTATATTAAT
780936 TTGATGAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATAAATAATTTATTATATTAATA
Found at i:782527 original size:35 final size:34
Alignment explanation
Indices: 782488--782561 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 34
782478 AATTAAATTA
782488 TATTAGTAATAAATTAAATCAATTATATTAACTCT
1 TATTAGTAATAAATTAAATCAATTATATTAA-TCT
* * * *
782523 TATTATTAATAAATTAAATTAATTATGTTAATTT
1 TATTAGTAATAAATTAAATCAATTATATTAATCT
782557 TATTA
1 TATTA
782562 TATTAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
34 7 0.20
35 28 0.80
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.49
Consensus pattern (34 bp):
TATTAGTAATAAATTAAATCAATTATATTAATCT
Found at i:782561 original size:14 final size:14
Alignment explanation
Indices: 782544--782575 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
782534 AATTAAATTA
*
782544 ATTATGTTAATTTT
1 ATTATATTAATTTT
782558 ATTATATTAATTTT
1 ATTATATTAATTTT
782572 ATTA
1 ATTA
782576 AATAATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
ATTATATTAATTTT
Found at i:785218 original size:2 final size:2
Alignment explanation
Indices: 785213--785239 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
785203 ATATATCTAT
785213 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
785240 CTTTTCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:785393 original size:19 final size:18
Alignment explanation
Indices: 785369--785427 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 18
785359 ATTTGATTTT
785369 AATTATTATTTTATAATAA
1 AATTATT-TTTTATAATAA
*
785388 AATTA-TTTTTAT-TTAA
1 AATTATTTTTTATAATAA
* *
785404 ATTTATTTTTTAAAATAA
1 AATTATTTTTTATAATAA
785422 ATATTA
1 A-ATTA
785428 ATATAAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 7 0.22
17 12 0.38
18 5 0.16
19 8 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTATTTTTTATAATAA
Found at i:786141 original size:21 final size:22
Alignment explanation
Indices: 786105--786146 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
786095 TATTTTTATT
*
786105 TAAATTTTATTATAAAAATATA
1 TAAATATTATTATAAAAATATA
786127 TAAATATTA-TATAAAAATAT
1 TAAATATTATTATAAAAATAT
786147 TTTTAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATATTATTATAAAAATATA
Found at i:786157 original size:23 final size:22
Alignment explanation
Indices: 786101--786162 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
786091 AAAATATTTT
*
786101 TATTTAAATTTTATTATAAAAA
1 TATTTAAATATTATTATAAAAA
*
786123 TATATAAATATTA-TATAAAAA
1 TATTTAAATATTATTATAAAAA
*
786144 TATTTTTAAATATTTTTAT
1 TA--TTTAAATATTATTAT
786163 TATTTTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.30
22 11 0.33
23 9 0.27
24 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTTAAATATTATTATAAAAA
Found at i:786160 original size:11 final size:10
Alignment explanation
Indices: 786141--786174 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
786131 TATTATATAA
786141 AAATATTTTT
1 AAATATTTTT
786151 AAATATTTTT
1 AAATATTTTT
*
786161 -ATTATTTTT
1 AAATATTTTT
786170 AAATA
1 AAATA
786175 ATAATTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
AAATATTTTT
Found at i:786589 original size:22 final size:22
Alignment explanation
Indices: 786542--786589 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
786532 GTTTTTTAAT
* *
786542 TATATATTATATATGTTATATT
1 TATATATTATATAAGTTATATC
*
786564 TATATATTATGTAAG-TATATCC
1 TATATATTATATAAGTTATAT-C
786586 TATA
1 TATA
786590 AAGAATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (22 bp):
TATATATTATATAAGTTATATC
Found at i:787888 original size:22 final size:21
Alignment explanation
Indices: 787861--787911 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 21
787851 ATACATTATT
787861 AATATAATATAAAAAATAATGA
1 AATATAATATAAAAAATAAT-A
*
787883 AATATAATATAAAATATAATA
1 AATATAATATAAAAAATAATA
787904 AGATATAA
1 A-ATATAA
787912 AAATTTTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (21 bp):
AATATAATATAAAAAATAATA
Found at i:787897 original size:12 final size:12
Alignment explanation
Indices: 787861--787903 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
787851 ATACATTATT
787861 AATATAATATAA
1 AATATAATATAA
* *
787873 AAAAT-A-ATGA
1 AATATAATATAA
787883 AATATAATATAA
1 AATATAATATAA
787895 AATATAATA
1 AATATAATA
787904 AGATATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 16 0.64
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (12 bp):
AATATAATATAA
Found at i:788659 original size:2 final size:2
Alignment explanation
Indices: 788654--788683 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
788644 CACAGAGAGC
*
788654 AT AT AT AT AT TT 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
788684 GTCCTGGTTA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:788766 original size:31 final size:31
Alignment explanation
Indices: 788723--788795 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
788713 CATATTTATT
*
788723 TTAATTATAAACATAATAAATATTATTATAA
1 TTAATTAAAAACATAATAAATATTATTATAA
* *
788754 TTAATTAAAAACATAATGAATGTTATTATAA
1 TTAATTAAAAACATAATAAATATTATTATAA
*
788785 TTAATTGAAAA
1 TTAATTAAAAA
788796 TAAATATTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (31 bp):
TTAATTAAAAACATAATAAATATTATTATAA
Found at i:789982 original size:2 final size:2
Alignment explanation
Indices: 789975--790020 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
789965 TTTCCTTAGG
*
789975 AT AT AT AT AC 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
790017 AT AT
1 AT AT
790021 TAGTGGAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:792017 original size:2 final size:2
Alignment explanation
Indices: 792010--792046 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
792000 TAAACGATCA
792010 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
792047 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:792051 original size:2 final size:2
Alignment explanation
Indices: 792046--792072 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
792036 TCTCTCTCTC
792046 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
792073 CATGCTGGAC
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:792252 original size:2 final size:2
Alignment explanation
Indices: 792245--792272 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
792235 AATTGGAACA
792245 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
792273 GAAAATCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:792959 original size:21 final size:21
Alignment explanation
Indices: 792913--792961 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
792903 TAATTATATA
*
792913 ATATATATTAATTTTATATTT
1 ATATATATTAATTGTATATTT
792934 ATATATATTAAGTTGT-T-TTT
1 ATATATATTAA-TTGTATATTT
792954 ATTATATA
1 A-TATATA
792962 AAATAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 4 0.16
21 18 0.72
22 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
ATATATATTAATTGTATATTT
Done.