Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold502
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: 762056
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 5 of 6
Found at i:616404 original size:13 final size:13
Alignment explanation
Indices: 616386--616420 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
616376 CGATTAATTG
*
616386 TAATAAATATCGA
1 TAATAAATATCAA
*
616399 TAATAAATATTAA
1 TAATAAATATCAA
616412 TAATAAATA
1 TAATAAATA
616421 AATTAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (13 bp):
TAATAAATATCAA
Found at i:617593 original size:17 final size:17
Alignment explanation
Indices: 617558--617623 Score: 61
Period size: 17 Copynumber: 4.1 Consensus size: 17
617548 AAATAAATAA
617558 TATTTTAT-T-TAATAAT
1 TATTTTATATATAA-AAT
*
617574 TATGTTATATATAAAAT
1 TATTTTATATATAAAAT
* *
617591 TATTTTAAAAATAAAA-
1 TATTTTATATATAAAAT
617607 TATTTTAT-TA-AAAAT
1 TATTTTATATATAAAAT
617622 TA
1 TA
617624 ACTTATACAA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
14 4 0.10
15 3 0.07
16 14 0.34
17 17 0.41
18 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TATTTTATATATAAAAT
Found at i:617771 original size:2 final size:2
Alignment explanation
Indices: 617764--617796 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
617754 AAATTATTAA
*
617764 AT AT AT AT TT A- 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
617797 CTAAAATTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:617772 original size:21 final size:22
Alignment explanation
Indices: 617747--617805 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 22
617737 TGATATTGAA
617747 ATATTTAAAATTAT-TAAATAT
1 ATATTTAAAATTATATAAATAT
*
617768 ATATTTAATATATATATATATATAT
1 ATATTTAA-A-AT-TATATAAATAT
*
617793 ATATCTAAAATTA
1 ATATTTAAAATTA
617806 CTCTCTCCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 8 0.25
22 3 0.09
23 4 0.12
24 4 0.12
25 13 0.41
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTTAAAATTATATAAATAT
Found at i:618142 original size:14 final size:13
Alignment explanation
Indices: 618123--618171 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
618113 TTTAAAAAAA
618123 TTAAAATTATATAT
1 TTAAAATT-TATAT
618137 TTAAAAATTTATAT
1 TT-AAAATTTATAT
* *
618151 TATTATATTTATAT
1 T-TAAAATTTATAT
618165 TTAAAAT
1 TTAAAAT
618172 AATATATGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 4 0.14
14 18 0.62
15 7 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTAAAATTTATAT
Found at i:618142 original size:22 final size:23
Alignment explanation
Indices: 618117--618161 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
618107 TAATTTTTTA
618117 AAAAAATTAAAATTA-TATATTT
1 AAAAAATTAAAATTATTATATTT
* *
618139 -AAAAATTTATATTATTATATTT
1 AAAAAATTAAAATTATTATATTT
618161 A
1 A
618162 TATTTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AAAAAATTAAAATTATTATATTT
Found at i:618316 original size:26 final size:25
Alignment explanation
Indices: 618263--618324 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
618253 CAAATTTCAT
618263 ATTTATATTTTTTAAAATTTAAGATA
1 ATTTATATTTTTTAAAATTT-AGATA
618289 ATTTATAATTTTTTTAAAAATTT-G-TA
1 ATTTAT-A-TTTTTT-AAAATTTAGATA
*
618315 ATTTTTATTT
1 ATTTATATTT
618325 ATTTTTGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
24 3 0.09
25 1 0.03
26 13 0.41
27 2 0.06
28 6 0.19
29 7 0.22
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (25 bp):
ATTTATATTTTTTAAAATTTAGATA
Found at i:618878 original size:22 final size:23
Alignment explanation
Indices: 618837--618883 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 23
618827 AAATTTTAAA
618837 AAATTATTTATATATTAATTTTT
1 AAATTATTTATATATTAATTTTT
*
618860 AAATT-TTTATA-ATTAA-ATTT
1 AAATTATTTATATATTAATTTTT
618880 AAAT
1 AAAT
618884 AAAATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 5 0.22
22 6 0.26
23 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AAATTATTTATATATTAATTTTT
Found at i:619915 original size:18 final size:18
Alignment explanation
Indices: 619892--619930 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
619882 AAAATTGAAT
*
619892 AATAAATATTCACA-TAAA
1 AATAAAAATTCA-ATTAAA
619910 AATAAAAATTCAATTAAA
1 AATAAAAATTCAATTAAA
619928 AAT
1 AAT
619931 TTGTAGTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (18 bp):
AATAAAAATTCAATTAAA
Found at i:622134 original size:3 final size:3
Alignment explanation
Indices: 622126--622158 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
622116 ATGACGAGAG
622126 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
622159 GGAGGAGGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:627504 original size:28 final size:28
Alignment explanation
Indices: 627464--627519 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
627454 CTTGTAAACA
*
627464 TACTCTTGTCTAGCCTTCAATACTCACG
1 TACTCTTGTCTAGCATTCAATACTCACG
627492 TACTCTTGTCTAGCATTCAATACTCACG
1 TACTCTTGTCTAGCATTCAATACTCACG
627520 GCTGTTTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.30, G:0.11, T:0.36
Consensus pattern (28 bp):
TACTCTTGTCTAGCATTCAATACTCACG
Found at i:629166 original size:23 final size:23
Alignment explanation
Indices: 629139--629184 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
629129 CAATCTGTTT
629139 GGTATAATTTGACTCAAATCTTC
1 GGTATAATTTGACTCAAATCTTC
629162 GGTATAATTTGACTCAAATCTTC
1 GGTATAATTTGACTCAAATCTTC
629185 TATGTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (23 bp):
GGTATAATTTGACTCAAATCTTC
Found at i:634871 original size:2 final size:2
Alignment explanation
Indices: 634864--634919 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
634854 GCCCTGCACA
634864 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
634906 AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT A
634920 ATTTGTTAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:640288 original size:17 final size:18
Alignment explanation
Indices: 640247--640293 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
640237 ATTTATTTTT
*
640247 AAATATATTAAAATATTAA
1 AAATATATT-TAATATTAA
640266 AAATAT-TTTAATATTAA
1 AAATATATTTAATATTAA
**
640283 TTATATATTTA
1 AAATATATTTA
640294 TAATTAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 12 0.50
18 6 0.25
19 6 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATATATTTAATATTAA
Found at i:640813 original size:2 final size:2
Alignment explanation
Indices: 640806--640844 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
640796 GATTTCTGTA
* *
640806 AT AT AT AT AT AT AT AT AT AT AT AT GAA AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
640845 TTAATGTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 31 0.97
3 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:640968 original size:2 final size:2
Alignment explanation
Indices: 640961--640995 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
640951 GCAGTAAACA
640961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
640996 GATAGATAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:642604 original size:14 final size:14
Alignment explanation
Indices: 642580--642623 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 14
642570 AGGTCGAGAT
642580 AATTATAAATATTAA
1 AATT-TAAATATTAA
642595 AATTTAAATATTAA
1 AATTTAAATATTAA
642609 AATTATTAAATATTA
1 AA-T-TTAAATATTA
642624 TTTATTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.44
15 5 0.19
16 10 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTTAAATATTAA
Found at i:643698 original size:2 final size:2
Alignment explanation
Indices: 643691--643717 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
643681 ATTACGACTT
643691 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
643718 GTGTGTATAA
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:645389 original size:2 final size:2
Alignment explanation
Indices: 645382--645415 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
645372 TTCCATTATT
645382 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
645416 AAGCAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:645870 original size:17 final size:17
Alignment explanation
Indices: 645848--645887 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
645838 ATACACAAAA
645848 AAAATA-AAATATAATAT
1 AAAATATAAAT-TAATAT
*
645865 AAAATATAACTTAATAT
1 AAAATATAAATTAATAT
645882 AAAATA
1 AAAATA
645888 GTATAAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATATAAATTAATAT
Found at i:648467 original size:130 final size:126
Alignment explanation
Indices: 648241--648473 Score: 310
Period size: 130 Copynumber: 1.8 Consensus size: 126
648231 GATTAAGATT
* * * **
648241 CAAATTGATATTAAGAAAAAAATGTCCTTTTTATTTGGTCAATTTCACCTAAATTTTTAATATTT
1 CAAATTAATATTAAGAAAAAAATGTCCTTTTTATTGGGTAAATTTCA-CTAAATCATTAATATTT
*
648306 TATTTCGAATTTTCATTTTTTATCTTTAATATTTGAATTGTTTCACTTGGAAAAAATTTAGCA
65 TATTTCGAATTTTCATTTTTAATCTTTAATA-TTGAATTGTTTCACTTGGAAAAAATTTAGCA
*
648369 CAAATTAATATTAAGAAAAAAAATATGTCCTTTTTATTGGGTAAATTTCA-TACAGTCATTAACT
1 CAAATTAATATTAAG--AAAAAA-ATGTCCTTTTTATTGGGTAAATTTCACTA-AATCATTAA-T
648433 -TTTTATTTCGAATTTT-ATTTTTAATCTTTAAATATTGAATT
61 ATTTTATTTCGAATTTTCATTTTTAATCTTT-AATATTGAATT
648474 ATTTAATTTG
Statistics
Matches: 92, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
128 14 0.15
129 21 0.23
130 32 0.35
131 25 0.27
ACGTcount: A:0.35, C:0.09, G:0.08, T:0.47
Consensus pattern (126 bp):
CAAATTAATATTAAGAAAAAAATGTCCTTTTTATTGGGTAAATTTCACTAAATCATTAATATTTT
ATTTCGAATTTTCATTTTTAATCTTTAATATTGAATTGTTTCACTTGGAAAAAATTTAGCA
Found at i:649288 original size:24 final size:25
Alignment explanation
Indices: 649261--649313 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
649251 TTTAATATAA
*
649261 AATTTGAGATTTAAAATTTGA-TTT
1 AATTTGAGATTTAAAATTTAAGTTT
* **
649285 AATTTTATTTTTAAAATTTAAGTTT
1 AATTTGAGATTTAAAATTTAAGTTT
649310 AATT
1 AATT
649314 AAAAATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.55
Consensus pattern (25 bp):
AATTTGAGATTTAAAATTTAAGTTT
Found at i:649516 original size:31 final size:31
Alignment explanation
Indices: 649439--649517 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 31
649429 AGTCTGAATC
*
649439 ATTATTTAA--AAAATAAATAAAATATTAAAA
1 ATTATTTAATTAAATTAAATAAAATA-TAAAA
*
649469 ATTATTT-TTTATAATTAAATAAAATA-AAAA
1 ATTATTTAATTA-AATTAAATAAAATATAAAA
649499 TATTATTTAATTAAATTAA
1 -ATTATTTAATTAAATTAA
649518 CTATGATTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
30 11 0.27
31 14 0.34
32 16 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
ATTATTTAATTAAATTAAATAAAATATAAAA
Found at i:650103 original size:24 final size:24
Alignment explanation
Indices: 650042--650103 Score: 56
Period size: 24 Copynumber: 2.6 Consensus size: 24
650032 TAATATATAA
* *
650042 AAATATT-TTTTAAATTTAATTTT
1 AAATATTAATTTAAAATTAATTTT
*
650065 AAATATTAATATAAAATTAATATTT
1 AAATATTAATTTAAAATTAAT-TTT
* *
650090 TAATGTT-ATTTAAA
1 AAATATTAATTTAAA
650104 GGGCTAACCC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 7 0.23
24 16 0.52
25 8 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
AAATATTAATTTAAAATTAATTTT
Found at i:651493 original size:20 final size:22
Alignment explanation
Indices: 651457--651508 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 22
651447 AAATTTAATT
651457 ATAAAAATATATAAAT-AT-TA
1 ATAAAAATATATAAATAATATA
* *
651477 ATAAAAATATTTTAATAATATA
1 ATAAAAATATATAAATAATATA
651499 ATAAATAATA
1 ATAAA-AATA
651509 AAATAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 14 0.52
21 2 0.07
22 7 0.26
23 4 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
ATAAAAATATATAAATAATATA
Found at i:652386 original size:16 final size:16
Alignment explanation
Indices: 652367--652416 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
652357 TAATCAAAAC
652367 TCAAAATAATTTGAAA
1 TCAAAATAATTTGAAA
* *
652383 TCAAAATGATTTGAAT
1 TCAAAATAATTTGAAA
* *
652399 TCGAAATTAATTTAAAA
1 TC-AAAATAATTTGAAA
652416 T
1 T
652417 TTTTAAATCT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 16 0.59
17 11 0.41
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (16 bp):
TCAAAATAATTTGAAA
Found at i:653313 original size:19 final size:20
Alignment explanation
Indices: 653282--653323 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
653272 TCAAATTACA
653282 TAATATATTAAT-ATTTTAT
1 TAATATATTAATAATTTTAT
*
653301 TAATAT-TTAAATAATTTTTT
1 TAATATATT-AATAATTTTAT
653321 TAA
1 TAA
653324 ACATCATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 9 0.45
20 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TAATATATTAATAATTTTAT
Found at i:653428 original size:14 final size:14
Alignment explanation
Indices: 653387--653429 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
653377 TTAAATTTAA
653387 TAATATAAAAATTT
1 TAATATAAAAATTT
653401 TAA-A-AAAATTATTT
1 TAATATAAAA--ATTT
653415 TAATATAAAAATTT
1 TAATATAAAAATTT
653429 T
1 T
653430 CAAAAAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 4 0.16
13 1 0.04
14 15 0.60
15 1 0.04
16 4 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAATATAAAAATTT
Found at i:655931 original size:13 final size:13
Alignment explanation
Indices: 655909--655959 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
655899 TTATAATTTT
*
655909 TATTTTTTATTAA
1 TATTTATTATTAA
655922 TATTTATTA-TAA
1 TATTTATTATTAA
* *
655934 TTAATTA-TAATAA
1 -TATTTATTATTAA
655947 TATTTATTATTAA
1 TATTTATTATTAA
655960 AAATATTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TATTTATTATTAA
Found at i:656008 original size:17 final size:17
Alignment explanation
Indices: 655980--656012 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
655970 AAATCGAATT
655980 AAATTTTATTATTATTTA
1 AAATTTTATTA-TATTTA
655998 AAATTTT-TTATATTT
1 AAATTTTATTATATTT
656013 TTATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 3 0.20
18 7 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
AAATTTTATTATATTTA
Found at i:656034 original size:22 final size:21
Alignment explanation
Indices: 655981--656034 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
655971 AATCGAATTA
* *
655981 AATTTTATTATTATTTAAAAT
1 AATTTAATTTTTATTTAAAAT
**
656002 TTTTTATATTTTTATTTAAAAAT
1 AATTTA-ATTTTTATTT-AAAAT
656025 AATTTAATTT
1 AATTTAATTT
656035 AAAAATTTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
21 3 0.12
22 13 0.52
23 9 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
AATTTAATTTTTATTTAAAAT
Found at i:656133 original size:18 final size:17
Alignment explanation
Indices: 656112--656164 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
656102 TATTAAATAA
656112 TAATTTAAATAAATAAAT
1 TAATTTAAATAAA-AAAT
*
656130 TAATTATAAATTAAAAAT
1 TAATT-TAAATAAAAAAT
*
656148 AATATTTAAAATAAAAA
1 TA-ATTT-AAATAAAAA
656165 TTTATTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 11 0.38
19 18 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAATTTAAATAAAAAAT
Found at i:656165 original size:18 final size:18
Alignment explanation
Indices: 656106--656165 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
656096 TTTTATTATT
656106 AAATAATAATTT-AAATAAA
1 AAATAAT-ATTTAAAAT-AA
* *
656125 TAAATTAAT-TATAAATTAA
1 -AAA-TAATATTTAAAATAA
656144 AAATAATATTTAAAATAA
1 AAATAATATTTAAAATAA
656162 AAAT
1 AAAT
656166 TTATTTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 4 0.12
18 15 0.45
19 4 0.12
20 6 0.18
21 4 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATAATATTTAAAATAA
Found at i:656529 original size:15 final size:15
Alignment explanation
Indices: 656500--656534 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
656490 TAAATCTTAA
*
656500 TTTAA-ATAAATTTT
1 TTTAATATAAAATTT
656514 TTTAATATAAAATTT
1 TTTAATATAAAATTT
656529 TTTAAT
1 TTTAAT
656535 TTAATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTAATATAAAATTT
Found at i:656532 original size:29 final size:28
Alignment explanation
Indices: 656500--656558 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
656490 TAAATCTTAA
*
656500 TTTAAATAAATT-TTTTTAATATAAAATTT
1 TTTAAATAAATTATTATT-AT-TAAAATTT
* *
656529 TTTAATTTAATTATTATTATTAAAATTT
1 TTTAAATAAATTATTATTATTAAAATTT
656557 TT
1 TT
656559 AATTTATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 10 0.38
29 12 0.46
30 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
TTTAAATAAATTATTATTATTAAAATTT
Found at i:657203 original size:12 final size:12
Alignment explanation
Indices: 657186--657211 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
657176 CATATTTAAA
657186 AAAATTAAATTT
1 AAAATTAAATTT
657198 AAAATTAAATTT
1 AAAATTAAATTT
657210 AA
1 AA
657212 TTGATTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAATTAAATTT
Found at i:657295 original size:23 final size:24
Alignment explanation
Indices: 657251--657297 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
657241 AAAATTAAAA
657251 TTTTAATATTTATAATTTTTTTAT
1 TTTTAATATTTATAATTTTTTTAT
*
657275 TTTTAA-A-TTATGATTTATTTTAT
1 TTTTAATATTTATAATTT-TTTTAT
657298 ATTAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 7 0.33
24 6 0.29
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (24 bp):
TTTTAATATTTATAATTTTTTTAT
Found at i:657302 original size:22 final size:22
Alignment explanation
Indices: 657260--657302 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
657250 ATTTTAATAT
*
657260 TTATAATTTTTTTATTTTTAAA
1 TTATAATTTTTTTATTATTAAA
*
657282 TTATGATTTATTTTA-TATTAA
1 TTATAATTT-TTTTATTATTAA
657303 TAAAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTATAATTTTTTTATTATTAAA
Found at i:660356 original size:25 final size:27
Alignment explanation
Indices: 660312--660362 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
660302 CTATATTTTT
* *
660312 TTATTTTTAAAAAATCATATCTTATAC
1 TTATATTTAAAAAATCATATCATATAC
660339 TTATATTT-AAAAAT-ATATCATATA
1 TTATATTTAAAAAATCATATCATATA
660363 AATATCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 9 0.41
26 6 0.27
27 7 0.32
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (27 bp):
TTATATTTAAAAAATCATATCATATAC
Found at i:660531 original size:2 final size:2
Alignment explanation
Indices: 660526--660561 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
660516 GCAAAAACCA
660526 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
660562 TCCAATTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:662057 original size:2 final size:2
Alignment explanation
Indices: 662050--662086 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
662040 TCTTATTGCT
662050 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
662087 TCCCATTTTT
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:662343 original size:26 final size:25
Alignment explanation
Indices: 662294--662343 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
662284 TAGATGTTTT
* **
662294 ATTTAAATTTAAATTTATCCAATGG
1 ATTTAAACTTAAATTTATAAAATGG
662319 ATTTAAACTTAGAATTTATAAAATG
1 ATTTAAACTTA-AATTTATAAAATG
662344 AAATTTGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (25 bp):
ATTTAAACTTAAATTTATAAAATGG
Found at i:662424 original size:14 final size:15
Alignment explanation
Indices: 662397--662443 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
662387 TTAACTTAAA
662397 AAAATTATAAATTTT
1 AAAATTATAAATTTT
662412 AAAATTA-AAATTTT
1 AAAATTATAAATTTT
* *
662426 AAATTTATTAAATATT
1 AAAATTA-TAAATTTT
662442 AA
1 AA
662444 TAAATTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 13 0.46
15 7 0.25
16 8 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATTATAAATTTT
Found at i:662519 original size:13 final size:13
Alignment explanation
Indices: 662501--662528 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
662491 AGATATTAAC
662501 TGTGGGTAATAGT
1 TGTGGGTAATAGT
662514 TGTGGGTAATAGT
1 TGTGGGTAATAGT
662527 TG
1 TG
662529 CTGCTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.39
Consensus pattern (13 bp):
TGTGGGTAATAGT
Found at i:662671 original size:20 final size:19
Alignment explanation
Indices: 662625--662671 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
662615 AAAAAATTTA
662625 TTTAAATTTAATTATAATT
1 TTTAAATTTAATTATAATT
*
662644 TTTAAAATTT-TTTAATAATAT
1 TTT-AAATTTAATT-ATAAT-T
662665 TTTAAAT
1 TTTAAAT
662672 AATATTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.21
20 15 0.62
21 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTAAATTTAATTATAATT
Found at i:662684 original size:11 final size:11
Alignment explanation
Indices: 662638--662678 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
662628 AAATTTAATT
662638 ATAAT-TTTTA
1 ATAATATTTTA
*
662648 A-AATTTTTTA
1 ATAATATTTTA
662658 ATAATATTTTAA
1 ATAATATTTT-A
662670 ATAATATTT
1 ATAATATTT
662679 ATATAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 7 0.26
11 7 0.26
12 10 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATAATATTTTA
Found at i:668752 original size:20 final size:20
Alignment explanation
Indices: 668727--668785 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
668717 ACTGCTAAGG
*
668727 AAATGTATCGATATATTAAT
1 AAATGTATCGATATATTAAC
*
668747 AAATGTATCGATATATGCTTAC
1 AAATGTATCGATATAT--TAAC
*
668769 AATTGTATCGATATATT
1 AAATGTATCGATATATT
668786 TCTCATTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 17 0.50
22 17 0.50
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (20 bp):
AAATGTATCGATATATTAAC
Found at i:668793 original size:20 final size:20
Alignment explanation
Indices: 668730--668801 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
668720 GCTAAGGAAA
** *
668730 TGTATCGATATATTAATAAA
1 TGTATCGATATATTTCTAAT
668750 TGTATCGATATATGCTTAC-AAT
1 TGTATCGATATAT--TT-CTAAT
*
668772 TGTATCGATATATTTCTCAT
1 TGTATCGATATATTTCTAAT
*
668792 TGTTTCGATA
1 TGTATCGATA
668802 CATTCTAGGT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
19 1 0.02
20 26 0.60
22 16 0.37
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.44
Consensus pattern (20 bp):
TGTATCGATATATTTCTAAT
Found at i:676348 original size:58 final size:59
Alignment explanation
Indices: 676224--676338 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 59
676214 TAAAAAAAAC
* *
676224 AAAAAAAATTACAAAAAAACTTGGTGAAACACAAGCTTCGAGATTCACCCAATCTTGAT
1 AAAAAAAATTACAAAAAAACTTAGTGAAACACAAGCTTCGAGATTCACCCAATCCTGAT
* *
676283 AAAAAAAA-TACAAAAAAACTTAGTGAGACACAAGCTTCGAGACTT-ACCCACTCCTG
1 AAAAAAAATTACAAAAAAACTTAGTGAAACACAAGCTTCGAGA-TTCACCCAATCCTG
676339 GTTTTAAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 41 0.80
59 10 0.20
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.20
Consensus pattern (59 bp):
AAAAAAAATTACAAAAAAACTTAGTGAAACACAAGCTTCGAGATTCACCCAATCCTGAT
Found at i:677388 original size:33 final size:33
Alignment explanation
Indices: 677348--677455 Score: 126
Period size: 33 Copynumber: 3.3 Consensus size: 33
677338 TCTCTTCTCC
* * * *
677348 AAGTCCACGATTCAGTGGCATCATTCTCCTTCA
1 AAGTCCACAACTCAGTGGCATCATTTTTCTTCA
* * *
677381 AAGTCCACAACTCAGCGGCATCTTTTTTCTTTA
1 AAGTCCACAACTCAGTGGCATCATTTTTCTTCA
* *
677414 AAGTCCACAACCCAGTGGCATTATTTTTCTTCA
1 AAGTCCACAACTCAGTGGCATCATTTTTCTTCA
*
677447 AAGCCCACA
1 AAGTCCACA
677456 TAAGTTGGTG
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.31
Consensus pattern (33 bp):
AAGTCCACAACTCAGTGGCATCATTTTTCTTCA
Found at i:677494 original size:42 final size:42
Alignment explanation
Indices: 677437--677590 Score: 154
Period size: 42 Copynumber: 4.0 Consensus size: 42
677427 AGTGGCATTA
* * *
677437 TTTTTC-T-TCAAAGCCCACATAAGTTGGTGGCATCCTTTTT
1 TTTTTCTTCTCAAAGCCCACACAAGCTGGTGGCAACCTTTTT
677477 TTTTTCTTCTCAAAGCCCACACAAGCTGGTGGCAACC-----
1 TTTTTCTTCTCAAAGCCCACACAAGCTGGTGGCAACCTTTTT
**
677514 ----T-TTCTCAAAGCCCACACAAG-TCGGTGGCATTCTTTTT
1 TTTTTCTTCTCAAAGCCCACACAAGCT-GGTGGCAACCTTTTT
*
677551 TTTTTCTTCTCAAAGCCCACATAAGCTGGTGGCAACCTTT
1 TTTTTCTTCTCAAAGCCCACACAAGCTGGTGGCAACCTTT
677591 CTCAAAGCCC
Statistics
Matches: 92, Mismatches: 8, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
31 1 0.01
32 27 0.29
33 1 0.01
40 6 0.07
41 2 0.02
42 54 0.59
43 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.35
Consensus pattern (42 bp):
TTTTTCTTCTCAAAGCCCACACAAGCTGGTGGCAACCTTTTT
Found at i:677523 original size:32 final size:31
Alignment explanation
Indices: 677482--677948 Score: 320
Period size: 32 Copynumber: 14.5 Consensus size: 31
677472 TTTTTTTTTT
677482 CTTCTCAAAGCCCACACAAGCTGGTGGCAACC
1 CTTCTCAAAGCCCACACAAG-TGGTGGCAACC
* * *
677514 TTTCTCAAAGCCCACACAAGTCGGTGGCATTCTTTTTTTTTT
1 CTTCTCAAAGCCCACACAAGT-GGTGGCA-AC---------C
*
677556 CTTCTCAAAGCCCACATAAGCTGGTGGCAACC
1 CTTCTCAAAGCCCACACAAG-TGGTGGCAACC
* *
677588 TTTCTCAAAGCCCACATAAGTCGGTGGCAACC
1 CTTCTCAAAGCCCACACAAGT-GGTGGCAACC
* * *
677620 CTTCTTAAAGCCTACACAAACTGGTGGCAACC
1 CTTCTCAAAGCCCACAC-AAGTGGTGGCAACC
*
677652 TTTCTCAAAGCCCACACAAGTTGGTGGCAACC
1 CTTCTCAAAGCCCACACAAG-TGGTGGCAACC
* **
677684 CTTCT-AAAGCCCGCGTAAGTCGGTGGCAACC
1 CTTCTCAAAGCCCACACAAGT-GGTGGCAACC
* * * *
677715 CTTCTCAAAGCTCACACAAATCGATGGCACCC
1 CTTCTCAAAGCCCACACAAGT-GGTGGCAACC
* * *
677747 CTTCT-AAAGCCTATAAAAGTTGGTGGCAACC
1 CTTCTCAAAGCCCACACAAG-TGGTGGCAACC
**
677778 CTTCTCAAAGCCCACACAAACCGGTGGCAA-C
1 CTTCTCAAAGCCCACAC-AAGTGGTGGCAACC
* * * *
677809 CTTCTTAAAACCCATACAAGTTAGTGGCAACC
1 CTTCTCAAAGCCCACACAAG-TGGTGGCAACC
* * * *
677841 CTTCTCAAAG-CCATACAAGTCGGTGGTATCA
1 CTTCTCAAAGCCCACACAAGT-GGTGGCAACC
* * *
677872 TTTCT-AAAGCCCACACAAGTCGTTAGCAACCC
1 CTTCTCAAAGCCCACACAAGT-GGTGGCAA-CC
* *
677904 CTT-TCAAAAGCTCACACAAGTCGGTGGCATCCC
1 CTTCTC-AAAGCCCACACAAGT-GGTGGCA-ACC
677937 CTTCT--AAGCCCA
1 CTTCTCAAAGCCCA
677949 ATGTCGTTGG
Statistics
Matches: 341, Mismatches: 65, Indels: 59
0.73 0.14 0.13
Matches are distributed among these distances:
30 8 0.02
31 114 0.33
32 160 0.47
33 31 0.09
34 1 0.00
41 1 0.00
42 25 0.07
43 1 0.00
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (31 bp):
CTTCTCAAAGCCCACACAAGTGGTGGCAACC
Found at i:677523 original size:74 final size:74
Alignment explanation
Indices: 677439--677680 Score: 315
Period size: 74 Copynumber: 3.4 Consensus size: 74
677429 TGGCATTATT
* *
677439 TTTCTTCAAAGCCCACATAAGTTGGTGGCATCCTTTTTTTTTTCTTCTCAAAGCCCACACAAGCT
1 TTTC-TCAAAGCCCACACAAGTCGGTGGCATCCTTTTTTTTTTCTTCTCAAAGCCCACACAAGCT
677504 GGTGGCAACC
65 GGTGGCAACC
* *
677514 TTTCTCAAAGCCCACACAAGTCGGTGGCATTCTTTTTTTTTTCTTCTCAAAGCCCACATAAGCTG
1 TTTCTCAAAGCCCACACAAGTCGGTGGCATCCTTTTTTTTTTCTTCTCAAAGCCCACACAAGCTG
677579 GTGGCAACC
66 GTGGCAACC
* * * * *
677588 TTTCTCAAAGCCCACATAAGTCGGTGGCAACC----------CTTCTTAAAGCCTACACAAACTG
1 TTTCTCAAAGCCCACACAAGTCGGTGGCATCCTTTTTTTTTTCTTCTCAAAGCCCACACAAGCTG
677643 GTGGCAACC
66 GTGGCAACC
*
677652 TTTCTCAAAGCCCACACAAGTTGGTGGCA
1 TTTCTCAAAGCCCACACAAGTCGGTGGCA
677681 ACCCTTCTAA
Statistics
Matches: 154, Mismatches: 13, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
64 55 0.36
74 95 0.62
75 4 0.03
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (74 bp):
TTTCTCAAAGCCCACACAAGTCGGTGGCATCCTTTTTTTTTTCTTCTCAAAGCCCACACAAGCTG
GTGGCAACC
Found at i:677724 original size:63 final size:63
Alignment explanation
Indices: 677556--677948 Score: 366
Period size: 63 Copynumber: 6.2 Consensus size: 63
677546 TTTTTTTTTT
* * *
677556 CTTCTCAAAGCCCACATAAG-CTGGTGGCAACCTTTCTCAAAGCCCACATAAGTCGGTGGCAACC
1 CTTCT-AAAGCCCACAAAAGTC-GGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTGGCAACC
* * * *
677620 CTTCTTAAAGCCTACACAAACT-GGTGGCAACCTTTCTCAAAGCCCACACAAGTTGGTGGCAACC
1 CTTC-TAAAGCCCACA-AAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTGGCAACC
* ** * * * *
677684 CTTCTAAAGCCCGCGTAAGTCGGTGGCAACCCTTCTCAAAGCTCACACAAATCGATGGCACCC
1 CTTCTAAAGCCCACAAAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTGGCAACC
* * * **
677747 CTTCTAAAGCCTATAAAAGTTGGTGGCAACCCTTCTCAAAGCCCACACAAACCGGTGGCAA-C
1 CTTCTAAAGCCCACAAAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTGGCAACC
* * * ** * * * *
677809 CTTCTTAAAACCCATACAAGTTAGTGGCAACCCTTCTCAAAG-CCATACAAGTCGGTGGTATCA
1 CTTC-TAAAGCCCACAAAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTGGCAACC
* * * * * *
677872 TTTCTAAAGCCCACACAAGTCGTTAGCAACCCCTT-TCAAAAGCTCACACAAGTCGGTGGCATCC
1 CTTCTAAAGCCCACAAAAGTCGGTGGCAA-CCCTTCTC-AAAGCCCACACAAGTCGGTGGCA-AC
677936 C
63 C
677937 CTTCT-AAGCCCA
1 CTTCTAAAGCCCA
677949 ATGTCGTTGG
Statistics
Matches: 270, Mismatches: 49, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
62 43 0.16
63 140 0.52
64 79 0.29
65 8 0.03
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (63 bp):
CTTCTAAAGCCCACAAAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTGGCAACC
Found at i:678082 original size:52 final size:52
Alignment explanation
Indices: 678001--678202 Score: 201
Period size: 52 Copynumber: 3.9 Consensus size: 52
677991 ATCTCTTTTT
* * * *
678001 AATATTGCTAGCCTTGAATCAACACATTGGCACCTTTTTCTTTCTTAAGTCC
1 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTCTTAAGTCC
* * ** * *
678053 AATATCGCTGGCCTTGAATTAGTATATTGGCACCTTTGTGATGT-TTAAGTCT
1 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-TTCTTTCTTAAGTCC
* * * *
678105 GATATCGCTGGCTTTGAATCAGCATATTGGCACCTTTGTC-ATCTTTAAGTCC
1 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTC-TTAAGTCC
* * * * *
678157 AATATCGCTGACCTTAAATCAGCATATCGGCACCTTTATCATTCTT
1 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTCTT
678203 CTCATCTTCA
Statistics
Matches: 120, Mismatches: 26, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
50 1 0.01
52 114 0.95
53 5 0.04
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (52 bp):
AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTCTTAAGTCC
Found at i:678304 original size:39 final size:39
Alignment explanation
Indices: 678248--678323 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
678238 GGCACATTTA
678248 CACCTTTGTCATCTTTAAGCCCAATATCGTTGGGCTTAG
1 CACCTTTGTCATCTTTAAGCCCAATATCGTTGGGCTTAG
*
678287 CACCTTTGTCATGTTTAAGCCCAATATCGTTGGGCTT
1 CACCTTTGTCATCTTTAAGCCCAATATCGTTGGGCTT
678324 GAATCAGCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (39 bp):
CACCTTTGTCATCTTTAAGCCCAATATCGTTGGGCTTAG
Found at i:678395 original size:61 final size:61
Alignment explanation
Indices: 678295--678533 Score: 246
Period size: 61 Copynumber: 3.9 Consensus size: 61
678285 AGCACCTTTG
* * ** * *
678295 TCATGTTTAAGCCCAATATCGTTGGGCTTGAATCAGCATATTGGCACCTTTATCATTCTTC
1 TCATCTTTAAGCCTAATATCACTGGCCTTAAATCAGCATATTGGCACCTTTATCATTCTTC
* *
678356 TCATCTTTAAGCCTAATATCACTGGCCTTAAATCAGCATATTGGCATCTTTATCATTCTTT
1 TCATCTTTAAGCCTAATATCACTGGCCTTAAATCAGCATATTGGCACCTTTATCATTCTTC
* * * * *
678417 TCATATTCAAGCCTGATATCACTAG-CTGTAAATCAGCATATTGGCACCTCTATCATTCTTC
1 TCATCTTTAAGCCTAATATCACTGGCCT-TAAATCAGCATATTGGCACCTTTATCATTCTTC
* * * * *** * * * *
678478 GCATCCTTAAGTCTAACATTGTTGACCTTAAATCAGTACATTGGCACCTTTCTCAT
1 TCATCTTTAAGCCTAATATCACTGGCCTTAAATCAGCATATTGGCACCTTTATCAT
678534 CTTTATCATT
Statistics
Matches: 145, Mismatches: 31, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
60 2 0.01
61 141 0.97
62 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (61 bp):
TCATCTTTAAGCCTAATATCACTGGCCTTAAATCAGCATATTGGCACCTTTATCATTCTTC
Found at i:688198 original size:22 final size:20
Alignment explanation
Indices: 688184--688221 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
688174 TACATGCTCA
688184 CAATTGTATCGATACATTAT
1 CAATTGTATCGATACATTAT
*
688204 CTATTGTATCGATACATT
1 CAATTGTATCGATACATT
688222 CTGGGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
CAATTGTATCGATACATTAT
Found at i:692055 original size:24 final size:23
Alignment explanation
Indices: 692018--692066 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
692008 TAATAATATA
**
692018 TTTTATATTATATTTTTAATTAT
1 TTTTATATTATATTTAAAATTAT
*
692041 TTTTATTATTGTATTTAAAATTAT
1 TTTTA-TATTATATTTAAAATTAT
692065 TT
1 TT
692067 GTACAAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTATATTATATTTAAAATTAT
Found at i:698783 original size:21 final size:21
Alignment explanation
Indices: 698749--698788 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
698739 TATTTTTATT
698749 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
698770 TAAATATTAA-TATAAAATA
1 TAAAT-TTAATTATAAAATA
698789 ATTTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:702154 original size:21 final size:22
Alignment explanation
Indices: 702112--702155 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
702102 ATATTAAAAA
*
702112 ATATATTTTTATATTACTATTT
1 ATATATTTTTATATTACAATTT
702134 ATATA-TTTTATAATTA-AATTT
1 ATATATTTTTAT-ATTACAATTT
702155 A
1 A
702156 AATAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
ATATATTTTTATATTACAATTT
Found at i:703015 original size:33 final size:33
Alignment explanation
Indices: 702978--703045 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
702968 TTTAAAAGTT
*
702978 TTAGAGATAACATTTATCTT-TAATACTATTAAA
1 TTAGAGATAACATTTAT-TTCCAATACTATTAAA
*
703011 TTAGAGATTACATTTATTTCCAATACTATTAAA
1 TTAGAGATAACATTTATTTCCAATACTATTAAA
703044 TT
1 TT
703046 CAAAATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 2 0.06
33 30 0.94
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (33 bp):
TTAGAGATAACATTTATTTCCAATACTATTAAA
Found at i:703105 original size:16 final size:16
Alignment explanation
Indices: 703084--703114 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
703074 CTCTTATCTC
703084 ATCTTTAAAAATCTTA
1 ATCTTTAAAAATCTTA
703100 ATCTTTAAAAATCTT
1 ATCTTTAAAAATCTT
703115 TTATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (16 bp):
ATCTTTAAAAATCTTA
Found at i:705102 original size:2 final size:2
Alignment explanation
Indices: 705097--705121 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
705087 ATAAAAAAGC
705097 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
705122 CATACTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:705366 original size:17 final size:17
Alignment explanation
Indices: 705324--705382 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
705314 ATTATATAAA
705324 TATATTAA-A-ATATTT
1 TATATTAATATATATTT
**
705339 TA-AAAAATATATATTT
1 TATATTAATATATATTT
705355 TATATTAATATATATTT
1 TATATTAATATATATTT
705372 TATAATTAATA
1 TAT-ATTAATA
705383 GTAAATAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 3 0.08
15 3 0.08
16 8 0.22
17 15 0.42
18 7 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATATTAATATATATTT
Found at i:705644 original size:32 final size:36
Alignment explanation
Indices: 705582--705705 Score: 118
Period size: 32 Copynumber: 3.6 Consensus size: 36
705572 TAATATGAAA
*
705582 ATAATATA-TAAATATATCAAAATATGTAT-AATAT
1 ATAATATATTAAATATATCAAAATATATATAAATAT
*
705616 A-AAT-TATTAAA-ATATCAAAATTTATATAAAATAT
1 ATAATATATTAAATATATCAAAATATATAT-AAATAT
** * *
705650 ATAATATATTAAATATTATCGTAATACATAAAAATAT
1 ATAATATATTAAATA-TATCAAAATATATATAAATAT
705687 ATAA-ATATATAAAT-TATCA
1 ATAATATAT-TAAATATATCA
705706 TATCGAAAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 15
0.76 0.08 0.15
Matches are distributed among these distances:
32 16 0.22
33 7 0.09
34 7 0.09
35 7 0.09
36 11 0.15
37 16 0.22
38 10 0.14
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (36 bp):
ATAATATATTAAATATATCAAAATATATATAAATAT
Found at i:705649 original size:34 final size:35
Alignment explanation
Indices: 705582--705705 Score: 116
Period size: 37 Copynumber: 3.6 Consensus size: 35
705572 TAATATGAAA
* *
705582 ATAATATA-TAAATATATCAAAATATGTATAATAT
1 ATAATATATTAAATATATCAAAATATATAAAATAT
705616 A-AAT-TATTAAA-ATATCAAAATTTATATAAAATAT
1 ATAATATATTAAATATATCAAAA--TATATAAAATAT
** *
705650 ATAATATATTAAATATTATCGTAATACATAAAAATAT
1 ATAATATATTAAATA-TATCAAAATATAT-AAAATAT
705687 ATAA-ATATATAAAT-TATCA
1 ATAATATAT-TAAATATATCA
705706 TATCGAAAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
32 11 0.15
33 7 0.09
34 12 0.16
35 7 0.09
36 15 0.20
37 17 0.23
38 6 0.08
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (35 bp):
ATAATATATTAAATATATCAAAATATATAAAATAT
Found at i:706088 original size:16 final size:15
Alignment explanation
Indices: 706027--706102 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 15
706017 ATAATTTAGT
*
706027 TTTTATTTATATTAT
1 TTTTATTTATATTAA
*
706042 TTTTATGTATTATT-A
1 TTTTATTTA-TATTAA
* * *
706057 TTGTATTTAAAATAA
1 TTTTATTTATATTAA
706072 TATTTATTTATATTAA
1 T-TTTATTTATATTAA
*
706088 TTTTA-ATATATTAA
1 TTTTATTTATATTAA
706102 T
1 T
706103 AATTTATATT
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
14 11 0.23
15 21 0.44
16 16 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TTTTATTTATATTAA
Found at i:706092 original size:27 final size:27
Alignment explanation
Indices: 706062--706113 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
706052 TATTATTGTA
* *
706062 TTTAAAATAATATTTATTTATATTAAT
1 TTTAAAATAATAATAATTTATATTAAT
* *
706089 TTTAATATATTAATAATTTATATTA
1 TTTAAAATAATAATAATTTATATTA
706114 TAATATATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTAAAATAATAATAATTTATATTAAT
Found at i:707885 original size:6 final size:6
Alignment explanation
Indices: 707874--707907 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
707864 TTCACGTTGT
707874 ATAAAA ATAAAA AT-AAA AT-AAA ATAAAA ATAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
707908 TATTAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.37
6 17 0.63
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:707898 original size:16 final size:16
Alignment explanation
Indices: 707877--707909 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
707867 ACGTTGTATA
707877 AAAATAAAAATAAAAT
1 AAAATAAAAATAAAAT
707893 AAAATAAAAATAAAAT
1 AAAATAAAAATAAAAT
707909 A
1 A
707910 TTAATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAATAAAAATAAAAT
Found at i:708494 original size:2 final size:2
Alignment explanation
Indices: 708487--708513 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
708477 ATACATATGC
708487 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
708514 AAGTTTGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:710476 original size:18 final size:18
Alignment explanation
Indices: 710450--710488 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
710440 GGAAGTTTTC
710450 TATGAATATAAAAATTAA
1 TATGAATATAAAAATTAA
* * *
710468 TATGGATATAGAAATTGA
1 TATGAATATAAAAATTAA
710486 TAT
1 TAT
710489 ATATATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (18 bp):
TATGAATATAAAAATTAA
Found at i:710492 original size:2 final size:2
Alignment explanation
Indices: 710485--710523 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
710475 ATAGAAATTG
710485 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
710524 GGTTGAGAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:713957 original size:76 final size:75
Alignment explanation
Indices: 713808--713996 Score: 245
Period size: 76 Copynumber: 2.5 Consensus size: 75
713798 GTCTCATATA
* * *
713808 ATTAAAAAATAAATAAATTATATTTAAATAATA-TTTTATTATAAATAATATATTAACTAAACTT
1 ATTAAAAATTAATTAAATTACATTTAAATAATATTTTTATTATAAATAATATATTAACTAAACTT
*
713872 AATCTAATAC
66 AATCCAATAC
* * * *
713882 ATTAAAAACTTAATTAAATTACATTTAAATAATATTTTTATTATAAATAATTTGTTGACTAAATT
1 ATTAAAAA-TTAATTAAATTACATTTAAATAATATTTTTATTATAAATAATATATTAACTAAACT
**
713947 TGGTCCAATAC
65 TAATCCAATAC
* *
713958 ATTAAAAATATAATTAAATTGCATTTAAAAAATATTTTT
1 ATTAAAAAT-TAATTAAATTACATTTAAATAATATTTTT
713997 TTGATCACAA
Statistics
Matches: 100, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
74 8 0.08
75 23 0.23
76 69 0.69
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (75 bp):
ATTAAAAATTAATTAAATTACATTTAAATAATATTTTTATTATAAATAATATATTAACTAAACTT
AATCCAATAC
Found at i:715786 original size:17 final size:17
Alignment explanation
Indices: 715750--715789 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
715740 AATTTTAATA
*
715750 TATTTATATATTTATAT
1 TATTTTTATATTTATAT
* *
715767 TATTTTTATATTTTTTT
1 TATTTTTATATTTATAT
715784 TATTTT
1 TATTTT
715790 ATTCGTGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TATTTTTATATTTATAT
Found at i:716692 original size:36 final size:33
Alignment explanation
Indices: 716636--716716 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 33
716626 AGTATAAACA
* **
716636 TTAAAAATATATTAAGTTATTTAAATTTTAAAATT
1 TTAAAAA-ATATTAAATTA-TTAAAAATTAAAATT
716671 TAATAAAAAATATTAAATTATTAAAAATTAAAATT
1 T--TAAAAAATATTAAATTATTAAAAATTAAAATT
716706 TTAAAAAATAT
1 TTAAAAAATAT
716717 GTTTAAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
33 10 0.24
35 15 0.37
36 10 0.24
37 6 0.15
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (33 bp):
TTAAAAAATATTAAATTATTAAAAATTAAAATT
Found at i:717043 original size:2 final size:2
Alignment explanation
Indices: 717036--717068 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
717026 ACTTTGGAGC
717036 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
717069 GGCTGAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:717309 original size:2 final size:2
Alignment explanation
Indices: 717297--717398 Score: 73
Period size: 2 Copynumber: 56.0 Consensus size: 2
717287 CTTCATACAT
* *
717297 TA TA T- TA TA TA TA TT TA T- TA TA T- TA TA TG T- TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
717334 TA TA TA TA TA TA T- TA TGC TA TA TA T- TA TA T- TA -A TA TA AA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
*
717373 TA TA TA TA -A TA TA TA CA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
717399 ACATATAATA
Statistics
Matches: 79, Mismatches: 9, Indels: 24
0.71 0.08 0.21
Matches are distributed among these distances:
1 11 0.14
2 67 0.85
3 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:717343 original size:25 final size:27
Alignment explanation
Indices: 717296--717363 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 27
717286 CCTTCATACA
717296 TTATATTATATATATTTATTATATTATATG-
1 TTATATTATATATA-TTA-TATA-T-TATGC
717326 TTATATTATATATA-TATATATTATGC
1 TTATATTATATATATTATATATTATGC
717352 TATATATTATAT
1 T-TATATTATAT
717364 TAATATAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
25 4 0.11
26 2 0.06
27 14 0.39
28 2 0.06
30 14 0.39
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.57
Consensus pattern (27 bp):
TTATATTATATATATTATATATTATGC
Found at i:717348 original size:32 final size:32
Alignment explanation
Indices: 717295--717387 Score: 113
Period size: 30 Copynumber: 3.0 Consensus size: 32
717285 CCCTTCATAC
717295 ATTATATTATATATAT-T-TATTATATTATAT
1 ATTATATTATATATATATATATTATATTATAT
* **
717325 GTTATATTATATATATATATATTATGCTATAT
1 ATTATATTATATATATATATATTATATTATAT
* *
717357 ATTATATTA-ATATAAATATA-TATAATATAT
1 ATTATATTATATATATATATATTATATTATAT
717387 A
1 A
717388 CATAATATAT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
30 24 0.44
31 11 0.20
32 19 0.35
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (32 bp):
ATTATATTATATATATATATATTATATTATAT
Found at i:717369 original size:25 final size:25
Alignment explanation
Indices: 717304--717398 Score: 76
Period size: 27 Copynumber: 3.8 Consensus size: 25
717294 CATTATATTA
717304 TATATATT-TATT-ATAT-TATATG
1 TATATATTATATTAATATATATATG
717326 T-TATATTATA-TATATATATATTATG
1 TATATATTATATTA-ATATATA-TATG
* *
717351 CTATATATTATATTAATATAAATATA
1 -TATATATTATATTAATATATATATG
*
717377 TATA-ATATATACATAATATATA
1 TATATAT-TATA-TTAATATATA
717399 ACATATAATA
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
21 7 0.12
22 3 0.05
23 4 0.07
24 4 0.07
25 12 0.20
26 12 0.20
27 15 0.25
28 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (25 bp):
TATATATTATATTAATATATATATG
Found at i:717522 original size:19 final size:20
Alignment explanation
Indices: 717489--717539 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
717479 ATATCTTGTA
717489 ATTTTTTTACATTTTACT-TT
1 ATTTTTTTACATTTT-CTATT
* *
717509 ATTTTTTTA-GTTTTGTATT
1 ATTTTTTTACATTTTCTATT
717528 ATTTTTTT-CATT
1 ATTTTTTTACATT
717540 AAGTTTCTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 1 0.04
19 16 0.62
20 9 0.35
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.73
Consensus pattern (20 bp):
ATTTTTTTACATTTTCTATT
Found at i:719665 original size:10 final size:8
Alignment explanation
Indices: 719638--719671 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
719628 TTCTCTTTTT
719638 TTTTTTAA
1 TTTTTTAA
719646 TTTTTTAA
1 TTTTTTAA
719654 TTTTTTAAA
1 TTTTTT-AA
*
719663 ATTTTTAA
1 TTTTTTAA
719671 T
1 T
719672 GTATCAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTTTAA
Found at i:719899 original size:14 final size:16
Alignment explanation
Indices: 719865--719897 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
719855 ACACATTTTG
719865 AAAAT-TAATTTTAAA
1 AAAATATAATTTTAAA
719880 AAAATATAA-TTTAAA
1 AAAATATAATTTTAAA
719895 AAA
1 AAA
719898 TAAAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATATAATTTTAAA
Found at i:720104 original size:13 final size:13
Alignment explanation
Indices: 720081--720135 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
720071 TTAATTTTTA
720081 AAATAATTATATTT
1 AAAT-ATTATATTT
*
720095 TAATATTATATTT
1 AAATATTATATTT
720108 AAATA-TATA-TT
1 AAATATTATATTT
*
720119 AAATATAAATATTT
1 AAATAT-TATATTT
720133 AAA
1 AAA
720136 AAATTAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
11 7 0.20
12 4 0.11
13 16 0.46
14 8 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AAATATTATATTT
Found at i:720119 original size:17 final size:17
Alignment explanation
Indices: 720097--720130 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
720087 TTATATTTTA
* *
720097 ATATTATATTTAAATAT
1 ATATTAAATATAAATAT
720114 ATATTAAATATAAATAT
1 ATATTAAATATAAATAT
720131 TTAAAAAATT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATTAAATATAAATAT
Found at i:720145 original size:16 final size:18
Alignment explanation
Indices: 720119--720151 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
720109 AATATATATT
720119 AAATATAAAT-ATTTAAA
1 AAATATAAATAATTTAAA
720136 AAAT-TAAATAATTTAA
1 AAATATAAATAATTTAA
720152 TATAGTCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATATAAATAATTTAAA
Found at i:720511 original size:24 final size:24
Alignment explanation
Indices: 720490--720544 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
720480 AATTATATTC
* *
720490 AAAATATTTTTATTATCAATATAT
1 AAAATAATTATATTATCAATATAT
* *
720514 AAAATAATTATATTATTATTATAAT
1 AAAATAATTATATTATCAATAT-AT
720539 AAAATA
1 AAAATA
720545 TATGAACCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 18 0.69
25 8 0.31
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
AAAATAATTATATTATCAATATAT
Found at i:720667 original size:1 final size:1
Alignment explanation
Indices: 720661--720687 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
720651 TTTGTTGAAG
720661 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
720688 AAAAAGTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:732828 original size:50 final size:50
Alignment explanation
Indices: 732753--732904 Score: 166
Period size: 50 Copynumber: 3.0 Consensus size: 50
732743 GTAAAGTGAT
* *
732753 TTAATTATTTTTTATTAATAT-TTGACAATCGAAAAAGATGATCGTAATTG
1 TTAATTATTTTTTATCAAT-TCTTGACAATCGAAAGAGATGATCGTAATTG
* * *
732803 TTAATTATTTTTTATCAATTCTTGACAATCGAGAGAGGTGGTCGTAATTG
1 TTAATTATTTTTTATCAATTCTTGACAATCGAAAGAGATGATCGTAATTG
* * * * *
732853 TTAACTATTTTTCA-CTAA-CCTTTGATAATCGAAAGAGATGAACGTAATTG
1 TTAATTATTTTTTATC-AATTC-TTGACAATCGAAAGAGATGATCGTAATTG
732903 TT
1 TT
732905 GACTATTCTT
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
49 3 0.03
50 83 0.97
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (50 bp):
TTAATTATTTTTTATCAATTCTTGACAATCGAAAGAGATGATCGTAATTG
Found at i:732910 original size:50 final size:48
Alignment explanation
Indices: 732773--732935 Score: 164
Period size: 50 Copynumber: 3.3 Consensus size: 48
732763 TTTATTAATA
* * * *
732773 TTTGACAATCGAAAAAGATGATCGTAATTGTTAATTATTTTTTATCAAT
1 TTTGACAATCGAAAGAGATGATCGTAATTGTTAACTATTTTTCAT-AAC
* * *
732822 TCTTGACAATCGAGAGAGGTGGTCGTAATTGTTAACTATTTTTCACTAACC
1 T-TTGACAATCGAAAGAGATGATCGTAATTGTTAACTATTTTTCA-TAA-C
* * * *
732873 TTTGATAATCGAAAGAGATGAACGTAATTGTTGACTATTCTTCATTAAC
1 TTTGACAATCGAAAGAGATGATCGTAATTGTTAACTATTTTTCA-TAAC
* *
732922 TTTGATAATAGAAA
1 TTTGACAATCGAAA
732936 AATGTTACCG
Statistics
Matches: 95, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
49 15 0.16
50 78 0.82
51 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (48 bp):
TTTGACAATCGAAAGAGATGATCGTAATTGTTAACTATTTTTCATAAC
Found at i:737391 original size:50 final size:50
Alignment explanation
Indices: 737311--737566 Score: 334
Period size: 50 Copynumber: 5.1 Consensus size: 50
737301 ACAAAGTGAT
* ** *
737311 TTGACTATTCTTCACCAACCTTTGATAATCGAGAGAGGTGGTCGTAATTA
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
*
737361 TTGACTATTCTTCACCAACTTTTGACAATCGAGAGAGGTGACCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
* * * *
737411 TTAACTGTTCTTTACCAACCTTTGACAATCGAGAGAGATGACCAGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACC-GTAATTG
* *
737462 TTGACTATTCTTCACCAACCTTTGACAATCAAGAGAGGTGGCCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
* * * * ** *
737512 TTAACTATTCTTCACAAACTTTTGATAATAAAGA-AAGTGACCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
737561 TTGACT
1 TTGACT
737567 CTAAGCATCT
Statistics
Matches: 181, Mismatches: 24, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
49 18 0.10
50 119 0.66
51 44 0.24
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (50 bp):
TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
Found at i:737497 original size:101 final size:99
Alignment explanation
Indices: 737314--737566 Score: 353
Period size: 101 Copynumber: 2.5 Consensus size: 99
737304 AAGTGATTTG
** *
737314 ACTATTCTTCACCAACCTTTGATAATCGAGAGAGGTGGTCGTAATTATTGACTATTCTTCACCAA
1 ACTATTCTTCACCAACCTTTGATAATCGAGAGA-GTGACCGTAATTGTTGACTATTCTTCACCAA
* *
737379 CTTTTGACAATCGAGAGAGGTGACCGTAATTGTTA
65 CCTTTGACAATCAAGAGAGGTGACCGTAATTGTTA
* * *
737414 ACTGTTCTTTACCAACCTTTGACAATCGAGAGAGATGACCAGTAATTGTTGACTATTCTTCACCA
1 ACTATTCTTCACCAACCTTTGATAATCGAGAGAG-TGACC-GTAATTGTTGACTATTCTTCACCA
*
737479 ACCTTTGACAATCAAGAGAGGTGGCCGTAATTGTTA
64 ACCTTTGACAATCAAGAGAGGTGACCGTAATTGTTA
* * ** *
737515 ACTATTCTTCACAAACTTTTGATAATAAAGAAAGTGACCGTAATTGTTGACT
1 ACTATTCTTCACCAACCTTTGATAATCGAGAGAGTGACCGTAATTGTTGACT
737567 CTAAGCATCT
Statistics
Matches: 134, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
99 14 0.10
100 38 0.28
101 82 0.61
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (99 bp):
ACTATTCTTCACCAACCTTTGATAATCGAGAGAGTGACCGTAATTGTTGACTATTCTTCACCAAC
CTTTGACAATCAAGAGAGGTGACCGTAATTGTTA
Found at i:737931 original size:22 final size:22
Alignment explanation
Indices: 737894--737952 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
737884 CGATTAGACA
*
737894 ATTTAATTAAATTAAATTTAAAT
1 ATTTAAAT-AATTAAATTTAAAT
737917 -TATTAAATAATTAAATTTAAAT
1 AT-TTAAATAATTAAATTTAAAT
*
737939 ATTTAAATATTTAA
1 ATTTAAATAATTAA
737953 TTTGAGTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 26 0.81
23 6 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTAAATAATTAAATTTAAAT
Found at i:738241 original size:19 final size:19
Alignment explanation
Indices: 738217--738284 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
738207 TAGATATGGT
738217 AAAATATAAATACAATATA
1 AAAATATAAATACAATATA
*
738236 AAAATATAAAATACAAAAT-
1 AAAATAT-AAATACAATATA
* *
738255 AAAATAT-GATAAAATATTA
1 AAAATATAAATACAATA-TA
738274 AAAATA-AAATA
1 AAAATATAAATA
738285 AAAATGATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
17 6 0.15
18 1 0.03
19 23 0.57
20 10 0.25
ACGTcount: A:0.71, C:0.03, G:0.01, T:0.25
Consensus pattern (19 bp):
AAAATATAAATACAATATA
Found at i:738249 original size:20 final size:20
Alignment explanation
Indices: 738217--738270 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
738207 TAGATATGGT
*
738217 AAAATAT-AAATACAATATA
1 AAAATATAAAATACAAAATA
738236 AAAATATAAAATACAAAATA
1 AAAATATAAAATACAAAATA
738256 AAATATGATAAAATA
1 AAA-AT-ATAAAATA
738271 TTAAAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 7 0.23
20 14 0.45
21 2 0.06
22 8 0.26
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAATATAAAATACAAAATA
Found at i:738258 original size:38 final size:37
Alignment explanation
Indices: 738216--738299 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 37
738206 TTAGATATGG
* *
738216 TAAAATATAAATACAATATAAAAATATAAAATACAAA-A
1 TAAAATAT-AATAAAATATAAAAA-ATAAAATAAAAAGA
* *
738254 TAAAATATGATAAAATATTAAAAATAAAATAAAAATGA
1 TAAAATATAATAAAATATAAAAAATAAAATAAAAA-GA
738292 TAAAATAT
1 TAAAATAT
738300 TAAAATTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
36 11 0.28
37 12 0.30
38 17 0.43
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (37 bp):
TAAAATATAATAAAATATAAAAAATAAAATAAAAAGA
Found at i:738279 original size:9 final size:10
Alignment explanation
Indices: 738253--738299 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
738243 AAAATACAAA
738253 ATAAAATATG
1 ATAAAATATG
*
738263 ATAAAATATT
1 ATAAAATATG
**
738273 A-AAAATAAA
1 ATAAAATATG
738282 ATAAAA-ATG
1 ATAAAATATG
738291 ATAAAATAT
1 ATAAAATAT
738300 TAAAATTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
9 14 0.47
10 16 0.53
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (10 bp):
ATAAAATATG
Found at i:738300 original size:28 final size:30
Alignment explanation
Indices: 738216--738305 Score: 111
Period size: 28 Copynumber: 3.2 Consensus size: 30
738206 TTAGATATGG
* *
738216 TAAAATA-TAAATACAATAT-A-AAAATA-
1 TAAAATACAAAATAAAATATGATAAAATAT
738242 TAAAATACAAAATAAAATATGATAAAATAT
1 TAAAATACAAAATAAAATATGATAAAATAT
*
738272 TAAAA-ATAAAATAAAA-ATGATAAAATAT
1 TAAAATACAAAATAAAATATGATAAAATAT
738300 TAAAAT
1 TAAAAT
738306 TTATATAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
26 7 0.12
27 10 0.18
28 18 0.32
29 16 0.29
30 5 0.09
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (30 bp):
TAAAATACAAAATAAAATATGATAAAATAT
Found at i:738303 original size:8 final size:7
Alignment explanation
Indices: 738216--738305 Score: 73
Period size: 7 Copynumber: 12.9 Consensus size: 7
738206 TTAGATATGG
738216 TAAAATA
1 TAAAATA
738223 T-AAATA
1 TAAAATA
* *
738229 CAATATA
1 TAAAATA
738236 -AAAATA
1 TAAAATA
738242 TAAAATA
1 TAAAATA
*
738249 CAAAATA
1 TAAAATA
738256 -AAATATGA
1 TAAA-AT-A
738264 TAAAATA
1 TAAAATA
738271 TTAAAA-A
1 -TAAAATA
738278 TAAAATA
1 TAAAATA
738285 -AAAATGA
1 TAAAAT-A
738292 TAAAATA
1 TAAAATA
738299 TTAAAAT
1 -TAAAAT
738306 TTATATAAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 19
0.75 0.04 0.21
Matches are distributed among these distances:
6 23 0.33
7 24 0.35
8 19 0.28
9 3 0.04
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (7 bp):
TAAAATA
Found at i:738367 original size:14 final size:17
Alignment explanation
Indices: 738317--738361 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
738307 TATATAAAAA
*
738317 TTATCAATATATCAAATTT
1 TTATAAATATAT--AATTT
738336 TTATAAATATATAATTT
1 TTATAAATATATAATTT
738353 TT-TAAATAT
1 TTATAAATAT
738362 TATTTTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 7 0.28
17 7 0.28
19 11 0.44
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (17 bp):
TTATAAATATATAATTT
Found at i:738596 original size:3 final size:3
Alignment explanation
Indices: 738588--738619 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
738578 TCTTTTCTAA
738588 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
738620 ATCTTAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:739033 original size:18 final size:18
Alignment explanation
Indices: 738973--739036 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
738963 GTTTTTTTGA
738973 AGAAAAGAAATTAATAAA-
1 AGAAAA-AAATTAATAAAG
* * *
738991 AAAAAAAGAATGAATGAATG
1 AGAAAAA-AATTAAT-AAAG
739011 AGAAAAAAATTAATAAAG
1 AGAAAAAAATTAATAAAG
739029 AGAAAAAA
1 AGAAAAAA
739037 TATATATTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 1 0.03
18 22 0.59
19 8 0.22
20 6 0.16
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (18 bp):
AGAAAAAAATTAATAAAG
Found at i:739249 original size:21 final size:22
Alignment explanation
Indices: 739218--739265 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
739208 TATCATATTT
739218 TTAATTATTTTTATATTATATA
1 TTAATTATTTTTATATTATATA
*
739240 TTAA-TATTTTTATATTTTATA
1 TTAATTATTTTTATATTATATA
739261 -TAATT
1 TTAATT
739266 TATCATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 3 0.12
21 17 0.71
22 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTAATTATTTTTATATTATATA
Found at i:740120 original size:19 final size:20
Alignment explanation
Indices: 740096--740140 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
740086 AAAATAAAAA
740096 TAAAAT-ATATT-TTAAATAT
1 TAAAATGATATTATT-AATAT
740115 TAAAATGATATTATTAATAT
1 TAAAATGATATTATTAATAT
*
740135 AAAAAT
1 TAAAAT
740141 TAAATTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.26
20 15 0.65
21 2 0.09
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
TAAAATGATATTATTAATAT
Found at i:742150 original size:2 final size:2
Alignment explanation
Indices: 742143--742187 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
742133 TGAGCCAACC
742143 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
742185 TA T
1 TA T
742188 CATGATCAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:744878 original size:30 final size:30
Alignment explanation
Indices: 744842--744902 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
744832 TTGAATGGTA
744842 TATTACGATAGTTATTTTATGAGTTTGATT
1 TATTACGATAGTTATTTTATGAGTTTGATT
*
744872 TATTACGGTAGTTATTTTATGAGTTTGATT
1 TATTACGATAGTTATTTTATGAGTTTGATT
744902 T
1 T
744903 TTTTTATCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.03, G:0.18, T:0.54
Consensus pattern (30 bp):
TATTACGATAGTTATTTTATGAGTTTGATT
Found at i:745826 original size:2 final size:2
Alignment explanation
Indices: 745757--745806 Score: 50
Period size: 2 Copynumber: 25.5 Consensus size: 2
745747 ATATTTACAC
* * *
745757 AT AT AT AT AT AT AT AT AT GT AT AT GT A- AT -T GAA 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
745798 AT AT AT AT A
1 AT AT AT AT A
745807 GGCTTGTATA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (2 bp):
AT
Found at i:746114 original size:3 final size:3
Alignment explanation
Indices: 746106--746148 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
746096 TATTGATTCT
746106 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
746149 GATGATATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:747203 original size:23 final size:24
Alignment explanation
Indices: 747177--747272 Score: 57
Period size: 23 Copynumber: 4.3 Consensus size: 24
747167 TATGATTATG
747177 TAAATATAAT-ATATATAAAATAT
1 TAAATATAATCATATATAAAATAT
*
747200 TAAATA-AATGATAT-TAAAA-A-
1 TAAATATAATCATATATAAAATAT
* *
747220 -AATTAT-AT-A-ATATAAATTAT
1 TAAATATAATCATATATAAAATAT
* *
747240 TAATATATTATCATTTATATAAATAT
1 TAA-ATATAATCATATATA-AAATAT
*
747266 AAAATAT
1 TAAATAT
747273 TTTAAATATA
Statistics
Matches: 56, Mismatches: 6, Indels: 20
0.68 0.07 0.24
Matches are distributed among these distances:
17 2 0.04
18 5 0.09
19 7 0.12
21 3 0.05
22 11 0.20
23 12 0.21
24 1 0.02
25 8 0.14
26 7 0.12
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (24 bp):
TAAATATAATCATATATAAAATAT
Found at i:747237 original size:14 final size:14
Alignment explanation
Indices: 747185--747322 Score: 57
Period size: 14 Copynumber: 10.1 Consensus size: 14
747175 TGTAAATATA
*
747185 ATAT-ATATAAAAT
1 ATATAATATAAATT
*
747198 AT-TAA-ATAAATG
1 ATATAATATAAATT
*
747210 ATATTAA-AAAAATT
1 ATA-TAATATAAATT
747224 ATATAATATAAATT
1 ATATAATATAAATT
747238 AT-TAATAT--ATT
1 ATATAATATAAATT
*
747249 ATCATTTATATAAA-T
1 AT-A-TAATATAAATT
*
747264 ATAAAATATTTTAAA-T
1 ATATAATA---TAAATT
* *
747280 ATA-ATTATAATATA
1 ATATAATATAA-ATT
747294 ATA-AAGTATAAA-T
1 ATATAA-TATAAATT
747307 ATATAATATAAATT
1 ATATAATATAAATT
747321 AT
1 AT
747323 TAAATTTAGA
Statistics
Matches: 96, Mismatches: 12, Indels: 33
0.68 0.09 0.23
Matches are distributed among these distances:
11 5 0.05
12 11 0.11
13 25 0.26
14 35 0.36
15 11 0.11
16 9 0.09
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (14 bp):
ATATAATATAAATT
Found at i:747293 original size:11 final size:12
Alignment explanation
Indices: 747225--747322 Score: 55
Period size: 11 Copynumber: 8.2 Consensus size: 12
747215 AAAAAAATTA
747225 TATAATATAAAT
1 TATAATATAAAT
*
747237 TATTAATATATTAT
1 TA-TAATATA-AAT
* *
747251 CATTTATATAAA-
1 TA-TAATATAAAT
* **
747263 TATAAAATATTT
1 TATAATATAAAT
747275 TA-AATAT-AAT
1 TATAATATAAAT
747285 TATAATAT-AA-
1 TATAATATAAAT
747295 TA-AAGTATAAAT
1 TATAA-TATAAAT
747307 ATATAATATAAAT
1 -TATAATATAAAT
747320 TAT
1 TAT
747323 TAAATTTAGA
Statistics
Matches: 65, Mismatches: 12, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
9 2 0.03
10 8 0.12
11 18 0.28
12 8 0.12
13 17 0.26
14 12 0.18
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (12 bp):
TATAATATAAAT
Found at i:747317 original size:20 final size:19
Alignment explanation
Indices: 747163--747319 Score: 74
Period size: 18 Copynumber: 7.9 Consensus size: 19
747153 TTAATAATTT
* *
747163 TAAATATGATTATGTAAATA
1 TAAATAT-ATAATATAAATA
747183 T-AATATAT-ATA-AAATA
1 TAAATATATAATATAAATA
* *
747199 TTAAATAAATGATATTAAA-A
1 -TAAATATATAATA-TAAATA
747219 -AAATTATATAATATAAATTA
1 TAAA-TATATAATATAAA-TA
* * **
747239 TTAATATATTATCATTTATA
1 TAAATATATAAT-ATAAATA
*
747259 TAAATATAAAATATTTTAAATA
1 TAAATATATAATA---TAAATA
*
747281 TAATTATAATATAATA-AAGTA
1 TAA--AT-ATATAATATAAATA
747302 TAAATATATAATATAAAT
1 TAAATATATAATATAAAT
747320 TATTAAATTT
Statistics
Matches: 104, Mismatches: 16, Indels: 35
0.67 0.10 0.23
Matches are distributed among these distances:
16 5 0.05
17 3 0.03
18 23 0.22
19 21 0.20
20 21 0.20
21 15 0.14
22 7 0.07
24 2 0.02
25 7 0.07
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.41
Consensus pattern (19 bp):
TAAATATATAATATAAATA
Found at i:747957 original size:32 final size:34
Alignment explanation
Indices: 747915--747978 Score: 87
Period size: 32 Copynumber: 1.9 Consensus size: 34
747905 GAAAAACTTT
747915 AAAATAATATTTA-TCTTAATACTA-TTAAATTA
1 AAAATAATATTTATTCTTAATACTATTTAAATTA
* * *
747947 AAAATTATATTTATTTTTAATATTATTTAAAT
1 AAAATAATATTTATTCTTAATACTATTTAAAT
747979 CAACATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 12 0.44
33 9 0.33
34 6 0.22
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (34 bp):
AAAATAATATTTATTCTTAATACTATTTAAATTA
Found at i:749598 original size:41 final size:41
Alignment explanation
Indices: 749545--749624 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
749535 AGCATGTTGA
749545 AATTGGTACTAATTACTTATATATATATATATATATATATT
1 AATTGGTACTAATTACTTATATATATATATATATATATATT
*
749586 AATTGGTACTAATTACTTTTATATATATATATATATATA
1 AATTGGTACTAATTACTTATATATATATATATATATATA
749625 ACAATCAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (41 bp):
AATTGGTACTAATTACTTATATATATATATATATATATATT
Found at i:749867 original size:21 final size:19
Alignment explanation
Indices: 749833--749893 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
749823 TTTATTTAAA
749833 AATTATAATAAATTTAATTT
1 AATT-TAATAAATTTAATTT
*
749853 AATTTAAATTAAATTT-ATTA
1 AATTT-AA-TAAATTTAATTT
749873 AATTTAATAAA--TAATTT
1 AATTTAATAAATTTAATTT
749890 AATT
1 AATT
749894 CATAAACATA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
16 1 0.03
17 7 0.19
18 4 0.11
19 3 0.08
20 14 0.39
21 7 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTTAATAAATTTAATTT
Found at i:749874 original size:9 final size:10
Alignment explanation
Indices: 749832--749884 Score: 58
Period size: 9 Copynumber: 5.4 Consensus size: 10
749822 TTTTATTTAA
749832 AAATTATAA-T
1 AAATT-TAATT
749842 AAATTTAATT
1 AAATTTAATT
*
749852 TAATTTAAATT
1 AAATTT-AATT
749863 AAATTT-ATT
1 AAATTTAATT
749872 AAATTTAA-T
1 AAATTTAATT
749881 AAAT
1 AAAT
749885 AATTTAATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
9 17 0.45
10 12 0.32
11 9 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AAATTTAATT
Found at i:750119 original size:23 final size:21
Alignment explanation
Indices: 750078--750124 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
750068 ATATCTATAA
*
750078 ATATTTTTATATTTAAAATTT
1 ATATTTTTATATTTAAAATAT
*
750099 ATATTTTTATACATTTCAAATAT
1 ATATTTTTAT--ATTTAAAATAT
750122 ATA
1 ATA
750125 ATCATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
23 12 0.55
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATTTTTATATTTAAAATAT
Found at i:750704 original size:17 final size:18
Alignment explanation
Indices: 750677--750721 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
750667 ATGATATGAT
750677 TATAAATATGATA-AAAAA
1 TATAAA-ATGATATAAAAA
750695 TATAAAATGATATAAAAA
1 TATAAAATGATATAAAAA
*
750713 -ATAAGATGA
1 TATAAAATGA
750722 ACTCAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (18 bp):
TATAAAATGATATAAAAA
Done.