Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold140
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: 3130556
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82166 characters in sequence are not A, C, G, or T
File 6 of 20
Found at i:938402 original size:18 final size:19
Alignment explanation
Indices: 938369--938410 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
938359 TTTATTATTA
*
938369 TAATTTAATTATATTTAAT
1 TAATTTAATAATATTTAAT
*
938388 TAATTT-ATAATATTTATT
1 TAATTTAATAATATTTAAT
938406 TAATT
1 TAATT
938411 AATTTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TAATTTAATAATATTTAAT
Found at i:938408 original size:22 final size:22
Alignment explanation
Indices: 938380--938425 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
938370 AATTTAATTA
938380 TATTTAATTAATTTATAATATT
1 TATTTAATTAATTTATAATATT
* *
938402 TATTTAATTAATTTTTAATTTT
1 TATTTAATTAATTTATAATATT
938424 TA
1 TA
938426 ATATAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTTAATTAATTTATAATATT
Found at i:938457 original size:18 final size:19
Alignment explanation
Indices: 938414--938479 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 19
938404 TTTAATTAAT
*
938414 TTTTAATTTT-TAATATAA
1 TTTTATTTTTATAATATAA
** *
938432 TAAATATTTTTAT-ATATAT
1 T-TTTATTTTTATAATATAA
*
938451 TTTTATTTGTATAATATAA
1 TTTTATTTTTATAATATAA
*
938470 TTTAATTTTT
1 TTTTATTTTT
938480 TAAAGATAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 5
0.70 0.20 0.10
Matches are distributed among these distances:
18 9 0.26
19 25 0.71
20 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTATTTTTATAATATAA
Found at i:938697 original size:3 final size:3
Alignment explanation
Indices: 938689--938716 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
938679 TCTTCACCCG
938689 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
938717 TACCTTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:948277 original size:13 final size:14
Alignment explanation
Indices: 948259--948292 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
948249 ACTTTTATTT
948259 TTATTAAA-TTATA
1 TTATTAAATTTATA
*
948272 TTATTAAATTTTTA
1 TTATTAAATTTATA
948286 TTATTAA
1 TTATTAA
948293 TAAATCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTAAATTTATA
Found at i:949415 original size:31 final size:29
Alignment explanation
Indices: 949351--949416 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
949341 AGATTTAAAA
** *
949351 ATTTA-TATAATTATATTATGATTTTATT
1 ATTTATTATAATTATATTAAAATATTATT
*
949379 TTTTATTATAATTATATATAAAATATTATAT
1 ATTTATTATAATTATAT-TAAAATATTAT-T
949410 ATTTATT
1 ATTTATT
949417 TAAATAAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 4 0.13
29 11 0.37
30 8 0.27
31 7 0.23
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
ATTTATTATAATTATATTAAAATATTATT
Found at i:949684 original size:16 final size:17
Alignment explanation
Indices: 949642--949692 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
949632 ATAATATGAA
*
949642 TTAATTAAATATATTAAT
1 TTAA-TAAATAAATTAAT
*
949660 TTAATAAATAAATTATT
1 TTAATAAATAAATTAAT
949677 TTAA-AAATAAATTAAT
1 TTAATAAATAAATTAAT
949693 ATGATAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
16 11 0.37
17 15 0.50
18 4 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAATAAATAAATTAAT
Found at i:949750 original size:18 final size:17
Alignment explanation
Indices: 949714--949777 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 17
949704 AAAAATATTT
* *
949714 AAATATTTTTTATTTAAA
1 AAATATTTATT-TTAAAA
949732 AAATATTTATTTTAAAA
1 AAATATTTATTTTAAAA
*
949749 AAA-ACTTAAATTTTAAAA
1 AAATA-TT-TATTTTAAAA
949767 AAATATTTATT
1 AAATATTTATT
949778 CAAATTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 1 0.03
17 13 0.33
18 24 0.62
19 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATATTTATTTTAAAA
Found at i:955112 original size:37 final size:37
Alignment explanation
Indices: 955060--955132 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
955050 GAATGCACGC
* *
955060 CTTAAAAGAATGCCAGCCATTGGAGCAGACTGCATAT
1 CTTAAAAGAAAGCCAGCCATCGGAGCAGACTGCATAT
955097 CTTAAAAGAAAGCCAGCCATCGGAGCAGACTGCATA
1 CTTAAAAGAAAGCCAGCCATCGGAGCAGACTGCATA
955133 CGCAAAGTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (37 bp):
CTTAAAAGAAAGCCAGCCATCGGAGCAGACTGCATAT
Found at i:955485 original size:18 final size:18
Alignment explanation
Indices: 955458--955493 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
955448 ATTGATTTAA
955458 TAAAAAAAATT-AATATT
1 TAAAAAAAATTAAATATT
955475 TAAATAAAAATTAAATATT
1 TAAA-AAAAATTAAATATT
955494 ATTTTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAAAAAAATTAAATATT
Found at i:955503 original size:23 final size:23
Alignment explanation
Indices: 955453--955509 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
955443 CGATTATTGA
955453 TTTAATAAAAA--AAATTAATAT
1 TTTAATAAAAATTAAATTAATAT
* *
955474 TTAAATAAAAATTAAA-TATTATT
1 TTTAATAAAAATTAAATTAATA-T
*
955497 TTTAATAACAATT
1 TTTAATAAAAATT
955510 GGTAACTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 10 0.34
22 4 0.14
23 15 0.52
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TTTAATAAAAATTAAATTAATAT
Found at i:960170 original size:17 final size:18
Alignment explanation
Indices: 960148--960191 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
960138 ATTAAAAATT
*
960148 TTTATATTGAATA-TATA
1 TTTATATTCAATATTATA
960165 TTTATATTCAATATTTATA
1 TTTATATTCAATA-TTATA
960184 TTTATATT
1 TTTATATT
960192 TGAGTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 12 0.50
19 12 0.50
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTATATTCAATATTATA
Found at i:962644 original size:20 final size:20
Alignment explanation
Indices: 962614--962658 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
962604 ATAATTTTAT
962614 AATAT-AAATATAGT-ATAAA
1 AATATAAAATATA-TAATAAA
*
962633 AATATAAAATATATAATATA
1 AATATAAAATATATAATAAA
962653 AATATA
1 AATATA
962659 TATAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AATATAAAATATATAATAAA
Found at i:962652 original size:22 final size:22
Alignment explanation
Indices: 962621--962666 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
962611 TATAATATAA
*
962621 ATATAGTATAAAAATATAAAAT
1 ATATAATATAAAAATATAAAAT
* *
962643 ATATAATATAAATATATATAAT
1 ATATAATATAAAAATATAAAAT
962665 AT
1 AT
962667 TTTAAATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
ATATAATATAAAAATATAAAAT
Found at i:962655 original size:13 final size:13
Alignment explanation
Indices: 962597--962660 Score: 59
Period size: 13 Copynumber: 5.4 Consensus size: 13
962587 TTAATTTTAA
*
962597 ATATAATATAATT
1 ATATAATATAAAT
*
962610 TTATAATAT-AA-
1 ATATAATATAAAT
*
962621 ATATAGTATAAA-
1 ATATAATATAAAT
962633 A-AT-ATA-AAAT
1 ATATAATATAAAT
962643 ATATAATATAAAT
1 ATATAATATAAAT
962656 ATATA
1 ATATA
962661 TAATATTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
9 3 0.07
10 3 0.07
11 11 0.27
12 7 0.17
13 17 0.41
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (13 bp):
ATATAATATAAAT
Found at i:964224 original size:84 final size:84
Alignment explanation
Indices: 964125--964280 Score: 240
Period size: 84 Copynumber: 1.9 Consensus size: 84
964115 TACAATTGGC
* * * * **
964125 TTTATTCTTCTTCCTTTCCCTTGCGATGATTTTTTATATTATTAGTTTTTTATCAGTGAAAATGG
1 TTTATTCATCCTCCTTTCCCTTGCGATGATTTTTCATATTATTAGTTATTTATCACAGAAAATGG
*
964190 GTTTTTCCGATAAGAATGA
66 CTTTTTCCGATAAGAATGA
*
964209 TTTATTCATCCTCCTTTCCCTTGCGATGATTTTTCATGTTATTAGTTATTTATCACAGAAAATGG
1 TTTATTCATCCTCCTTTCCCTTGCGATGATTTTTCATATTATTAGTTATTTATCACAGAAAATGG
964274 CTTTTTC
66 CTTTTTC
964281 AAAAATGCTA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 64 1.00
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.49
Consensus pattern (84 bp):
TTTATTCATCCTCCTTTCCCTTGCGATGATTTTTCATATTATTAGTTATTTATCACAGAAAATGG
CTTTTTCCGATAAGAATGA
Found at i:966370 original size:17 final size:17
Alignment explanation
Indices: 966348--966397 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
966338 TTTATTGATT
966348 TTATTTTATTTAAATAA
1 TTATTTTATTTAAATAA
*
966365 TTATTTAATTAATAAA-AA
1 TTATTTTATT--TAAATAA
966383 -TATTTTAATTTAAAT
1 TTATTTT-ATTTAAAT
966398 TTATTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
16 4 0.15
17 14 0.52
18 5 0.19
19 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATTTTATTTAAATAA
Found at i:967169 original size:34 final size:34
Alignment explanation
Indices: 967123--967307 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
967113 GTAAAAACCA
*
967123 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
967157 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
*
967191 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
967225 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
** * *
967259 CCATTTGGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
967292 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
967308 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 17 0.13
34 114 0.84
35 4 0.03
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:971769 original size:34 final size:34
Alignment explanation
Indices: 971723--971905 Score: 235
Period size: 34 Copynumber: 5.4 Consensus size: 34
971713 GTAAAAACCA
*
971723 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
971757 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
*
971791 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
971825 CCATTTAATCAACAATGGTAAGCTATCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* ** * *
971859 TCATTTGGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
971892 CCATTTAATCAACA
1 CCATTTAATCAACA
971906 TCATCATCAA
Statistics
Matches: 129, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
33 14 0.11
34 111 0.86
35 4 0.03
ACGTcount: A:0.39, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:971870 original size:102 final size:101
Alignment explanation
Indices: 971723--971905 Score: 294
Period size: 102 Copynumber: 1.8 Consensus size: 101
971713 GTAAAAACCA
971723 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
971788 CACCCATTTAATCAACAATGGTAAGCTACCAAATCTC
66 CA-CCATTTAATCAACAATGGTAAGCTACCAAATCTC
* * * * * * *
971825 CCATTTAATCAACAATGGTAAGCTATCAAATTTCTCATTTGGTCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
971890 CACCATTTAATCAACA
66 CACCATTTAATCAACA
971906 TCATCATCAA
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
101 14 0.19
102 60 0.81
ACGTcount: A:0.39, C:0.26, G:0.08, T:0.26
Consensus pattern (101 bp):
CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
CACCATTTAATCAACAATGGTAAGCTACCAAATCTC
Found at i:973013 original size:15 final size:16
Alignment explanation
Indices: 972970--973014 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
972960 ATTTAAATCA
972970 AATTAAATTTAATTTG
1 AATTAAATTTAATTTG
*
972986 AATTATAA--AAATTTG
1 AATTA-AATTTAATTTG
973001 AA-TAAATTTAATTT
1 AATTAAATTTAATTT
973015 TGATTAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
13 2 0.08
14 2 0.08
15 13 0.54
16 5 0.21
17 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (16 bp):
AATTAAATTTAATTTG
Found at i:973932 original size:25 final size:25
Alignment explanation
Indices: 973900--973957 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
973890 TAATATTAGG
973900 TATAATATAAAAAAAATA-ATTAATA
1 TATAATATAAAAAAAATATA-TAATA
*
973925 TATAATATAAAAAATATATATAATA
1 TATAATATAAAAAAAATATATAATA
973950 TA-AATATA
1 TATAATATA
973958 TAAATATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
24 6 0.19
25 24 0.77
26 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
TATAATATAAAAAAAATATATAATA
Found at i:973934 original size:5 final size:5
Alignment explanation
Indices: 973924--974068 Score: 53
Period size: 5 Copynumber: 30.2 Consensus size: 5
973914 AATAATTAAT
* * *
973924 ATATA ATATA A-AAA ATAT- ATATA ATATA A-AT- ATATA A-ATA TTTTA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * * * *
973969 AAATTA ATATA ATATA A-ATT AT-TA ATTTTTA A-AAA AT-TT ATATA
1 ATA-TA ATATA ATATA ATATA ATATA A--TATA ATATA ATATA ATATA
* *
974013 ATATA AAATA A-ATTAA ATATA ATTATA ATATA ATAAA ATAT- ATA-A
1 ATATA ATATA ATA-T-A ATATA A-TATA ATATA ATATA ATATA ATATA
*
974058 ACATA ATATA A
1 ATATA ATATA A
974069 ATACACGAAT
Statistics
Matches: 102, Mismatches: 20, Indels: 36
0.65 0.13 0.23
Matches are distributed among these distances:
3 1 0.01
4 29 0.28
5 55 0.54
6 13 0.13
7 4 0.04
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:973962 original size:23 final size:22
Alignment explanation
Indices: 973900--974069 Score: 81
Period size: 22 Copynumber: 7.8 Consensus size: 22
973890 TAATATTAGG
973900 TATAATATAAA-A-AAAATA-A
1 TATAATATAAATATAAAATATA
973919 T-TAATATATAATATAAAAAATATA
1 TATAATATA-AATAT--AAAATATA
973943 TATAATATAAATATATAAATAT-
1 TATAATATAAATATA-AAATATA
* * * * *
973965 TTTAAAATTAATATAATATAAA
1 TATAATATAAATATAAAATATA
** * *
973987 TTATTAAT-T-TTTAAAAAATTTA
1 -TA-TAATATAAATATAAAATATA
* *
974009 TATAATATAAA-ATAAATTAAA
1 TATAATATAAATATAAAATATA
974030 TATAATTATAATATAATAAAATATA
1 TATAA-TATAA-AT-ATAAAATATA
*
974055 TA-AACAT-AATATAAA
1 TATAATATAAATATAAA
974070 TACACGAATC
Statistics
Matches: 112, Mismatches: 22, Indels: 33
0.67 0.13 0.20
Matches are distributed among these distances:
18 7 0.06
19 3 0.03
20 10 0.09
21 20 0.18
22 26 0.23
23 17 0.15
24 12 0.11
25 17 0.15
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (22 bp):
TATAATATAAATATAAAATATA
Found at i:973972 original size:33 final size:31
Alignment explanation
Indices: 973934--974026 Score: 102
Period size: 33 Copynumber: 2.9 Consensus size: 31
973924 ATATAATATA
973934 AAAAATATATATAATATAAATATATAAATATTTT
1 AAAAAT-TATATAATATAAAT-TATAAAT-TTTT
*
973968 -AAAATTAATATAATATAAATTATTAATTTTT
1 AAAAATT-ATATAATATAAATTATAAATTTTT
973999 AAAAAATTTATATAATATAAA--ATAAATT
1 -AAAAA-TTATATAATATAAATTATAAATT
974027 AAATATAATT
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
31 10 0.19
32 7 0.13
33 34 0.64
34 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
AAAAATTATATAATATAAATTATAAATTTTT
Found at i:974324 original size:17 final size:17
Alignment explanation
Indices: 974304--974364 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
974294 TATTTTTTAA
974304 AATTTTTTATTTATTTT
1 AATTTTTTATTTATTTT
* *
974321 AATTTTTTAATT-TTTA
1 AATTTTTTATTTATTTT
974337 AATTATTATTA-TTA-TTT
1 AATT-TT-TTATTTATTTT
*
974354 AATTATTTATT
1 AATTTTTTATT
974365 ATTGAAAGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
15 3 0.08
16 9 0.25
17 21 0.58
18 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
AATTTTTTATTTATTTT
Found at i:974326 original size:26 final size:25
Alignment explanation
Indices: 974287--974364 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
974277 AATCGAATTT
*
974287 TTTATTATATTTTTTAAAATTTTTTA
1 TTTATTATAATTTTT-AAATTTTTTA
* * *
974313 TTTATTTTAATTTTTTAATTTTTAA
1 TTTATTATAATTTTTAAATTTTTTA
* * *
974338 ATTATTATTATTATTT-AATTATTTA
1 TTTATTATAATT-TTTAAATTTTTTA
974363 TT
1 TT
974365 ATTGAAAGTT
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
25 25 0.61
26 16 0.39
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTATTATAATTTTTAAATTTTTTA
Found at i:974340 original size:33 final size:34
Alignment explanation
Indices: 974288--974362 Score: 84
Period size: 33 Copynumber: 2.2 Consensus size: 34
974278 ATCGAATTTT
*
974288 TTATTATATTTTTTAAAATT-TT-TTATTTATTTTAA
1 TTATT-TAATTTTTAAAATTATTATTA-TTA-TTTAA
*
974323 TTTTTTAATTTTT-AAATTATTATTATTATTTAA
1 TTATTTAATTTTTAAAATTATTATTATTATTTAA
974356 TTATTTA
1 TTATTTA
974363 TTATTGAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
33 16 0.46
34 12 0.34
35 7 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (34 bp):
TTATTTAATTTTTAAAATTATTATTATTATTTAA
Found at i:974391 original size:17 final size:17
Alignment explanation
Indices: 974366--974405 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
974356 TTATTTATTA
*
974366 TTGAAAGTTTAATCAAT
1 TTGATAGTTTAATCAAT
974383 TTGATAGTTTAATCAAT
1 TTGATAGTTTAATCAAT
974400 TTGATA
1 TTGATA
974406 TCTGATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (17 bp):
TTGATAGTTTAATCAAT
Found at i:977661 original size:21 final size:21
Alignment explanation
Indices: 977637--977676 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
977627 TACAAAGACT
977637 ATGCAGCTGAGAAAGCAAAGG
1 ATGCAGCTGAGAAAGCAAAGG
** *
977658 ATGCTTCTGAGAAGGCAAA
1 ATGCAGCTGAGAAAGCAAA
977677 AGAGGTAAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.15, G:0.30, T:0.15
Consensus pattern (21 bp):
ATGCAGCTGAGAAAGCAAAGG
Found at i:979572 original size:8 final size:8
Alignment explanation
Indices: 979559--979583 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
979549 AAAATTTTGA
979559 TTTAAAAT
1 TTTAAAAT
979567 TTTAAAAT
1 TTTAAAAT
979575 TTTAAAAT
1 TTTAAAAT
979583 T
1 T
979584 ATGATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTAAAAT
Found at i:979579 original size:73 final size:73
Alignment explanation
Indices: 979488--979631 Score: 195
Period size: 73 Copynumber: 2.0 Consensus size: 73
979478 AAGTTGGGTA
**
979488 TAAAATTTAAAAAATTTAAAATTAT-AGTTCAATTT-AATTTCAAGTTTAATA-AGAAATTTTAA
1 TAAAATTTAAAAAATTTAAAATTATGA-TTCAATTTAAATTT-AAACTTAATATA-AAATTTTAA
979550 AAATTTTGATT
63 AAATTTTGATT
* * *
979561 TAAAATTTTAAAATTTTAAAATTATGATTTAATTTAAATTTAAACTTAATATAAAATTTTAAAAA
1 TAAAATTTAAAAAATTTAAAATTATGATTCAATTTAAATTTAAACTTAATATAAAATTTTAAAAA
979626 TTTTGA
66 TTTTGA
979632 AATACAATTA
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
73 56 0.89
74 7 0.11
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (73 bp):
TAAAATTTAAAAAATTTAAAATTATGATTCAATTTAAATTTAAACTTAATATAAAATTTTAAAAA
TTTTGATT
Found at i:982008 original size:32 final size:32
Alignment explanation
Indices: 981901--982009 Score: 76
Period size: 33 Copynumber: 3.2 Consensus size: 32
981891 TGACAATAGA
* *
981901 AAAAAACAAAACAAAAATACGTAGGTTTTA-GCG
1 AAAAAA-AAAACAAAATTATGTAGGTTTTATG-G
* * * *
981934 AAAAATAAAAATAAAATCATGTGGGCTTTCTGACAATAG
1 AAAAA-AAAAACAAAATTATGTAGG-TTT-T----ATGG
981973 AAAAAAAAAACAAAATTATGTAGGTTTTATGG
1 AAAAAAAAAACAAAATTATGTAGGTTTTATGG
982005 AAAAA
1 AAAAA
982010 TATAAAATAA
Statistics
Matches: 58, Mismatches: 10, Indels: 17
0.68 0.12 0.20
Matches are distributed among these distances:
32 8 0.14
33 18 0.31
34 4 0.07
35 1 0.02
36 1 0.02
37 3 0.05
38 16 0.28
39 7 0.12
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (32 bp):
AAAAAAAAAACAAAATTATGTAGGTTTTATGG
Found at i:987724 original size:24 final size:25
Alignment explanation
Indices: 987697--987744 Score: 80
Period size: 24 Copynumber: 1.9 Consensus size: 25
987687 AAGCTGAAAT
987697 CAATCAATATC-TTTCGGATACTGA
1 CAATCAATATCATTTCGGATACTGA
987721 CAATCAATATCGATTTCGGATACT
1 CAATCAATATC-ATTTCGGATACT
987745 CGTTGCCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 11 0.50
26 11 0.50
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (25 bp):
CAATCAATATCATTTCGGATACTGA
Found at i:988379 original size:22 final size:23
Alignment explanation
Indices: 988348--988434 Score: 73
Period size: 22 Copynumber: 4.0 Consensus size: 23
988338 TATTTTATAT
988348 TAATATTTATAATTAAATTTAAA
1 TAATATTTATAATTAAATTTAAA
988371 TAAT-TTTAT-ATTAAA--TAAA
1 TAATATTTATAATTAAATTTAAA
*
988390 TAATAATTTA-AA-TAAAATTAAA
1 TAAT-ATTTATAATTAAATTTAAA
* *
988412 TTATAATT-TAATATAAA-TTAAA
1 TAATATTTATAAT-TAAATTTAAA
988434 T
1 T
988435 TTATTAAATG
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
19 8 0.15
20 4 0.07
21 16 0.30
22 18 0.33
23 8 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TAATATTTATAATTAAATTTAAA
Found at i:988391 original size:19 final size:22
Alignment explanation
Indices: 988348--988434 Score: 85
Period size: 21 Copynumber: 4.0 Consensus size: 22
988338 TATTTTATAT
988348 TAATATTTATAATTAAATTTAAA
1 TAATATTTATAATTAAA-TTAAA
988371 TAAT-TTTAT-ATTAAA-TAAA
1 TAATATTTATAATTAAATTAAA
*
988390 TAATAATTTA-AATAAAATTAAA
1 TAAT-ATTTATAATTAAATTAAA
* *
988412 TTATAATT-TAATATAAATTAAA
1 TAATATTTATAAT-TAAATTAAA
988434 T
1 T
988435 TTATTAAATG
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
19 8 0.15
21 21 0.39
22 21 0.39
23 4 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATATTTATAATTAAATTAAA
Found at i:988401 original size:31 final size:34
Alignment explanation
Indices: 988339--988404 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
988329 TAAATTTTTT
**
988339 ATTTTATATTAATATTTATAATTAAATTTAAATA
1 ATTTTATATTAATATAAATAATTAAATTTAAATA
988373 ATTTTATATTAA-ATAAATAA-T-AATTTAAATA
1 ATTTTATATTAATATAAATAATTAAATTTAAATA
988404 A
1 A
988405 AATTAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 11 0.37
32 1 0.03
33 6 0.20
34 12 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (34 bp):
ATTTTATATTAATATAAATAATTAAATTTAAATA
Found at i:988413 original size:16 final size:16
Alignment explanation
Indices: 988358--988413 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
988348 TAATATTTAT
988358 AATTAAATTTAAATAA
1 AATTAAATTTAAATAA
** *
988374 TTTTATA-TTAAAT-A
1 AATTAAATTTAAATAA
*
988388 AATAATAATTTAAATAA
1 AATTA-AATTTAAATAA
988405 AATTAAATT
1 AATTAAATT
988414 ATAATTTAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
14 3 0.10
15 7 0.24
16 14 0.48
17 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTAAATTTAAATAA
Found at i:988435 original size:22 final size:22
Alignment explanation
Indices: 988370--988435 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
988360 TTAAATTTAA
* *
988370 ATAATTTTATATTAAA-TAAATA
1 ATAATTTAATA-TAAATTAAATT
988392 ATAATTTAA-ATAAAATTAAATT
1 ATAATTTAATAT-AAATTAAATT
988414 ATAATTTAATATAAATTAAATT
1 ATAATTTAATATAAATTAAATT
988436 TATTAAATGG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.03
21 4 0.10
22 32 0.82
23 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAATTTAATATAAATTAAATT
Found at i:988756 original size:13 final size:12
Alignment explanation
Indices: 988726--988767 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
988716 TTATTTATAT
988726 TTAAATAT-ATA
1 TTAAATATAATA
*
988737 TTGAATATAATTA
1 TTAAATATAA-TA
988750 TTAAATATAAATA
1 TTAAATAT-AATA
988763 TTAAA
1 TTAAA
988768 AAAAAAGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 7 0.27
12 1 0.04
13 16 0.62
14 2 0.08
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (12 bp):
TTAAATATAATA
Found at i:994281 original size:19 final size:19
Alignment explanation
Indices: 994259--994296 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
994249 TTTGTGATAT
*
994259 TATTAATATATTAATATTA
1 TATTAATATATTAACATTA
*
994278 TATTAATATTTTAACATTA
1 TATTAATATATTAACATTA
994297 ATTTTATGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTAATATATTAACATTA
Found at i:995320 original size:26 final size:25
Alignment explanation
Indices: 995281--995329 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
995271 AGATTTTTCT
* *
995281 TAAAAAATGCATTATTAGAAATAAAA
1 TAAAAAATGAATTAATA-AAATAAAA
*
995307 TAAAAAATTAATTAATAAAATAA
1 TAAAAAATGAATTAATAAAATAA
995330 TTTTTAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 6 0.30
26 14 0.70
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (25 bp):
TAAAAAATGAATTAATAAAATAAAA
Found at i:995883 original size:18 final size:19
Alignment explanation
Indices: 995855--995892 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
995845 GCGTAGGGGG
995855 TTTTCTATTTTTTTAATAA
1 TTTTCTATTTTTTTAATAA
*
995874 TTTT-TATTTTTTTCATAA
1 TTTTCTATTTTTTTAATAA
995892 T
1 T
995893 AAATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTCTATTTTTTTAATAA
Found at i:996342 original size:22 final size:22
Alignment explanation
Indices: 996317--996377 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
996307 AATGTTAAAT
996317 ATATTATTTAAAAATAAAATAA
1 ATATTATTTAAAAATAAAATAA
* * *
996339 ATA-TAATTAATTAATAAAATAG
1 ATATTATTTAA-AAATAAAATAA
* *
996361 TTGTT-TTTAAAAATAAA
1 ATATTATTTAAAAATAAA
996378 TCATTATAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
21 12 0.40
22 17 0.57
23 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (22 bp):
ATATTATTTAAAAATAAAATAA
Found at i:997137 original size:29 final size:32
Alignment explanation
Indices: 997077--997137 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
997067 ATAAAATTAC
* *
997077 TTAAAAATTATTTATTTATAAATTATATAATA
1 TTAAAAATTAATTATTTATAAAATATATAATA
*
997109 TTAATAATTAATT-TTTA-AAAATATA-AATA
1 TTAAAAATTAATTATTTATAAAATATATAATA
997138 AAAAGTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 4 0.15
30 7 0.27
31 4 0.15
32 11 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
TTAAAAATTAATTATTTATAAAATATATAATA
Found at i:999007 original size:13 final size:13
Alignment explanation
Indices: 998989--999018 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
998979 GTACAAGTGG
998989 ATTTAAAGAGATT
1 ATTTAAAGAGATT
999002 ATTT-AAGAGATT
1 ATTTAAAGAGATT
999014 ATTTA
1 ATTTA
999019 TTGTTTGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (13 bp):
ATTTAAAGAGATT
Found at i:1002962 original size:28 final size:28
Alignment explanation
Indices: 1002920--1002996 Score: 72
Period size: 28 Copynumber: 2.8 Consensus size: 28
1002910 TCATTTTTTG
1002920 TTAA-TTATTATTAATCTAATGTTATAAA-A
1 TTAATTTATTA-TAAT-TAAT-TTATAAACA
*
1002949 -TAATTTATTATAATTTATTTATAAACA
1 TTAATTTATTATAATTAATTTATAAACA
*
1002976 TTAGTTTATTAT-ATATAATTT
1 TTAATTTATTATAAT-TAATTT
1002997 TAGTGTATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
26 7 0.17
27 6 0.15
28 22 0.54
29 6 0.15
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (28 bp):
TTAATTTATTATAATTAATTTATAAACA
Found at i:1003027 original size:19 final size:19
Alignment explanation
Indices: 1003005--1003048 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1002995 TTTAGTGTAT
*
1003005 ATATTTACTATATAT-TAAA
1 ATATTTA-TATAAATATAAA
*
1003024 ATATATATATAAATATAAA
1 ATATTTATATAAATATAAA
1003043 ATATTT
1 ATATTT
1003049 TAAAACATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATTTATATAAATATAAA
Found at i:1003408 original size:23 final size:23
Alignment explanation
Indices: 1003357--1003417 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
1003347 TATAAAATAT
*
1003357 TTTAA-ATATAATTATAATAAAA
1 TTTAATATATAAATATAATAAAA
** *
1003379 TAAAATATATAAATATTATAAAA
1 TTTAATATATAAATATAATAAAA
1003402 TTTAATA-ATAAA-ATAA
1 TTTAATATATAAATATAA
1003418 AATTTTAACT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 3 0.10
22 8 0.26
23 20 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TTTAATATATAAATATAATAAAA
Found at i:1004118 original size:3 final size:3
Alignment explanation
Indices: 1004110--1004143 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1004100 GAAAGATTTT
1004110 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1004144 AAAGAATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1005877 original size:2 final size:2
Alignment explanation
Indices: 1005870--1005906 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1005860 CATTGCATAA
1005870 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 A
1005907 CACAATAAAG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1006248 original size:29 final size:29
Alignment explanation
Indices: 1006210--1006268 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1006200 ACACATCTTT
*
1006210 ATACATACATGCATATATATATATATATA
1 ATACATACATACATATATATATATATATA
* * *
1006239 ATACATACATATATATTTTTATATATATA
1 ATACATACATACATATATATATATATATA
1006268 A
1 A
1006269 ATAGAATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.42
Consensus pattern (29 bp):
ATACATACATACATATATATATATATATA
Found at i:1006338 original size:20 final size:18
Alignment explanation
Indices: 1006313--1006352 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
1006303 TTTTTATATT
1006313 AATTATATAAATATAATAAA
1 AATTAT-TAAA-ATAATAAA
*
1006333 AATTATTAAAATATTAAA
1 AATTATTAAAATAATAAA
1006351 AA
1 AA
1006353 ATAATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 4 0.21
20 6 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AATTATTAAAATAATAAA
Found at i:1006720 original size:20 final size:18
Alignment explanation
Indices: 1006656--1006723 Score: 58
Period size: 17 Copynumber: 4.0 Consensus size: 18
1006646 ATAAATACAA
* *
1006656 TAAATATATA-AATGTAT
1 TAAATTTATATAATATAT
1006673 TAAATTTATAT-A-ATA-
1 TAAATTTATATAATATAT
1006688 TAAA-TTAT-TAATATAT
1 TAAATTTATATAATATAT
1006704 TAAATTTTATATAAATATAT
1 TAAA-TTTATAT-AATATAT
1006724 AATATTTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
13 1 0.02
14 5 0.12
15 7 0.17
16 6 0.15
17 10 0.24
18 4 0.10
19 1 0.02
20 7 0.17
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (18 bp):
TAAATTTATATAATATAT
Found at i:1006743 original size:27 final size:27
Alignment explanation
Indices: 1006661--1006744 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
1006651 TACAATAAAT
1006661 ATATAAATGTATTAA-AT-TT--ATATA
1 ATATAAAT-TATTAATATATTAAATATA
* *
1006685 ATATAAATTATTAATATATTAAATTTT
1 ATATAAATTATTAATATATTAAATATA
1006712 ATATAAA-TATATAATAT-TTAAATATA
1 ATATAAATTAT-TAATATATTAAATATA
1006738 ATTATAA
1 A-TATAA
1006745 TAAATAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
23 6 0.12
24 10 0.20
25 2 0.04
26 11 0.22
27 21 0.42
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (27 bp):
ATATAAATTATTAATATATTAAATATA
Found at i:1006748 original size:15 final size:14
Alignment explanation
Indices: 1006711--1006764 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
1006701 TATTAAATTT
*
1006711 TATATAAATATATAA
1 TATATAAATA-AAAA
* * *
1006726 TATTTAAATATAAT
1 TATATAAATAAAAA
1006740 TATAATAAATAAAAA
1 TAT-ATAAATAAAAA
1006755 TATATAAATA
1 TATATAAATA
1006765 CAATATGAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 11 0.35
15 20 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TATATAAATAAAAA
Found at i:1006769 original size:19 final size:19
Alignment explanation
Indices: 1006731--1006783 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
1006721 TATAATATTT
1006731 AAATATAATTATAATAAATAA
1 AAATAT-ATTA-AATAAATAA
*
1006752 AAATATA-TAAATACAATAT
1 AAATATATTAAATA-AATAA
*
1006771 GAATATATTAAAT
1 AAATATATTAAAT
1006784 CTAATCACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 4 0.14
19 12 0.43
20 6 0.21
21 6 0.21
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
AAATATATTAAATAAATAA
Found at i:1007259 original size:29 final size:29
Alignment explanation
Indices: 1007222--1007284 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
1007212 AATTCTGATT
*
1007222 TAATCTAATAAATAAAATTTATAATTATA
1 TAATATAATAAATAAAATTTATAATTATA
** *
1007251 TAATATAATAAATAATTTTTATTATTATA
1 TAATATAATAAATAAAATTTATAATTATA
*
1007280 AAATA
1 TAATA
1007285 AAGTAATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (29 bp):
TAATATAATAAATAAAATTTATAATTATA
Found at i:1007324 original size:26 final size:24
Alignment explanation
Indices: 1007286--1007333 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
1007276 TATAAAATAA
*
1007286 AGTAATATAATAAATAAATTTTATC
1 AGTAATATAAT-AATAAAATTTATC
*
1007311 AGTATATATTATAATAAAATTTA
1 AGTA-ATATAATAATAAAATTTA
1007334 ATTATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (24 bp):
AGTAATATAATAATAAAATTTATC
Found at i:1013953 original size:160 final size:159
Alignment explanation
Indices: 1013686--1014002 Score: 499
Period size: 160 Copynumber: 2.0 Consensus size: 159
1013676 TTACCAAAAG
* *
1013686 TCCCATTCCAAGATATATGTAGCTTATTCCATCTATATGCCCCAGGTAAAAGAAAAATCGACAAG
1 TCCCATTCCAAGAAATATGTAGCTTAATCCATCTATATGCCCCAGGTAAAAGAAAAATCGACAAG
* *
1013751 CAATTAATTCTACTTTATGCTTCTTCAAGCAATCAATACAAAAATCCAACATGATTGATGAAAAC
66 CAATTAATTCTACTTTATGCTTCTTCAAGCAATCAATACAAAAATCCAACATGATGGATAAAAAC
1013816 CTTACTAAAAATATTTCAAGATACAAGTA
131 CTTACTAAAAATATTTCAAGATACAAGTA
* * *
1013845 TCCCATTCCAAGAAATATGTAGCTTAATCCATCTATATGCTCCATGTAGAAGCAAAAATCGACAA
1 TCCCATTCCAAGAAATATGTAGCTTAATCCATCTATATGCCCCAGGTAAAAG-AAAAATCGACAA
* * ** * *
1013910 GCAATTAATTCTACTTTATGCTTCTTCAAGCAATCATTACAAAAATCCTAGTTGGTGGTTAAAAA
65 GCAATTAATTCTACTTTATGCTTCTTCAAGCAATCAATACAAAAATCCAACATGATGGATAAAAA
*
1013975 CCTTACTAGAAATATTTCAAGATACAAG
130 CCTTACTAAAAATATTTCAAGATACAAG
1014003 AATCTCAATC
Statistics
Matches: 143, Mismatches: 14, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
159 47 0.33
160 96 0.67
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (159 bp):
TCCCATTCCAAGAAATATGTAGCTTAATCCATCTATATGCCCCAGGTAAAAGAAAAATCGACAAG
CAATTAATTCTACTTTATGCTTCTTCAAGCAATCAATACAAAAATCCAACATGATGGATAAAAAC
CTTACTAAAAATATTTCAAGATACAAGTA
Found at i:1014348 original size:2 final size:2
Alignment explanation
Indices: 1014338--1014378 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1014328 TATGTGTGTG
*
1014338 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1014379 TCCAATCATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1015619 original size:14 final size:14
Alignment explanation
Indices: 1015600--1015628 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1015590 TATCACATTA
1015600 ATTAAAATTTAGCT
1 ATTAAAATTTAGCT
1015614 ATTAAAATTTAGCT
1 ATTAAAATTTAGCT
1015628 A
1 A
1015629 ACGTTTTTTA
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:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
ATTAAAATTTAGCT
Found at i:1016284 original size:3 final size:3
Alignment explanation
Indices: 1016276--1016301 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1016266 CAGTATCATC
1016276 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1016302 TTGTTATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1018084 original size:22 final size:22
Alignment explanation
Indices: 1018040--1018080 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1018030 CATGATAAAA
*
1018040 TATTTAATTAAATTTAAATTAT
1 TATTTAATTAAATATAAATTAT
1018062 TATTTAATT-AATATAAATT
1 TATTTAATTAAATATAAATT
1018081 TATTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTTAATTAAATATAAATTAT
Found at i:1019344 original size:26 final size:27
Alignment explanation
Indices: 1019297--1019348 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
1019287 ATAACATATA
*
1019297 AATATATTAAAATTTATTTAAATTATT
1 AATATATTAAAATTTATATAAATTATT
1019324 AATATATT-AAATTTATATAAATTAT
1 AATATATTAAAATTTATATAAATTAT
1019349 ATCTTAAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
AATATATTAAAATTTATATAAATTATT
Found at i:1019748 original size:17 final size:17
Alignment explanation
Indices: 1019728--1019879 Score: 71
Period size: 17 Copynumber: 8.6 Consensus size: 17
1019718 TCTTAATAAT
1019728 TTATATATTTTATTATA
1 TTATATATTTTATTATA
**
1019745 TTATAATTATATTTAAAATA
1 TTAT-A-TAT-TTTATTATA
*
1019765 TTTTATATTTATATTA-A
1 TTATATATTT-TATTATA
*
1019782 TTTTAATATTTTATTA-A
1 TTAT-ATATTTTATTATA
* * *
1019799 TTA-ATATTATATAAAA
1 TTATATATTTTATTATA
* *
1019815 TT-TAAATATATATTTATA
1 TTATATAT-TTTA-TTATA
*
1019833 TTATAGTATTTT-TTATT
1 TTATA-TATTTTATTATA
*
1019850 TTATATAATTTTTTTAATA
1 TTATAT-ATTTTATT-ATA
1019869 TTACTATATTT
1 TTA-TATATTT
1019880 AAAGAAAAAA
Statistics
Matches: 105, Mismatches: 15, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
15 9 0.09
16 7 0.07
17 37 0.35
18 20 0.19
19 17 0.16
20 15 0.14
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.60
Consensus pattern (17 bp):
TTATATATTTTATTATA
Found at i:1019770 original size:27 final size:25
Alignment explanation
Indices: 1019724--1019795 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 25
1019714 TATTTCTTAA
*
1019724 TAATTTATATATTTTATTATATTATAAT
1 TAATTTAAATATTTTA-TAT-TTAT-AT
1019752 TATATTTAAAATATTTTATATTTATAT
1 TA-ATTT-AAATATTTTATATTTATAT
*
1019779 TAATTTTAATATTTTAT
1 TAATTTAAATATTTTAT
1019796 TAATTAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
25 10 0.25
26 4 0.10
27 4 0.10
28 6 0.15
29 7 0.17
30 9 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TAATTTAAATATTTTATATTTATAT
Found at i:1019805 original size:27 final size:27
Alignment explanation
Indices: 1019727--1019810 Score: 91
Period size: 27 Copynumber: 3.0 Consensus size: 27
1019717 TTCTTAATAA
1019727 TTTATATATTTTATTATATTATAATTATAT
1 TTTA-ATATTTTATTA-ATTAT-ATTATAT
* *
1019757 TTAAAATATTTTA-TATTTATATTA-AT
1 TT-TAATATTTTATTAATTATATTATAT
1019783 TTTAATATTTTATTAATTAATATTATAT
1 TTTAATATTTTATTAATT-ATATTATAT
1019811 AAAATTTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
25 9 0.20
26 8 0.17
27 10 0.22
28 6 0.13
29 2 0.04
30 10 0.22
31 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTAATATTTTATTAATTATATTATAT
Found at i:1027151 original size:29 final size:30
Alignment explanation
Indices: 1027105--1027167 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
1027095 TTATAATAAA
*
1027105 AATATTTAATTTTTATATTATT-AAATT-T
1 AATATTTAATATTTATATTATTAAAATTAT
*
1027133 AATATTTTAATATTTATATTTTTAAAATTAT
1 AATA-TTTAATATTTATATTATTAAAATTAT
1027164 AATA
1 AATA
1027168 AATAAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 4 0.13
29 16 0.53
30 5 0.17
31 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
AATATTTAATATTTATATTATTAAAATTAT
Found at i:1027153 original size:21 final size:21
Alignment explanation
Indices: 1027106--1027153 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1027096 TATAATAAAA
1027106 ATATTTAATTTTTATATTATT
1 ATATTTAATTTTTATATTATT
*
1027127 AAATTTAATATTTTA-A-TATTT
1 ATATTTAAT-TTTTATATTA-TT
1027148 ATATTT
1 ATATTT
1027154 TTAAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.09
21 16 0.70
22 5 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATTTAATTTTTATATTATT
Found at i:1027163 original size:14 final size:14
Alignment explanation
Indices: 1027116--1027164 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1027106 ATATTTAATT
*
1027116 TTTATATTATTAAA
1 TTTATATTTTTAAA
1027130 TTTA-ATATTTTAATA
1 TTTATAT-TTTTAA-A
1027145 TTTATATTTTTAAA
1 TTTATATTTTTAAA
*
1027159 ATTATA
1 TTTATA
1027165 ATAAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 2 0.07
14 15 0.50
15 11 0.37
16 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTATATTTTTAAA
Found at i:1027213 original size:19 final size:19
Alignment explanation
Indices: 1027170--1027225 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
1027160 TTATAATAAA
1027170 TAAAA-ATTAACAGTATTA-
1 TAAAATATTAACA-TATTAT
*
1027188 AAAAATATTTAA-ATATTAT
1 TAAAATA-TTAACATATTAT
1027207 TAAAATATTAACATATTAT
1 TAAAATATTAACATATTAT
1027226 ATAATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 13 0.41
19 15 0.47
20 4 0.12
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (19 bp):
TAAAATATTAACATATTAT
Found at i:1027427 original size:28 final size:29
Alignment explanation
Indices: 1027386--1027441 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
1027376 TAATTTATTA
1027386 TAATTCTAAAAATATA-AAAATAAAATAT
1 TAATTCTAAAAATATACAAAATAAAATAT
* * *
1027414 TAATTTTAATAATATACAAATTAAAATA
1 TAATTCTAAAAATATACAAAATAAAATA
1027442 CTCTTACCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (29 bp):
TAATTCTAAAAATATACAAAATAAAATAT
Found at i:1028385 original size:27 final size:27
Alignment explanation
Indices: 1028355--1028409 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1028345 ATAATAATAC
1028355 GTTAATAATTCCGATCATATTAATTTT
1 GTTAATAATTCCGATCATATTAATTTT
1028382 GTTAATAATTCCGATCATATTAATTTT
1 GTTAATAATTCCGATCATATTAATTTT
1028409 G
1 G
1028410 ATATGCACGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (27 bp):
GTTAATAATTCCGATCATATTAATTTT
Found at i:1030869 original size:30 final size:30
Alignment explanation
Indices: 1030833--1030893 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1030823 ACAACAAAAC
* *
1030833 AAGTATTTGCTATTCGAGCTTGATGCATGT
1 AAGTATTTGCCATTCGAACTTGATGCATGT
1030863 AAGTATTTGCCATTCGAACTTGATGCATGT
1 AAGTATTTGCCATTCGAACTTGATGCATGT
1030893 A
1 A
1030894 TGTTTTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (30 bp):
AAGTATTTGCCATTCGAACTTGATGCATGT
Found at i:1030903 original size:26 final size:27
Alignment explanation
Indices: 1030843--1030903 Score: 70
Period size: 30 Copynumber: 2.2 Consensus size: 27
1030833 AAGTATTTGC
*
1030843 TATTCGAGCTTGATGCATGTAAGTATT
1 TATTCGAACTTGATGCATGTAAGTATT
*
1030870 TGCCATTCGAACTTGATGCATGTATGT-TT
1 T---ATTCGAACTTGATGCATGTAAGTATT
1030899 TATTC
1 TATTC
1030904 ATGTAAATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
26 4 0.14
27 1 0.03
29 3 0.10
30 21 0.72
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.43
Consensus pattern (27 bp):
TATTCGAACTTGATGCATGTAAGTATT
Found at i:1041830 original size:35 final size:37
Alignment explanation
Indices: 1041769--1041841 Score: 89
Period size: 35 Copynumber: 2.0 Consensus size: 37
1041759 ACTTAGTTTT
1041769 TTTATAAAAAAAAATTAATTTAATTTAA-ATT-ATTA
1 TTTATAAAAAAAAATTAATTTAATTTAATATTAATTA
* * *
1041804 TTTATATAATAAAAA-TATTTTTATTTAATATTAATTA
1 TTTATA-AAAAAAAATTAATTTAATTTAATATTAATTA
1041841 T
1 T
1041842 AAATATATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 17 0.53
36 10 0.31
37 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (37 bp):
TTTATAAAAAAAAATTAATTTAATTTAATATTAATTA
Found at i:1043182 original size:2 final size:2
Alignment explanation
Indices: 1043177--1043201 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1043167 ATATATAGAA
1043177 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 A
1043202 ACTTTTGTTT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1044919 original size:29 final size:30
Alignment explanation
Indices: 1044886--1044943 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
1044876 TTAGTATTTA
* *
1044886 ATAAAAAATATTATTATT-TATAATTAATT
1 ATAAAAAATATAAATATTATATAATTAATT
*
1044915 ATAAAATATATAAATATTAATATAATTAA
1 ATAAAAAATATAAATATT-ATATAATTAA
1044944 ATAATATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.62
31 9 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
ATAAAAAATATAAATATTATATAATTAATT
Found at i:1045453 original size:3 final size:3
Alignment explanation
Indices: 1045445--1045481 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1045435 TGACTAAAAC
1045445 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1045482 CATCATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1045585 original size:3 final size:3
Alignment explanation
Indices: 1045577--1045615 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
1045567 GACGTTGCAA
1045577 AAT AAT AAT AAT AAT AAT AAT AAT AATT AA- AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
1045616 TGCATCTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1046389 original size:23 final size:24
Alignment explanation
Indices: 1046337--1046389 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 24
1046327 TTCAACGAAG
*
1046337 ATATT-ATTTAATTTATTAATAAT
1 ATATTAATTTAATATATTAATAAT
* * *
1046360 ATGTTAATTT-ATATATTATTAGT
1 ATATTAATTTAATATATTAATAAT
1046383 ATATTAA
1 ATATTAA
1046390 ATATAAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (24 bp):
ATATTAATTTAATATATTAATAAT
Found at i:1050832 original size:15 final size:15
Alignment explanation
Indices: 1050809--1050842 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1050799 AAAAAAATGA
*
1050809 TATTCACTTTCTAAT
1 TATTAACTTTCTAAT
*
1050824 TATTAACTTTCTATT
1 TATTAACTTTCTAAT
1050839 TATT
1 TATT
1050843 CATAATTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTAACTTTCTAAT
Found at i:1051075 original size:2 final size:2
Alignment explanation
Indices: 1051063--1051095 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1051053 AACCTAACCA
1051063 AT AT A- 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
1051096 TCTCCTGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1053044 original size:4 final size:4
Alignment explanation
Indices: 1053035--1053068 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
1053025 AAACATATTA
*
1053035 AAAT AAAT AAAT AAAT AAAT ATAAA AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT A
1053069 TATTAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 24 0.89
5 3 0.11
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1053063 original size:17 final size:17
Alignment explanation
Indices: 1053033--1053068 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1053023 TTAAACATAT
1053033 TAAAATAAATAAATAAA
1 TAAAATAAATAAATAAA
1053050 TAAATATAAA-AAATAAA
1 TAAA-ATAAATAAATAAA
1053067 TA
1 TA
1053069 TATTAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
TAAAATAAATAAATAAA
Found at i:1053069 original size:13 final size:13
Alignment explanation
Indices: 1053034--1053070 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1053024 TAAACATATT
1053034 AAAATAAATA-AA
1 AAAATAAATATAA
*
1053046 TAAATAAATATAA
1 AAAATAAATATAA
1053059 AAAATAAATATA
1 AAAATAAATATA
1053071 TTAAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATAAATATAA
Found at i:1053089 original size:32 final size:32
Alignment explanation
Indices: 1053053--1053115 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
1053043 AAATAAATAA
1053053 ATATAAAAAATAAATATATTAAAATTTATATT
1 ATATAAAAAATAAATATATTAAAATTTATATT
* * *
1053085 ATATAAGATATTAATATATTAAAATTTATAT
1 ATATAAAAAATAAATATATTAAAATTTATAT
1053116 AATTATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (32 bp):
ATATAAAAAATAAATATATTAAAATTTATATT
Found at i:1053324 original size:4 final size:4
Alignment explanation
Indices: 1053315--1053347 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
1053305 TAATAATGTA
1053315 AATT AATT AATT AATT AATT AATT AATT -ATT AA
1 AATT AATT AATT AATT AATT AATT AATT AATT AA
1053348 AAAGAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:1053482 original size:2 final size:2
Alignment explanation
Indices: 1053475--1053502 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1053465 TATTCCTTTA
1053475 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
1053503 TATTAAATGA
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:1055372 original size:27 final size:30
Alignment explanation
Indices: 1055316--1055414 Score: 91
Period size: 31 Copynumber: 3.3 Consensus size: 30
1055306 CATTGCTAGT
*
1055316 ATATATTTATATATTTATTATAACTTTTTTA
1 ATATATTTATATATTTATTATAAC-ATTTTA
*
1055347 ATATATTT-TATATTTA-TATAA-ATTTTT
1 ATATATTTATATATTTATTATAACATTTTA
* *
1055374 ATATATTAATA-ATTTATATTATATATATTTT-
1 ATATATTTATATA-TT-TATTATA-ACATTTTA
1055405 ATATATTTAT
1 ATATATTTAT
1055415 GTTATAGTCT
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
27 12 0.21
28 4 0.07
29 7 0.12
30 12 0.21
31 18 0.31
32 5 0.09
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (30 bp):
ATATATTTATATATTTATTATAACATTTTA
Found at i:1055375 original size:18 final size:18
Alignment explanation
Indices: 1055352--1055414 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
1055342 TTTTAATATA
1055352 TTTTATATTTATATAAAT
1 TTTTATATTTATATAAAT
1055370 TTTTATATATTA-AT-AA-
1 TTTTATAT-TTATATAAAT
*
1055386 -TTTATA-TTATATATAT
1 TTTTATATTTATATAAAT
1055402 TTTATATATTTAT
1 TTT-TATATTTAT
1055415 GTTATAGTCT
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 3 0.08
14 2 0.05
15 7 0.19
17 4 0.11
18 14 0.38
19 7 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTATATTTATATAAAT
Found at i:1056659 original size:37 final size:36
Alignment explanation
Indices: 1056600--1056670 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
1056590 TAAAATTTTG
**
1056600 TTTTTAAATATATAAGGATAAAAATATTAAATATAAA
1 TTTTTAAATATATAAAAATAAAAA-ATTAAATATAAA
*
1056637 TTTTTAAATATA-AAAAATTAAAAAATTTAATATA
1 TTTTTAAATATATAAAAA-TAAAAAATTAAATATA
1056671 CTCATATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 12 0.40
37 18 0.60
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (36 bp):
TTTTTAAATATATAAAAATAAAAAATTAAATATAAA
Found at i:1057350 original size:33 final size:33
Alignment explanation
Indices: 1057303--1057366 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1057293 CGGTTAAAAA
*
1057303 TTTAAAAATAATAAAATTATT-ATTATAATATTT
1 TTTAAAAATAATAAAATAATTAATTA-AATATTT
* *
1057336 TTTAAATATTATAAAATAATTAATTAAATAT
1 TTTAAAAATAATAAAATAATTAATTAAATAT
1057367 AAAAAATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 23 0.85
34 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
TTTAAAAATAATAAAATAATTAATTAAATATTT
Found at i:1057387 original size:23 final size:23
Alignment explanation
Indices: 1057361--1057406 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1057351 ATAATTAATT
*
1057361 AAATATAAAAAATATTTTTAAAA
1 AAATATAAAAAATATTTATAAAA
* * *
1057384 AAATTTAACAAATGTTTATAAAA
1 AAATATAAAAAATATTTATAAAA
1057407 GCTCATTAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
AAATATAAAAAATATTTATAAAA
Found at i:1059014 original size:16 final size:15
Alignment explanation
Indices: 1058993--1059026 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
1058983 AATAACATCA
1058993 TATTAATAATATAAAT
1 TATTAATAAT-TAAAT
1059009 TATTAATAATTAAAT
1 TATTAATAATTAAAT
1059024 TAT
1 TAT
1059027 ATTATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTAATAATTAAAT
Found at i:1059033 original size:16 final size:16
Alignment explanation
Indices: 1058992--1059035 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
1058982 TAATAACATC
1058992 ATATTAATAATATAAATT
1 ATATT-ATAAT-TAAATT
*
1059010 AT-TAATAATTAAATT
1 ATATTATAATTAAATT
1059025 ATATTATAATT
1 ATATTATAATT
1059036 TTATAACCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 8 0.35
16 12 0.52
17 1 0.04
18 2 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATTATAATTAAATT
Found at i:1063932 original size:16 final size:15
Alignment explanation
Indices: 1063911--1063949 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1063901 TTTAAAAATT
1063911 AATTAATATTTAAGAA
1 AATTAATATTTAA-AA
*
1063927 AATTAA-ATTTAAAT
1 AATTAATATTTAAAA
1063941 AATTAATAT
1 AATTAATAT
1063950 AATTATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AATTAATATTTAAAA
Found at i:1063952 original size:60 final size:58
Alignment explanation
Indices: 1063860--1063978 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 58
1063850 TCAAATGATA
* * *
1063860 ATTTAAAAAATTAGTTTAATTAATTAACATAATTATATATCTTTAAAAATTAATTAAT
1 ATTTAAAAAATTAATTTAAATAATTAACATAATTATATATCTTTAAAAAATAATTAAT
* * *
1063918 ATTTAAGAAAATTAAATTTAAATAATTAATATAATTATATATTTTTAAAAAATATTTAAT
1 ATTTAA-AAAATT-AATTTAAATAATTAACATAATTATATATCTTTAAAAAATAATTAAT
1063978 A
1 A
1063979 AATTTTAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 6 0.11
59 6 0.11
60 41 0.77
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (58 bp):
ATTTAAAAAATTAATTTAAATAATTAACATAATTATATATCTTTAAAAAATAATTAAT
Found at i:1063971 original size:30 final size:30
Alignment explanation
Indices: 1063880--1063982 Score: 79
Period size: 30 Copynumber: 3.5 Consensus size: 30
1063870 TTAGTTTAAT
* * *
1063880 TAATTAACATAATTATATATCTTTAAAAAT
1 TAATTAATATAATTATATATATTTAAAAAA
* * *
1063910 TAATTAATAT--TTA-AGAAAATTAAATTTAAA
1 TAATTAATATAATTATATATATTTAAA---AAA
*
1063940 TAATTAATATAATTATATATTTTTAAAAAA
1 TAATTAATATAATTATATATATTTAAAAAA
*
1063970 TATTTAATA-AATT
1 TAATTAATATAATT
1063983 TTAAATTCAA
Statistics
Matches: 56, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
27 7 0.12
28 3 0.05
29 4 0.07
30 32 0.57
32 3 0.05
33 7 0.12
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (30 bp):
TAATTAATATAATTATATATATTTAAAAAA
Found at i:1065420 original size:15 final size:15
Alignment explanation
Indices: 1065402--1065444 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1065392 CATTTATAAA
1065402 TATAAATTTTAAAAT
1 TATAAATTTTAAAAT
*
1065417 TATAAATATTT-ATAT
1 TATAAAT-TTTAAAAT
*
1065432 TTTAAATTTTAAA
1 TATAAATTTTAAA
1065445 TATAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 3 0.13
15 17 0.74
16 3 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATAAATTTTAAAAT
Found at i:1065657 original size:17 final size:16
Alignment explanation
Indices: 1065637--1065683 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1065627 TATTTGGTAT
1065637 AAAATTATATTAATAGC
1 AAAATTATATTAA-AGC
**
1065654 AAAATTAT-TATAAATT
1 AAAATTATAT-TAAAGC
1065670 AAAATTATATTAAA
1 AAAATTATATTAAA
1065684 AATTATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
AAAATTATATTAAAGC
Found at i:1065791 original size:10 final size:10
Alignment explanation
Indices: 1065772--1065932 Score: 52
Period size: 9 Copynumber: 15.5 Consensus size: 10
1065762 TACTAAATTT
1065772 TTAT-TAAAA
1 TTATATAAAA
1065781 TTATATAAAA
1 TTATATAAAA
*
1065791 TTTATAAAAAA
1 -TTATATAAAA
* *
1065802 TTACATTAAA
1 TTATATAAAA
1065812 -TAT-TAAAAA
1 TTATAT-AAAA
1065821 TTATCA-AAAA
1 TTAT-ATAAAA
**
1065831 TTATATTAATGG
1 TTATA-TAA-AA
1065843 TTAT-TAAAA
1 TTATATAAAA
*
1065852 TTATAGACATAA
1 TTATATA-A-AA
*
1065864 -TA-ATAAAG
1 TTATATAAAA
1065872 TTATATTATTCAAA
1 TTATA-TA---AAA
1065886 TTATA-AAAA
1 TTATATAAAA
*
1065895 ATATATTAAAAA
1 TTATA-T-AAAA
1065907 TTAT-TAAAA
1 TTATATAAAA
1065916 TTATATCAAATA
1 TTATAT-AAA-A
1065928 TTATA
1 TTATA
1065933 ATAATGATTA
Statistics
Matches: 112, Mismatches: 16, Indels: 45
0.65 0.09 0.26
Matches are distributed among these distances:
8 2 0.02
9 32 0.29
10 32 0.29
11 19 0.17
12 20 0.18
14 7 0.06
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (10 bp):
TTATATAAAA
Found at i:1065812 original size:21 final size:20
Alignment explanation
Indices: 1065777--1065820 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1065767 AATTTTTATT
* *
1065777 AAAATTATATAAAATTTATAA
1 AAAATTACATAAAATAT-TAA
*
1065798 AAAATTACATTAAATATTAA
1 AAAATTACATAAAATATTAA
1065818 AAA
1 AAA
1065821 TTATCAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATTACATAAAATATTAA
Found at i:1065907 original size:21 final size:21
Alignment explanation
Indices: 1065883--1065933 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1065873 TATATTATTC
*
1065883 AAATTATAAAAAATATATTAA
1 AAATTATAAAAAATATATCAA
* *
1065904 AAATTATTAAAATTATATCAA
1 AAATTATAAAAAATATATCAA
*
1065925 ATATTATAA
1 AAATTATAA
1065934 TAATGATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AAATTATAAAAAATATATCAA
Found at i:1065927 original size:30 final size:30
Alignment explanation
Indices: 1065876--1065945 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
1065866 ATAAAGTTAT
*
1065876 ATTATTCAAATTATAAAAAATA-TATTAAAA
1 ATTATTAAAATTATAAAAAATATTA-TAAAA
** *
1065906 ATTATTAAAATTATATCAAATATTATAATA
1 ATTATTAAAATTATAAAAAATATTATAAAA
*
1065936 ATGATTAAAA
1 ATTATTAAAA
1065946 AATGTTATCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 32 0.94
31 2 0.06
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (30 bp):
ATTATTAAAATTATAAAAAATATTATAAAA
Found at i:1066075 original size:10 final size:9
Alignment explanation
Indices: 1066046--1066084 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1066036 ATCAAAATTA
*
1066046 TATAAAAAA
1 TATAAAAAT
*
1066055 TATCAAAAT
1 TATAAAAAT
1066064 TATAAAACAT
1 TATAAAA-AT
1066074 TATAAAAAT
1 TATAAAAAT
1066083 TA
1 TA
1066085 AAGATAAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (9 bp):
TATAAAAAT
Found at i:1066329 original size:20 final size:20
Alignment explanation
Indices: 1066260--1066329 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
1066250 TATGCCCATG
*
1066260 ATTATCCAATTATATTCAAA
1 ATTATCAAATTATATTCAAA
* *
1066280 ATTATTAAAATTTTA-T-AAA
1 ATTA-TCAAATTATATTCAAA
1066299 ATTTATCCAAATTATATTCAAA
1 A-TTAT-CAAATTATATTCAAA
1066321 ATTATCAAA
1 ATTATCAAA
1066330 ATAATAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
19 5 0.12
20 19 0.47
21 12 0.30
22 4 0.10
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTATCAAATTATATTCAAA
Found at i:1068248 original size:18 final size:20
Alignment explanation
Indices: 1068205--1068249 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
1068195 AAATTTTTAA
*
1068205 AAATAATTTTTATTAATTTT
1 AAATAAATTTTATTAATTTT
1068225 -AATAAATTTT-TT-ATTTT
1 AAATAAATTTTATTAATTTT
1068242 AAATAAAT
1 AAATAAAT
1068250 AATTTCATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 5 0.22
18 9 0.39
19 9 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AAATAAATTTTATTAATTTT
Found at i:1068262 original size:26 final size:29
Alignment explanation
Indices: 1068233--1068286 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 29
1068223 TTAATAAATT
*
1068233 TTTTATTTTAA-ATAA-ATAATT-TCATA
1 TTTTATTTAAATATAACATAATTATCATA
1068259 TTTTATTTAAATATAACATAATTATCAT
1 TTTTATTTAAATATAACATAATTATCAT
1068287 CTTCCGTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 10 0.42
27 4 0.17
28 6 0.25
29 4 0.17
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTTATTTAAATATAACATAATTATCATA
Found at i:1070034 original size:21 final size:20
Alignment explanation
Indices: 1070000--1070040 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
1069990 AAAATAAATT
1070000 TTATAATTTATATATTTATA
1 TTATAATTTATATATTTATA
1070020 TTATAATTATATATATTTATA
1 TTATAATT-TATATATTTATA
1070041 AAAAAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATAATTTATATATTTATA
Found at i:1070048 original size:21 final size:20
Alignment explanation
Indices: 1070004--1070052 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
1069994 TAAATTTTAT
** *
1070004 AATTTATATATTTATATTAT
1 AATTTATATATTTATAAAAA
1070024 AATTATATATATTTATAAAAA
1 AATT-TATATATTTATAAAAA
1070045 AATTTATA
1 AATTTATA
1070053 AAAATTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTTATATATTTATAAAAA
Found at i:1080114 original size:2 final size:2
Alignment explanation
Indices: 1080107--1080149 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1080097 CTAGTAAGCT
1080107 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
1080149 T
1 T
1080150 TGTCAATGGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1085589 original size:15 final size:15
Alignment explanation
Indices: 1085569--1085601 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1085559 CAGATATCAG
*
1085569 ATATGAATATTTCGA
1 ATATGAATATTTCAA
1085584 ATATGAATATTTCAA
1 ATATGAATATTTCAA
1085599 ATA
1 ATA
1085602 AAATAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.39
Consensus pattern (15 bp):
ATATGAATATTTCAA
Found at i:1086862 original size:15 final size:15
Alignment explanation
Indices: 1086842--1086887 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
1086832 GGATTGTAGA
*
1086842 TTAAATTTTTTTTAT
1 TTAAATTTTATTTAT
*
1086857 TTAAATTTAAATTTAT
1 TTAAATTT-TATTTAT
*
1086873 TTAGATTTTATTTAT
1 TTAAATTTTATTTAT
1086888 AGGTTAGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TTAAATTTTATTTAT
Found at i:1086947 original size:21 final size:21
Alignment explanation
Indices: 1086923--1086962 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1086913 AATAAAAATT
1086923 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
1086944 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
1086963 AATAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:1086980 original size:52 final size:55
Alignment explanation
Indices: 1086909--1087025 Score: 145
Period size: 56 Copynumber: 2.1 Consensus size: 55
1086899 ATTATTTTTA
* *
1086909 AAATAATAAAAATTTATTTTA-T-ATTAAT-ATTTATATATT-TTATAAT-TAAATTT
1 AAATAA-AAAAATTTATTTTATTAATAAATAATTTA-A-ATTATTAAAATATAAATTT
1086962 AAATAAAAAAATTTATTTTATTAAATAAATAATTTAAATTATTAAAATATAAATTT
1 AAATAAAAAAATTTATTTTATT-AATAAATAATTTAAATTATTAAAATATAAATTT
1087018 AAATAAAA
1 AAATAAAA
1087026 TTTAGTGTAA
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
52 14 0.25
53 7 0.12
54 3 0.05
55 12 0.21
56 20 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (55 bp):
AAATAAAAAAATTTATTTTATTAATAAATAATTTAAATTATTAAAATATAAATTT
Found at i:1086997 original size:21 final size:22
Alignment explanation
Indices: 1086960--1087021 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
1086950 ATAATTAAAT
**
1086960 TTAAATAAAAAAATTTATTTTA
1 TTAAATAAAAAAATTTAAATTA
*
1086982 TTAAAT-AAATAATTTAAATTA
1 TTAAATAAAAAAATTTAAATTA
* *
1087003 TTAAA-ATATAAATTTAAAT
1 TTAAATAAAAAAATTTAAAT
1087022 AAAATTTAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 27 0.82
22 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTAAATAAAAAAATTTAAATTA
Found at i:1087410 original size:21 final size:21
Alignment explanation
Indices: 1087386--1087439 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 21
1087376 TTCAAAACTC
*
1087386 TAATTTAAAATTAAATTATTT
1 TAATTTAAAATTAAATAATTT
1087407 TAATTTTAAAATTAAATAATTT
1 TAA-TTTAAAATTAAATAATTT
*
1087429 AAATTTAAAAT
1 TAATTTAAAAT
1087440 AATTCATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 11 0.37
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATTTAAAATTAAATAATTT
Found at i:1087416 original size:22 final size:21
Alignment explanation
Indices: 1087387--1087439 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1087377 TCAAAACTCT
*
1087387 AATTTAAAATTAAATTATTTTA
1 AATTTAAAATTAAA-TAATTTA
*
1087409 ATTTTAAAATTAAATAATTTA
1 AATTTAAAATTAAATAATTTA
1087430 AATTTAAAAT
1 AATTTAAAAT
1087440 AATTCATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTTAAAATTAAATAATTTA
Done.