Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold106
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: 4928209
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8888 characters in sequence are not A, C, G, or T
File 7 of 27
Found at i:938367 original size:35 final size:35
Alignment explanation
Indices: 938328--938396 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
938318 AAAAATAAAT
*
938328 TAAAAATATATTTTATGTTAA-ATAATAATTAAAAA
1 TAAAAATATA-TTTATATTAATATAATAATTAAAAA
938363 TAAAAATATATTTATATTAATATAATAATTAAAA
1 TAAAAATATATTTATATTAATATAATAATTAAAA
938397 TTATATTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 9 0.28
35 23 0.72
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (35 bp):
TAAAAATATATTTATATTAATATAATAATTAAAAA
Found at i:938373 original size:64 final size:65
Alignment explanation
Indices: 938292--938434 Score: 166
Period size: 64 Copynumber: 2.2 Consensus size: 65
938282 ATAATTATAG
* * *
938292 TAAATAATAAAATTATATTTATAACAA-AAAATAAATTAAAAATATATTT-TATGTTAAATAA-T
1 TAAA-AATAAAAATATATTTATAACAATAAAAT-AATTAAAAATATATTTATAT-TTAAAAAACA
938354 AAT
63 AAT
** * *
938357 TAAAAATAAAAATATATTTATATTAATATAATAATTAAAATTATATTTATATTTAAAAAACAAAT
1 TAAAAATAAAAATATATTTATAACAATAAAATAATTAAAAATATATTTATATTTAAAAAACAAAT
938422 TAACAAATAAAAA
1 TAA-AAATAAAAA
938435 AAAAACTATG
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
64 41 0.61
65 17 0.25
66 9 0.13
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (65 bp):
TAAAAATAAAAATATATTTATAACAATAAAATAATTAAAAATATATTTATATTTAAAAAACAAAT
Found at i:938650 original size:18 final size:18
Alignment explanation
Indices: 938613--938647 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
938603 CATCGAAATT
*
938613 TTAATATTTGAAAATTAA
1 TTAATATTTAAAAATTAA
938631 TTAAT-TTTAAAAATTAA
1 TTAATATTTAAAAATTAA
938648 ATTTTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
TTAATATTTAAAAATTAA
Found at i:938869 original size:28 final size:29
Alignment explanation
Indices: 938801--938870 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 29
938791 TAAAATAGAT
*
938801 CAATTATATTATTATATATCATATAACATA
1 CAATTATATT-TTATATATAATATAACATA
*
938831 CAACTAT-TTTTATATAATAATATAA-ATA
1 CAATTATATTTTATAT-ATAATATAACATA
*
938859 -ATTTATATTTTA
1 CAATTATATTTTA
938871 AAATTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 4 0.12
28 14 0.41
29 10 0.29
30 6 0.18
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (29 bp):
CAATTATATTTTATATATAATATAACATA
Found at i:944252 original size:2 final size:2
Alignment explanation
Indices: 944245--944269 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
944235 ACGATACCCA
944245 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
944270 GCATGCCTCT
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:949471 original size:42 final size:43
Alignment explanation
Indices: 949396--949494 Score: 114
Period size: 42 Copynumber: 2.3 Consensus size: 43
949386 AATTTGGCCG
* * *
949396 AATGTTCAATCAAATGTCTCAAAGTCTAAAGTTAACTTTGTCA
1 AATGTTCAATCAAATGTCCCAAAGTCTAAAGTTAAATTGGTCA
* * *
949439 AATGTTCAATC-AATGTCCCAAAAT-TCAGAGTTAAATTGGTCG
1 AATGTTCAATCAAATGTCCCAAAGTCT-AAAGTTAAATTGGTCA
949481 AATGTTCAAT-AAAT
1 AATGTTCAATCAAAT
949495 TATTTTTTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
41 1 0.02
42 36 0.75
43 11 0.23
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (43 bp):
AATGTTCAATCAAATGTCCCAAAGTCTAAAGTTAAATTGGTCA
Found at i:949922 original size:24 final size:23
Alignment explanation
Indices: 949894--949956 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
949884 ACCTAACTTT
*
949894 ATTTTTAATTATATAATTTTTATA
1 ATTTTTAATTATATAA-TTATATA
949918 ATTTTTATATCTATAT-ATTATATA
1 ATTTTTA-AT-TATATAATTATATA
*
949942 ATTTAT-ATTATATAA
1 ATTTTTAATTATATAA
949957 AAATAAACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
21 5 0.15
22 3 0.09
24 18 0.53
25 3 0.09
26 5 0.15
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
ATTTTTAATTATATAATTATATA
Found at i:952498 original size:21 final size:21
Alignment explanation
Indices: 952474--952517 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
952464 TTAAGCTAAC
952474 AAATGTGCCCTCTACATTCCA
1 AAATGTGCCCTCTACATTCCA
**
952495 AAATGTGTTCTCTACATTCCA
1 AAATGTGCCCTCTACATTCCA
952516 AA
1 AA
952518 GCTTTATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.32
Consensus pattern (21 bp):
AAATGTGCCCTCTACATTCCA
Found at i:958159 original size:2 final size:2
Alignment explanation
Indices: 958152--958184 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
958142 ACGTACGTAC
958152 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
958185 ACACTCTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:963231 original size:10 final size:10
Alignment explanation
Indices: 963210--963242 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
963200 TATTTTTAAA
963210 TTAATAATTT
1 TTAATAATTT
963220 TTAATTAATTT
1 TTAA-TAATTT
963231 TTAATAATTT
1 TTAATAATTT
963241 TT
1 TT
963243 TAATTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTAATAATTT
Found at i:966263 original size:12 final size:12
Alignment explanation
Indices: 966246--966271 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
966236 GACTAAGATA
966246 TGGTTGAAAATG
1 TGGTTGAAAATG
966258 TGGTTGAAAATG
1 TGGTTGAAAATG
966270 TG
1 TG
966272 ACTAAATCTC
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:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (12 bp):
TGGTTGAAAATG
Found at i:967403 original size:15 final size:15
Alignment explanation
Indices: 967378--967418 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
967368 CGAGTACCTC
967378 GAGATGAAATCCGAGA
1 GAGA-GAAATCCGAGA
967394 GAGAGAAATCCGAGA
1 GAGAGAAATCCGAGA
967409 GAGAGAAATC
1 GAGAGAAATC
967419 AAGTTTGACC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.46, C:0.12, G:0.32, T:0.10
Consensus pattern (15 bp):
GAGAGAAATCCGAGA
Found at i:969551 original size:19 final size:18
Alignment explanation
Indices: 969527--969624 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
969517 TAGCTTAAAT
969527 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
969546 TGTATCGATAC--A-TTA
1 TGTATCGATACAAACTTA
969561 --TATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
969578 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
969591 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
969611 TGTATCGATACAAA
1 TGTATCGATACAAA
969625 TAGTTAAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 20 0.30
14 1 0.02
15 3 0.05
16 4 0.06
17 3 0.05
19 22 0.33
20 13 0.20
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:969570 original size:32 final size:32
Alignment explanation
Indices: 969529--969622 Score: 161
Period size: 32 Copynumber: 2.9 Consensus size: 32
969519 GCTTAAATTG
*
969529 TATCGATACAAAACTTATGTATCGATACATTA
1 TATCGATACAACACTTATGTATCGATACATTA
*
969561 TATCGATACAACACTTATGTATCGATACATTG
1 TATCGATACAACACTTATGTATCGATACATTA
969593 TATCGATACAACACTTTATGTATCGATACA
1 TATCGATACAACAC-TTATGTATCGATACA
969623 AATAGTTAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 44 0.75
33 15 0.25
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (32 bp):
TATCGATACAACACTTATGTATCGATACATTA
Found at i:970319 original size:20 final size:20
Alignment explanation
Indices: 970294--970347 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
970284 TAACTGAAAG
970294 TATCGATACA-TTGAAAAATA
1 TATCGATACATTTG-AAAATA
*
970314 TATCGATACATTTGAGAATA
1 TATCGATACATTTGAAAATA
*
970334 TATCGATATATTTG
1 TATCGATACATTTG
970348 GGTCAAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 28 0.90
21 3 0.10
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (20 bp):
TATCGATACATTTGAAAATA
Found at i:973877 original size:21 final size:21
Alignment explanation
Indices: 973851--973890 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
973841 AAAAGCTCAA
973851 ACTGAACAATTATTATACAAT
1 ACTGAACAATTATTATACAAT
973872 ACTGAACAATTATTATACA
1 ACTGAACAATTATTATACA
973891 GCTGCAACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.33
Consensus pattern (21 bp):
ACTGAACAATTATTATACAAT
Found at i:975885 original size:18 final size:18
Alignment explanation
Indices: 975864--975904 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
975854 GTCAGAGTTG
*
975864 GAGTTTCGAATAGAGTCA
1 GAGTTTCGAATAGAATCA
* *
975882 GAGTTTTGAATGGAATCA
1 GAGTTTCGAATAGAATCA
975900 GAGTT
1 GAGTT
975905 AAATCCTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.07, G:0.29, T:0.32
Consensus pattern (18 bp):
GAGTTTCGAATAGAATCA
Found at i:981902 original size:23 final size:21
Alignment explanation
Indices: 981858--981902 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
981848 AACACTTCAC
*
981858 TTATAATTTTTTATTATAATA
1 TTATAATTTTTAATTATAATA
*
981879 TTATAATTAATTTAATTATGATA
1 TTATAATT--TTTAATTATAATA
981902 T
1 T
981903 AAAATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
23 12 0.60
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TTATAATTTTTAATTATAATA
Found at i:981995 original size:12 final size:12
Alignment explanation
Indices: 981978--982002 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
981968 AATTTTATTT
981978 TTTAAAATTAAA
1 TTTAAAATTAAA
981990 TTTAAAATTAAA
1 TTTAAAATTAAA
982002 T
1 T
982003 CAAATGATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTTAAAATTAAA
Found at i:982036 original size:22 final size:22
Alignment explanation
Indices: 981982--982036 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
981972 TTATTTTTTA
981982 AAATTAAATTTAAAATTAAATC
1 AAATTAAATTTAAAATTAAATC
* * * * *
982004 AAATGATATTTACAATTGATTC
1 AAATTAAATTTAAAATTAAATC
*
982026 TAATTAAATTT
1 AAATTAAATTT
982037 TATTAATTTA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (22 bp):
AAATTAAATTTAAAATTAAATC
Found at i:982536 original size:16 final size:16
Alignment explanation
Indices: 982517--982558 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
982507 TTTAATAATT
982517 TTAATATTAAATATAA
1 TTAATATTAAATATAA
*
982533 TTAATA-T-AATATAT
1 TTAATATTAAATATAA
982547 TTAATATATAAA
1 TTAATAT-TAAA
982559 AATTTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 12 0.55
15 1 0.05
16 7 0.32
17 2 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAATATTAAATATAA
Found at i:987525 original size:2 final size:2
Alignment explanation
Indices: 987518--987545 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
987508 TTATCAAAAT
987518 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
987546 ACATCGTCAA
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):
TA
Found at i:988260 original size:22 final size:21
Alignment explanation
Indices: 988235--988276 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
988225 AAATTAAACA
988235 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
988255 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
988276 A
1 A
988277 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:988649 original size:40 final size:40
Alignment explanation
Indices: 988604--988685 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
988594 ATATTTTTAT
* *
988604 TTTAATATAAATATAGTGTAAATTATTAATTATTTAAAAA
1 TTTAATATAAATATAATATAAATTATTAATTATTTAAAAA
988644 TTTAATATAAATATAATATAAATTATTAATTATTTAAAAA
1 TTTAATATAAATATAATATAAATTATTAATTATTTAAAAA
988684 TT
1 TT
988686 ATTATTTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (40 bp):
TTTAATATAAATATAATATAAATTATTAATTATTTAAAAA
Found at i:988686 original size:18 final size:18
Alignment explanation
Indices: 988623--988689 Score: 71
Period size: 18 Copynumber: 3.5 Consensus size: 18
988613 AATATAGTGT
988623 AAATTATTAATTATTTAA
1 AAATTATTAATTATTTAA
* * *
988641 AAATTTAATATAAATATAATAT
1 AAA-TT-AT-TAATTAT-TTAA
988663 AAATTATTAATTATTTAA
1 AAATTATTAATTATTTAA
988681 AAATTATTA
1 AAATTATTA
988690 TTTAAATTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 14 0.36
19 8 0.21
20 4 0.10
21 8 0.21
22 5 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATTATTAATTATTTAA
Found at i:989649 original size:42 final size:38
Alignment explanation
Indices: 989600--989722 Score: 108
Period size: 42 Copynumber: 3.1 Consensus size: 38
989590 ATAAAAATAA
989600 TATATTTTTAATATTATAATGTAAATATTATGTTAAATTATT
1 TATATTTTTAATATT-TAAT-TAAATA-TAT-TTAAATTATT
* *
989642 TATA-TTTTAAAATTTAA-TAAAAATATATTAAA-TATT
1 TATATTTTTAATATTTAATTAAATATAT-TTAAATTATT
* *
989678 TTTATTTTTTAAAATATTTAATATAAATAAATTTAAATTATT
1 TATA-TTTTT--AATATTTAAT-TAAATATATTTAAATTATT
989720 TAT
1 TAT
989723 TTTAAAATAT
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
36 7 0.11
37 8 0.12
38 9 0.14
40 11 0.17
41 14 0.21
42 17 0.26
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (38 bp):
TATATTTTTAATATTTAATTAAATATATTTAAATTATT
Found at i:989697 original size:40 final size:39
Alignment explanation
Indices: 989632--989732 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 39
989622 AAATATTATG
*
989632 TTAAATTATTTATATTTT-AAA-ATTTAATAAAAATATA-
1 TTAAATTATTTAT-TTTTAAAATATTTAATAAAAATAAAT
* *
989669 TTAAATATTTTTATTTTTTAAAATATTTAATATAAATAAAT
1 TTAAAT-TATTTA-TTTTTAAAATATTTAATAAAAATAAAT
989710 TTAAATTATTTA-TTTTAAAATAT
1 TTAAATTATTTATTTTTAAAATAT
989733 AAATATATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
37 6 0.11
38 20 0.36
39 4 0.07
40 19 0.35
41 6 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (39 bp):
TTAAATTATTTATTTTTAAAATATTTAATAAAAATAAAT
Found at i:989726 original size:38 final size:38
Alignment explanation
Indices: 989609--989732 Score: 126
Period size: 40 Copynumber: 3.1 Consensus size: 38
989599 ATATATTTTT
* *
989609 AATATTATAATGTAAATATTATGTTAAATTATTTATATTTTA
1 AATATT-TAATATAAATA-TAT-TTAAATTATTTAT-TTTAA
* *
989651 AA-ATTTAATAAAAATATA-TTAAATATTTTTATTTTTTAA
1 AATATTTAATATAAATATATTTAAAT-TATTTA--TTTTAA
*
989690 AATATTTAATATAAATAAATTTAAATTATTTATTTTAA
1 AATATTTAATATAAATATATTTAAATTATTTATTTTAA
989728 AATAT
1 AATAT
989733 AAATATATTT
Statistics
Matches: 70, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
37 6 0.09
38 16 0.23
39 8 0.11
40 29 0.41
41 9 0.13
42 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (38 bp):
AATATTTAATATAAATATATTTAAATTATTTATTTTAA
Found at i:990060 original size:16 final size:16
Alignment explanation
Indices: 990009--990062 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
989999 ATTATATATT
* *
990009 TATATAAAATTTAATA
1 TATATAAATTTTAAAA
* *
990025 TAT-TAATATTTTATAT
1 TATATAA-ATTTTAAAA
990041 TATATAAATTTTAAAA
1 TATATAAATTTTAAAA
990057 TATATA
1 TATATA
990063 TTATAATTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 3 0.10
16 24 0.80
17 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATATAAATTTTAAAA
Found at i:990721 original size:21 final size:21
Alignment explanation
Indices: 990695--990742 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
990685 CTTACCGATT
*
990695 TATATAT-TTATGTAATTTTTA
1 TATATATATT-TGTAATTATTA
*
990716 TATATATATTTGTTATTATTA
1 TATATATATTTGTAATTATTA
990737 TATATA
1 TATATA
990743 AAGTGTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (21 bp):
TATATATATTTGTAATTATTA
Found at i:990772 original size:15 final size:17
Alignment explanation
Indices: 990751--990800 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
990741 TAAAGTGTTT
990751 TATATTTTTATAT-TAA
1 TATATTTTTATATATAA
990767 -ATA-TTTTATTATATAA
1 TATATTTTTA-TATATAA
990783 TATTATTTTTATACTATA
1 TA-TATTTTTATA-TATA
990801 TTTTATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 5 0.18
15 6 0.21
16 3 0.11
17 1 0.04
18 4 0.14
19 9 0.32
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATTTTTATATATAA
Found at i:992658 original size:2 final size:2
Alignment explanation
Indices: 992653--992684 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
992643 CCCCCCCCCT
992653 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
992685 CACTAGAGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:992897 original size:48 final size:49
Alignment explanation
Indices: 992827--992924 Score: 180
Period size: 48 Copynumber: 2.0 Consensus size: 49
992817 TTTAGATTCC
*
992827 TTCCTTTTTGTAAGGACCATTCACTGGGAGATATATATAT-TATATATA
1 TTCCTTTTTGTAAAGACCATTCACTGGGAGATATATATATATATATATA
992875 TTCCTTTTTGTAAAGACCATTCACTGGGAGATATATATATATATATATA
1 TTCCTTTTTGTAAAGACCATTCACTGGGAGATATATATATATATATATA
992924 T
1 T
992925 ATATATATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 39 0.81
49 9 0.19
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (49 bp):
TTCCTTTTTGTAAAGACCATTCACTGGGAGATATATATATATATATATA
Found at i:992912 original size:2 final size:2
Alignment explanation
Indices: 992905--992936 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
992895 TCACTGGGAG
992905 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
992937 TTTGTCTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:994923 original size:14 final size:15
Alignment explanation
Indices: 994901--994957 Score: 55
Period size: 14 Copynumber: 3.8 Consensus size: 15
994891 TTTGAAAATA
*
994901 ATTTTAATTT-TTTT
1 ATTTAAATTTATTTT
994915 ATTTAAATTTATTTTT
1 ATTTAAATTTA-TTTT
*
994931 AATTT-AATTTATATT
1 -ATTTAAATTTATTTT
*
994946 ATTTATATTTAT
1 ATTTAAATTTAT
994958 GATATAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
14 13 0.36
15 9 0.25
16 10 0.28
17 4 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTAAATTTATTTT
Found at i:994929 original size:17 final size:16
Alignment explanation
Indices: 994909--994942 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
994899 TAATTTTAAT
*
994909 TTTTTTATTTAAATTTA
1 TTTTTAATTT-AATTTA
994926 TTTTTAATTTAATTTA
1 TTTTTAATTTAATTTA
994942 T
1 T
994943 ATTATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTAATTTAATTTA
Found at i:994931 original size:16 final size:16
Alignment explanation
Indices: 994910--994957 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
994900 AATTTTAATT
994910 TTTTTATTTAAATTTA
1 TTTTTATTTAAATTTA
994926 TTTTTAATTT-AATTTA
1 TTTTT-ATTTAAATTTA
* *
994942 -TATTATTTATATTTA
1 TTTTTATTTAAATTTA
994957 T
1 T
994958 GATATAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 4 0.15
15 8 0.30
16 11 0.41
17 4 0.15
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTTATTTAAATTTA
Found at i:997899 original size:12 final size:12
Alignment explanation
Indices: 997882--997938 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
997872 TATTTTTGTT
997882 ATTAAATATTAA
1 ATTAAATATTAA
997894 ATTAAATA-TAA
1 ATTAAATATTAA
*
997905 A-TATAT-TTATA
1 ATTAAATATTA-A
997916 ATTAAATA-TAA
1 ATTAAATATTAA
*
997927 ATAAAAATATTA
1 AT-TAAATATTA
997939 TTTATATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
10 6 0.17
11 9 0.25
12 19 0.53
13 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTAAATATTAA
Found at i:997928 original size:40 final size:35
Alignment explanation
Indices: 997834--997936 Score: 122
Period size: 34 Copynumber: 3.0 Consensus size: 35
997824 AAAAATTAAA
**
997834 AAATATTTTTA-TATTTTATAATTAAATATAAATAT
1 AAATATTTTTATTATTAAAT-ATTAAATATAAATAT
*
997869 AAATATTTTTGTTATTAAATATTAAAT-TAAATAT
1 AAATATTTTTATTATTAAATATTAAATATAAATAT
* * *
997903 AAATATATTTATAATTAAATA-TAAATAAAAATAT
1 AAATATTTTTATTATTAAATATTAAATATAAATAT
997937 TATTTATATT
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
33 5 0.08
34 31 0.53
35 17 0.29
36 6 0.10
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (35 bp):
AAATATTTTTATTATTAAATATTAAATATAAATAT
Found at i:997947 original size:28 final size:26
Alignment explanation
Indices: 997887--997947 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 26
997877 TTGTTATTAA
*
997887 ATATTAAATTAAATATAAATATATTT
1 ATATTAAATTAAATAAAAATATATTT
997913 ATAATTAAATATAAATAAAAATATTATTT
1 AT-ATTAAAT-TAAATAAAAATA-TATTT
997942 ATATTA
1 ATATTA
997948 TTTATTGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 2 0.06
27 7 0.23
28 15 0.48
29 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATATTAAATTAAATAAAAATATATTT
Found at i:1003086 original size:3 final size:3
Alignment explanation
Indices: 1003078--1003112 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1003068 ACATATAAAA
1003078 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1003113 ATTTGTCGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1003544 original size:12 final size:10
Alignment explanation
Indices: 1003514--1003550 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
1003504 AATAAGTTTT
1003514 TTAATTTAAA
1 TTAATTTAAA
1003524 TTAATTTAAA
1 TTAATTTAAA
1003534 TTATTATTTAAA
1 TTA--ATTTAAA
1003546 TTAAT
1 TTAAT
1003551 AAAATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 15 0.60
12 10 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TTAATTTAAA
Found at i:1003547 original size:28 final size:29
Alignment explanation
Indices: 1003490--1003561 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 29
1003480 CCGATATATA
*
1003490 TTAAATTAAATTTAAATAAGTTTTTTAAT
1 TTAAATTAAATTTAAATAAGTTTTTAAAT
*
1003519 TTAAATT-AATTTAAATTA-TTATTTAAAT
1 TTAAATTAAATTTAAATAAGTT-TTTAAAT
*
1003547 TAATAAAATAAATTT
1 T--TAAATTAAATTT
1003562 TTAAATTAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 2 0.06
28 17 0.47
29 7 0.19
30 5 0.14
31 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (29 bp):
TTAAATTAAATTTAAATAAGTTTTTAAAT
Found at i:1004598 original size:18 final size:17
Alignment explanation
Indices: 1004575--1004608 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1004565 TATCAAAAGC
*
1004575 TATATAACATATTAAACT
1 TATATAA-ATATAAAACT
1004593 TATATAAATATAAAAC
1 TATATAAATATAAAAC
1004609 ATTCTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (17 bp):
TATATAAATATAAAACT
Found at i:1008359 original size:6 final size:6
Alignment explanation
Indices: 1008350--1008413 Score: 66
Period size: 6 Copynumber: 11.2 Consensus size: 6
1008340 GTGAATGTGA
1008350 TTATAT TTATAAT TT-TA- -TATAT TTATA- TTATAT TTATAT TTATAT
1 TTATAT TTAT-AT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
*
1008395 TT-TAT ATTATAA TTATAT T
1 TTATAT -TTATAT TTATAT T
1008414 AAAAATAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
3 1 0.02
4 2 0.04
5 9 0.18
6 31 0.63
7 6 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
TTATAT
Found at i:1008383 original size:11 final size:11
Alignment explanation
Indices: 1008350--1008513 Score: 73
Period size: 11 Copynumber: 15.1 Consensus size: 11
1008340 GTGAATGTGA
1008350 TTATATTTATAAT
1 TTATA-TTAT-AT
1008363 TT-TA-TATAT
1 TTATATTATAT
1008372 TTATATTATAT
1 TTATATTATAT
1008383 TTATATTTATATT
1 TTATA-TTATA-T
*
1008396 TTATATTATAA
1 TTATATTATAT
1008407 TTATATTA-A-
1 TTATATTATAT
** *
1008416 AAATAATATAT
1 TTATATTATAT
*
1008427 TAATAATT-TA-
1 TTAT-ATTATAT
*
1008437 ATATATTTAATAT
1 TTATA-TT-ATAT
1008450 TTATATTATAT
1 TTATATTATAT
1008461 TT-TGATT-T-T
1 TTAT-ATTATAT
*
1008470 TTAATATTTTAT
1 TT-ATATTATAT
*
1008482 TTTTA-T-TAT
1 TTATATTATAT
1008491 TTA-ATTATAT
1 TTATATTATAT
*
1008501 TGTATATAATAT
1 T-TATATTATAT
1008513 T
1 T
1008514 ATCTGATTTA
Statistics
Matches: 119, Mismatches: 12, Indels: 41
0.69 0.07 0.24
Matches are distributed among these distances:
8 1 0.01
9 19 0.16
10 21 0.18
11 38 0.32
12 28 0.24
13 12 0.10
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (11 bp):
TTATATTATAT
Found at i:1008403 original size:24 final size:25
Alignment explanation
Indices: 1008349--1008462 Score: 99
Period size: 27 Copynumber: 4.4 Consensus size: 25
1008339 TGTGAATGTG
1008349 ATTATATTTATAATTTTATATATTTAT
1 ATTATATTTAT-A-TTTATATATTTAT
1008376 ATTATATTTATATTTATAT-TTTAT
1 ATTATATTTATATTTATATATTTAT
* * * *
1008400 ATTATAATTATA-TTAAAAATAATAT
1 ATTATATTTATATTTATATAT-TTAT
1008425 ATTAATAATTTAATATATT-TAATATTTAT
1 ATT-AT-ATTT-ATAT-TTAT-ATATTTAT
1008454 ATTATATTT
1 ATTATATTT
1008463 TGATTTTTTA
Statistics
Matches: 71, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
23 4 0.06
24 17 0.24
25 13 0.18
26 3 0.04
27 18 0.25
28 5 0.07
29 6 0.08
30 5 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTATATTTATATTTATATATTTAT
Found at i:1008440 original size:16 final size:16
Alignment explanation
Indices: 1008363--1008462 Score: 61
Period size: 16 Copynumber: 6.2 Consensus size: 16
1008353 TATTTATAAT
1008363 TTTATATATTTATATTATA
1 TTTA-ATATTTA-A-TATA
1008382 TTT-ATATTT-ATAT-
1 TTTAATATTTAATATA
1008395 TTT-ATATTATAAT-TA
1 TTTAATATT-TAATATA
**
1008410 TATTAA-AAATAATATA
1 T-TTAATATTTAATATA
1008426 -TTAATAATTTAATATA
1 TTTAAT-ATTTAATATA
1008442 TTTAATATTTATATTATA
1 TTTAATATTTA-A-TATA
1008460 TTT
1 TTT
1008463 TGATTTTTTA
Statistics
Matches: 66, Mismatches: 4, Indels: 23
0.71 0.04 0.25
Matches are distributed among these distances:
13 8 0.12
14 9 0.14
15 8 0.12
16 18 0.27
17 13 0.20
18 7 0.11
19 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTAATATTTAATATA
Found at i:1008482 original size:21 final size:21
Alignment explanation
Indices: 1008447--1008495 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1008437 ATATATTTAA
1008447 TATTT-ATATTATATTTTGAT
1 TATTTAATATTATATTTTGAT
* * *
1008467 TTTTTAATATTTTATTTTTAT
1 TATTTAATATTATATTTTGAT
1008488 TATTTAAT
1 TATTTAAT
1008496 TATATTGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TATTTAATATTATATTTTGAT
Found at i:1013591 original size:54 final size:54
Alignment explanation
Indices: 1013509--1013617 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
1013499 CCCTTTGTTT
1013509 GCAAGCACTAGGCCAGGTAATTTGGTTAAAGACCTAAAAATATCTAAACAATTA
1 GCAAGCACTAGGCCAGGTAATTTGGTTAAAGACCTAAAAATATCTAAACAATTA
1013563 GCAAGCACTAGGCCAGGTAATTTGGTTAAAGACCTAAAAATATCTAAACAATTA
1 GCAAGCACTAGGCCAGGTAATTTGGTTAAAGACCTAAAAATATCTAAACAATTA
1013617 G
1 G
1013618 ACAATCTTTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (54 bp):
GCAAGCACTAGGCCAGGTAATTTGGTTAAAGACCTAAAAATATCTAAACAATTA
Found at i:1014117 original size:6 final size:6
Alignment explanation
Indices: 1014108--1014134 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1014098 TACATATACA
1014108 TAGATT TAGATT TAGATT TAGATT TAG
1 TAGATT TAGATT TAGATT TAGATT TAG
1014135 GGTGAAGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (6 bp):
TAGATT
Found at i:1017146 original size:15 final size:15
Alignment explanation
Indices: 1017109--1017164 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
1017099 AAAATTAATA
*
1017109 ATTTAAAATTG-ATT
1 ATTTAAATTTGAATT
*
1017123 AATTCAAATTTGAATT
1 -ATTTAAATTTGAATT
*
1017139 ATTTAAATTTAAAATT
1 ATTTAAATTT-GAATT
1017155 ATTTAAATTT
1 ATTTAAATTT
1017165 AAAATATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
15 18 0.51
16 17 0.49
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (15 bp):
ATTTAAATTTGAATT
Found at i:1017154 original size:16 final size:16
Alignment explanation
Indices: 1017135--1017169 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1017125 TTCAAATTTG
1017135 AATTATTTAAATTTAA
1 AATTATTTAAATTTAA
1017151 AATTATTTAAATTTAA
1 AATTATTTAAATTTAA
1017167 AAT
1 AAT
1017170 ATTCATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTATTTAAATTTAA
Found at i:1017241 original size:37 final size:38
Alignment explanation
Indices: 1017200--1017276 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
1017190 TAAAATAATC
1017200 AAATTGATAAATTTTAA-TATTAAATTTAATTAACTTA
1 AAATTGATAAATTTTAATTATTAAATTTAATTAACTTA
* * *
1017237 AAATTGATTAATTTTAATTGTTAAATTTAATTAATTTA
1 AAATTGATAAATTTTAATTATTAAATTTAATTAACTTA
1017275 AA
1 AA
1017277 TTTAAAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
37 16 0.44
38 20 0.56
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (38 bp):
AAATTGATAAATTTTAATTATTAAATTTAATTAACTTA
Found at i:1017265 original size:13 final size:14
Alignment explanation
Indices: 1017238--1017281 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
1017228 ATTAACTTAA
*
1017238 AATTGATTAATTTT
1 AATTGATTAAATTT
1017252 AATTG-TTAAATTT
1 AATTGATTAAATTT
*
1017265 AATTAATTTAAATTT
1 AATTGA-TTAAATTT
1017280 AA
1 AA
1017282 AATAATTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 11 0.42
14 5 0.19
15 10 0.38
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (14 bp):
AATTGATTAAATTT
Found at i:1017269 original size:23 final size:23
Alignment explanation
Indices: 1017234--1017278 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1017224 TTTAATTAAC
* *
1017234 TTAAAATTGATTAATTTTAATTG
1 TTAAAATTAATTAATTTAAATTG
*
1017257 TTAAATTTAATTAATTTAAATT
1 TTAAAATTAATTAATTTAAATT
1017279 TAAAATAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
TTAAAATTAATTAATTTAAATTG
Found at i:1017277 original size:15 final size:15
Alignment explanation
Indices: 1017257--1017305 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
1017247 ATTTTAATTG
1017257 TTAAATTTAATTAAT
1 TTAAATTTAATTAAT
*
1017272 TTAAATTTAAAATAAT
1 TTAAATTT-AATTAAT
** *
1017288 TCGATTTTAATTAAT
1 TTAAATTTAATTAAT
1017303 TTA
1 TTA
1017306 TAATCTAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
TTAAATTTAATTAAT
Found at i:1017284 original size:22 final size:22
Alignment explanation
Indices: 1017234--1017284 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
1017224 TTTAATTAAC
* *
1017234 TTAAAA-TTGATTAATTTTAAT
1 TTAAAATTTAATTAATTTAAAT
*
1017255 TGTTAAATTTAATTAATTTAAAT
1 T-TAAAATTTAATTAATTTAAAT
1017278 TTAAAAT
1 TTAAAAT
1017285 AATTCGATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 1 0.04
22 9 0.38
23 14 0.58
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (22 bp):
TTAAAATTTAATTAATTTAAAT
Found at i:1017369 original size:48 final size:47
Alignment explanation
Indices: 1017268--1017371 Score: 127
Period size: 48 Copynumber: 2.2 Consensus size: 47
1017258 TAAATTTAAT
* * ** * *
1017268 TAATTTAAATTTAAAATAATTCGATTTTAATTAATTTATAATCTAAA
1 TAATTTAAAATCAAAATAATTCGATTAAAATTAATTTAAAATCAAAA
* *
1017315 TGATTTAAAATCAAAATTATTCGAATTAAAATTAATTTAAAATCAAAA
1 TAATTTAAAATCAAAATAATTCG-ATTAAAATTAATTTAAAATCAAAA
1017363 TAATTTAAA
1 TAATTTAAA
1017372 CTTAAAAATG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
47 19 0.40
48 28 0.60
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (47 bp):
TAATTTAAAATCAAAATAATTCGATTAAAATTAATTTAAAATCAAAA
Found at i:1017378 original size:16 final size:17
Alignment explanation
Indices: 1017296--1017378 Score: 59
Period size: 16 Copynumber: 5.1 Consensus size: 17
1017286 ATTCGATTTT
*
1017296 AATTAATTTATAATCT-A
1 AATTAATTTAAAAT-TAA
* *
1017313 AA-TGATTTAAAATCAA
1 AATTAATTTAAAATTAA
**
1017329 AATT-A-TTCGAATTAA
1 AATTAATTTAAAATTAA
*
1017344 AATTAATTTAAAATCAA
1 AATTAATTTAAAATTAA
*
1017361 AA-TAATTTAAACTTAA
1 AATTAATTTAAAATTAA
1017377 AA
1 AA
1017379 ATGACTTAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
15 11 0.22
16 28 0.55
17 12 0.24
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.37
Consensus pattern (17 bp):
AATTAATTTAAAATTAA
Found at i:1017379 original size:17 final size:16
Alignment explanation
Indices: 1017338--1017397 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
1017328 AAATTATTCG
*
1017338 AATTAAAATTAATTTA
1 AATTAAAAATAATTTA
* *
1017354 AAATCAAAATAATTTA
1 AATTAAAAATAATTTA
* *
1017370 AACTTAAAAATGACTTA
1 AA-TTAAAAATAATTTA
1017387 AATTTAAAAAT
1 AA-TTAAAAAT
1017398 CTAAAATGAT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
16 15 0.43
17 20 0.57
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (16 bp):
AATTAAAAATAATTTA
Found at i:1017664 original size:22 final size:22
Alignment explanation
Indices: 1017622--1017665 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1017612 AATAATTACT
*
1017622 AAATATAAAATATACTTAATAA
1 AAATATAAAATATACTGAATAA
*
1017644 AAATAT-ATATATAACTGAATAA
1 AAATATAAAATAT-ACTGAATAA
1017666 TATGATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (22 bp):
AAATATAAAATATACTGAATAA
Found at i:1023013 original size:33 final size:37
Alignment explanation
Indices: 1022943--1023016 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 37
1022933 ATAGTTATTT
*
1022943 AATAAAAATATATTAAATAATTATTTTAATATTAAATAA
1 AATAAAAATATA-TAAATAATTATTTT-ATATAAAATAA
1022982 AATAAAAATA-A-AAATAATTATTTT-TA-AAAATAA
1 AATAAAAATATATAAATAATTATTTTATATAAAATAA
1023015 AA
1 AA
1023017 ATTAAATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
33 8 0.24
34 2 0.06
36 13 0.38
38 1 0.03
39 10 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (37 bp):
AATAAAAATATATAAATAATTATTTTATATAAAATAA
Found at i:1023808 original size:13 final size:14
Alignment explanation
Indices: 1023777--1023808 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1023767 TAACTTGCTC
1023777 TCTCTTTTTTTCTT
1 TCTCTTTTTTTCTT
1023791 T-TCTTTTTTT-TT
1 TCTCTTTTTTTCTT
1023803 TCTCTT
1 TCTCTT
1023809 GGATCATCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 13 0.76
14 1 0.06
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TCTCTTTTTTTCTT
Found at i:1024570 original size:17 final size:16
Alignment explanation
Indices: 1024530--1024571 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1024520 TTAGAAAAAA
*
1024530 TTGA-ACATACTTGTT
1 TTGACACATACTTGTC
1024545 TTGAGCACATACTTGTAC
1 TTGA-CACATACTTGT-C
1024563 TTGACACAT
1 TTGACACAT
1024572 CCGAATTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 4 0.17
17 15 0.65
18 4 0.17
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (16 bp):
TTGACACATACTTGTC
Found at i:1025327 original size:2 final size:2
Alignment explanation
Indices: 1025320--1025358 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1025310 ATTTAAGGAT
1025320 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1025359 TAGTATTAGA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1028437 original size:10 final size:10
Alignment explanation
Indices: 1028404--1028437 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1028394 TAATTTATTC
1028404 TTAAAAAATA
1 TTAAAAAATA
* *
1028414 TTTAAAAATT
1 TTAAAAAATA
1028424 TTAAAAAATA
1 TTAAAAAATA
1028434 TTAA
1 TTAA
1028438 CAATGGATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TTAAAAAATA
Found at i:1028812 original size:21 final size:19
Alignment explanation
Indices: 1028782--1028832 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 19
1028772 TTTATTTCAC
*
1028782 ATTTATTATAATATTTTTA
1 ATTTAATATAATATTTTTA
1028801 TATTTTAATAT-AT-TTTTTA
1 -A-TTTAATATAATATTTTTA
1028820 ATTTAAT-TAATAT
1 ATTTAATATAATAT
1028833 CACTTGTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
16 1 0.04
17 8 0.30
18 2 0.07
19 6 0.22
20 3 0.11
21 7 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTAATATAATATTTTTA
Found at i:1028832 original size:19 final size:19
Alignment explanation
Indices: 1028789--1028832 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
1028779 CACATTTATT
*
1028789 ATAATATTTTTATATTTTA
1 ATAATATTTTTATAATTTA
1028808 AT-ATATTTTT-TAATTTA
1 ATAATATTTTTATAATTTA
1028825 ATTAATAT
1 A-TAATAT
1028833 CACTTGTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 9 0.41
19 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATAATATTTTTATAATTTA
Found at i:1030126 original size:1 final size:1
Alignment explanation
Indices: 1030120--1030146 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1030110 CCTGTATACT
1030120 CCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCC
1030147 AAGAAAAAAG
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:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1030952 original size:25 final size:24
Alignment explanation
Indices: 1030924--1030981 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
1030914 TATATCGATT
1030924 TAATATAATTTAAATTATTATTTAA
1 TAATATAATTTAAATTATTATTT-A
* * * *
1030949 TAATAAAAATTATATTTTTATTTA
1 TAATATAATTTAAATTATTATTTA
1030973 -AATATAATT
1 TAATATAATT
1030982 AAAAATATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
23 7 0.26
24 1 0.04
25 19 0.70
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TAATATAATTTAAATTATTATTTA
Found at i:1030979 original size:28 final size:28
Alignment explanation
Indices: 1030947--1031010 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
1030937 ATTATTATTT
* *
1030947 AATAATAAAAATTATATTTTTATT-TAAA
1 AATAATAAAAA-TATAATATTATTATAAA
*
1030975 TATAATTAAAAATATAATATTATTATAAA
1 AATAA-TAAAAATATAATATTATTATAAA
1031004 AATAATA
1 AATAATA
1031011 TTTTAATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 16 0.53
29 14 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
AATAATAAAAATATAATATTATTATAAA
Found at i:1031003 original size:29 final size:29
Alignment explanation
Indices: 1030947--1031009 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
1030937 ATTATTATTT
* *
1030947 AATAA-TAAAAATTATATTTTTATTTAAA
1 AATAATTAAAAATTATAATATTATTTAAA
*
1030975 TATAATTAAAAA-TATAATATTATTATAAA
1 AATAATTAAAAATTATAATATTATT-TAAA
1031004 AATAAT
1 AATAAT
1031010 ATTTTAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
AATAATTAAAAATTATAATATTATTTAAA
Found at i:1031003 original size:48 final size:47
Alignment explanation
Indices: 1030921--1031014 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 47
1030911 ATTTATATCG
* * * *
1030921 ATTTAATATAATTTAAATTATTATTTAATAATAAAAATTATATTTTT
1 ATTTAATATAATTAAAAATATAATTTAATAATAAAAATAATATTTTT
*
1030968 ATTTAAATATAATTAAAAATATAATATT-ATTATAAAAATAATATTTT
1 ATTT-AATATAATTAAAAATATAAT-TTAATAATAAAAATAATATTTT
1031015 AATAATATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
47 4 0.10
48 34 0.85
49 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (47 bp):
ATTTAATATAATTAAAAATATAATTTAATAATAAAAATAATATTTTT
Found at i:1031007 original size:31 final size:28
Alignment explanation
Indices: 1030948--1031007 Score: 66
Period size: 31 Copynumber: 2.0 Consensus size: 28
1030938 TTATTATTTA
* **
1030948 ATAATAAAAATTATATTTTTATTTAAAT
1 ATAATAAAAATTATATTATTATAAAAAT
1030976 ATAATTAAAAATATAATATTATTATAAAAAT
1 ATAA-TAAAAAT-T-ATATTATTATAAAAAT
1031007 A
1 A
1031008 ATATTTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 4 0.15
29 7 0.27
30 1 0.04
31 14 0.54
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
ATAATAAAAATTATATTATTATAAAAAT
Found at i:1031012 original size:17 final size:17
Alignment explanation
Indices: 1030973--1031023 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
1030963 TTTTTATTTA
*
1030973 AATATAATTAAAAATAT
1 AATATTATTAAAAATAT
1030990 AATATTATTATAAAA-AT
1 AATATTATTA-AAAATAT
*
1031007 AATATT-TTAATAATAT
1 AATATTATTAAAAATAT
1031023 A
1 A
1031024 TTAAATAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 3 0.10
16 6 0.20
17 17 0.57
18 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATTATTAAAAATAT
Found at i:1039471 original size:27 final size:24
Alignment explanation
Indices: 1039441--1039500 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 24
1039431 TTTTTATACT
*
1039441 AATATTAATATTTTATAATTAAATTTA
1 AATATTAATATTTTAAAATT--A-TTA
**
1039468 AATAAAAATATTTTAAAATTATTA
1 AATATTAATATTTTAAAATTATTA
1039492 AATATTAAT
1 AATATTAAT
1039501 TTAAATTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 10 0.36
25 1 0.04
27 17 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AATATTAATATTTTAAAATTATTA
Found at i:1039483 original size:21 final size:22
Alignment explanation
Indices: 1039455--1039510 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 22
1039445 TTAATATTTT
1039455 ATAA-TTAAATTTAAATAAA-A
1 ATAATTTAAATTTAAATAAATA
* * *
1039475 ATATTTTAAAATT-ATTAAATA
1 ATAATTTAAATTTAAATAAATA
*
1039496 TTAATTTAAATTTAA
1 ATAATTTAAATTTAA
1039511 TGACTCAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
20 8 0.30
21 18 0.67
22 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAATTTAAATTTAAATAAATA
Found at i:1039704 original size:24 final size:25
Alignment explanation
Indices: 1039677--1039735 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
1039667 AAATATCATT
*
1039677 AATCAAAAAAC-TTATCAAAA-AGTA
1 AATCAAAAAACATTAACAAAATA-TA
1039701 AATCAATAAAACATTAACAAAATATA
1 AATCAA-AAAACATTAACAAAATATA
*
1039727 AATTAAAAA
1 AATCAAAAA
1039736 TATATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 6 0.20
25 8 0.27
26 15 0.50
27 1 0.03
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.22
Consensus pattern (25 bp):
AATCAAAAAACATTAACAAAATATA
Found at i:1039753 original size:19 final size:21
Alignment explanation
Indices: 1039729--1039770 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 21
1039719 AAAATATAAA
1039729 TTAAAAATAT-ATTT-TTTAT
1 TTAAAAATATAATTTATTTAT
1039748 TT-AAAATATAATTTATTTAT
1 TTAAAAATATAATTTATTTAT
1039768 TTA
1 TTA
1039771 TTTACATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 7 0.35
19 6 0.30
20 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAAAAATATAATTTATTTAT
Found at i:1039768 original size:20 final size:18
Alignment explanation
Indices: 1039732--1039770 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 18
1039722 ATATAAATTA
1039732 AAAATATATTTTTTATTT
1 AAAATATATTTTTTATTT
1039750 AAAATATAATTTATTTATTT
1 AAAATAT-ATTT-TTTATTT
1039770 A
1 A
1039771 TTTACATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 4 0.21
20 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAAATATATTTTTTATTT
Found at i:1047452 original size:24 final size:24
Alignment explanation
Indices: 1047425--1047481 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
1047415 AAGTATTGAG
* * *
1047425 TTTTAATTTGTTAGTTTATTCAAT
1 TTTTAATTTGTAAGTTTAATAAAT
* * *
1047449 TTTTAAATGGTAATTTTAATAAAT
1 TTTTAATTTGTAAGTTTAATAAAT
1047473 TTTTAATTT
1 TTTTAATTT
1047482 AAATTTAAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.60
Consensus pattern (24 bp):
TTTTAATTTGTAAGTTTAATAAAT
Found at i:1048291 original size:7 final size:7
Alignment explanation
Indices: 1048279--1048307 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1048269 GGTGCAGCAC
1048279 CTTTCAA
1 CTTTCAA
1048286 CTTTCAA
1 CTTTCAA
1048293 CTTTCAA
1 CTTTCAA
1048300 CTTTCAA
1 CTTTCAA
1048307 C
1 C
1048308 GCCGTTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (7 bp):
CTTTCAA
Found at i:1048435 original size:27 final size:27
Alignment explanation
Indices: 1048397--1048448 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1048387 TGGAGCTATC
*
1048397 AATATAATATAAAAATAATTAATATAA
1 AATATAATATAAAAATAATAAATATAA
*
1048424 AATATAATATAAATATAATAAATAT
1 AATATAATATAAAAATAATAAATAT
1048449 TTTAATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (27 bp):
AATATAATATAAAAATAATAAATATAA
Found at i:1048462 original size:34 final size:34
Alignment explanation
Indices: 1048397--1048506 Score: 103
Period size: 34 Copynumber: 3.4 Consensus size: 34
1048387 TGGAGCTATC
1048397 AATAT-AATATAA-AAATAATTAATATAAAATAT
1 AATATAAATATAATAAATAATTAATATAAAATAT
* *
1048429 AATATAAATATAATAAATATTTTAATAT-TAATAT
1 AATATAAATATAATAAATA-ATTAATATAAAATAT
* *
1048463 AATTTAAATATAAT---T-ATT-ATATAATAAAAT
1 AATATAAATATAATAAATAATTAATATAA-AATAT
1048493 -ATATAAATATAATA
1 AATATAAATATAATA
1048507 TCGATATATA
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
28 4 0.06
29 14 0.22
30 4 0.06
31 1 0.02
32 5 0.08
33 7 0.11
34 23 0.35
35 7 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AATATAAATATAATAAATAATTAATATAAAATAT
Found at i:1048496 original size:23 final size:21
Alignment explanation
Indices: 1048420--1048507 Score: 63
Period size: 23 Copynumber: 4.0 Consensus size: 21
1048410 AATAATTAAT
*
1048420 ATAAA-ATATAATATAAATATA
1 ATAAATATATAATAT-TATATA
*
1048441 ATAAATATTTTAATATTAATATA
1 ATAAATA-TATAATATT-ATATA
*
1048464 ATTTAAATATA-ATTATTATATA
1 A--TAAATATATAATATTATATA
*
1048486 ATAAAATATATAAATATAATAT
1 AT-AAATATAT-AATATTATAT
1048508 CGATATATAA
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
20 1 0.02
21 12 0.23
22 7 0.13
23 26 0.49
24 1 0.02
25 6 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAAATATATAATATTATATA
Found at i:1048546 original size:18 final size:18
Alignment explanation
Indices: 1048525--1048565 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1048515 TAAATTACTT
1048525 AATTTAATTTAATTT-TTA
1 AATTT-ATTTAATTTATTA
*
1048543 AATTTTTTTAATTTATTA
1 AATTTATTTAATTTATTA
1048561 AATTT
1 AATTT
1048566 TGACAGGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
AATTTATTTAATTTATTA
Found at i:1048552 original size:17 final size:18
Alignment explanation
Indices: 1048532--1048566 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1048522 CTTAATTTAA
1048532 TTTAATTT-TTAAATTTT
1 TTTAATTTATTAAATTTT
1048549 TTTAATTTATTAAATTTT
1 TTTAATTTATTAAATTTT
1048567 GACAGGATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTAATTTATTAAATTTT
Found at i:1048688 original size:25 final size:25
Alignment explanation
Indices: 1048623--1048688 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 25
1048613 AAAAATAATA
1048623 TTTTAAAATTTTAAAAAATAAATTAGT
1 TTTTAAAA--TTAAAAAATAAATTAGT
1048650 TTTT-AAA-TAAAAAATAAAAATTAGT
1 TTTTAAAATTAAAAAAT--AAATTAGT
1048675 TTTTAAAATTAAAA
1 TTTTAAAATTAAAA
1048689 GGCCACAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
23 8 0.23
25 12 0.34
26 6 0.17
27 9 0.26
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (25 bp):
TTTTAAAATTAAAAAATAAATTAGT
Found at i:1052634 original size:28 final size:28
Alignment explanation
Indices: 1052600--1052655 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1052590 ATAATATCTC
*
1052600 CTAAATTAGTATTGACTGTGACATATGG
1 CTAAATTAGTATTGACCGTGACATATGG
* * *
1052628 CTAAATTATTGTTGACCGTGATATATGG
1 CTAAATTAGTATTGACCGTGACATATGG
1052656 TTTGTTATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (28 bp):
CTAAATTAGTATTGACCGTGACATATGG
Found at i:1052907 original size:3 final size:3
Alignment explanation
Indices: 1052899--1052930 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1052889 CTTGATTTGA
1052899 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1052931 GTAATAAAAA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1062542 original size:25 final size:25
Alignment explanation
Indices: 1062486--1062550 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
1062476 CGAGTTATTT
* *
1062486 TAATTTTAAATCTTTTCAATTTTGAG
1 TAATTTTAAAT-TATTCAATTTTGAA
1062512 TAATTTTAAATTATTCGAA-TTTGAA
1 TAATTTTAAATTATTC-AATTTTGAA
*
1062537 TCATTTTAAATTAT
1 TAATTTTAAATTAT
1062551 CTTTGAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
25 22 0.63
26 13 0.37
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (25 bp):
TAATTTTAAATTATTCAATTTTGAA
Found at i:1068529 original size:22 final size:22
Alignment explanation
Indices: 1068508--1068548 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1068498 ACAATAATAT
* *
1068508 TATTTTCT-ATTAATATTTATA
1 TATTTTATAATTAAAATTTATA
1068529 TATTTTATAATTAAAATTTA
1 TATTTTATAATTAAAATTTA
1068549 ATAAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTTTATAATTAAAATTTATA
Found at i:1073180 original size:29 final size:27
Alignment explanation
Indices: 1073122--1073187 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
1073112 TAATGTAAGT
1073122 ATTTAAATTTAAATTTTAAATTTAATAA
1 ATTT-AATTTAAATTTTAAATTTAATAA
* *
1073150 ATATTATATTTAAATTTTGATTATTAA-AA
1 AT-TTA-ATTTAAATTTTAAAT-TTAATAA
1073179 ATTTAATTT
1 ATTTAATTT
1073188 TTTAAAGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
27 4 0.12
28 6 0.18
29 19 0.58
30 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
ATTTAATTTAAATTTTAAATTTAATAA
Found at i:1073335 original size:28 final size:27
Alignment explanation
Indices: 1073299--1073351 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
1073289 TTTAATTTAA
*
1073299 TTATTTATT-ATATTATTAAAATATTATT
1 TTATATATTAATATT-TTAAAA-ATTATT
1073327 TTATATATTAATATTTTAAAAATTA
1 TTATATATTAATATTTTAAAAATTA
1073352 AATTTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 14 0.61
29 5 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTATATATTAATATTTTAAAAATTATT
Found at i:1073357 original size:28 final size:28
Alignment explanation
Indices: 1073295--1073371 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 28
1073285 AAAATTTAAT
*
1073295 TTAA-TTATTTATT-ATATTATTAAAATA
1 TTAATTTATATATTAATATT-TTAAAATA
*
1073322 TTATTTTATATATTAATATTTTAAAA-A
1 TTAATTTATATATTAATATTTTAAAATA
* **
1073349 TTAAATTTAAATAAAAATATTTT
1 TT-AATTTATATATTAATATTTT
1073372 TATTATTAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
27 6 0.15
28 30 0.73
29 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TTAATTTATATATTAATATTTTAAAATA
Found at i:1073496 original size:21 final size:21
Alignment explanation
Indices: 1073454--1073497 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1073444 TTTAAAGTAA
*
1073454 AAAAATAATATTATATTTAAT
1 AAAAATAATATTATATTCAAT
*
1073475 AAAAATATTATT-TAATTCAAT
1 AAAAATAATATTAT-ATTCAAT
1073496 AA
1 AA
1073498 TTATATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAAATAATATTATATTCAAT
Found at i:1078610 original size:2 final size:2
Alignment explanation
Indices: 1078603--1078633 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1078593 ATCCCATCCA
1078603 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 A
1078634 ACTACAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1079638 original size:27 final size:25
Alignment explanation
Indices: 1079619--1079678 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 25
1079609 AATATTTACA
1079619 AATTTTAATATTTTATAAATATAAATTC
1 AATTTTAATA-TTTATAAATAT--ATTC
*
1079647 AATTTTAATATTTATAAATTATAATC
1 AATTTTAATATTTATAAA-TATATTC
1079673 -ATTTTA
1 AATTTTA
1079679 TAAAAATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 6 0.20
26 3 0.10
27 8 0.27
28 13 0.43
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (25 bp):
AATTTTAATATTTATAAATATATTC
Found at i:1079859 original size:12 final size:12
Alignment explanation
Indices: 1079842--1079869 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1079832 AAAGGTAAGG
1079842 GAGAGTTATAAT
1 GAGAGTTATAAT
1079854 GAGAGTTATAAT
1 GAGAGTTATAAT
1079866 GAGA
1 GAGA
1079870 ATGAAATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (12 bp):
GAGAGTTATAAT
Found at i:1084543 original size:51 final size:51
Alignment explanation
Indices: 1084466--1084654 Score: 164
Period size: 51 Copynumber: 3.5 Consensus size: 51
1084456 ATATGAGGTC
* * * *
1084466 GGAGCAGGCCGCTGAATCAAGGAAAGAGGTTGGAATATCTGGGAAAAGTTT
1 GGAGCAGGCCGCTGAATCAAGAAAAGAAGTTGGAATAGCTGAGAAAAGTTT
* *
1084517 GGAGCAGGCTGCTGAATCAAGAAAAGAAGTTGGAATAGCTGAGAGAAGTTT
1 GGAGCAGGCCGCTGAATCAAGAAAAGAAGTTGGAATAGCTGAGAAAAGTTT
* * *
1084568 GGAGCCAAGCCAGCCGGCTGTTGAATCTAGAAAAGAAGCTGGAATAGCTG-GAAGAACTTT
1 GGAG-C-AG---GCC-GC---TGAATCAAGAAAAGAAGTTGGAATAGCTGAGAA-AAGTTT
** * *
1084628 GGAGCAGGGAGCTGATTCTAGAAAAGA
1 GGAGCAGGCCGCTGAATCAAGAAAAGA
1084655 CCTTGGTATT
Statistics
Matches: 114, Mismatches: 14, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
51 63 0.55
52 1 0.01
53 2 0.02
54 2 0.02
55 1 0.01
56 2 0.02
57 2 0.02
58 2 0.02
59 3 0.03
60 36 0.32
ACGTcount: A:0.35, C:0.13, G:0.33, T:0.19
Consensus pattern (51 bp):
GGAGCAGGCCGCTGAATCAAGAAAAGAAGTTGGAATAGCTGAGAAAAGTTT
Found at i:1088669 original size:21 final size:21
Alignment explanation
Indices: 1088628--1088670 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1088618 AAAAGGGTTA
* *
1088628 TTTTTTATTAATCCTTTTTGT
1 TTTTTTATTAATACTTATTGT
1088649 TTTTTTATTAA-ACTTAATTGT
1 TTTTTTATTAATACTT-ATTGT
1088670 T
1 T
1088671 ATTTATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTTTTATTAATACTTATTGT
Found at i:1091279 original size:2 final size:2
Alignment explanation
Indices: 1091272--1091301 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1091262 CTATAGTGCT
1091272 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
1091302 AAGAGTTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1091746 original size:319 final size:319
Alignment explanation
Indices: 1091221--1091883 Score: 957
Period size: 319 Copynumber: 2.1 Consensus size: 319
1091211 TCACGTGAGG
* *
1091221 AAAATTTTATTTTTATTTTCTTTAAATATGTTAGAAATGCACTATAGTGCTTATATATATATATA
1 AAAATTTTATTTTTATTTTATTTAAATAAGTTAGAAATGCACTATAGTGCTTATATATATATATA
* * * *
1091286 TATATATATATATATAAAGAGTTGAATTTTATTTTATATTATAATTTTTATTGAACAATTAAATC
66 TATATAAAAACATATAAAGAGTTGAATTTTATTTCATATTATAATTTTTATTGAACAATTAAATC
**
1091351 TTTAAAAAAATATAATTTATAGATTTTATTTATATTAAATCGAGTCTTATAAATATTTCAAATAA
131 TTTAAAAAAATATAATTTATAGATTTTATTTATATTAAATCGAGTCCGATAAATATTTCAAATAA
* *
1091416 ATTAAATTAATTTGACATGATTTAAATAATTTTTTAGATAATAAAAATAATTTTTATTTAAATTA
196 ATTAAATTAATTCGACATGATTTAAATAATTATTTAGATAATAAAAATAA-TTTTATTTAAATTA
** * * *
1091481 AATAAAAATATTAATACAATTTTTTAATATT-TCTTGAATTTAAATCAATTTGAAGCTAATA
260 AATAAAAATATTAATACAAAATATTAAT-TTCTCTT-AATTTAAATCAATTTAAAACTAATA
1091542 AAAATTTTATTTTTATTTTATTTAAATAAAGTTAGAAATGCACTATAGTGCTTATA-A-A-A-A-
1 AAAATTTTATTTTTATTTTATTTAAAT-AAGTTAGAAATGCACTATAGTGCTTATATATATATAT
*
1091602 A-A-ATGAAAAACATATAGAGAGTTGAATTTTATTTCATATTATAATTTTTTATTGAACAATTAA
65 ATATAT-AAAAACATATAAAGAGTTGAATTTTATTTCATATTATAA-TTTTTATTGAACAATTAA
* *
1091665 ATCTTTAAAATATATATAATTTATAGATTTTATTTTATATTAAATCGAGTCCGATAAATATTTTA
128 ATCTTTAAAA-AAATATAATTTATAGATTTTA-TTTATATTAAATCGAGTCCGATAAATATTTCA
* * *
1091730 AATGAATTAGATTAATTCGACATGATTTAAATAATTATTTATATAATAAAAATAATTTTATTTAA
191 AATAAATTAAATTAATTCGACATGATTTAAATAATTATTTAGATAATAAAAATAATTTTATTTAA
* *
1091795 ATTAAATAAAAATATTAATATAAAATATTAATTTCTCTTTATTTAAATCAATTTAAAACTAATA
256 ATTAAATAAAAATATTAATACAAAATATTAATTTCTCTTAATTTAAATCAATTTAAAACTAATA
* *
1091859 AAAATTATA-ATTTATTTATATTTAA
1 AAAATTTTATTTTTATTT-TATTTAA
1091884 TTACAAATAT
Statistics
Matches: 310, Mismatches: 25, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
315 2 0.01
316 42 0.14
317 68 0.22
318 63 0.20
319 80 0.26
320 1 0.00
321 27 0.09
322 27 0.09
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (319 bp):
AAAATTTTATTTTTATTTTATTTAAATAAGTTAGAAATGCACTATAGTGCTTATATATATATATA
TATATAAAAACATATAAAGAGTTGAATTTTATTTCATATTATAATTTTTATTGAACAATTAAATC
TTTAAAAAAATATAATTTATAGATTTTATTTATATTAAATCGAGTCCGATAAATATTTCAAATAA
ATTAAATTAATTCGACATGATTTAAATAATTATTTAGATAATAAAAATAATTTTATTTAAATTAA
ATAAAAATATTAATACAAAATATTAATTTCTCTTAATTTAAATCAATTTAAAACTAATA
Found at i:1094742 original size:2 final size:2
Alignment explanation
Indices: 1094735--1094769 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1094725 ATCATCATTA
1094735 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1094770 TAAAATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1101963 original size:13 final size:13
Alignment explanation
Indices: 1101945--1101969 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1101935 TATTCCGAGC
1101945 TTGATAACTGATA
1 TTGATAACTGATA
1101958 TTGATAACTGAT
1 TTGATAACTGAT
1101970 GATTACTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (13 bp):
TTGATAACTGATA
Found at i:1104266 original size:21 final size:20
Alignment explanation
Indices: 1104242--1104284 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1104232 AATTTCATCA
* *
1104242 AATTTATCTATTTTTAAATTT
1 AATTAATCTA-TTTAAAATTT
*
1104263 AATTAATTTATTTAAAATTT
1 AATTAATCTATTTAAAATTT
1104283 AA
1 AA
1104285 ACTTTTATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
AATTAATCTATTTAAAATTT
Found at i:1105481 original size:108 final size:108
Alignment explanation
Indices: 1105268--1105472 Score: 252
Period size: 108 Copynumber: 1.9 Consensus size: 108
1105258 GTTTACGAAA
* * *
1105268 TTTAGGTCTTGAATTTATCGGTTTTTCCAATCAAATACTAAAATAGCTACCTTTCCTTGTTATTG
1 TTTACGTCTTGAATTGATCGGTTTTTCCAATCAAATACTAAAATAGCTACCTTTCCGTGTTATTG
* ** * * *
1105333 TCAATACTGCTTTTTGTTTGTATTGTTCCTTTCTATTACTAAG
66 TCAATACTGCCTTTTAATTGGATTATTCCTTTCTAGTACTAAG
* * *
1105376 TTTACGTCTTGAATTGATCTGGTTTTT-GAGTCAAATTA-TAAAATAGCTGCCTTTCCGTGTTAT
1 TTTACGTCTTGAATTGATC-GGTTTTTCCAATCAAA-TACTAAAATAGCTACCTTTCCGTGTTAT
* *
1105439 TGTTAATACTGCCTTTTAATTGGATTATTACTTT
64 TGTCAATACTGCCTTTTAATTGGATTATTCCTTT
1105473 TCGGTACTAT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
108 73 0.89
109 9 0.11
ACGTcount: A:0.23, C:0.15, G:0.14, T:0.48
Consensus pattern (108 bp):
TTTACGTCTTGAATTGATCGGTTTTTCCAATCAAATACTAAAATAGCTACCTTTCCGTGTTATTG
TCAATACTGCCTTTTAATTGGATTATTCCTTTCTAGTACTAAG
Found at i:1105493 original size:108 final size:108
Alignment explanation
Indices: 1105271--1105500 Score: 234
Period size: 108 Copynumber: 2.1 Consensus size: 108
1105261 TACGAAATTT
* *
1105271 AGGTCTTGAATTTATCGGTTTTTCCAATCAAATACTAAAATAGCTACCTTTCCTTGTTATTGTCA
1 AGGTCTTGAATTGATCGGTTTTTCCAATCAAATACTAAAATAGCTACCTTTCCGTGTTATTGTCA
* ** * * * **
1105336 ATACTGCTTTTTGTTTGTATTGTTCCTTTCTATTACTAAGTTT
66 ATACTGCCTTTTAATTGGATTATTCCTTTCTAGTACTAAGTAA
* * * *
1105379 ACGTCTTGAATTGATCTGGTTTTT-GAGTCAAATTA-TAAAATAGCTGCCTTTCCGTGTTATTGT
1 AGGTCTTGAATTGATC-GGTTTTTCCAATCAAA-TACTAAAATAGCTACCTTTCCGTGTTATTGT
* * *
1105442 TAATACTGCCTTTTAATTGGATTATTACTTT-TCGGTACTATA-TAA
64 CAATACTGCCTTTTAATTGGATTATTCCTTTCT-AGTACTA-AGTAA
1105487 AGGTCTTGTAATTG
1 AGGTCTTG-AATTG
1105501 TATTAGGGAC
Statistics
Matches: 99, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
107 1 0.01
108 83 0.84
109 15 0.15
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (108 bp):
AGGTCTTGAATTGATCGGTTTTTCCAATCAAATACTAAAATAGCTACCTTTCCGTGTTATTGTCA
ATACTGCCTTTTAATTGGATTATTCCTTTCTAGTACTAAGTAA
Found at i:1108030 original size:92 final size:92
Alignment explanation
Indices: 1107929--1108112 Score: 359
Period size: 92 Copynumber: 2.0 Consensus size: 92
1107919 AAGAGTCGGA
1107929 TGGTTTTTATAACTAATTGTCTACAAGCATGCAGTACCTGTGGCAGTCTCTAATGCTTATTCTCT
1 TGGTTTTTATAACTAATTGTCTACAAGCATGCAGTACCTGTGGCAGTCTCTAATGCTTATTCTCT
1107994 TTATATCATAACTAATAACCTCAGTCC
66 TTATATCATAACTAATAACCTCAGTCC
*
1108021 TGGTTTTTATAACTAATTGTCTCCAAGCATGCAGTACCTGTGGCAGTCTCTAATGCTTATTCTCT
1 TGGTTTTTATAACTAATTGTCTACAAGCATGCAGTACCTGTGGCAGTCTCTAATGCTTATTCTCT
1108086 TTATATCATAACTAATAACCTCAGTCC
66 TTATATCATAACTAATAACCTCAGTCC
1108113 CTAACACACT
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (92 bp):
TGGTTTTTATAACTAATTGTCTACAAGCATGCAGTACCTGTGGCAGTCTCTAATGCTTATTCTCT
TTATATCATAACTAATAACCTCAGTCC
Found at i:1110719 original size:20 final size:20
Alignment explanation
Indices: 1110675--1110712 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1110665 TTTGCATTTA
*
1110675 AAAATTAAAAAAAAATCCAC
1 AAAATTAAAAAAAAACCCAC
1110695 AAAATTAAAAAAAAACCC
1 AAAATTAAAAAAAAACCC
1110713 GTTAAATCTC
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:0.71, C:0.16, G:0.00, T:0.13
Consensus pattern (20 bp):
AAAATTAAAAAAAAACCCAC
Found at i:1117330 original size:18 final size:18
Alignment explanation
Indices: 1117307--1117341 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1117297 TCATATATGC
1117307 CTTAAATTTCACAATCAA
1 CTTAAATTTCACAATCAA
1117325 CTTAAATTTCACAATCA
1 CTTAAATTTCACAATCA
1117342 CAAAATCTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (18 bp):
CTTAAATTTCACAATCAA
Found at i:1118636 original size:2 final size:2
Alignment explanation
Indices: 1118631--1118657 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1118621 CTTTTTTTTA
1118631 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
1118658 GGGATTAGAG
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:1122038 original size:21 final size:21
Alignment explanation
Indices: 1121995--1122041 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1121985 AAATGAAAAT
* *
1121995 ATTTATTTTTGAATTATTAAA
1 ATTTATTTTTAAATTAATAAA
1122016 ATTTATTTTTAAATATAAT-AA
1 ATTTATTTTTAAAT-TAATAAA
1122037 ATTTA
1 ATTTA
1122042 AAATATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTTATTTTTAAATTAATAAA
Found at i:1122079 original size:11 final size:11
Alignment explanation
Indices: 1122053--1122099 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
1122043 AATATATTTA
*
1122053 ATAATATTAAAA
1 ATAATA-TAAAT
1122065 ATAATATAAAT
1 ATAATATAAAT
1122076 ATAATATAAAT
1 ATAATATAAAT
* *
1122087 AAAATAAAAAT
1 ATAATATAAAT
1122098 AT
1 AT
1122100 GATGTCATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
11 25 0.81
12 6 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:1122080 original size:26 final size:24
Alignment explanation
Indices: 1122025--1122090 Score: 59
Period size: 26 Copynumber: 2.8 Consensus size: 24
1122015 AATTTATTTT
*
1122025 TAAATATAATAAATTTAAAATATA
1 TAAATATAATAAATTAAAAATATA
1122049 T---T-TAATAATATTAAAAATAATA
1 TAAATATAATAA-ATTAAAAAT-ATA
*
1122071 TAAATATAATATAAATAAAA
1 TAAATATAATA-AATTAAAA
1122091 TAAAAATATG
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
20 6 0.18
21 9 0.27
22 4 0.12
24 1 0.03
25 1 0.03
26 11 0.33
27 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
TAAATATAATAAATTAAAAATATA
Found at i:1124859 original size:18 final size:15
Alignment explanation
Indices: 1124825--1124863 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 15
1124815 AAATATATTT
1124825 AATTTTTTATTTTAA
1 AATTTTTTATTTTAA
1124840 AATTTTTATATATTTAAA
1 AATTTTT-TAT-TTT-AA
1124858 AATTTT
1 AATTTT
1124864 AAAAAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 3 0.14
17 3 0.14
18 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AATTTTTTATTTTAA
Found at i:1134956 original size:16 final size:16
Alignment explanation
Indices: 1134932--1134966 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1134922 CGCCAAACGA
1134932 AAATGATTGATTTAAT
1 AAATGATTGATTTAAT
* *
1134948 AAATTATTGTTTTAAT
1 AAATGATTGATTTAAT
1134964 AAA
1 AAA
1134967 ATCTCAACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (16 bp):
AAATGATTGATTTAAT
Found at i:1137679 original size:20 final size:20
Alignment explanation
Indices: 1137656--1137723 Score: 68
Period size: 18 Copynumber: 3.5 Consensus size: 20
1137646 GTAAAAAATT
1137656 TATACATATAATAAAAATAA
1 TATACATATAATAAAAATAA
* *
1137676 TAT--ATATAATATAATTATA
1 TATACATATAATAAAAATA-A
* * *
1137695 TGTACATATAGTGAAAATAA
1 TATACATATAATAAAAATAA
1137715 TATACATAT
1 TATACATAT
1137724 GTACCTTAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
18 12 0.32
19 3 0.08
20 12 0.32
21 10 0.27
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (20 bp):
TATACATATAATAAAAATAA
Found at i:1138860 original size:24 final size:24
Alignment explanation
Indices: 1138833--1138904 Score: 63
Period size: 28 Copynumber: 2.8 Consensus size: 24
1138823 AAATCATTTC
1138833 ATATTATTAACAATAAAATTAACA
1 ATATTATTAACAATAAAATTAACA
* * ** *
1138857 ATATATATAAAAATATATAAAATTTCCT
1 ATAT-TAT--TAACA-ATAAAATTAACA
1138885 ATATTATTAACAATAAAATT
1 ATATTATTAACAATAAAATT
1138905 TTTAACAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
24 12 0.32
25 6 0.16
27 6 0.16
28 13 0.35
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATTATTAACAATAAAATTAACA
Done.