Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold40
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: 3440810
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 28138 characters in sequence are not A, C, G, or T
File 18 of 24
Found at i:2325020 original size:7 final size:7
Alignment explanation
Indices: 2325008--2325039 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
2324998 TTTTTTCAAA
2325008 CCTGGAC
1 CCTGGAC
2325015 CCTGGAC
1 CCTGGAC
2325022 CCTGGAC
1 CCTGGAC
2325029 CCTGG-C
1 CCTGGAC
2325035 CCTGG
1 CCTGG
2325040 TCCTGGTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.09, C:0.44, G:0.31, T:0.16
Consensus pattern (7 bp):
CCTGGAC
Found at i:2325980 original size:13 final size:13
Alignment explanation
Indices: 2325962--2325986 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2325952 TATTCAAATT
2325962 TTTAAATTTAAAA
1 TTTAAATTTAAAA
2325975 TTTAAATTTAAA
1 TTTAAATTTAAA
2325987 TTTTGAAATC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTAAATTTAAAA
Found at i:2326024 original size:13 final size:13
Alignment explanation
Indices: 2326006--2326030 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2325996 CTGGATAGAA
2326006 TAAAATTTAAATT
1 TAAAATTTAAATT
2326019 TAAAATTTAAAT
1 TAAAATTTAAAT
2326031 AACACTTTTT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAAAATTTAAATT
Found at i:2330686 original size:3 final size:3
Alignment explanation
Indices: 2330678--2330703 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2330668 ATATACTAAG
2330678 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2330704 ATACGTATGG
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2332626 original size:3 final size:3
Alignment explanation
Indices: 2332618--2332651 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2332608 TACTAGTTAC
*
2332618 TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2332652 GAAAACAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2333160 original size:13 final size:13
Alignment explanation
Indices: 2333121--2333160 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
2333111 ATTTATATAT
2333121 ATTTTATAATTAA
1 ATTTTATAATTAA
2333134 ATTTATATAA--AA
1 ATTT-TATAATTAA
2333146 ATTTTATAATTAA
1 ATTTTATAATTAA
2333159 AT
1 AT
2333161 AATAATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 5 0.21
12 6 0.25
13 8 0.33
14 5 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTTTATAATTAA
Found at i:2333454 original size:16 final size:16
Alignment explanation
Indices: 2333412--2333446 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2333402 TTTGGGTTAT
* *
2333412 TTTCAAGTTCAGATTA
1 TTTCGAGTTCGGATTA
2333428 TTTCGAGTTCGGATTA
1 TTTCGAGTTCGGATTA
2333444 TTT
1 TTT
2333447 GGGGTTCGAG
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:0.23, C:0.11, G:0.17, T:0.49
Consensus pattern (16 bp):
TTTCGAGTTCGGATTA
Found at i:2333481 original size:15 final size:16
Alignment explanation
Indices: 2333451--2333481 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2333441 TTATTTGGGG
2333451 TTCGAGTCACTTTGGA
1 TTCGAGTCACTTTGGA
2333467 TTCGAGTCA-TTTGGA
1 TTCGAGTCACTTTGGA
2333482 GTTTAAGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.39
Consensus pattern (16 bp):
TTCGAGTCACTTTGGA
Found at i:2333501 original size:16 final size:16
Alignment explanation
Indices: 2333482--2333548 Score: 71
Period size: 16 Copynumber: 4.2 Consensus size: 16
2333472 GTCATTTGGA
2333482 GTTTAAGTCATTTCAG
1 GTTTAAGTCATTTCAG
* *
2333498 GTTTAATTCATTTCAT
1 GTTTAAGTCATTTCAG
* *
2333514 ATTTAAGTCATTTCAA
1 GTTTAAGTCATTTCAG
* * *
2333530 GTTCAGGCCATTTCAG
1 GTTTAAGTCATTTCAG
2333546 GTT
1 GTT
2333549 CGGATTGATT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (16 bp):
GTTTAAGTCATTTCAG
Found at i:2333542 original size:32 final size:32
Alignment explanation
Indices: 2333483--2333544 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
2333473 TCATTTGGAG
* * **
2333483 TTTAAGTCATTTCAGGTTTAATTCATTTCATA
1 TTTAAGTCATTTCAAGTTCAAGCCATTTCATA
*
2333515 TTTAAGTCATTTCAAGTTCAGGCCATTTCA
1 TTTAAGTCATTTCAAGTTCAAGCCATTTCA
2333545 GGTTCGGATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.45
Consensus pattern (32 bp):
TTTAAGTCATTTCAAGTTCAAGCCATTTCATA
Found at i:2334669 original size:15 final size:13
Alignment explanation
Indices: 2334634--2334688 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 13
2334624 AATAAATAAT
2334634 TAAATAATTTTTA
1 TAAATAATTTTTA
2334647 -AAATAATTTTTAA
1 TAAATAATTTTT-A
* *
2334660 TAAATAAATTATA
1 TAAATAATTTTTA
*
2334673 AAAAT-ATTTATTA
1 TAAATAATTT-TTA
2334686 TAA
1 TAA
2334689 TTTAATTGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
12 14 0.42
13 10 0.30
14 9 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAATAATTTTTA
Found at i:2339440 original size:93 final size:92
Alignment explanation
Indices: 2339336--2339506 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 92
2339326 TAGATATTTT
* *
2339336 GATACATTGAAAAATGTATCAACACATTCATACATGTATCGCTATATTGAAAAATATATCGATAC
1 GATACATTGAAAAATATATCAACACATTCATACATGTATCGATATATTGAAAAATATATCGAT-C
2339401 ATCT-GAGTAAAAAAACATAATGTGCATC
65 ATCTAG-GTAAAAAAACATAATGTGCATC
* * *
2339429 GATACATTGAAAAATATATCGATACATTCATACATGTATCGATATATTGAAAAATTTATCGATCA
1 GATACATTGAAAAATATATCAACACATTCATACATGTATCGATATATTGAAAAATATATCGATCA
2339494 TCTAGGTAAAAAA
66 TCTAGGTAAAAAA
2339507 TAGAATGTAT
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
92 13 0.18
93 59 0.82
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.30
Consensus pattern (92 bp):
GATACATTGAAAAATATATCAACACATTCATACATGTATCGATATATTGAAAAATATATCGATCA
TCTAGGTAAAAAAACATAATGTGCATC
Found at i:2339451 original size:20 final size:20
Alignment explanation
Indices: 2339426--2339491 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
2339416 CATAATGTGC
2339426 ATCGATACATTGAAAAATAT
1 ATCGATACATTGAAAAATAT
* * * *
2339446 ATCGATACATTCATACATGT
1 ATCGATACATTGAAAAATAT
* *
2339466 ATCGATATATTGAAAAATTT
1 ATCGATACATTGAAAAATAT
2339486 ATCGAT
1 ATCGAT
2339492 CATCTAGGTA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (20 bp):
ATCGATACATTGAAAAATAT
Found at i:2343688 original size:17 final size:16
Alignment explanation
Indices: 2343640--2343691 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
2343630 TAAATTAATT
* *
2343640 ATTCGAATCATTTTAG
1 ATTCGGATCATTTTAA
*
2343656 GTTCGGATCATTTTAA
1 ATTCGGATCATTTTAA
2343672 ATTCGGATCATTTTTAA
1 ATTCGGATCA-TTTTAA
2343689 ATT
1 ATT
2343692 TAAATTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 22 0.71
17 9 0.29
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (16 bp):
ATTCGGATCATTTTAA
Found at i:2343695 original size:6 final size:6
Alignment explanation
Indices: 2343684--2343757 Score: 54
Period size: 6 Copynumber: 13.3 Consensus size: 6
2343674 TCGGATCATT
* * **
2343684 TTTAAA TTTAAA -TT-AA -TTAAT TTTAAA TTAATAA TTTTTA -TTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA
2343729 -TTAAA -TTAAA -TTAAA TTTAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT
2343758 AATTAATCAA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
4 4 0.07
5 21 0.38
6 27 0.48
7 4 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:2343714 original size:5 final size:5
Alignment explanation
Indices: 2343685--2343763 Score: 58
Period size: 5 Copynumber: 15.8 Consensus size: 5
2343675 CGGATCATTT
* * **
2343685 TTAAA TTTAAA TT-AA TTAATT TTAAA TT-AA -TAAT TTTTA TTAAA TTAAA
1 TTAAA -TTAAA TTAAA TTAA-A TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
2343734 TTAAA TTAAA TTTAAA TTTAAA TT-AA TTAA
1 TTAAA TTAAA -TTAAA -TTAAA TTAAA TTAA
2343764 TCAAATTTCT
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
3 1 0.02
4 11 0.19
5 27 0.46
6 20 0.34
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (5 bp):
TTAAA
Found at i:2343718 original size:14 final size:15
Alignment explanation
Indices: 2343685--2343764 Score: 76
Period size: 15 Copynumber: 5.3 Consensus size: 15
2343675 CGGATCATTT
*
2343685 TTAAATTTAAATTAA
1 TTAATTTTAAATTAA
2343700 TTAATTTTAAATTAA
1 TTAATTTTAAATTAA
*
2343715 -TAATTTT-TATTAAA
1 TTAATTTTAAATT-AA
*
2343729 TTAA-ATTAAATTAAA
1 TTAATTTTAAATT-AA
*
2343744 TTTAAATTTAAATTAA
1 -TTAATTTTAAATTAA
2343760 TTAAT
1 TTAAT
2343765 CAAATTTCTG
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
13 3 0.06
14 11 0.20
15 27 0.50
16 6 0.11
17 7 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATTTTAAATTAA
Found at i:2344141 original size:16 final size:16
Alignment explanation
Indices: 2344117--2344165 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
2344107 AATTAATATG
*
2344117 TTAAAATTTTATATTA
1 TTAATATTTTATATTA
*
2344133 TTAATA-TTTATTATAA
1 TTAATATTTTA-TATTA
2344149 TTAAT-TTTTATATTA
1 TTAATATTTTATATTA
2344164 TT
1 TT
2344166 TATTATGATC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATATTTTATATTA
Found at i:2344375 original size:13 final size:13
Alignment explanation
Indices: 2344357--2344383 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2344347 TAATAATTTT
2344357 AAATATAATATAA
1 AAATATAATATAA
2344370 AAATATAATATAA
1 AAATATAATATAA
2344383 A
1 A
2344384 TATAATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATATAATATAA
Found at i:2344384 original size:11 final size:11
Alignment explanation
Indices: 2344356--2344389 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 11
2344346 ATAATAATTT
2344356 TAAATATAATA
1 TAAATATAATA
2344367 TAAAAATATAATA
1 T--AAATATAATA
2344380 TAAATATAAT
1 TAAATATAAT
2344390 TTATTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 10 0.48
13 11 0.52
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAATATAATA
Found at i:2344720 original size:2 final size:2
Alignment explanation
Indices: 2344715--2344744 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2344705 TCTATATAAA
2344715 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
2344745 GAAGTCAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2345950 original size:2 final size:2
Alignment explanation
Indices: 2345943--2345977 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2345933 CCAACATTAC
2345943 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 T
2345978 CACTAAATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2346531 original size:8 final size:8
Alignment explanation
Indices: 2346521--2346550 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
2346511 TATTTTCTCT
*
2346521 TTTTTATT
1 TTTTTATA
2346529 TTTTTATA
1 TTTTTATA
2346537 TTTTTATA
1 TTTTTATA
2346545 TTTTTA
1 TTTTTA
2346551 GTAGCTATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTATA
Found at i:2346961 original size:3 final size:3
Alignment explanation
Indices: 2346953--2346998 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
2346943 ATTAAACAAG
2346953 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2346999 TTCATTAATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2350169 original size:19 final size:19
Alignment explanation
Indices: 2350132--2350169 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2350122 GTTCATAATG
*
2350132 TCATATTTAAAGAGGTTAA
1 TCATATTTAAAGAGATTAA
*
2350151 TCATATTTAAATAGATTAA
1 TCATATTTAAAGAGATTAA
2350170 CTATGTTGAG
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:0.05, G:0.11, T:0.39
Consensus pattern (19 bp):
TCATATTTAAAGAGATTAA
Found at i:2357038 original size:2 final size:2
Alignment explanation
Indices: 2357031--2357061 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2357021 AAATGAACGC
2357031 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2357062 TGGAAGGGGG
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2357296 original size:33 final size:35
Alignment explanation
Indices: 2357254--2357349 Score: 90
Period size: 36 Copynumber: 2.7 Consensus size: 35
2357244 AATAATATAA
*
2357254 ATATTATATAAATATATAATTATATTAAA-ATT-T
1 ATATAATATAAATATATAATTATATTAAATATTAT
* *
2357287 ATATAATATAAATTATTAACAAATATATTAAATATTAT
1 ATATAATATAAA-TA-T-ATAATTATATTAAATATTAT
*
2357325 ATAATAATATTTAA-ATATAATTATA
1 AT-ATAATA-TAAATATATAATTATA
2357350 ATATAATAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
33 11 0.22
34 2 0.04
35 1 0.02
36 19 0.38
37 4 0.08
38 4 0.08
39 6 0.12
40 3 0.06
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (35 bp):
ATATAATATAAATATATAATTATATTAAATATTAT
Found at i:2357320 original size:26 final size:27
Alignment explanation
Indices: 2357228--2357321 Score: 69
Period size: 26 Copynumber: 3.7 Consensus size: 27
2357218 TATGAATATA
*
2357228 ATAAAAATA-ATTAAA-AAATAA-TAT
1 ATAAAAATATATTAAATATATAATTAT
* *
2357252 A-AATATTATA-TAAATATATAATTAT
1 ATAAAAATATATTAAATATATAATTAT
* *
2357277 ATTAAAATTTA-TATAATATA-AATTAT
1 ATAAAAATATATTA-AATATATAATTAT
2357303 -TAACAAATATATTAAATAT
1 ATAA-AAATATATTAAATAT
2357322 TATATAATAA
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
23 9 0.17
24 7 0.13
25 6 0.11
26 24 0.44
27 8 0.15
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (27 bp):
ATAAAAATATATTAAATATATAATTAT
Found at i:2357323 original size:22 final size:20
Alignment explanation
Indices: 2357241--2357347 Score: 56
Period size: 20 Copynumber: 5.0 Consensus size: 20
2357231 AAAATAATTA
*
2357241 AAAAATAATATAAATATTA-T
1 AAAAAT-ATTTAAATATTATT
* * *
2357261 ATAAATATATAATTA-TATT
1 AAAAATATTTAAATATTATT
* *
2357280 AAAATTTATATAATATAAATTATT
1 AAAA-ATATTTAA-AT--ATTATT
2357304 AACAAATATATTAAATATTATAT
1 AA-AAATAT-TTAAATATTAT-T
* *
2357327 AATAATATTTAAATATAATT
1 AAAAATATTTAAATATTATT
2357347 A
1 A
2357348 TAATATAATA
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
18 2 0.03
19 12 0.17
20 14 0.20
21 11 0.16
22 10 0.14
23 4 0.06
24 11 0.16
25 5 0.07
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAAATATTTAAATATTATT
Found at i:2357325 original size:36 final size:36
Alignment explanation
Indices: 2357274--2357390 Score: 104
Period size: 36 Copynumber: 3.3 Consensus size: 36
2357264 AATATATAAT
2357274 TATATTAAA-ATTTATATAATATAAATTATTAACAAA
1 TATATTAAATA-TTATATAATATAAATTATTAACAAA
* *
2357310 TATATTAAATATTATATAATA-ATA-T-TTAA-ATA
1 TATATTAAATATTATATAATATAAATTATTAACAAA
* *
2357342 TA-ATTATAATATAATAAAAT-TAAATTAAATTAACAAA
1 TATATTA-AATATTATATAATATAAATT--ATTAACAAA
*
2357379 TTTATTAAATAT
1 TATATTAAATAT
2357391 CGTTCACCGA
Statistics
Matches: 65, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
31 4 0.06
32 17 0.26
33 5 0.08
34 1 0.02
35 2 0.03
36 23 0.35
37 9 0.14
38 4 0.06
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (36 bp):
TATATTAAATATTATATAATATAAATTATTAACAAA
Found at i:2357349 original size:22 final size:22
Alignment explanation
Indices: 2357267--2357352 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 22
2357257 TTATATAAAT
* *
2357267 ATATAATTATATTAAAATTTATATA
1 ATATAATTATAATAATA-TT-TA-A
*
2357292 ATATAAATTATTAACAAATATATTAA
1 ATAT-AATTA-TAA-TAATAT-TTAA
*
2357318 ATATTA-TATAATAATATTTAA
1 ATATAATTATAATAATATTTAA
2357339 ATATAATTATAATA
1 ATATAATTATAATA
2357353 TAATAAAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
21 9 0.18
22 12 0.24
23 3 0.06
24 2 0.04
25 5 0.10
26 10 0.20
27 5 0.10
28 4 0.08
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATAATTATAATAATATTTAA
Found at i:2357355 original size:24 final size:24
Alignment explanation
Indices: 2357267--2357357 Score: 66
Period size: 26 Copynumber: 3.8 Consensus size: 24
2357257 TTATATAAAT
* *
2357267 ATATAATTATATTAAAAT-TTATATA
1 ATATAATTATAATATAATATT-TA-A
*
2357292 ATATAAATTATTAACA-AATATATTAA
1 ATAT-AATTA-TAATATAATAT-TTAA
*
2357318 ATATTA-TAT-A-ATAATATTTAA
1 ATATAATTATAATATAATATTTAA
2357339 ATATAATTATAATATAATA
1 ATATAATTATAATATAATA
2357358 AAATTAAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
21 10 0.19
22 9 0.17
23 2 0.04
24 8 0.15
25 5 0.09
26 13 0.24
27 6 0.11
28 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (24 bp):
ATATAATTATAATATAATATTTAA
Found at i:2357369 original size:64 final size:65
Alignment explanation
Indices: 2357222--2357370 Score: 175
Period size: 64 Copynumber: 2.3 Consensus size: 65
2357212 ATATTATATG
* *
2357222 AATATAATAAAAATAATTAAAAAATAATATAAATATTATATAAATATATAATTATATTAAAATTT
1 AATATAATAAAATTAATTAAAAAATAATATAAATATTATATAAATATATAATTATAATAAAATTT
* * *
2357287 -ATATAATATAAATT-ATTAACAAAT-ATATTAAATATTATAT-AATA-ATATTTA-AATATAAT
1 AATATAATA-AAATTAATTAAAAAATAATA-TAAATATTATATAAATATATAATTATAATAAAAT
2357346 TAT
64 T-T
2357349 AATATAATAAAATTAAATTAAA
1 AATATAATAAAATT-AATTAAA
2357371 TTAACAAATT
Statistics
Matches: 72, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
61 7 0.10
62 12 0.17
63 15 0.21
64 34 0.47
65 4 0.06
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.40
Consensus pattern (65 bp):
AATATAATAAAATTAATTAAAAAATAATATAAATATTATATAAATATATAATTATAATAAAATTT
Found at i:2357389 original size:69 final size:64
Alignment explanation
Indices: 2357209--2357390 Score: 172
Period size: 64 Copynumber: 2.8 Consensus size: 64
2357199 ACAACATTCG
* * * * * *
2357209 AATATATT-ATATGAATATAATAAAAATAATTAAAAAATA-ATATAAATATTATATAAATATATA
1 AATATATTAAAATTAATAAAATATAAATTATTAACAAATATAT-TAAATATTATATAAATATATA
* * * *
2357272 ATTATATTAAAATTTATATAATATAAATTATTAACAAATATATTAAATATTATATAATAATATTT
1 AATATATTAAAATTAATAAAATATAAATTATTAACAAATATATTAAATATTATAT-A-AATATAT
2357337 A
64 A
* *
2357338 AATATAATTATAATATAATAAAAT-TAAATTAAATTAACAAATTTATTAAATAT
1 AATAT-ATTAAAAT-TAATAAAATATAAATT--ATTAACAAATATATTAAATAT
2357391 CGTTCACCGA
Statistics
Matches: 98, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
63 7 0.07
64 37 0.38
65 3 0.03
66 11 0.11
67 13 0.13
68 7 0.07
69 20 0.20
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.41
Consensus pattern (64 bp):
AATATATTAAAATTAATAAAATATAAATTATTAACAAATATATTAAATATTATATAAATATATA
Found at i:2357751 original size:14 final size:14
Alignment explanation
Indices: 2357722--2357783 Score: 72
Period size: 15 Copynumber: 4.3 Consensus size: 14
2357712 TAATGAATAA
*
2357722 AATATTTTAATTTT
1 AATATTTTAAATTT
*
2357736 TATATTATTAAATTT
1 AATATT-TTAAATTT
2357751 AATATTTT-AATTT
1 AATATTTTAAATTT
2357764 AATATTTTTAAATTAT
1 AATA-TTTTAAATT-T
2357780 AATA
1 AATA
2357784 AATAAATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
13 9 0.22
14 11 0.27
15 16 0.39
16 5 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
AATATTTTAAATTT
Found at i:2357761 original size:29 final size:29
Alignment explanation
Indices: 2357722--2357783 Score: 90
Period size: 28 Copynumber: 2.1 Consensus size: 29
2357712 TAATGAATAA
*
2357722 AATATTTTAATTTTTATATTATTAAATT-T
1 AATATTTTAA-TTTAATATTATTAAATTAT
*
2357751 AATATTTTAATTTAATATTTTTAAATTAT
1 AATATTTTAATTTAATATTATTAAATTAT
2357780 AATA
1 AATA
2357784 AATAAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 15 0.50
29 15 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
AATATTTTAATTTAATATTATTAAATTAT
Found at i:2357764 original size:13 final size:13
Alignment explanation
Indices: 2357722--2357771 Score: 64
Period size: 13 Copynumber: 3.6 Consensus size: 13
2357712 TAATGAATAA
2357722 AATATTTTAATTTT
1 AATATTTTAA-TTT
*
2357736 TATATTATTAAATTT
1 AATATT-TT-AATTT
2357751 AATATTTTAATTT
1 AATATTTTAATTT
2357764 AATATTTT
1 AATATTTT
2357772 TAAATTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 13 0.41
14 7 0.22
15 10 0.31
16 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AATATTTTAATTT
Found at i:2357942 original size:20 final size:20
Alignment explanation
Indices: 2357892--2357942 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
2357882 ATATGATACG
2357892 TTAA-TATTTTATTAATATT
1 TTAATTATTTTATTAATATT
* *
2357911 TAAATAATTTT-TATAATATT
1 TTAATTATTTTAT-TAATATT
2357931 ATTAATTATTTT
1 -TTAATTATTTT
2357943 TCTTCATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 4 0.16
20 12 0.48
21 9 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAATTATTTTATTAATATT
Found at i:2358183 original size:17 final size:18
Alignment explanation
Indices: 2358158--2358198 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
2358148 TTGATCAAAT
*
2358158 CAATTTAAAA-AATATTA
1 CAATATAAAATAATATTA
2358175 CAATATAAAATTAATATTA
1 CAATATAAAA-TAATATTA
2358194 -AATAT
1 CAATAT
2358199 GATAAAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 9 0.43
18 5 0.24
19 7 0.33
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (18 bp):
CAATATAAAATAATATTA
Found at i:2358864 original size:25 final size:24
Alignment explanation
Indices: 2358830--2358896 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 24
2358820 TTATATAAAT
*
2358830 AAAAATTAAT-TCAATTATTAATTTA
1 AAAAATTAATATCAA--ATTAATTAA
2358855 AAAAATTAATAATCAAATTAATTAA
1 AAAAATTAAT-ATCAAATTAATTAA
*
2358880 AAAAATTAA-ATTAAATT
1 AAAAATTAATATCAAATT
2358897 CATTGAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.18
25 27 0.71
27 4 0.11
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAAATTAATATCAAATTAATTAA
Found at i:2359623 original size:20 final size:19
Alignment explanation
Indices: 2359587--2359626 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2359577 TAATAGTGTT
**
2359587 ATAAATGAATATCATTTTA
1 ATAAATGAATAAAATTTTA
2359606 ATAAATAGAATAAAATTTTA
1 ATAAAT-GAATAAAATTTTA
2359626 A
1 A
2359627 GTATTCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (19 bp):
ATAAATGAATAAAATTTTA
Found at i:2359769 original size:26 final size:26
Alignment explanation
Indices: 2359727--2359776 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2359717 ATATTAATTT
*
2359727 AATTAATAAAATTATAAAAATAAATA
1 AATTAATAAAATAATAAAAATAAATA
* *
2359753 AATTAATATAATAATAAAGATAAA
1 AATTAATAAAATAATAAAAATAAA
2359777 CAAAAATACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (26 bp):
AATTAATAAAATAATAAAAATAAATA
Found at i:2360046 original size:21 final size:22
Alignment explanation
Indices: 2360017--2360057 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
2360007 TGGGTAAATT
2360017 AATCAACTTTTAAAAATAACAA
1 AATCAACTTTTAAAAATAACAA
2360039 AATC-ACTTTTAAAAATAAC
1 AATCAACTTTTAAAAATAAC
2360058 TTTTAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (22 bp):
AATCAACTTTTAAAAATAACAA
Found at i:2360404 original size:22 final size:22
Alignment explanation
Indices: 2360379--2360424 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2360369 TAATTAAATA
*
2360379 TATATTTGTA-TTAAATATTTAT
1 TATATTTATACTTAAATA-TTAT
*
2360401 TATATTTATACTTATATATTAT
1 TATATTTATACTTAAATATTAT
2360423 TA
1 TA
2360425 AAATTACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
TATATTTATACTTAAATATTAT
Found at i:2361208 original size:24 final size:22
Alignment explanation
Indices: 2361181--2361234 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
2361171 TGTAAATTAT
*
2361181 ATTTATATTAATAAAATTTATCTA
1 ATTTATATTAATAAAAATT-T-TA
2361205 ATTTATA--AATAAAAATTTTA
1 ATTTATATTAATAAAAATTTTA
2361225 ATTT-TATTAA
1 ATTTATATTAA
2361235 AATATTTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 2 0.07
20 6 0.22
21 3 0.11
22 9 0.33
24 7 0.26
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTATATTAATAAAAATTTTA
Found at i:2361932 original size:18 final size:19
Alignment explanation
Indices: 2361906--2361949 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
2361896 AAAATAATTT
*
2361906 AATATATTTTACATA-TAA
1 AATAAATTTTACATATTAA
*
2361924 AATAAATTTTATATATTAA
1 AATAAATTTTACATATTAA
*
2361943 TATAAAT
1 AATAAAT
2361950 CTAACTAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
AATAAATTTTACATATTAA
Found at i:2367527 original size:23 final size:24
Alignment explanation
Indices: 2367486--2367536 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 24
2367476 TAAGATATGA
2367486 ATATTTAAATATAATTATTATATT
1 ATATTTAAATATAATTATTATATT
2367510 ATATTTAATATATATATT-TTAT-TT
1 ATATTTAA-ATATA-ATTATTATATT
2367534 ATA
1 ATA
2367537 ATTTTAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 13 0.52
25 9 0.36
26 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATATTTAAATATAATTATTATATT
Found at i:2367536 original size:13 final size:13
Alignment explanation
Indices: 2367489--2367542 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
2367479 GATATGAATA
*
2367489 TTTAAATATA-AT
1 TTTATATATATAT
2367501 TATTATAT-TATAT
1 T-TTATATATATAT
*
2367514 TTAATATATATAT
1 TTTATATATATAT
*
2367527 TTTATTTATA-AT
1 TTTATATATATAT
2367539 TTTA
1 TTTA
2367543 ACATATTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 14 0.40
13 21 0.60
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTATATATATAT
Found at i:2368033 original size:21 final size:21
Alignment explanation
Indices: 2367982--2368035 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 21
2367972 CCTACCAAAT
*
2367982 CTACCATTTAGTCAACAATGG
1 CTACCATTTAATCAACAATGG
2368003 -TAAGCCATTTAATCAACAATGG
1 CT-A-CCATTTAATCAACAATGG
2368025 CTACCATTTAA
1 CTACCATTTAA
2368036 GCCACCAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 1 0.03
21 9 0.31
22 18 0.62
23 1 0.03
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (21 bp):
CTACCATTTAATCAACAATGG
Found at i:2368071 original size:34 final size:34
Alignment explanation
Indices: 2368033--2368199 Score: 210
Period size: 34 Copynumber: 4.9 Consensus size: 34
2368023 GGCTACCATT
* * *
2368033 TAAGCCACCAAATCACCCATTTAATCAATAACGG
1 TAAGCTACCAAATCACCCATTTAATCAACAATGG
** *
2368067 TAAGCTACCAAATTTCTCATTTAATCAACAATGG
1 TAAGCTACCAAATCACCCATTTAATCAACAATGG
** *
2368101 TAAGCTACCAAATCTTCCATTTAGTCAACAATGG
1 TAAGCTACCAAATCACCCATTTAATCAACAATGG
* * *
2368135 CAAACCACCAAATCACCCATTTAATCAACAATGG
1 TAAGCTACCAAATCACCCATTTAATCAACAATGG
*
2368169 TAAACTACCAAATCA-CCATTTAATCAACAAT
1 TAAGCTACCAAATCACCCATTTAATCAACAAT
2368200 TCTCTCACTT
Statistics
Matches: 115, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
33 16 0.14
34 99 0.86
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (34 bp):
TAAGCTACCAAATCACCCATTTAATCAACAATGG
Found at i:2370913 original size:36 final size:36
Alignment explanation
Indices: 2370866--2370936 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
2370856 TTTTGAGTCC
2370866 AGGAAGCAATCCACTATCAGATAGAATCTTTATACA
1 AGGAAGCAATCCACTATCAGATAGAATCTTTATACA
2370902 AGGAAGCAATCCACTATCAGATAGAATCTTTATAC
1 AGGAAGCAATCCACTATCAGATAGAATCTTTATAC
2370937 CTCGTTCTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (36 bp):
AGGAAGCAATCCACTATCAGATAGAATCTTTATACA
Found at i:2372692 original size:34 final size:33
Alignment explanation
Indices: 2372642--2372857 Score: 229
Period size: 34 Copynumber: 6.4 Consensus size: 33
2372632 TGGTAAAAAC
* *
2372642 CACCATTTAATAAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
* *
2372675 CTATCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* * *
2372709 CACCCATTTAATCAATAATGGTAAGCTATCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
2372743 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * **
2372777 CTCCATTTAGTCAACAATGACAAACC-ACCAAAT
1 CACCATTTAATCAACAATG-GTAACCTACCAAAT
*
2372810 CACCTATTTAATCAACAATGGTAAACTACCAAAT
1 CACC-ATTTAATCAACAATGGTAACCTACCAAAT
2372844 CACCATTTAATCAA
1 CACCATTTAATCAA
2372858 TATAGGTAAA
Statistics
Matches: 152, Mismatches: 23, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
33 42 0.28
34 108 0.71
35 2 0.01
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:2372758 original size:68 final size:67
Alignment explanation
Indices: 2372642--2372857 Score: 263
Period size: 67 Copynumber: 3.2 Consensus size: 67
2372632 TGGTAAAAAC
* * * * *
2372642 CACCATTTAATAAACAATGGCAACCTACCAAATCTATCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCTCATTTAATCAACAATGGTAAGCTACCAA
2372707 AT
66 AT
* * * * *
2372709 CACCCATTTAATCAATAATGGTAAGCTATCAAATTTCTCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCTCATTTAATCAACAATGGTAAGCTACCA
2372774 AAT
65 AAT
* * * * * *
2372777 CTCCATTTAGTCAACAATGACAAACCACCAAATCAC-CTATTTAATCAACAATGGTAAACTACCA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCTC-ATTTAATCAACAATGGTAAGCTACCA
2372841 AAT
65 AAT
2372844 CACCATTTAATCAA
1 CACCATTTAATCAA
2372858 TATAGGTAAA
Statistics
Matches: 125, Mismatches: 22, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
66 1 0.01
67 67 0.54
68 57 0.46
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCTCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:2372811 original size:101 final size:101
Alignment explanation
Indices: 2372642--2372857 Score: 299
Period size: 101 Copynumber: 2.1 Consensus size: 101
2372632 TGGTAAAAAC
* * ** *
2372642 CACCATTTAATAAACAATGGCAACCTACCAAATCTATCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGACAAACCACCAA
* * *
2372707 ATCACCCATTTAATCAATAATGGTAAGCTATCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * *
2372743 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCT-CCATTTAGTCAACAATGACAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGACAAACCACCA
*
2372807 AATCACCTATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
2372844 CACCATTTAATCAA
1 CACCATTTAATCAA
2372858 TATAGGTAAA
Statistics
Matches: 99, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
100 11 0.11
101 59 0.60
102 29 0.29
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGACAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:2375074 original size:53 final size:54
Alignment explanation
Indices: 2375010--2375119 Score: 204
Period size: 53 Copynumber: 2.1 Consensus size: 54
2375000 AGGTACATAC
2375010 TTAATACTAACATTTAAATCCGAATAATATA-TTTTTTTAAGTGTGAATTACAG
1 TTAATACTAACATTTAAATCCGAATAATATATTTTTTTTAAGTGTGAATTACAG
*
2375063 TTAATATTAACATTTAAATCCGAATAATATATTTTTTTTAAGTGTGAATTACAG
1 TTAATACTAACATTTAAATCCGAATAATATATTTTTTTTAAGTGTGAATTACAG
2375117 TTA
1 TTA
2375120 CGCCTAACAT
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 30 0.55
54 25 0.45
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44
Consensus pattern (54 bp):
TTAATACTAACATTTAAATCCGAATAATATATTTTTTTTAAGTGTGAATTACAG
Found at i:2375128 original size:54 final size:53
Alignment explanation
Indices: 2375010--2375129 Score: 186
Period size: 54 Copynumber: 2.2 Consensus size: 53
2375000 AGGTACATAC
*
2375010 TTAATACTAACATTTAAATCCGAATAATATATTTTTTTAAGTGTGAATTACAG
1 TTAAGACTAACATTTAAATCCGAATAATATATTTTTTTAAGTGTGAATTACAG
* *
2375063 TTAATATTAACATTTAAATCCGAATAATATATTTTTTTTAAGTGTGAATTACAG
1 TTAAGACTAACATTTAAATCCGAATAATATA-TTTTTTTAAGTGTGAATTACAG
* *
2375117 TTACGCCTAACAT
1 TTAAGACTAACAT
2375130 GATTTTCACT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
53 30 0.49
54 31 0.51
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (53 bp):
TTAAGACTAACATTTAAATCCGAATAATATATTTTTTTAAGTGTGAATTACAG
Found at i:2377108 original size:13 final size:13
Alignment explanation
Indices: 2377072--2377114 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2377062 TTATATTATT
**
2377072 ATTTTAAAAATAA
1 ATTTTAAATTTAA
2377085 ATTTAATAAATTTAA
1 ATTT--TAAATTTAA
2377100 ATTTTAAATTTAA
1 ATTTTAAATTTAA
2377113 AT
1 AT
2377115 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 15 0.58
15 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTTAAATTTAA
Found at i:2377409 original size:21 final size:22
Alignment explanation
Indices: 2377383--2377428 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2377373 TATTTTTAAT
2377383 ATTTTTAAATAATA-AAATAAA
1 ATTTTTAAATAATACAAATAAA
* * *
2377404 ATTTTTTAATCATACAAATCAA
1 ATTTTTAAATAATACAAATAAA
2377426 ATT
1 ATT
2377429 AAATCTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTTTTAAATAATACAAATAAA
Found at i:2378175 original size:11 final size:11
Alignment explanation
Indices: 2378161--2378192 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
2378151 ATTTAAATGC
2378161 TATTTAATTAT
1 TATTTAATTAT
2378172 TATTTAATTAT
1 TATTTAATTAT
2378183 TATTTTAATT
1 TA-TTTAATT
2378193 TAAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATTTAATTAT
Found at i:2383179 original size:23 final size:23
Alignment explanation
Indices: 2383153--2383203 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2383143 TCAAATTATA
2383153 AAAAATAAAATAAATATTATTTT
1 AAAAATAAAATAAATATTATTTT
*** *
2383176 AAAAATTTGATTAATATTATTTT
1 AAAAATAAAATAAATATTATTTT
2383199 AAAAA
1 AAAAA
2383204 GTAACATGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
AAAAATAAAATAAATATTATTTT
Found at i:2388360 original size:4 final size:4
Alignment explanation
Indices: 2388353--2388378 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2388343 CAAACGCATA
2388353 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
2388379 TTGTAATGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:2391470 original size:18 final size:20
Alignment explanation
Indices: 2391435--2391474 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2391425 AAGTGAACAG
*
2391435 TATTTTATTTATTAATATAA
1 TATTATATTTATTAATATAA
2391455 TATTATATTT-TT-ATATAA
1 TATTATATTTATTAATATAA
2391473 TA
1 TA
2391475 AAAAGTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 2 0.11
20 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTATATTTATTAATATAA
Found at i:2392649 original size:38 final size:34
Alignment explanation
Indices: 2392586--2392681 Score: 95
Period size: 37 Copynumber: 2.6 Consensus size: 34
2392576 ACTATTTAAA
*
2392586 TAATA-AAAAAAATTTATTAAATTTAATTATAAATAT
1 TAATATAAAAATATTT-TTAAATTTAA-TATAAAT-T
*
2392622 TAATATAAAAATATTTTTAAATTTTTAATATTAATT
1 TAATATAAAAATATTTTTAAA--TTTAATATAAATT
2392658 TAAATAGTAAAATATATTTTTAAA
1 T-AATA-TAAAA-ATATTTTTAAA
2392682 CTAATTCTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
36 12 0.23
37 19 0.37
38 10 0.19
39 11 0.21
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (34 bp):
TAATATAAAAATATTTTTAAATTTAATATAAATT
Found at i:2393565 original size:2 final size:2
Alignment explanation
Indices: 2393558--2393585 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2393548 AGATAAACGA
2393558 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
2393586 TTTTTAATTG
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:2394198 original size:3 final size:3
Alignment explanation
Indices: 2394190--2394235 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
2394180 AATTTCATAT
*
2394190 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2394236 CATTGGAGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2394480 original size:18 final size:21
Alignment explanation
Indices: 2394449--2394495 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
2394439 TCTCAAAATC
2394449 TATATAAAATAAATTAT-T-AA
1 TATAT-AAATAAATTATATAAA
2394469 TATATAAA-AAATTATATAAA
1 TATATAAATAAATTATATAAA
2394489 TATATAA
1 TATATAA
2394496 TATCTTAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.28
19 4 0.16
20 14 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TATATAAATAAATTATATAAA
Found at i:2394596 original size:2 final size:2
Alignment explanation
Indices: 2394589--2394635 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
2394579 AATATTAGGC
*
2394589 AT AT AT AT AT A- AT AT A- AT AC A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2394628 AT TT AT AT
1 AT AT AT AT
2394636 CAAAGAAACT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2396830 original size:2 final size:2
Alignment explanation
Indices: 2396765--2396814 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
2396755 CGTGTGTATC
*
2396765 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2396806 TA AA TA TA T
1 TA TA TA TA T
2396815 TTAATTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2397286 original size:33 final size:33
Alignment explanation
Indices: 2397221--2397287 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
2397211 ATTATAAATT
* * * * *
2397221 AAATAAAATTAACTTAATTAATAAAAATATAAA
1 AAATAAAATAAAATCAACTAATAAAAAGATAAA
*
2397254 AAATAAAATAAAATCAACTAATTAAAAGATAAA
1 AAATAAAATAAAATCAACTAATAAAAAGATAAA
2397287 A
1 A
2397288 TAGAGAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.69, C:0.04, G:0.01, T:0.25
Consensus pattern (33 bp):
AAATAAAATAAAATCAACTAATAAAAAGATAAA
Found at i:2398092 original size:17 final size:17
Alignment explanation
Indices: 2398070--2398104 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2398060 AGAAGGCTGT
*
2398070 GATGTGTATAAATATTA
1 GATGTGTATAAACATTA
*
2398087 GATGTGTGTAAACATTA
1 GATGTGTATAAACATTA
2398104 G
1 G
2398105 TTAGATGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (17 bp):
GATGTGTATAAACATTA
Found at i:2398654 original size:22 final size:22
Alignment explanation
Indices: 2398637--2398678 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2398627 ATATTAGTTG
*
2398637 ACATATCACTTGTAATTAATTA
1 ACATATCACATGTAATTAATTA
*
2398659 ACGTATCACATGTAATTAAT
1 ACATATCACATGTAATTAAT
2398679 GTAGTACAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.38
Consensus pattern (22 bp):
ACATATCACATGTAATTAATTA
Found at i:2399287 original size:21 final size:22
Alignment explanation
Indices: 2399252--2399295 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2399242 TATTTATATT
2399252 TTATATAATACATATAAAAATAA
1 TTATATAATA-ATATAAAAATAA
*
2399275 TTATATAAT-ATATAAATATAA
1 TTATATAATAATATAAAAATAA
2399296 AAAATATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
23 9 0.45
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TTATATAATAATATAAAAATAA
Found at i:2399639 original size:2 final size:2
Alignment explanation
Indices: 2399632--2399662 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2399622 TGTAATTTGT
2399632 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2399663 AACAAAGGGG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2400159 original size:21 final size:21
Alignment explanation
Indices: 2400118--2400169 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
2400108 AAATTTAAAA
2400118 AAATATTTTATATGAATATTT
1 AAATATTTTATATGAATATTT
* *
2400139 ATATATTTTATAATTAA-ATTT
1 AAATATTTTAT-ATGAATATTT
2400160 AAATAATTTT
1 AAAT-ATTTT
2400170 TTTTTAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
AAATATTTTATATGAATATTT
Found at i:2401307 original size:17 final size:18
Alignment explanation
Indices: 2401285--2401336 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 18
2401275 ATTTAATTTT
2401285 TATAATTTATTATAA-AA
1 TATAATTTATTATAATAA
* *
2401302 TATAA-TGATTATAATTA
1 TATAATTTATTATAATAA
*
2401319 TATAATTT-TTTTAATAA
1 TATAATTTATTATAATAA
2401336 T
1 T
2401337 TTTTGAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 8 0.29
17 19 0.68
18 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TATAATTTATTATAATAA
Found at i:2401645 original size:22 final size:21
Alignment explanation
Indices: 2401620--2401660 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2401610 TTATTACAAA
2401620 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
2401640 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
2401661 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:2404895 original size:2 final size:2
Alignment explanation
Indices: 2404888--2404919 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2404878 TACAAGAAAT
2404888 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
2404920 ACTCCTTTTT
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):
TA
Found at i:2405350 original size:2 final size:2
Alignment explanation
Indices: 2405343--2405379 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2405333 TATTATTGGT
*
2405343 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2405380 TTCTCTCTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2411159 original size:2 final size:2
Alignment explanation
Indices: 2411152--2411185 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2411142 TCGAGAACAC
2411152 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2411186 TTGATCTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2411978 original size:12 final size:12
Alignment explanation
Indices: 2411939--2411987 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
2411929 TTATTTATAT
*
2411939 ATTTAATGTTAA
1 ATTTAATATTAA
*
2411951 ATTATAA-ATTAT
1 ATT-TAATATTAA
2411963 ATTTAATATTAA
1 ATTTAATATTAA
2411975 ATTT-AT-TTAA
1 ATTTAATATTAA
2411985 ATT
1 ATT
2411988 ATTTATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
10 7 0.22
11 5 0.16
12 17 0.53
13 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:2411995 original size:24 final size:25
Alignment explanation
Indices: 2411915--2411996 Score: 79
Period size: 24 Copynumber: 3.5 Consensus size: 25
2411905 AAGAAATTTT
*
2411915 TTATTTAAT-TT-AATTTATTTATA
1 TTATTTAATATTAAATTTATTTAAA
*
2411938 -TATTTAATGTTAAA-TTA--TAAA
1 TTATTTAATATTAAATTTATTTAAA
2411959 TTATATTTAATATTAAATTTATTTAAA
1 -T-TATTTAATATTAAATTTATTTAAA
2411986 TTATTT-ATATT
1 TTATTTAATATT
2411997 TTATTTTAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
21 3 0.06
22 8 0.16
23 5 0.10
24 20 0.41
25 8 0.16
26 1 0.02
27 4 0.08
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (25 bp):
TTATTTAATATTAAATTTATTTAAA
Found at i:2412002 original size:24 final size:25
Alignment explanation
Indices: 2411913--2412008 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 25
2411903 AAAAGAAATT
*
2411913 TTTTATTTAATTTAATTTATTTATA
1 TTTTATTTAATTTAAATTATTTATA
2411938 TATTTAATGTTAAATTATAAATTATATTTAATA
1 T-TTT-AT-TT-AATT-TAAA-T-TATTT-ATA
**
2411971 TTAAATTT-ATTTAAATTATTTATA
1 TTTTATTTAATTTAAATTATTTATA
2411995 TTTTATTTTAATTT
1 TTTTA-TTTAATTT
2412009 TTATATTTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 19
0.70 0.06 0.24
Matches are distributed among these distances:
24 6 0.11
25 9 0.16
26 8 0.14
27 6 0.11
28 5 0.09
29 4 0.07
30 5 0.09
31 3 0.05
32 6 0.11
33 4 0.07
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (25 bp):
TTTTATTTAATTTAAATTATTTATA
Found at i:2412011 original size:19 final size:20
Alignment explanation
Indices: 2411908--2412033 Score: 81
Period size: 19 Copynumber: 6.6 Consensus size: 20
2411898 ATCAAAAAAG
*
2411908 AAATT-TTT-TATTTAATTT
1 AAATTATTTATATTTTATTT
*
2411926 AATTTATTTATATATTTAATGTT
1 AAATTATTTATAT-TTT-AT-TT
* *
2411949 AAATTA--TAAATTATATTT
1 AAATTATTTATATTTTATTT
*
2411967 -AA-TA-TTA-AATTTATTT
1 AAATTATTTATATTTTATTT
2411983 AAATTATTTATATTTTATTT
1 AAATTATTTATATTTTATTT
* *
2412003 TAATT-TTTATATTTTATAT
1 AAATTATTTATATTTTATTT
* *
2412022 ATATTATATATA
1 AAATTATTTATA
2412034 ATACAAAAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
16 9 0.11
17 6 0.07
18 8 0.10
19 24 0.29
20 22 0.26
21 6 0.07
22 2 0.02
23 7 0.08
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (20 bp):
AAATTATTTATATTTTATTT
Found at i:2412699 original size:9 final size:8
Alignment explanation
Indices: 2412629--2412749 Score: 55
Period size: 8 Copynumber: 15.9 Consensus size: 8
2412619 ATTTATATTT
2412629 ATATATAA
1 ATATATAA
2412637 ATAGTAT-A
1 ATA-TATAA
*
2412645 ATATATTA
1 ATATATAA
* *
2412653 ATTTTTAA
1 ATATATAA
2412661 A-ATATAA
1 ATATATAA
2412668 AT-TA-AA
1 ATATATAA
2412674 A-A-AT-A
1 ATATATAA
2412679 ATAT-TAA
1 ATATATAA
2412686 TATATCATAA
1 -ATAT-ATAA
2412696 ATATATAA
1 ATATATAA
*
2412704 ATGTATAA
1 ATATATAA
*
2412712 AAATAT-A
1 ATATATAA
* *
2412719 ATAAAATTA
1 AT-ATATAA
*
2412728 AT-TATTA
1 ATATATAA
*
2412735 ATATAAAA
1 ATATATAA
2412743 ATATATA
1 ATATATA
2412750 TAAAATTTAT
Statistics
Matches: 85, Mismatches: 14, Indels: 28
0.67 0.11 0.22
Matches are distributed among these distances:
5 3 0.04
6 5 0.06
7 19 0.22
8 45 0.53
9 10 0.12
10 3 0.04
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (8 bp):
ATATATAA
Found at i:2412738 original size:39 final size:38
Alignment explanation
Indices: 2412632--2412755 Score: 103
Period size: 39 Copynumber: 3.2 Consensus size: 38
2412622 TATATTTATA
* * *
2412632 TATAAATAGTATAAT-ATATTAATTTTTAAAATATAAAT
1 TATAAA-AATATAATAATATTAATTATTAATATATAAAT
* * *
2412670 TA-AAAAATAATATTAATA-T-ATCATAAATATATAAAT
1 TATAAAAAT-ATAATAATATTAATTATTAATATATAAAT
* *
2412706 GTATAAAAATATAATAAAATTAATTATTAATATAAAAAT
1 -TATAAAAATATAATAATATTAATTATTAATATATAAAT
2412745 ATATATAAAAT
1 -TATA-AAAAT
2412756 TTATAATGTA
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
36 15 0.22
37 17 0.25
38 12 0.18
39 18 0.27
40 5 0.07
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (38 bp):
TATAAAAATATAATAATATTAATTATTAATATATAAAT
Found at i:2413192 original size:20 final size:19
Alignment explanation
Indices: 2413164--2413212 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
2413154 AAACAAAATG
2413164 GAAAATAAAAATTAAAAAA
1 GAAAATAAAAATTAAAAAA
** *
2413183 GAAAATTAAATTTTGAAAAA
1 GAAAA-TAAAAATTAAAAAA
2413203 GAAAA-AAAAA
1 GAAAATAAAAA
2413213 AGAAGAGTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
18 3 0.12
19 5 0.21
20 16 0.67
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.18
Consensus pattern (19 bp):
GAAAATAAAAATTAAAAAA
Found at i:2413625 original size:22 final size:21
Alignment explanation
Indices: 2413599--2413677 Score: 76
Period size: 20 Copynumber: 3.8 Consensus size: 21
2413589 TTAAAATTTT
2413599 TATTTTTAAAAATCTTTTTTGA
1 TATTTTTAAAAAT-TTTTTTGA
*
2413621 TATTTTT-AAAATTTTTTTTA
1 TATTTTTAAAAATTTTTTTGA
* *
2413641 TAAGTTTTATAAAA-GTTTTTGA
1 T-ATTTTTA-AAAATTTTTTTGA
2413663 -ATTTTT-AAAATTTTT
1 TATTTTTAAAAATTTTT
2413678 ATTTTATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
18 4 0.09
19 3 0.06
20 13 0.28
21 10 0.21
22 13 0.28
23 4 0.09
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.61
Consensus pattern (21 bp):
TATTTTTAAAAATTTTTTTGA
Found at i:2413686 original size:20 final size:19
Alignment explanation
Indices: 2413573--2413687 Score: 85
Period size: 21 Copynumber: 5.8 Consensus size: 19
2413563 TTTTTAATTC
*
2413573 AATTTTTATTATATATTTAA
1 AATTTTT-TTATATTTTTAA
*
2413593 AA--TTTTTAT-TTTTAAA
1 AATTTTTTTATATTTTTAA
2413609 AATCTTTTTTGATATTTTTAA
1 AAT-TTTTTT-ATATTTTTAA
2413630 AATTTTTTTTATAAGTTTTATAA
1 AA-TTTTTTTAT-A-TTTT-TAA
* *
2413653 AAGTTTTTGA-ATTTTTAA
1 AATTTTTTTATATTTTTAA
*
2413671 AATTTTTATTTTATTTT
1 AATTTTT-TTATATTTT
2413688 CTTAATAATG
Statistics
Matches: 76, Mismatches: 8, Indels: 22
0.72 0.08 0.21
Matches are distributed among these distances:
16 7 0.09
17 4 0.05
18 12 0.16
19 10 0.13
20 12 0.16
21 15 0.20
22 11 0.14
23 5 0.07
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (19 bp):
AATTTTTTTATATTTTTAA
Found at i:2413774 original size:17 final size:19
Alignment explanation
Indices: 2413741--2413783 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
2413731 ATCATATTTT
2413741 TATTATT-TATTATTTTAA
1 TATTATTATATTATTTTAA
2413759 TATTATTAT-TTA-TTTAA
1 TATTATTATATTATTTTAA
*
2413776 TAATATTA
1 TATTATTA
2413784 AAATAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 12 0.52
18 10 0.43
19 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTATTATATTATTTTAA
Found at i:2413791 original size:31 final size:31
Alignment explanation
Indices: 2413768--2413827 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2413758 ATATTATTAT
*
2413768 TTATTTAATAATATTAAAATAATATATTAAA
1 TTATTTAATAAAATTAAAATAATATATTAAA
* *
2413799 TTATTTGATAAAATTAAATTACATATATT
1 TTATTTAATAAAATTAAAATA-ATATATT
2413828 CAATAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (31 bp):
TTATTTAATAAAATTAAAATAATATATTAAA
Found at i:2418123 original size:127 final size:126
Alignment explanation
Indices: 2417897--2418130 Score: 346
Period size: 127 Copynumber: 1.8 Consensus size: 126
2417887 TAATATCTTG
*
2417897 TTTGAGAATATGTTGCTTGAAAATGTAGAAAAATCTATCAGTGGATCTTAATGATTCATGAACAT
1 TTTGAGAATATGTTGCTTGAAAATGTAGAAAAATCTATCAGTGGACCTTAATGATTCATGAACAT
* *
2417962 AAGAGCTCCATGTTAGCTTCTTTCTCAGTTAAATGTGTGACTTGTATACGATACAATCGTTT
66 AAGAGCTCCATGTTAGCTTCTTTCGCAATTAAATGTG-GACTTGTATACGATACAATCGTTT
* * * *
2418024 TTTGAGAGTATGTTGCTTGAAAATGTAGAAAAATCTGTCAGTGGACCTTAATGTTTCATGACCAT
1 TTTGAGAATATGTTGCTTGAAAATGTAGAAAAATCTATCAGTGGACCTTAATGATTCATGAACAT
* *
2418089 AAAGAGCTTCAT-TCTAGGTTCTTT-GCAATTAAATGTGGACTT
66 -AAGAGCTCCATGT-TAGCTTCTTTCGCAATTAAATGTGGACTT
2418131 CTAGATTTTC
Statistics
Matches: 96, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
126 5 0.05
127 72 0.75
128 19 0.20
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (126 bp):
TTTGAGAATATGTTGCTTGAAAATGTAGAAAAATCTATCAGTGGACCTTAATGATTCATGAACAT
AAGAGCTCCATGTTAGCTTCTTTCGCAATTAAATGTGGACTTGTATACGATACAATCGTTT
Found at i:2419576 original size:22 final size:21
Alignment explanation
Indices: 2419548--2419604 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 21
2419538 AGAGAAAGAA
2419548 AAAAAAAAAGAAAGGAAGAGGG
1 AAAAAAAAAGAAAGG-AGAGGG
* *
2419570 -AAAAAAAAGGAAGGAGAGTG
1 AAAAAAAAAGAAAGGAGAGGG
2419590 AAAGAGAAAAAGAAA
1 AAA-A-AAAAAGAAA
2419605 AATCTGTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 5 0.17
21 15 0.52
22 1 0.03
23 8 0.28
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (21 bp):
AAAAAAAAAGAAAGGAGAGGG
Found at i:2419587 original size:20 final size:21
Alignment explanation
Indices: 2419549--2419592 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2419539 GAGAAAGAAA
2419549 AAAAAAAAGAAAGGAAGAGGG
1 AAAAAAAAGAAAGGAAGAGGG
* *
2419570 AAAAAAAAGGAAGG-AGAGTG
1 AAAAAAAAGAAAGGAAGAGGG
2419590 AAA
1 AAA
2419593 GAGAAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (21 bp):
AAAAAAAAGAAAGGAAGAGGG
Found at i:2420877 original size:2 final size:2
Alignment explanation
Indices: 2420872--2420902 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2420862 TTTTTTTTTT
2420872 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2420903 CCTTCTTGAT
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2428718 original size:16 final size:16
Alignment explanation
Indices: 2428693--2428727 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2428683 TTAATTTTAT
*
2428693 ATTTTATATTAATCAA
1 ATTTTATATTAATAAA
*
2428709 ATTTTTTATTAATAAA
1 ATTTTATATTAATAAA
2428725 ATT
1 ATT
2428728 ATTAAAAATA
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:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTTATATTAATAAA
Found at i:2428852 original size:17 final size:17
Alignment explanation
Indices: 2428824--2428876 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
2428814 ATTTTTTAAT
2428824 AATTTT-ATTAATAAAA
1 AATTTTAATTAATAAAA
*
2428840 AATTTTAATTAATATAA
1 AATTTTAATTAATAAAA
* *
2428857 AATATTAA--AATTAAA
1 AATTTTAATTAATAAAA
2428872 AATTT
1 AATTT
2428877 AATAAAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 9 0.29
16 6 0.19
17 16 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTTTAATTAATAAAA
Found at i:2429257 original size:15 final size:16
Alignment explanation
Indices: 2429237--2429266 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2429227 CACTTTTTTT
2429237 TTTAAAA-TATTAAAA
1 TTTAAAATTATTAAAA
2429252 TTTAAAATTATTAAA
1 TTTAAAATTATTAAA
2429267 TAATATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTAAAATTATTAAAA
Found at i:2434149 original size:18 final size:18
Alignment explanation
Indices: 2434101--2434154 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
2434091 GATAAATTGG
*
2434101 ATTTAAA-ATTATTTTATT
1 ATTTAAATATT-TTTTAAT
*
2434119 ATTTAAATTTTTTTTAAT
1 ATTTAAATATTTTTTAAT
* *
2434137 ATTTATATATTTTATAAT
1 ATTTAAATATTTTTTAAT
2434155 TAAATATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 28 0.93
19 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTAAATATTTTTTAAT
Found at i:2435374 original size:11 final size:11
Alignment explanation
Indices: 2435358--2435400 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
2435348 AAAGTTTTAA
2435358 ATTTATTTATT
1 ATTTATTTATT
2435369 ATTTATTT-TT
1 ATTTATTTATT
2435379 AATCTTATTTTATT
1 -AT-TTA-TTTATT
2435393 ATTTATTT
1 ATTTATTT
2435401 TAAAATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 2 0.07
11 13 0.46
12 6 0.21
13 5 0.18
14 2 0.07
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTATTTATT
Found at i:2435378 original size:23 final size:24
Alignment explanation
Indices: 2435352--2435408 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
2435342 AAATTAAAAG
2435352 TTTTAAATTTA-TTTATTATTTAT
1 TTTTAAATTTATTTTATTATTTAT
2435375 TTTT-AATCTTATTTTATTATTTAT
1 TTTTAAAT-TTATTTTATTATTTAT
*
2435399 TTTAAAATTT
1 TTTTAAATTT
2435409 TTATTCAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 3 0.10
23 7 0.23
24 17 0.57
25 3 0.10
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTTAAATTTATTTTATTATTTAT
Found at i:2435398 original size:12 final size:12
Alignment explanation
Indices: 2435358--2435402 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
2435348 AAAGTTTTAA
2435358 ATTTA-TTTATT
1 ATTTATTTTATT
*
2435369 ATTTATTTT-TA
1 ATTTATTTTATT
2435380 ATCTTATTTTATT
1 AT-TTATTTTATT
2435393 ATTTATTTTA
1 ATTTATTTTA
2435403 AAATTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 8 0.28
12 18 0.62
13 3 0.10
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (12 bp):
ATTTATTTTATT
Found at i:2435408 original size:12 final size:12
Alignment explanation
Indices: 2435352--2435408 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
2435342 AAATTAAAAG
2435352 TTTTA-AATTTA
1 TTTTATAATTTA
*
2435363 -TTTATTATTTA
1 TTTTATAATTTA
2435374 TTTT-TAATCTTA
1 TTTTATAAT-TTA
*
2435386 TTTTATTATTTA
1 TTTTATAATTTA
*
2435398 TTTTAAAATTT
1 TTTTATAATTT
2435409 TTATTCAAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
10 4 0.11
11 8 0.22
12 22 0.59
13 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTATAATTTA
Found at i:2435962 original size:25 final size:26
Alignment explanation
Indices: 2435929--2435992 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
2435919 AAATAATTTT
* *
2435929 TAATTTAATATAAAAATTTA-AAATA
1 TAATATAATATAAAAAATTATAAATA
2435954 TAATATAATATAAAAAATTATAAATA
1 TAATATAATATAAAAAATTATAAATA
2435980 TAATATATATATA
1 TAATATA-ATATA
2435993 TATATATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 18 0.51
26 12 0.34
27 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
TAATATAATATAAAAAATTATAAATA
Found at i:2435987 original size:2 final size:2
Alignment explanation
Indices: 2435972--2436033 Score: 58
Period size: 2 Copynumber: 32.0 Consensus size: 2
2435962 TATAAAAAAT
* *
2435972 TA TA AA TA TA -A TA TA TA TA TA TA TA TA TA TA TCA -A AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
* *
2436013 TA AA TA TA -A TA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
2436034 AATTAAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
1 3 0.06
2 45 0.92
3 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (2 bp):
TA
Found at i:2436015 original size:39 final size:37
Alignment explanation
Indices: 2435935--2436044 Score: 124
Period size: 39 Copynumber: 3.1 Consensus size: 37
2435925 TTTTTAATTT
* *
2435935 AATATAAAAATTTAA-A-ATATA-ATATAATATAAAA
1 AATATATAAATATAATATATATATATATAATATAAAA
*
2435969 AAT-TATAAATATAATATATATATATATATATATATCAA
1 AATATATAAATATAATATATATATATATA-ATATA-AAA
*
2436007 AATATATAAATATAATATAAATATATA-AAT-TAAAA
1 AATATATAAATATAATATATATATATATAATATAAAA
2436042 AAT
1 AAT
2436045 CTTAAAATTT
Statistics
Matches: 65, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
33 9 0.14
34 4 0.06
35 10 0.15
36 7 0.11
37 7 0.11
38 6 0.09
39 22 0.34
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (37 bp):
AATATATAAATATAATATATATATATATAATATAAAA
Found at i:2436034 original size:8 final size:8
Alignment explanation
Indices: 2435935--2436036 Score: 59
Period size: 8 Copynumber: 12.4 Consensus size: 8
2435925 TTTTTAATTT
*
2435935 AATATAAA
1 AATATATA
*
2435943 AATTTA-A
1 AATATATA
2435950 AATATAATA
1 AATAT-ATA
2435959 TAATATA-A
1 -AATATATA
*
2435967 AAAATTATA
1 AATA-TATA
2435976 AATATA-A
1 AATATATA
*
2435983 TATATATA
1 AATATATA
*
2435991 TATATATA
1 AATATATA
*
2435999 TATATCA-A
1 AATAT-ATA
2436007 AATATATAA
1 AATATAT-A
2436016 ATATAATATA
1 A-AT-ATATA
2436026 AATATATA
1 AATATATA
2436034 AAT
1 AAT
2436037 TAAAAAATCT
Statistics
Matches: 77, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
7 15 0.19
8 38 0.49
9 11 0.14
10 9 0.12
11 4 0.05
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (8 bp):
AATATATA
Found at i:2436182 original size:2 final size:2
Alignment explanation
Indices: 2436175--2436205 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2436165 ATAATGACAT
2436175 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 T
2436206 TCTATTTTAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2436339 original size:17 final size:16
Alignment explanation
Indices: 2436317--2436365 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
2436307 GAATTAATTT
2436317 AAATTTAATTTAATAAA
1 AAATTTAATTTAA-AAA
*
2436334 AAATTTAAATTAAAAA
1 AAATTTAATTTAAAAA
*
2436350 TAATTTAAATTTAAAA
1 AAATTT-AATTTAAAA
2436366 TGATTTGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 8 0.29
17 20 0.71
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATTTAATTTAAAAA
Found at i:2436356 original size:16 final size:16
Alignment explanation
Indices: 2436318--2436371 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
2436308 AATTAATTTA
* *
2436318 AATTTAATTTAATAAAA
1 AATTTAAATTAA-AAAT
2436335 AATTTAAATTAAAAAT
1 AATTTAAATTAAAAAT
*
2436351 AATTTAAATTTAAAAT
1 AATTTAAATTAAAAAT
*
2436367 GATTT
1 AATTT
2436372 GAATCTTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
16 22 0.67
17 11 0.33
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
AATTTAAATTAAAAAT
Found at i:2437247 original size:16 final size:15
Alignment explanation
Indices: 2437203--2437258 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
2437193 ACCTAAATTT
*
2437203 AAAATATCTAAACTTAA
1 AAAATATTTAAA--TAA
*
2437220 AAAA-ATTAAAATAA
1 AAAATATTTAAATAA
*
2437234 AAAATGATTTAAATAT
1 AAAAT-ATTTAAATAA
2437250 AAAATATTT
1 AAAATATTT
2437259 CGAATTCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 7 0.21
15 4 0.12
16 18 0.55
17 4 0.12
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (15 bp):
AAAATATTTAAATAA
Found at i:2437720 original size:13 final size:13
Alignment explanation
Indices: 2437702--2437735 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2437692 ATGCATAAAT
2437702 CATTAAAATATAA
1 CATTAAAATATAA
*
2437715 CATTAATATATAA
1 CATTAAAATATAA
2437728 C-TTAAAAT
1 CATTAAAAT
2437736 CTATATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (13 bp):
CATTAAAATATAA
Found at i:2441805 original size:18 final size:18
Alignment explanation
Indices: 2441782--2441818 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2441772 TTTAACAATA
2441782 TCTAAAGAATA-ATTATTT
1 TCTAAA-AATATATTATTT
2441800 TCTAAAAATATATTATTT
1 TCTAAAAATATATTATTT
2441818 T
1 T
2441819 TTTACTCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (18 bp):
TCTAAAAATATATTATTT
Found at i:2442419 original size:38 final size:38
Alignment explanation
Indices: 2442364--2442437 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
2442354 TCTGTCAATA
*
2442364 ACATAAATTTCATAATTTTATTACTTCTTATTACATCT
1 ACATAAATTTCACAATTTTATTACTTCTTATTACATCT
2442402 ACATAAATTTCACAATTTTATTACTTCTTATTACAT
1 ACATAAATTTCACAATTTTATTACTTCTTATTACAT
2442438 ATAAACAGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (38 bp):
ACATAAATTTCACAATTTTATTACTTCTTATTACATCT
Found at i:2442707 original size:2 final size:2
Alignment explanation
Indices: 2442700--2442740 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2442690 GCATCGTCCC
*
2442700 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2442741 AAAGATACTG
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:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2443141 original size:22 final size:22
Alignment explanation
Indices: 2443082--2443130 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
2443072 ATAATTAATT
*
2443082 TAATTAGTAAAAATTT-AATTTA
1 TAATTAAT-AAAATTTAAATTTA
*
2443104 TAATTAATAAAATTTAAATTTT
1 TAATTAATAAAATTTAAATTTA
2443126 TAATT
1 TAATT
2443131 CATTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TAATTAATAAAATTTAAATTTA
Found at i:2443605 original size:21 final size:20
Alignment explanation
Indices: 2443575--2443630 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 20
2443565 ATTAGACTTT
2443575 ATAAGATATTTTTTTAAAAAA
1 ATAA-ATATTTTTTTAAAAAA
*
2443596 ATTATATATTTTTTTAAAAAA
1 A-TAAATATTTTTTTAAAAAA
2443617 ATAAATATTTTTTT
1 ATAAATATTTTTTT
2443631 TTTATATTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 12 0.38
21 18 0.56
22 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
ATAAATATTTTTTTAAAAAA
Found at i:2443824 original size:5 final size:5
Alignment explanation
Indices: 2443814--2443839 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2443804 ATGAATAACG
2443814 AAATT AAATT AAATT AAATT AAATT A
1 AAATT AAATT AAATT AAATT AAATT A
2443840 TATAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AAATT
Found at i:2444858 original size:19 final size:17
Alignment explanation
Indices: 2444834--2444878 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 17
2444824 AGTATAAATA
2444834 TAAATATAATAAAATTTAT
1 TAAATATAATAAAA-TT-T
*
2444853 TAAATATATTAAAATTT
1 TAAATATAATAAAATTT
2444870 TAAATATAA
1 TAAATATAA
2444879 ATATAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.38
18 2 0.08
19 13 0.54
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATATAATAAAATTT
Found at i:2445730 original size:28 final size:27
Alignment explanation
Indices: 2445678--2445741 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 27
2445668 TCTTATTTAT
*
2445678 ATTTTTC-TTCTAATTTCTTGCTCATG
1 ATTTTTCTTTCTAATTTCTTACTCATG
* *
2445704 CTTTTTCTTATCTAATTT-TTACGTCATT
1 ATTTTTCTT-TCTAATTTCTTAC-TCATG
2445732 ATTTTTCTTT
1 ATTTTTCTTT
2445742 TGATTTACGG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
26 6 0.19
27 5 0.16
28 20 0.65
ACGTcount: A:0.16, C:0.17, G:0.05, T:0.62
Consensus pattern (27 bp):
ATTTTTCTTTCTAATTTCTTACTCATG
Found at i:2446730 original size:2 final size:2
Alignment explanation
Indices: 2446723--2446757 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2446713 ACATTAATTT
2446723 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 T
2446758 CAAGTTAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.