Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold25
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: 9553305
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 6276 characters in sequence are not A, C, G, or T
File 18 of 56
Found at i:3326301 original size:11 final size:11
Alignment explanation
Indices: 3326287--3326408 Score: 51
Period size: 11 Copynumber: 11.2 Consensus size: 11
3326277 ATAAAAATTT
3326287 AATTAATTTTA
1 AATTAATTTTA
*
3326298 AATTTATATTT-
1 AATTAAT-TTTA
3326309 AATT-ATTTTCA
1 AATTAATTTT-A
3326320 AATTAAATTTT-
1 AATT-AATTTTA
*
3326331 AATTAA-ATTA
1 AATTAATTTTA
* * *
3326341 TATTATAATTCA
1 AATTA-ATTTTA
*
3326353 AA-TATATATTA
1 AATTA-ATTTTA
3326364 AA-T-ATTTTA
1 AATTAATTTTA
* *
3326373 AAATAATCTTGA
1 AATTAAT-TTTA
*
3326385 ATTTAATTTTA
1 AATTAATTTTA
*
3326396 TATTAATTTTA
1 AATTAATTTTA
3326407 AA
1 AA
3326409 ATAAATTTAT
Statistics
Matches: 83, Mismatches: 17, Indels: 22
0.68 0.14 0.18
Matches are distributed among these distances:
9 12 0.14
10 9 0.11
11 43 0.52
12 14 0.17
13 5 0.06
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (11 bp):
AATTAATTTTA
Found at i:3326308 original size:22 final size:22
Alignment explanation
Indices: 3326281--3326336 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
3326271 CAAATAATAA
3326281 AAATTTAATTAATTTT-AAATTT
1 AAATTTAATTAATTTTCAAA-TT
*
3326303 ATATTTAATT-ATTTTCAAATT
1 AAATTTAATTAATTTTCAAATT
3326324 AAATTTTAATTAA
1 AAA-TTTAATTAA
3326337 ATTATATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 9 0.31
22 19 0.66
23 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
AAATTTAATTAATTTTCAAATT
Found at i:3326325 original size:27 final size:26
Alignment explanation
Indices: 3326295--3326374 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 26
3326285 TTAATTAATT
3326295 TTAAATTTATATTTAATTATTTTCAAA
1 TTAAATTTATATTTAATTATTTT-AAA
* *
3326322 TTAAATTT-TAATTAAATTATATTATAA
1 TTAAATTTAT-ATTTAATTATTTTA-AA
* *
3326349 TTCAAATATATA-TTAAATATTTTAAA
1 TT-AAATTTATATTTAATTATTTTAAA
3326375 ATAATCTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
26 4 0.09
27 32 0.74
28 6 0.14
29 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (26 bp):
TTAAATTTATATTTAATTATTTTAAA
Found at i:3326358 original size:16 final size:17
Alignment explanation
Indices: 3326316--3326363 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
3326306 TTTAATTATT
* *
3326316 TTCAAATTAAATTTTAA
1 TTCAAATTATATTATAA
3326333 TT-AAATTATATTATAA
1 TTCAAATTATATTATAA
3326349 TTCAAATATATATTA
1 TTCAAAT-TATATTA
3326364 AATATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 14 0.52
17 6 0.22
18 7 0.26
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (17 bp):
TTCAAATTATATTATAA
Found at i:3326427 original size:28 final size:28
Alignment explanation
Indices: 3326402--3326453 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
3326392 TTTATATTAA
*
3326402 TTTT-AAAATAAATTTATTG-AATTATT
1 TTTTAAAAATAAATTAATTGTAATTATT
3326428 TTTTAAAAATAAATTAATTGTAATTA
1 TTTTAAAAATAAATTAATTGTAATTA
3326454 CCTAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 4 0.17
27 14 0.61
28 5 0.22
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (28 bp):
TTTTAAAAATAAATTAATTGTAATTATT
Found at i:3327005 original size:3 final size:3
Alignment explanation
Indices: 3326997--3327032 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3326987 CTCTTTTTGT
*
3326997 TTC TTC TTC TTC TTC TTC TTC TTC TTC CTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3327033 CCTTAAACCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:3327490 original size:25 final size:26
Alignment explanation
Indices: 3327462--3327513 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
3327452 AGAAACAATA
*
3327462 AATTATATATATTT-TTTATTTTTTT
1 AATTATATATATTTATTTATATTTTT
*
3327487 AATTATATATTTTTATTTATATTTTT
1 AATTATATATATTTATTTATATTTTT
3327513 A
1 A
3327514 TAAATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (26 bp):
AATTATATATATTTATTTATATTTTT
Found at i:3327507 original size:12 final size:12
Alignment explanation
Indices: 3327467--3327514 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
3327457 CAATAAATTA
*
3327467 TATATATTT-TT
1 TATATTTTTATT
*
3327478 TATTTTTTTAATT
1 TATATTTTT-ATT
3327491 ATATATTTTTATT
1 -TATATTTTTATT
3327504 TATATTTTTAT
1 TATATTTTTAT
3327515 AAATTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 7 0.23
12 11 0.35
13 5 0.16
14 8 0.26
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TATATTTTTATT
Found at i:3333947 original size:22 final size:22
Alignment explanation
Indices: 3333919--3333962 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3333909 AAAATATTAT
*
3333919 TTTTAT-ATTAATATTTATATAA
1 TTTTATAATTAA-ATTTAAATAA
3333941 TTTTATAATTAAATTTAAATAA
1 TTTTATAATTAAATTTAAATAA
3333963 AAATATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTATAATTAAATTTAAATAA
Found at i:3335564 original size:178 final size:182
Alignment explanation
Indices: 3334949--3335735 Score: 915
Period size: 184 Copynumber: 4.3 Consensus size: 182
3334939 ACAAGAGGTT
* * * * * * *
3334949 TGATTACTCATTCAGAATAGTGTGATAGTTTATCCACTTAACATTGCCTCATAAGCTTCTTCGAC
1 TGATGACTCATTCAGAATAGCGAGA-GGTTTATGCACTTAACATTGCCTCATAAACTTCTTTGAC
* * * * * *
3335014 TACCTATTGGAAATCATACGCGAGCTTATAGTTTCATATGTTCATATCAGCTTCATAATGCAATC
65 CACCTATTGGAAATCATACACAAACTTACAGTTTTATATGTTCATATCAGCTTCATAATGCAATC
* *
3335079 CACAAAAGAAGATTCCTCCCACACGCTCCCCTA--CTTAAAGGAATTGGGAGA
130 CACAAAAGAAGGTTCCTCCCACATGCTCCCCTACTCTTAAAGGAATTGGGAGA
* * * * * * * * *
3335130 TGTTGTCTCATTCAGAATTGTGAGATGGTTTATGCACTTAACATCGCCTCATGAACCTCCTTAAC
1 TGATGACTCATTCAGAATAGCGAGA-GGTTTATGCACTTAACATTGCCTCATAAACTTCTTTGAC
* * ** ** * * * **
3335195 TACCTATTGCAAGCCATATGCAAATTCCTTATAGTTTTATTTATTCATATCAGCTAAATAATGCA
65 CACCTATTGGAAATCATACACAAA---CTTACAGTTTTATATGTTCATATCAGCTTCATAATGCA
*
3335260 ATCCACAAAAGAAGCTTCCTCTCC-CATGCTCCCCTACTTCTTAAAGGAATTGGGAGA
127 ATCCACAAAAGAAGGTTCCTC-CCACATGCTCCCCTAC-TCTTAAAGGAATTGGGAGA
3335317 TGATGACTCATTCAGAATAGCGAGATGGTTTATGCACTTAACATTGCCTCATAAACTTCTTTGAC
1 TGATGACTCATTCAGAATAGCGAGA-GGTTTATGCACTTAACATTGCCTCATAAACTTCTTTGAC
* * *
3335382 CACCTATTGGAAATCATACACAAACTTACAGTTTTGTATGTTCATATCAGCTTCATAATGCAGTT
65 CACCTATTGGAAATCATACACAAACTTACAGTTTTATATGTTCATATCAGCTTCATAATGCAATC
* * *
3335447 CACAGATGGAGGTTCCTCCCACATGCT-CCC-A-TCTTAAAGGAATTGGGAGA
130 CACAAAAGAAGGTTCCTCCCACATGCTCCCCTACTCTTAAAGGAATTGGGAGA
**
3335497 TGATGACTCATTCAGAATAGCGA-AGGTTTATAAACTTAACATTGCCTCATAAACTTCTTTGACC
1 TGATGACTCATTCAGAATAGCGAGAGGTTTATGCACTTAACATTGCCTCATAAACTTCTTTGACC
* * * *
3335561 ACCTATTGGAAATCATACAAAAACTTACAGTTTTACATGTTCATATCAGCTTCATAATGCAGTTC
66 ACCTATTGGAAATCATACACAAACTTACAGTTTTATATGTTCATATCAGCTTCATAATGCAATCC
**
3335626 ACAGATTG-AGGTTCCTCCCACATGCTCCCCTACTTCTTAAAGGAATTGGGAGA
131 ACA-AAAGAAGGTTCCTCCCACATGCTCCCCTAC-TCTTAAAGGAATTGGGAGA
* * * * * *
3335679 CGATAACTCATACAGAATAGTGAGAAAGTTTATGCACTTAACATTGCCGCATAAACT
1 TGATGACTCATTCAGAATAGCGAG-AGGTTTATGCACTTAACATTGCCTCATAAACT
3335736 AAAAAAGGAG
Statistics
Matches: 522, Mismatches: 69, Indels: 27
0.84 0.11 0.04
Matches are distributed among these distances:
178 121 0.23
179 6 0.01
180 43 0.08
181 69 0.13
182 39 0.07
183 5 0.01
184 145 0.28
185 2 0.00
187 92 0.18
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (182 bp):
TGATGACTCATTCAGAATAGCGAGAGGTTTATGCACTTAACATTGCCTCATAAACTTCTTTGACC
ACCTATTGGAAATCATACACAAACTTACAGTTTTATATGTTCATATCAGCTTCATAATGCAATCC
ACAAAAGAAGGTTCCTCCCACATGCTCCCCTACTCTTAAAGGAATTGGGAGA
Found at i:3336004 original size:14 final size:14
Alignment explanation
Indices: 3335985--3336015 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3335975 CTTCAACTGA
3335985 AAAAAAAAAAGAAG
1 AAAAAAAAAAGAAG
*
3335999 AAAAAAAGAAGAAG
1 AAAAAAAAAAGAAG
3336013 AAA
1 AAA
3336016 CAATGAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGAAG
Found at i:3336740 original size:3 final size:3
Alignment explanation
Indices: 3336732--3336757 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3336722 CTGTTTCCTA
3336732 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
3336758 TTAATCTTTT
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:3337073 original size:16 final size:16
Alignment explanation
Indices: 3337041--3337074 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3337031 ATTTAATATG
**
3337041 ATTATATATTTTTAAA
1 ATTATATATTTAAAAA
3337057 ATTATATATTTAAAAA
1 ATTATATATTTAAAAA
3337073 AT
1 AT
3337075 ATAAAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTATATATTTAAAAA
Found at i:3337765 original size:14 final size:14
Alignment explanation
Indices: 3337732--3337764 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
3337722 TTCAAAATAG
3337732 ATTTTTTGAAAAAT
1 ATTTTTTGAAAAAT
3337746 ATTTTTTG--AAAT
1 ATTTTTTGAAAAAT
3337758 ATTTTTT
1 ATTTTTT
3337765 TCACAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
14 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (14 bp):
ATTTTTTGAAAAAT
Found at i:3337967 original size:10 final size:10
Alignment explanation
Indices: 3337936--3337987 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
3337926 ATTTTTAATT
3337936 TTTAATTAAA
1 TTTAATTAAA
**
3337946 TAAAATTGAAA
1 TTTAATT-AAA
3337957 TTTAATTAAA
1 TTTAATTAAA
**
3337967 TTTAAAAAAA
1 TTTAATTAAA
3337977 TTTATATTAAA
1 TTTA-ATTAAA
3337988 ATATCAAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
10 20 0.62
11 12 0.38
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (10 bp):
TTTAATTAAA
Found at i:3338013 original size:76 final size:72
Alignment explanation
Indices: 3337869--3338035 Score: 191
Period size: 74 Copynumber: 2.3 Consensus size: 72
3337859 AGATAGATAA
* * *
3337869 AATTAAA-AAAATAAATTTTAATTAAATTAAAAAATTCACATTGAAATTAATATATTAATTTTTA
1 AATTAAATAAAATAAATTTTAATTAAATTAAAAAATTCACATTAAAATTAAAATATTAATTATTA
3337933 A-TTTTT
66 ATTTTTT
* *
3337939 AATTAAATAAAATTGAAA-TTTAATTAAATTTAAAAAAATTTATATTAAAATATCAAAATATTAA
1 AATTAAATAAAA-T-AAATTTTAATTAAA-TT-AAAAAATTCACATTAAAAT-T-AAAATATTAA
3338003 TTATTAATTTTTT
60 TTATTAATTTTTT
*
3338016 AATAAAAT-AAA-AAATTTTAA
1 AATTAAATAAAATAAATTTTAA
3338036 AAATAAAGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
70 7 0.09
71 4 0.05
72 11 0.13
73 8 0.10
74 21 0.26
75 1 0.01
76 18 0.22
77 12 0.15
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (72 bp):
AATTAAATAAAATAAATTTTAATTAAATTAAAAAATTCACATTAAAATTAAAATATTAATTATTA
ATTTTTT
Found at i:3338023 original size:72 final size:71
Alignment explanation
Indices: 3337870--3338014 Score: 170
Period size: 76 Copynumber: 2.0 Consensus size: 71
3337860 GATAGATAAA
* * *
3337870 ATTAAA-AAAA-T-AAATTTTAATTAAATTAAAAAATTCACATTGAAATTAATATATTAATTTTT
1 ATTAAATAAAATTGAAA-TTTAATTAAATTAAAAAATTCACATTAAAATTAAAATATTAATTATT
3337932 AATTTTT
65 AATTTTT
* *
3337939 AATTAAATAAAATTGAAATTTAATTAAATTTAAAAAAATTTATATTAAAATATCAAAATATTAAT
1 -ATTAAATAAAATTGAAATTTAATTAAA-TT-AAAAAATTCACATTAAAAT-T-AAAATATTAAT
3338004 TATTAATTTTT
61 TATTAATTTTT
3338015 TAATAAAATA
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
70 6 0.10
71 4 0.06
72 11 0.17
73 5 0.08
74 16 0.25
75 1 0.02
76 20 0.32
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (71 bp):
ATTAAATAAAATTGAAATTTAATTAAATTAAAAAATTCACATTAAAATTAAAATATTAATTATTA
ATTTTT
Found at i:3338359 original size:40 final size:39
Alignment explanation
Indices: 3338315--3338440 Score: 112
Period size: 40 Copynumber: 3.4 Consensus size: 39
3338305 TAGAGTATGA
3338315 TTATACGAA-TTTAAATTTTAAAAGTATAATTTATTTTTAT
1 TTATA-GAAGTTTAAATTTT-AAAGTATAATTTATTTTTAT
* *
3338355 TTATAGAAGTTTAAA---T-ATGT-T--TTTA-TTTGA-
1 TTATAGAAGTTTAAATTTTAAAGTATAATTTATTTTTAT
*
3338385 TTATGCGAA-TTTAAATTTTGAAAGTATAATTTATTTTTAT
1 TTAT-AGAAGTTTAAATTTT-AAAGTATAATTTATTTTTAT
3338425 TTATAGAAGTTTAAAT
1 TTATAGAAGTTTAAAT
3338441 ATGTTTTTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 26
0.68 0.06 0.26
Matches are distributed among these distances:
30 10 0.15
31 7 0.10
32 4 0.06
33 1 0.01
34 1 0.01
35 6 0.09
36 1 0.01
37 1 0.01
38 4 0.06
39 10 0.15
40 22 0.33
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.52
Consensus pattern (39 bp):
TTATAGAAGTTTAAATTTTAAAGTATAATTTATTTTTAT
Found at i:3338394 original size:70 final size:69
Alignment explanation
Indices: 3338310--3338656 Score: 418
Period size: 70 Copynumber: 5.0 Consensus size: 69
3338300 ATTTGTAGAG
3338310 TATGATTATACGAATTTAAATTTTAAAAGTATAATTTATTTTTATTTATAGAAGTTTAAATATGT
1 TATGATTATACGAATTTAAATTTT-AAAGTATAATTTATTTTTATTTATAGAAGTTTAAATATGT
3338375 TTTTA
65 TTTTA
* *
3338380 TTTGATTATGCGAATTTAAATTTTGAAAGTATAATTTATTTTTATTTATAGAAGTTTAAATATGT
1 TATGATTATACGAATTTAAATTTT-AAAGTATAATTTATTTTTATTTATAGAAGTTTAAATATGT
3338445 TTTTA
65 TTTTA
* * * * * *
3338450 TTTGATTATGCGAATTTAAATTTTGAAGATATAATTTATTTTTAATTTGTAAAAGTTTAAATGTG
1 TATGATTATACGAATTTAAATTTTAAAG-TATAATTTATTTTT-ATTTATAGAAGTTTAAATATG
3338515 TTATTTAA
64 TT-TTT-A
* * *
3338523 GTATGATTATACGAGTTTAAATTTTTGAAGGTATAATTT-TTTTTATTTGTAGAAGTTT-AAT-T
1 -TATGATTATACGAATTTAAA-TTTT-AAAGTATAATTTATTTTTATTTATAGAAGTTTAAATAT
*
3338585 -TTTTTG
63 GTTTTTA
* * ** *
3338591 TATGATAATACGATTTTAAATTTTAGGGTATAA-TT-TTTTTATTTATAGAAGTTTAAATGTGTT
1 TATGATTATACGAATTTAAATTTTAAAGTATAATTTATTTTTATTTATAGAAGTTTAAATATGTT
3338654 TTT
66 TTT
3338657 TAAATTTTTG
Statistics
Matches: 249, Mismatches: 18, Indels: 23
0.86 0.06 0.08
Matches are distributed among these distances:
64 20 0.08
65 11 0.04
66 5 0.02
67 23 0.09
69 6 0.02
70 107 0.43
71 21 0.08
72 6 0.02
73 14 0.06
74 22 0.09
75 12 0.05
76 2 0.01
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.52
Consensus pattern (69 bp):
TATGATTATACGAATTTAAATTTTAAAGTATAATTTATTTTTATTTATAGAAGTTTAAATATGTT
TTTA
Found at i:3338400 original size:30 final size:30
Alignment explanation
Indices: 3338364--3338470 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
3338354 TTTATAGAAG
3338364 TTTAAATATGTTTTTATTTGATTATGCGAA
1 TTTAAATATGTTTTTATTTGATTATGCGAA
* * *
3338394 TTTAAATTTTGAAAGTATAATTTATTTTTATTTAT-AGAA
1 TTTAAA---T--ATGT-T--TTTA-TTTGA-TTATGCGAA
3338433 GTTTAAATATGTTTTTATTTGATTATGCGAA
1 -TTTAAATATGTTTTTATTTGATTATGCGAA
3338464 TTTAAAT
1 TTTAAAT
3338471 TTTGAAGATA
Statistics
Matches: 59, Mismatches: 6, Indels: 24
0.66 0.07 0.27
Matches are distributed among these distances:
30 17 0.29
31 7 0.12
32 4 0.07
33 1 0.02
34 1 0.02
35 6 0.10
36 1 0.02
37 1 0.02
38 4 0.07
39 7 0.12
40 10 0.17
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.53
Consensus pattern (30 bp):
TTTAAATATGTTTTTATTTGATTATGCGAA
Found at i:3338458 original size:140 final size:138
Alignment explanation
Indices: 3338310--3338656 Score: 443
Period size: 141 Copynumber: 2.5 Consensus size: 138
3338300 ATTTGTAGAG
*
3338310 TATGATTATACGAATTTAAATTTTAAAAGTATAATTTATTTTTATTTATAGAAGTTTAAATATGT
1 TATGATTATACGAATTTAAATTTT-AAAGTATAATTTATTTTTATTTATAGAAGTTTAAATGTGT
* *
3338375 TTTT-A-TTTGATTATGCGAATTTAAA-TTTTGAAAGTATAATTTATTTTTATTTATAGAAGTTT
65 TTTTAAGTATGATTATACGAATTTAAATTTTTGAAAGTATAATTT-TTTTTATTTATAGAAGTTT
3338437 AAATATGTTTTTA
129 -AAT-T-TTTTTA
* * * * *
3338450 TTTGATTATGCGAATTTAAATTTTGAAGATATAATTTATTTTTAATTTGTAAAAGTTTAAATGTG
1 TATGATTATACGAATTTAAATTTTAAAG-TATAATTTATTTTT-ATTTATAGAAGTTTAAATGTG
* * *
3338515 TTATTTAAGTATGATTATACGAGTTTAAATTTTTGAAGGTATAATTTTTTTTATTTGTAGAAGTT
64 TT-TTTAAGTATGATTATACGAATTTAAATTTTTGAAAGTATAATTTTTTTTATTTATAGAAGTT
*
3338580 TAATTTTTTTG
128 TAATTTTTTTA
* * **
3338591 TATGATAATACGATTTTAAATTTTAGGGTATAA-TT-TTTTTATTTATAGAAGTTTAAATGTGTT
1 TATGATTATACGAATTTAAATTTTAAAGTATAATTTATTTTTATTTATAGAAGTTTAAATGTGTT
3338654 TTT
66 TTT
3338657 TAAATTTTTG
Statistics
Matches: 180, Mismatches: 21, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
136 3 0.02
137 21 0.12
138 5 0.03
139 5 0.03
140 41 0.23
141 46 0.26
142 4 0.02
143 4 0.02
144 35 0.19
145 16 0.09
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.52
Consensus pattern (138 bp):
TATGATTATACGAATTTAAATTTTAAAGTATAATTTATTTTTATTTATAGAAGTTTAAATGTGTT
TTTAAGTATGATTATACGAATTTAAATTTTTGAAAGTATAATTTTTTTTATTTATAGAAGTTTAA
TTTTTTTA
Found at i:3338748 original size:72 final size:72
Alignment explanation
Indices: 3338655--3339427 Score: 782
Period size: 73 Copynumber: 10.7 Consensus size: 72
3338645 AAATGTGTTT
* * * *
3338655 TTTAAATTTTTGAT-AGTATAATTT-TTTTAATTTATAAAAGTTTAAATGTGTTTTTTGGTATGA
1 TTTAAATTTTT-ATGA-TATAATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTGGTATGA
*
3338718 TTATACAAG
64 TTATACGAG
*
3338727 TTAATAATTTTTATGATATAATTTATTTTTATTTGTAGAAA-TTTAAATTTATTTTTTGG-ATTG
1 TTTA-AATTTTTATGATATAATTTATTTTTATTTGTA-AAAGTTTAAATTTATTTTTTGGTA-TG
*
3338790 ATTATATGAG
63 ATTATACGAG
* * * *
3338800 TTTAAATTTTTAAGATATTATTTATCTTTATTTGTAGAAA-TTTAAA---ATTTTTTTGTATGAT
1 TTTAAATTTTTATGATATAATTTATTTTTATTTGTA-AAAGTTTAAATTTATTTTTTGGTATGAT
**
3338861 TATGTGAG
65 TATACGAG
* * *
3338869 TTTATATTTTTAAGATATAATTTATTTTTATTTGTATAAGTTTAAATTTATTTTTTAGGT-TGAT
1 TTTAAATTTTTATGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTT-GGTATGAT
3338933 TATACGAG
65 TATACGAG
* * * * *
3338941 TCTAAATTTTTAGGGTATTATTTATCTTTATTTGTAAAAGTTTAAATTTATTTTTTGTGTATGAT
1 TTTAAATTTTTATGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTG-GTATGAT
3339006 TATACGAG
65 TATACGAG
* * * * * * * *
3339014 TTTAAATTTTTA-AAGTATAATATATTTTGATTTTTAGATGTTTAAATGTGTTTTTTGGGTATGA
1 TTTAAATTTTTATGA-TATAATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTT-GGTATGA
*
3339078 TTATATGAG
64 TTATACGAG
* * ** * * *
3339087 TTTAAATTTTTTATGGTATAGTTTATTTTTATTTGTCGAAGTTTAAATATGTTTTTAGGTATGAT
1 TTTAAA-TTTTTATGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTGGTATGAT
3339152 TATACGAG
65 TATACGAG
* * * * * *
3339160 TTTATATTTTAATGGTATAATTTATTTTTATTTATAGAAGTTTAAGTTTATTTTTTGGGT-TGAT
1 TTTAAATTTTTATGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTT-GGTATGAT
*
3339224 TATACAAG
65 TATACGAG
* * * * * *
3339232 TTTAAATTTTTAGGGTATTATTTATCTATATTTGTAAAACTTTAAATTTATTTTTTGAGTATGAT
1 TTTAAATTTTTATGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTG-GTATGAT
3339297 TATACGAG
65 TATACGAG
* * *
3339305 TTTAAATTTTTA-GAGTATAATTTATTTTTATTCGTAAAAGTTTAAATGTGTTTTTTGAGTATGA
1 TTTAAATTTTTATGA-TATAATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTG-GTATGA
*
3339369 TTATATGAG
64 TTATACGAG
* *
3339378 TTTATATTTTTTAT-AGTATAATTTATTTTTATTTATAGAAA-TTTAAATTT
1 TTTA-AATTTTTATGA-TATAATTTATTTTTATTTGTA-AAAGTTTAAATTT
3339428 GATCTTGGTT
Statistics
Matches: 592, Mismatches: 85, Indels: 46
0.82 0.12 0.06
Matches are distributed among these distances:
68 2 0.00
69 58 0.10
70 1 0.00
71 2 0.00
72 223 0.38
73 224 0.38
74 79 0.13
75 3 0.01
ACGTcount: A:0.31, C:0.02, G:0.13, T:0.55
Consensus pattern (72 bp):
TTTAAATTTTTATGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTGGTATGATT
ATACGAG
Found at i:3339212 original size:291 final size:287
Alignment explanation
Indices: 3338684--3339425 Score: 1017
Period size: 291 Copynumber: 2.6 Consensus size: 287
3338674 AATTTTTTTA
* * * * * *
3338684 ATTTATAAAAGTTTAAATGTGTTTTTTGGTATGATTATACAAGTTAATAATTTTT-ATGATATAA
1 ATTTGTAAAAGTTTAAATTTATTTTTTGGTATGATTATACGAGTTTA-AATTTTTAAAG-TATAA
* * * *
3338748 TTTATTTTTATTTGTAGAAATTTAAATTTATTTTTTGGAT-TGATTATATGAGTTTAAA-TTTTT
64 TTTATTTTTATTTGTAGAAGTTTAAATGTGTTTTTTGGGTATGATTATATGAGTTTAAATTTTTT
* * * * **
3338811 AAGATATTATTTATCTTTATTTGTAGAAATTTAAA-ATTTTTTTGTATGATTATGTGAGTTTATA
129 ATGGTA-TATTTATTTTTATTTGTAGAAATTTAAATATTTTTTGGTATGATTATACGAGTTTATA
* * *
3338875 TTTTTAAGATATAATTTATTTTTATTTGTATAAGTTTAAATTTATTTTTTAGGTTGATTATACGA
193 TTTTTAAGATATAATTTATTTTTATTTATAGAAGTTTAAATTTATTTTTTAGGTTGATTATACAA
*
3338940 GTCTAAATTTTTAGGGTATTATTTATCTTT
258 GTCTAAATTTTTAGGGTATTATTTATCTAT
3338970 ATTTGTAAAAGTTTAAATTTATTTTTTGTGTATGATTATACGAGTTTAAATTTTTAAAGTATAAT
1 ATTTGTAAAAGTTTAAATTTATTTTTTG-GTATGATTATACGAGTTTAAATTTTTAAAGTATAAT
* * * *
3339035 ATATTTTGATTTTTAGATGTTTAAATGTGTTTTTTGGGTATGATTATATGAGTTTAAATTTTTTA
65 TTATTTTTATTTGTAGAAGTTTAAATGTGTTTTTTGGGTATGATTATATGAGTTTAAATTTTTTA
* *
3339100 TGGTATAGTTTATTTTTATTTGTCGAAGTTTAAATATGTTTTTAGGTATGATTATACGAGTTTAT
130 TGGTATA-TTTATTTTTATTTGTAGAAATTTAAATAT-TTTTT-GGTATGATTATACGAGTTTAT
* * *
3339165 A-TTTTAATGGTATAATTTATTTTTATTTATAGAAGTTTAAGTTTATTTTTTGGGTTGATTATAC
192 ATTTTTAA-GATATAATTTATTTTTATTTATAGAAGTTTAAATTTATTTTTTAGGTTGATTATAC
*
3339229 AAGTTTAAATTTTTAGGGTATTATTTATCTAT
256 AAGTCTAAATTTTTAGGGTATTATTTATCTAT
* *
3339261 ATTTGTAAAACTTTAAATTTATTTTTTGAGTATGATTATACGAGTTTAAATTTTTAGAGTATAAT
1 ATTTGTAAAAGTTTAAATTTATTTTTTG-GTATGATTATACGAGTTTAAATTTTTAAAGTATAAT
* * * *
3339326 TTATTTTTATTCGTAAAAGTTTAAATGTGTTTTTTGAGTATGATTATATGAGTTTATATTTTTTA
65 TTATTTTTATTTGTAGAAGTTTAAATGTGTTTTTTGGGTATGATTATATGAGTTTAAATTTTTTA
* *
3339391 TAGTATAATTTATTTTTATTTATAGAAATTTAAAT
130 TGGTAT-ATTTATTTTTATTTGTAGAAATTTAAAT
3339426 TTGATCTTGG
Statistics
Matches: 401, Mismatches: 45, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
286 69 0.17
287 39 0.10
288 32 0.08
289 2 0.00
290 11 0.03
291 247 0.62
292 1 0.00
ACGTcount: A:0.31, C:0.02, G:0.13, T:0.54
Consensus pattern (287 bp):
ATTTGTAAAAGTTTAAATTTATTTTTTGGTATGATTATACGAGTTTAAATTTTTAAAGTATAATT
TATTTTTATTTGTAGAAGTTTAAATGTGTTTTTTGGGTATGATTATATGAGTTTAAATTTTTTAT
GGTATATTTATTTTTATTTGTAGAAATTTAAATATTTTTTGGTATGATTATACGAGTTTATATTT
TTAAGATATAATTTATTTTTATTTATAGAAGTTTAAATTTATTTTTTAGGTTGATTATACAAGTC
TAAATTTTTAGGGTATTATTTATCTAT
Found at i:3339420 original size:20 final size:21
Alignment explanation
Indices: 3339378--3339427 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
3339368 ATTATATGAG
3339378 TTTATATTTTTTATAGTATAA
1 TTTATATTTTTTATAGTATAA
*
3339399 TTTATTTTTATTTATAG-A-AA
1 TTTATATTT-TTTATAGTATAA
*
3339419 TTTAAATTT
1 TTTATATTT
3339428 GATCTTGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 9 0.36
21 9 0.36
22 7 0.28
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTATATTTTTTATAGTATAA
Found at i:3340979 original size:40 final size:40
Alignment explanation
Indices: 3340932--3341075 Score: 263
Period size: 40 Copynumber: 3.6 Consensus size: 40
3340922 ATTTAAACTT
3340932 TTACAAATAAAAATAAATAATACCTTTAATCAAATTAAAC
1 TTACAAATAAAAATAAATAATACCTTTAATCAAATTAAAC
3340972 TTACAAATAAAAATAAATAATACCTTTAATCAAATTAAAC
1 TTACAAATAAAAATAAATAATACCTTTAATCAAATTAAAC
3341012 TTACAAATAAAAATAAATAATACCTTTAATCAAATTAAAC
1 TTACAAATAAAAATAAATAATACCTTTAATCAAATTAAAC
* *
3341052 TTACAAA-AAAAATTAATCATACCT
1 TTACAAATAAAAATAAATAATACCT
3341076 AAAAATAAAA
Statistics
Matches: 102, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
39 15 0.15
40 87 0.85
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (40 bp):
TTACAAATAAAAATAAATAATACCTTTAATCAAATTAAAC
Found at i:3341495 original size:23 final size:21
Alignment explanation
Indices: 3341450--3341499 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
3341440 TTTTCAATAT
3341450 AATTTTTTTAAATTTAATTAA
1 AATTTTTTTAAATTTAATTAA
* *
3341471 AATTTATTTTTAATTTTATTAA
1 AATTT-TTTTAAATTTAATTAA
*
3341493 AAATTTT
1 AATTTTT
3341500 AATTCATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AATTTTTTTAAATTTAATTAA
Found at i:3342037 original size:3 final size:3
Alignment explanation
Indices: 3342029--3342058 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3342019 ATGAAGATAC
3342029 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3342059 ATTCTGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3346657 original size:14 final size:15
Alignment explanation
Indices: 3346631--3346660 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3346621 ATTATTAATA
3346631 TTAAAAAATATTATT
1 TTAAAAAATATTATT
3346646 TTAAAAAA-ATTATT
1 TTAAAAAATATTATT
3346660 T
1 T
3346661 AATTACTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAAAAAATATTATT
Found at i:3347068 original size:2 final size:2
Alignment explanation
Indices: 3347061--3347111 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
3347051 AGGTATAAAC
3347061 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3347103 TA TA TA TA T
1 TA TA TA TA T
3347112 TGCTGGGTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3347697 original size:23 final size:23
Alignment explanation
Indices: 3347671--3347714 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3347661 AATTAAAAGA
3347671 TAAAATATTTAAATATATATTTT
1 TAAAATATTTAAATATATATTTT
* * *
3347694 TAAAATTTTTTAATTTATATT
1 TAAAATATTTAAATATATATT
3347715 AATATTTAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TAAAATATTTAAATATATATTTT
Found at i:3349952 original size:2 final size:2
Alignment explanation
Indices: 3349945--3349974 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3349935 AAATATGATA
3349945 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
3349975 CGTTGGTACA
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:3350195 original size:18 final size:18
Alignment explanation
Indices: 3350155--3350199 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3350145 ATTTATCAAT
*
3350155 TTATATATTTATATTATAT
1 TTATAT-TTTATATTATAA
* *
3350174 TTATATTTTTTATTTTAA
1 TTATATTTTATATTATAA
3350192 TTATATTT
1 TTATATTT
3350200 AAAATATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATATTTTATATTATAA
Found at i:3350214 original size:27 final size:26
Alignment explanation
Indices: 3350155--3350228 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 26
3350145 ATTTATCAAT
3350155 TTATATA-TTTATATTATATTT--ATA
1 TTATATATTTTA-ATTATATTTAAATA
* *
3350179 TTTTTTATTTTAATTATATTTAAAATA
1 TTATATATTTTAATTATATTT-AAATA
* *
3350206 TTATATATTTTAAATAAATTTAA
1 TTATATATTTTAATTATATTTAA
3350229 TAAGTTAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
24 14 0.35
25 4 0.10
26 2 0.05
27 20 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
TTATATATTTTAATTATATTTAAATA
Found at i:3350844 original size:14 final size:14
Alignment explanation
Indices: 3350825--3350854 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3350815 TGGTATCTAA
3350825 ATCTTAATAGATAT
1 ATCTTAATAGATAT
3350839 ATCTTAATAGATAT
1 ATCTTAATAGATAT
3350853 AT
1 AT
3350855 ATATATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
ATCTTAATAGATAT
Found at i:3351184 original size:3 final size:3
Alignment explanation
Indices: 3351178--3351222 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
3351168 ATTATTAAAT
3351178 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3351223 AAAGAAAGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3351375 original size:12 final size:11
Alignment explanation
Indices: 3351351--3351386 Score: 56
Period size: 12 Copynumber: 3.3 Consensus size: 11
3351341 TAAATTTAAT
3351351 TATAAAAAT-A
1 TATAAAAATAA
3351361 TATAAAAATTAA
1 TATAAAAA-TAA
3351373 TATAAAAATAA
1 TATAAAAATAA
3351384 TAT
1 TAT
3351387 TTTGATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 8 0.33
11 7 0.29
12 9 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TATAAAAATAA
Found at i:3353248 original size:16 final size:16
Alignment explanation
Indices: 3353185--3353261 Score: 56
Period size: 17 Copynumber: 4.9 Consensus size: 16
3353175 TTATTTTGTT
3353185 ATTAAAATATCAATAAA
1 ATTAAAAT-TCAATAAA
*
3353202 ATTAAAA-AC-ATAATA
1 ATTAAAATTCAATAA-A
*
3353217 TATATAAAATTTAATAAA
1 -AT-TAAAATTCAATAAA
*
3353235 ATTAAAATGCAAT--A
1 ATTAAAATTCAATAAA
3353249 ATT-AAATTCAATA
1 ATTAAAATTCAATA
3353262 TTTACTAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 15
0.70 0.09 0.22
Matches are distributed among these distances:
13 8 0.17
14 8 0.17
15 2 0.04
16 11 0.23
17 14 0.29
18 1 0.02
19 4 0.08
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.32
Consensus pattern (16 bp):
ATTAAAATTCAATAAA
Found at i:3353554 original size:5 final size:5
Alignment explanation
Indices: 3353544--3353588 Score: 72
Period size: 5 Copynumber: 9.0 Consensus size: 5
3353534 ATGACACCTA
* *
3353544 AACCC AACCC AAACC AACCC AACCC AACCC AACGC AACCC AACCC
1 AACCC AACCC AACCC AACCC AACCC AACCC AACCC AACCC AACCC
3353589 TTTTTCTCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.42, C:0.56, G:0.02, T:0.00
Consensus pattern (5 bp):
AACCC
Found at i:3353901 original size:21 final size:22
Alignment explanation
Indices: 3353861--3353901 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3353851 TAAGCAAAAT
*
3353861 AAATTAAATAATTAATTTTAAA
1 AAATTAAAAAATTAATTTTAAA
3353883 AAATTAAAAAATT-ATTTTA
1 AAATTAAAAAATTAATTTTA
3353902 GTATGGATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AAATTAAAAAATTAATTTTAAA
Found at i:3354012 original size:42 final size:44
Alignment explanation
Indices: 3353933--3354032 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 44
3353923 ACCAAAAGTG
* * * *
3353933 TATTTTTTTAATTTTATTAAAAAATTATTATATA-TTTT-A-TT
1 TATTTTTTAAATTATATTAAAAAATTATCATAAATTTTTAATTT
3353974 TATTTTTTAAATATATATT-AAAAATATATCATAAATTTTTAATTT
1 TATTTTTTAAAT-TATATTAAAAAAT-TATCATAAATTTTTAATTT
*
3354019 TATTTATTAAATTA
1 TATTTTTTAAATTA
3354033 AAAAAATTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
41 17 0.35
42 12 0.24
43 4 0.08
44 3 0.06
45 13 0.27
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (44 bp):
TATTTTTTAAATTATATTAAAAAATTATCATAAATTTTTAATTT
Found at i:3357530 original size:10 final size:11
Alignment explanation
Indices: 3357494--3357535 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
3357484 TCTCACAGAA
*
3357494 ATATTATATAT
1 ATATTACATAT
*
3357505 ATATATATATAT
1 ATAT-TACATAT
3357517 ATATTACATA-
1 ATATTACATAT
3357527 ATATTACAT
1 ATATTACAT
3357536 TCAAATGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 9 0.31
11 9 0.31
12 11 0.38
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (11 bp):
ATATTACATAT
Found at i:3362024 original size:2 final size:2
Alignment explanation
Indices: 3362017--3362043 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3362007 TCAGATGACA
3362017 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
3362044 ATTGTAGTTT
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:3363068 original size:2 final size:2
Alignment explanation
Indices: 3363061--3363097 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3363051 ACAAGCTGTG
3363061 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3363098 AAAGAAGCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3363366 original size:22 final size:22
Alignment explanation
Indices: 3363332--3363375 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3363322 TTTATTTCAT
*
3363332 TATTATAATTAATTATAATAAA
1 TATTATAATTAATAATAATAAA
*
3363354 TATTAGTAA-TAATAATGATAAA
1 TATTA-TAATTAATAATAATAAA
3363376 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (22 bp):
TATTATAATTAATAATAATAAA
Found at i:3364507 original size:2 final size:2
Alignment explanation
Indices: 3364500--3364530 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3364490 CAACCCCACG
3364500 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
3364531 AGATTTCATC
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:3366776 original size:14 final size:14
Alignment explanation
Indices: 3366757--3366790 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
3366747 AAAATGTGGA
3366757 AAAAAAAAAAGAAAAG
1 AAAAAAAAAAG--AAG
3366773 AAAAAAAAAAGAAG
1 AAAAAAAAAAGAAG
3366787 AAAA
1 AAAA
3366791 GGCTAAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
16 11 0.61
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGAAG
Found at i:3377291 original size:27 final size:28
Alignment explanation
Indices: 3377225--3377291 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
3377215 CTGAATATTA
* *
3377225 TTTTTATTATTTAATAAATAAAATTATT
1 TTTTTAATATTTAATAAATAAAATAATT
* *
3377253 TTATTTGA-ATTTAAT-TATAAAATAATT
1 TT-TTTAATATTTAATAAATAAAATAATT
3377280 TTTTTAATATTT
1 TTTTTAATATTT
3377292 TTATTTTCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
26 4 0.12
27 16 0.50
28 9 0.28
29 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (28 bp):
TTTTTAATATTTAATAAATAAAATAATT
Found at i:3377401 original size:10 final size:10
Alignment explanation
Indices: 3377386--3377420 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
3377376 GATCTACCCA
*
3377386 ATAAATAAAT
1 ATAAATATAT
3377396 ATAAATATAT
1 ATAAATATAT
*
3377406 ATATATATAT
1 ATAAATATAT
3377416 ATAAA
1 ATAAA
3377421 ACAGTTTGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATAAATATAT
Found at i:3377720 original size:23 final size:26
Alignment explanation
Indices: 3377676--3377727 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
3377666 TTTAATTTGC
3377676 TAAAGAGTTGTTGAAGGAATAA-AAT
1 TAAAGAGTTGTTGAAGGAATAATAAT
*
3377701 TAAAGA-TTTTTGAA-GAATAATAAT
1 TAAAGAGTTGTTGAAGGAATAATAAT
3377725 TAA
1 TAA
3377728 CTAAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 6 0.24
24 13 0.52
25 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (26 bp):
TAAAGAGTTGTTGAAGGAATAATAAT
Found at i:3381990 original size:12 final size:12
Alignment explanation
Indices: 3381975--3381999 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3381965 CAGTAACAAA
3381975 ATGAATAAATTT
1 ATGAATAAATTT
3381987 ATGAATAAATTT
1 ATGAATAAATTT
3381999 A
1 A
3382000 CTGCAGTGAT
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:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGAATAAATTT
Found at i:3383902 original size:21 final size:21
Alignment explanation
Indices: 3383878--3383943 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 21
3383868 ATCCACAAAG
*
3383878 ATATGTCCACTCAAATTACTT
1 ATATCTCCACTCAAATTACTT
* *
3383899 ATATCTCC-CAC-AA--A--G
1 ATATCTCCACTCAAATTACTT
*
3383914 ATATGTCCACTCAAATTACTT
1 ATATCTCCACTCAAATTACTT
3383935 ATATCTCCA
1 ATATCTCCA
3383944 GAAAGACACA
Statistics
Matches: 32, Mismatches: 7, Indels: 12
0.63 0.14 0.24
Matches are distributed among these distances:
15 7 0.22
16 2 0.06
17 3 0.09
19 3 0.09
20 2 0.06
21 15 0.47
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (21 bp):
ATATCTCCACTCAAATTACTT
Found at i:3383910 original size:36 final size:36
Alignment explanation
Indices: 3383870--3383942 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
3383860 ATGTTCATAT
3383870 CCACAAAGATATGTCCACTCAAATTACTTATATCTC
1 CCACAAAGATATGTCCACTCAAATTACTTATATCTC
3383906 CCACAAAGATATGTCCACTCAAATTACTTATATCTC
1 CCACAAAGATATGTCCACTCAAATTACTTATATCTC
3383942 C
1 C
3383943 AGAAAGACAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.29, G:0.05, T:0.30
Consensus pattern (36 bp):
CCACAAAGATATGTCCACTCAAATTACTTATATCTC
Found at i:3386562 original size:7 final size:7
Alignment explanation
Indices: 3386550--3386578 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3386540 ACTATTTTTT
3386550 AAAATTA
1 AAAATTA
3386557 AAAATTA
1 AAAATTA
3386564 AAAATT-
1 AAAATTA
3386570 AAAATTA
1 AAAATTA
3386577 AA
1 AA
3386579 TATTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAAATTA
Found at i:3386566 original size:13 final size:14
Alignment explanation
Indices: 3386550--3386578 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3386540 ACTATTTTTT
3386550 AAAATTAAAAATTA
1 AAAATTAAAAATTA
3386564 AAAATT-AAAATTA
1 AAAATTAAAAATTA
3386577 AA
1 AA
3386579 TATTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATTAAAAATTA
Found at i:3387690 original size:15 final size:15
Alignment explanation
Indices: 3387656--3387687 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3387646 AATAATAAAA
3387656 ATTT-AAAAATTTAT
1 ATTTAAAAAATTTAT
3387670 ATTTAAAAAATTT-T
1 ATTTAAAAAATTTAT
3387684 ATTT
1 ATTT
3387688 TAATTAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTAAAAAATTTAT
Found at i:3389022 original size:19 final size:20
Alignment explanation
Indices: 3388967--3389022 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
3388957 GATAAATTTT
**
3388967 TTAATTTATATACTTATATTA
1 TTAATTTATATA-AAATATTA
*
3388988 TTTATTTATACTTAAAATATTA
1 TTAATTTATA--TAAAATATTA
3389010 -TAATTTATATAAA
1 TTAATTTATATAAA
3389023 TTTTGATACA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
19 4 0.14
21 17 0.59
22 6 0.21
23 2 0.07
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTTATATAAAATATTA
Found at i:3389045 original size:34 final size:32
Alignment explanation
Indices: 3388968--3389058 Score: 87
Period size: 34 Copynumber: 2.7 Consensus size: 32
3388958 ATAAATTTTT
* * *
3388968 TAATTTATATACTTATATTATTTATTTATACTTAA
1 TAATTTATA-A-TTATATAAATT-TTGATACTTAA
3389003 -AATATTATAATTTATATAAATTTTGATACATTAA
1 TAAT-TTATAA-TTATATAAATTTTGATAC-TTAA
3389037 TAATTTAT-ATTATATAAATTTT
1 TAATTTATAATTATATAAATTTT
3389059 AATATAATCA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
32 13 0.27
33 7 0.14
34 21 0.43
35 8 0.16
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (32 bp):
TAATTTATAATTATATAAATTTTGATACTTAA
Found at i:3389105 original size:28 final size:27
Alignment explanation
Indices: 3389069--3389135 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
3389059 AATATAATCA
3389069 TATATTTATATCATAATTATT-TTATTTTT
1 TATA-TTATATCAT-ATT-TTATTATTTTT
*
3389098 TATATTATAACATATTTTAATTATTTTT
1 TATATTATATCATATTTT-ATTATTTTT
3389126 TATATTATAT
1 TATATTATAT
3389136 TCATTCCATC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 2 0.06
27 3 0.09
28 25 0.74
29 4 0.12
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (27 bp):
TATATTATATCATATTTTATTATTTTT
Found at i:3395039 original size:19 final size:19
Alignment explanation
Indices: 3395015--3395051 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3395005 TAATAATTCT
3395015 TATA-TTTTTATTATATTAA
1 TATATTTTTTA-TATATTAA
3395034 TATATTTTTTATATATTA
1 TATATTTTTTATATATTA
3395052 TAATCGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATATTTTTTATATATTAA
Found at i:3395126 original size:12 final size:13
Alignment explanation
Indices: 3395114--3395163 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
3395104 AATTTAAATA
3395114 TATTTTTATATAT
1 TATTTTTATATAT
* *
3395127 T-TTATTATTTTAT
1 TATTTTTA-TATAT
3395140 TATTTTT-TATAT
1 TATTTTTATATAT
*
3395152 TATATTTATATA
1 TATTTTTATATA
3395164 ATGTAATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
12 15 0.52
13 10 0.34
14 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TATTTTTATATAT
Found at i:3395135 original size:8 final size:8
Alignment explanation
Indices: 3395117--3395158 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
3395107 TTAAATATAT
3395117 TTTTATATA
1 TTTTAT-TA
3395126 TTTTATTA
1 TTTTATTA
3395134 TTTTATTA
1 TTTTATTA
3395142 TTTT-TTA
1 TTTTATTA
*
3395149 TATTA-TA
1 TTTTATTA
3395156 TTT
1 TTT
3395159 ATATAATGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 10 0.33
8 14 0.47
9 6 0.20
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTATTA
Found at i:3395137 original size:17 final size:16
Alignment explanation
Indices: 3395117--3395156 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
3395107 TTAAATATAT
3395117 TTTTATATATTTTATTA
1 TTTTATATATTTT-TTA
3395134 TTTTAT-TATTTTTTA
1 TTTTATATATTTTTTA
*
3395149 TATTATAT
1 TTTTATAT
3395157 TTATATAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
17 6 0.29
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTATATATTTTTTA
Found at i:3395457 original size:27 final size:30
Alignment explanation
Indices: 3395394--3395463 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 30
3395384 TGTATCACGG
*
3395394 ATTAATTTAGTATGTTATTAAAATTATCAA
1 ATTAATTTAATATGTTATTAAAATTATCAA
*
3395424 A--ATTTTAATA-GTTATT-AAATTAT-AA
1 ATTAATTTAATATGTTATTAAAATTATCAA
3395449 ATTAATTTAATATGT
1 ATTAATTTAATATGT
3395464 CATAATGATA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
25 3 0.09
26 7 0.21
27 14 0.41
28 9 0.26
30 1 0.03
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (30 bp):
ATTAATTTAATATGTTATTAAAATTATCAA
Found at i:3396086 original size:21 final size:20
Alignment explanation
Indices: 3396030--3396086 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 20
3396020 TTAAAAAATT
*
3396030 AATATATAATTTATTTTTTAA
1 AATATATATTTTA-TTTTTAA
3396051 AAT-TAATAGTTTTATTTTTAA
1 AATAT-ATA-TTTTATTTTTAA
3396072 AATATATATTATTAT
1 AATATATATT-TTAT
3396087 CTTATTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
20 3 0.10
21 23 0.74
22 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
AATATATATTTTATTTTTAA
Found at i:3396640 original size:23 final size:24
Alignment explanation
Indices: 3396614--3396660 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3396604 AAGTTTTGTA
*
3396614 TAAAAT-TATTAAT-AATATTAAAT
1 TAAAATATA-TAATAAATAATAAAT
3396637 TAAAATATATAATAAATAATAAAT
1 TAAAATATATAATAAATAATAAAT
3396661 AATTAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
TAAAATATATAATAAATAATAAAT
Found at i:3396659 original size:24 final size:23
Alignment explanation
Indices: 3396614--3396660 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3396604 AAGTTTTGTA
*
3396614 TAAAATTATTAATAATATTAAAT
1 TAAAATTATTAATAATAATAAAT
3396637 TAAAA-TATATAATAAATAATAAAT
1 TAAAATTAT-TAAT-AATAATAAAT
3396661 AATTAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 3 0.14
23 9 0.43
24 9 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAAATTATTAATAATAATAAAT
Found at i:3396991 original size:15 final size:14
Alignment explanation
Indices: 3396965--3397007 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
3396955 TTATCATATT
3396965 TTAAAATTATTATA
1 TTAAAATTATTATA
3396979 TTAAAATTTATTA-A
1 TTAAAA-TTATTATA
*
3396993 AT-AAATTATTATA
1 TTAAAATTATTATA
3397006 TT
1 TT
3397008 TAATATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 6 0.24
13 5 0.20
14 8 0.32
15 6 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAAAATTATTATA
Found at i:3397036 original size:25 final size:24
Alignment explanation
Indices: 3397008--3397058 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 24
3396998 TTATTATATT
3397008 TAATATAA-AATATTATTATAAATAA
1 TAATATAATAATATT-TTA-AAATAA
*
3397033 TAATTTAATTAATATTTTAAAATAA
1 TAATATAA-TAATATTTTAAAATAA
3397058 T
1 T
3397059 CGTGGCCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 14 0.61
26 3 0.13
27 6 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TAATATAATAATATTTTAAAATAA
Found at i:3397432 original size:24 final size:26
Alignment explanation
Indices: 3397400--3397454 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
3397390 TAATATATAT
* *
3397400 AAATATATATTTT-AT-TTTAATTAA
1 AAATTTATATTTTAATATTTAAATAA
3397424 AAATTTATATTTTAATATTTAAATAA
1 AAATTTATATTTTAATATTTAAATAA
3397450 AAATT
1 AAATT
3397455 ATACATCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 12 0.44
25 2 0.07
26 13 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
AAATTTATATTTTAATATTTAAATAA
Found at i:3397457 original size:25 final size:23
Alignment explanation
Indices: 3397400--3397457 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 23
3397390 TAATATATAT
*
3397400 AAATATATATTTTATTTTAATTAA
1 AAAT-TATATTTTATTTTAAATAA
3397424 AAATTTATATTTTAATATTTAAATAA
1 AAA-TTATATTTT-AT-TTTAAATAA
3397450 AAATTATA
1 AAATTATA
3397458 CATCAATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 11 0.37
25 8 0.27
26 11 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATTATATTTTATTTTAAATAA
Found at i:3397476 original size:26 final size:27
Alignment explanation
Indices: 3397418--3397476 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 27
3397408 ATTTTATTTT
** * *
3397418 AATTAAAAATTTATATTTTAATATTTA
1 AATTAAAAATTTATACATCAATAATTA
3397445 AA-TAAAAA-TTATACATCAATAATTA
1 AATTAAAAATTTATACATCAATAATTA
3397470 AATTAAA
1 AATTAAA
3397477 TAAAAATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 15 0.56
26 10 0.37
27 2 0.07
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (27 bp):
AATTAAAAATTTATACATCAATAATTA
Found at i:3397476 original size:30 final size:32
Alignment explanation
Indices: 3397442--3397500 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 32
3397432 ATTTTAATAT
*
3397442 TTAAATAAAAATTA-TA-CATCAATAATTAAA
1 TTAAATAAAAATTATTATCATAAATAATTAAA
3397472 TTAAATAAAAATTATTATCATAAATAATT
1 TTAAATAAAAATTATTATCATAAATAATT
3397501 TTTAAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 14 0.54
31 2 0.08
32 10 0.38
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (32 bp):
TTAAATAAAAATTATTATCATAAATAATTAAA
Found at i:3397506 original size:30 final size:28
Alignment explanation
Indices: 3397436--3397507 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 28
3397426 ATTTATATTT
* *
3397436 TAATATTTAAATAAAAATTATACATCAA
1 TAATTTTTAAATAAAAATTATACATAAA
*
3397464 TAATTAAATTAAATAAAAATTATTATCATAAA
1 TAATT--TTTAAATAAAAATTA-TA-CATAAA
3397496 TAATTTTTAAAT
1 TAATTTTTAAAT
3397508 TTTATAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 4 0.11
30 20 0.56
31 2 0.06
32 10 0.28
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (28 bp):
TAATTTTTAAATAAAAATTATACATAAA
Found at i:3398230 original size:20 final size:20
Alignment explanation
Indices: 3398194--3398232 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3398184 TTAGGGTTTT
*
3398194 TTTTTTTTAATTTTTTTAGG
1 TTTTTTTTAATTATTTTAGG
3398214 TTTTTTTT-ATCTATTTTAG
1 TTTTTTTTAAT-TATTTTAG
3398233 TTTATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.15, C:0.03, G:0.08, T:0.74
Consensus pattern (20 bp):
TTTTTTTTAATTATTTTAGG
Found at i:3398236 original size:25 final size:25
Alignment explanation
Indices: 3398183--3398230 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
3398173 TATCTCTCGC
* *
3398183 TTTAGGGTTTTTTTTTTTTAATTTT
1 TTTAGGGTTTTTTTTATCTAATTTT
3398208 TTTA-GGTTTTTTTTATCT-ATTTT
1 TTTAGGGTTTTTTTTATCTAATTTT
3398231 AGTTTATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.12, C:0.02, G:0.10, T:0.75
Consensus pattern (25 bp):
TTTAGGGTTTTTTTTATCTAATTTT
Found at i:3399419 original size:21 final size:21
Alignment explanation
Indices: 3399393--3399434 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3399383 TTTAAAATTT
*
3399393 TTAATA-AATTTATTTTTAATA
1 TTAATATAATTTA-ATTTAATA
3399414 TTAATATAATTTAATTTAATA
1 TTAATATAATTTAATTTAATA
3399435 AAAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAATATAATTTAATTTAATA
Found at i:3399636 original size:22 final size:21
Alignment explanation
Indices: 3399613--3399655 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 21
3399603 AATAATTTTT
3399613 AAATATAATATTTAATAAATTTAA
1 AAAT-TAAT-TTTAA-AAATTTAA
3399637 AAATTAATTTTAAAAATTT
1 AAATTAATTTTAAAAATTT
3399656 GTTTATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 5 0.26
23 4 0.21
24 4 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATTAATTTTAAAAATTTAA
Found at i:3400658 original size:16 final size:16
Alignment explanation
Indices: 3400639--3400686 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
3400629 CGAAAATAAC
3400639 TCGAACCTAAAATGAT
1 TCGAACCTAAAATGAT
* *
3400655 TCGAACTTAAAATAAT
1 TCGAACCTAAAATGAT
3400671 TCGAA-CTAAAACTGAT
1 TCGAACCTAAAA-TGAT
3400687 CCAAACTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 5 0.19
16 22 0.81
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (16 bp):
TCGAACCTAAAATGAT
Found at i:3400675 original size:32 final size:32
Alignment explanation
Indices: 3400620--3400697 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
3400610 AAATTGACTT
*
3400620 ATCCAAACTCGAAAATAACTCGAACCTAAAA-TG
1 ATCCAAACT-TAAAATAACTCGAA-CTAAAACTG
* * *
3400653 ATTCGAACTTAAAATAATTCGAACTAAAACTG
1 ATCCAAACTTAAAATAACTCGAACTAAAACTG
3400685 ATCCAAACTTAAA
1 ATCCAAACTTAAA
3400698 TTAAGTATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
31 6 0.16
32 25 0.66
33 7 0.18
ACGTcount: A:0.49, C:0.21, G:0.08, T:0.23
Consensus pattern (32 bp):
ATCCAAACTTAAAATAACTCGAACTAAAACTG
Found at i:3401586 original size:15 final size:15
Alignment explanation
Indices: 3401547--3401584 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
3401537 AAAATTTTAA
* *
3401547 AACTCGAAATAATCT
1 AACTCAAAATAACCT
3401562 AACTCAAAATAACCT
1 AACTCAAAATAACCT
3401577 AAC-CAAAA
1 AACTCAAAA
3401585 ATCAACTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.55, C:0.24, G:0.03, T:0.18
Consensus pattern (15 bp):
AACTCAAAATAACCT
Found at i:3401651 original size:7 final size:7
Alignment explanation
Indices: 3401641--3401715 Score: 64
Period size: 7 Copynumber: 10.7 Consensus size: 7
3401631 TCTAAATAAA
3401641 AAATTTT
1 AAATTTT
3401648 AAATTTAT
1 AAATTT-T
*
3401656 AAATTTG
1 AAATTTT
**
3401663 ATAATCAT
1 A-AATTTT
*
3401671 AAATTTC
1 AAATTTT
*
3401678 AAATTTA
1 AAATTTT
3401685 AAATTTT
1 AAATTTT
*
3401692 AAAATTT
1 AAATTTT
3401699 AAA-TTT
1 AAATTTT
3401705 AAA-TTT
1 AAATTTT
3401711 AAATT
1 AAATT
3401716 AAAATTTTTA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
6 12 0.22
7 32 0.58
8 11 0.20
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (7 bp):
AAATTTT
Found at i:3401661 original size:15 final size:15
Alignment explanation
Indices: 3401641--3401711 Score: 69
Period size: 15 Copynumber: 4.9 Consensus size: 15
3401631 TCTAAATAAA
3401641 AAATTTTAAATTTAT
1 AAATTTTAAATTTAT
* *
3401656 AAATTTGATAA-TCAT
1 AAATTTTA-AATTTAT
*
3401671 AAATTTCAAATTTA-
1 AAATTTTAAATTTAT
*
3401685 AAATTTTAAAATT-T
1 AAATTTTAAATTTAT
3401699 AAA-TTTAAATTTA
1 AAATTTTAAATTTA
3401712 AATTAAAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
13 8 0.18
14 16 0.36
15 19 0.42
16 2 0.04
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (15 bp):
AAATTTTAAATTTAT
Found at i:3401704 original size:6 final size:6
Alignment explanation
Indices: 3401670--3401722 Score: 61
Period size: 6 Copynumber: 8.2 Consensus size: 6
3401660 TTGATAATCA
*
3401670 TAAATT TCAAATT TAAAATTT TAAAATT TAAATT TAAATT TAAATT AAAATT
1 TAAATT T-AAATT T-AAA-TT T-AAATT TAAATT TAAATT TAAATT TAAATT
3401722 T
1 T
3401723 TTAAACACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
6 23 0.55
7 12 0.29
8 7 0.17
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (6 bp):
TAAATT
Found at i:3403077 original size:18 final size:19
Alignment explanation
Indices: 3403038--3403080 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
3403028 ATAAAGAACC
*
3403038 TTTAAACTTTATAATTTTA
1 TTTAAACTTTATAATTTCA
3403057 TTTAATACTTT-T-ATTTCA
1 TTTAA-ACTTTATAATTTCA
3403075 TTTAAA
1 TTTAAA
3403081 TAATTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 10 0.45
19 6 0.27
20 5 0.23
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTAAACTTTATAATTTCA
Found at i:3403112 original size:30 final size:29
Alignment explanation
Indices: 3403065--3403184 Score: 127
Period size: 30 Copynumber: 4.1 Consensus size: 29
3403055 TATTTAATAC
*
3403065 TTTTA-TTTCATTTAAATAATTTTTTAAA
1 TTTTATTTTCATTTAAATAAATTTTTAAA
* * *
3403093 TTTTATTTTACATTGAAATAAACTTTTAAT
1 TTTTATTTT-CATTTAAATAAATTTTTAAA
* * *
3403123 TTTTAGTTTTTATCTAAATAAATTTTTAAT
1 TTTTA-TTTTCATTTAAATAAATTTTTAAA
3403153 TTTTAATTTAT-ATTTAAATAAATTTTTAAA
1 TTTT-ATTT-TCATTTAAATAAATTTTTAAA
3403183 TT
1 TT
3403185 AAATCATTAG
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
28 5 0.06
29 3 0.04
30 63 0.82
31 6 0.08
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (29 bp):
TTTTATTTTCATTTAAATAAATTTTTAAA
Found at i:3404083 original size:17 final size:18
Alignment explanation
Indices: 3404058--3404104 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
3404048 ATTAAAGTAT
*
3404058 AATAAAAAATATGAGA-G
1 AATATAAAATATGAGATG
*
3404075 AATATAAAA-ATGATATG
1 AATATAAAATATGAGATG
3404092 AATATACAAATAT
1 AATATA-AAATAT
3404105 TTTAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 5 0.20
17 15 0.60
18 3 0.12
19 2 0.08
ACGTcount: A:0.62, C:0.02, G:0.11, T:0.26
Consensus pattern (18 bp):
AATATAAAATATGAGATG
Found at i:3404715 original size:20 final size:20
Alignment explanation
Indices: 3404677--3404715 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3404667 CAGATGACAT
*
3404677 TATTTTCTTAAACTTAAATC
1 TATTTTCTTAAAATTAAATC
3404697 TATTTT-TTAAAATTCAAAT
1 TATTTTCTTAAAATT-AAAT
3404716 TTCCATGGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTTTCTTAAAATTAAATC
Found at i:3411360 original size:15 final size:15
Alignment explanation
Indices: 3411331--3411374 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
3411321 CTATAAAGGT
3411331 TTATAAA-TA-TTAA
1 TTATAAATTATTTAA
3411344 TTATAAATTATTTAA
1 TTATAAATTATTTAA
3411359 TTATTAAATT-TTTAA
1 TTA-TAAATTATTTAA
3411374 T
1 T
3411375 ACATAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.25
14 2 0.07
15 13 0.46
16 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATAAATTATTTAA
Found at i:3411403 original size:23 final size:23
Alignment explanation
Indices: 3411359--3411404 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3411349 AATTATTTAA
**
3411359 TTATTAAATTTTTAATACATAAT
1 TTATTAAATTTAAAATACATAAT
3411382 TTATTAAATTTAAAAATA-ATAAT
1 TTATTAAATTT-AAAATACATAAT
3411405 ACATTAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TTATTAAATTTAAAATACATAAT
Found at i:3411505 original size:36 final size:37
Alignment explanation
Indices: 3411465--3411552 Score: 115
Period size: 38 Copynumber: 2.3 Consensus size: 37
3411455 ACATTAACTA
3411465 ATAATTCTTAATAATATTTAATTTTTATCTT-TTATT
1 ATAATTCTTAATAATATTTAATTTTTATCTTGTTATT
* *
3411501 ATAATTTTTAATATAATATTTAATTTTTATTTTGTTATT
1 ATAATTCTT-A-ATAATATTTAATTTTTATCTTGTTATT
*
3411540 TTAATTTCTTAAT
1 ATAA-TTCTTAAT
3411553 GTATTTTGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
36 8 0.18
37 1 0.02
38 22 0.50
39 9 0.20
40 4 0.09
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (37 bp):
ATAATTCTTAATAATATTTAATTTTTATCTTGTTATT
Found at i:3411507 original size:19 final size:18
Alignment explanation
Indices: 3411479--3411546 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 18
3411469 TTCTTAATAA
*
3411479 TATTTAATTTTTATCTTT
1 TATTTAATTTTTATATTT
**
3411497 TATTATAATTTTTAATATAA
1 TATT-TAATTTTT-ATATTT
*
3411517 TATTTAATTTTTATTTTGT
1 TATTTAATTTTTATATT-T
3411536 TATTTTAATTT
1 TA-TTTAATTT
3411547 CTTAATGTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
18 7 0.17
19 18 0.45
20 15 0.38
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (18 bp):
TATTTAATTTTTATATTT
Found at i:3411524 original size:38 final size:40
Alignment explanation
Indices: 3411475--3411552 Score: 124
Period size: 38 Copynumber: 2.0 Consensus size: 40
3411465 ATAATTCTTA
3411475 ATAATATTTAATTTTTATCTT-TTATTATAATTT-TTAAT
1 ATAATATTTAATTTTTATCTTGTTATTATAATTTCTTAAT
* *
3411513 ATAATATTTAATTTTTATTTTGTTATTTTAATTTCTTAAT
1 ATAATATTTAATTTTTATCTTGTTATTATAATTTCTTAAT
3411553 GTATTTTGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 20 0.56
39 11 0.31
40 5 0.14
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (40 bp):
ATAATATTTAATTTTTATCTTGTTATTATAATTTCTTAAT
Found at i:3411668 original size:21 final size:21
Alignment explanation
Indices: 3411644--3411684 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3411634 ATTTTATTAA
3411644 TTATA-ATTTAAATTTAAATTT
1 TTATATATTTAAA-TTAAATTT
*
3411665 TTATATTTTTAAATTAAATT
1 TTATATATTTAAATTAAATT
3411685 AATATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATATATTTAAATTAAATTT
Found at i:3411681 original size:27 final size:29
Alignment explanation
Indices: 3411644--3411715 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 29
3411634 ATTTTATTAA
3411644 TTATAAT-TTAAATTTAA-ATT-TTTATAT
1 TTATAATATTAAATTTAATATTATTTA-AT
*
3411671 TTTTAA-ATTAAA-TTAATATTATTTAAT
1 TTATAATATTAAATTTAATATTATTTAAT
3411698 TTATAATATT-AATTTAAT
1 TTATAATATTAAATTTAAT
3411716 TAATCACGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
26 4 0.11
27 22 0.58
28 12 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TTATAATATTAAATTTAATATTATTTAAT
Found at i:3411693 original size:22 final size:22
Alignment explanation
Indices: 3411650--3411694 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3411640 TTAATTATAA
**
3411650 TTTAAATTTAAATTTTTATATT
1 TTTAAATTTAAATTAATATATT
3411672 TTTAAA-TTAAATTAATATTATT
1 TTTAAATTTAAATTAATA-TATT
3411694 T
1 T
3411695 AATTTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTAAATTTAAATTAATATATT
Found at i:3412656 original size:14 final size:15
Alignment explanation
Indices: 3412629--3412658 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3412619 ATCTTCACAT
3412629 TTTAAAATATATTTA
1 TTTAAAATATATTTA
3412644 TTTAAAA-ATATTTA
1 TTTAAAATATATTTA
3412658 T
1 T
3412659 AAATTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAAAATATATTTA
Found at i:3412844 original size:14 final size:14
Alignment explanation
Indices: 3412796--3412852 Score: 53
Period size: 15 Copynumber: 4.0 Consensus size: 14
3412786 CTTGGATATA
*
3412796 TTAATATTATATTTT
1 TTAAT-TTAAATTTT
* *
3412811 TAAATTTAATATTTA
1 TTAATTTAA-ATTTT
*
3412826 ATAATTTAAATTTT
1 TTAATTTAAATTTT
3412840 TTAA-TTAAATTTT
1 TTAATTTAAATTTT
3412853 AAAATATAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
13 9 0.26
14 10 0.29
15 15 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTAATTTAAATTTT
Found at i:3413297 original size:24 final size:24
Alignment explanation
Indices: 3413269--3413322 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
3413259 ATTTTTACAT
*
3413269 AATTTA-TAATTAAATATTAATAAA
1 AATTTATTAA-TAAATAATAATAAA
**
3413293 AATTTATTAATAAATAATAATTTA
1 AATTTATTAATAAATAATAATAAA
3413317 AATTTA
1 AATTTA
3413323 ATTTAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
AATTTATTAATAAATAATAATAAA
Found at i:3413883 original size:2 final size:2
Alignment explanation
Indices: 3413876--3413921 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3413866 TCGGTAAATA
3413876 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3413918 AT AT
1 AT AT
3413922 TGGAAGCGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3417623 original size:2 final size:2
Alignment explanation
Indices: 3417612--3417646 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3417602 GGGAAAAATC
3417612 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3417647 GATGTTGTAT
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):
TA
Found at i:3417867 original size:18 final size:16
Alignment explanation
Indices: 3417834--3417879 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
3417824 TTTGATATGT
3417834 TTAA-AAATTATATAAAA
1 TTAATAAATT-TAT-AAA
3417851 TTATATAAATTTATAAA
1 TTA-ATAAATTTATAAA
3417868 TTAAT-AATTTAT
1 TTAATAAATTTAT
3417880 TTTATGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 7 0.26
16 2 0.07
17 9 0.33
18 4 0.15
19 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAATAAATTTATAAA
Found at i:3422273 original size:17 final size:16
Alignment explanation
Indices: 3422236--3422266 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3422226 TAAGTTTAAA
3422236 TATAATTTTTTATATT
1 TATAATTTTTTATATT
3422252 TATAATTTTTT-TATT
1 TATAATTTTTTATATT
3422267 ATTATAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATAATTTTTTATATT
Found at i:3422404 original size:2 final size:2
Alignment explanation
Indices: 3422397--3422434 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3422387 TTACATGTGA
3422397 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3422435 GTACTTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3425703 original size:3 final size:3
Alignment explanation
Indices: 3425697--3425736 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3425687 ATATAATTAT
3425697 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
3425737 ACATACAGCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3426146 original size:26 final size:26
Alignment explanation
Indices: 3426117--3426179 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
3426107 GGTAGCGTTA
3426117 TTCGATAGGGAAAAGAATAGGGAATG
1 TTCGATAGGGAAAAGAATAGGGAATG
3426143 TTCGATAGGGAAAAGAATAGGGAATG
1 TTCGATAGGGAAAAGAATAGGGAATG
*
3426169 TTCAATAGGGA
1 TTCGATAGGGA
3426180 GCACGGGAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.41, C:0.05, G:0.33, T:0.21
Consensus pattern (26 bp):
TTCGATAGGGAAAAGAATAGGGAATG
Found at i:3430357 original size:2 final size:2
Alignment explanation
Indices: 3430350--3430400 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
3430340 ACCTTAATTT
3430350 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3430392 TA TA TA TA T
1 TA TA TA TA T
3430401 GGAAGATTGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3431179 original size:23 final size:23
Alignment explanation
Indices: 3431146--3431224 Score: 72
Period size: 23 Copynumber: 3.3 Consensus size: 23
3431136 AAAATTTTTT
3431146 TAAAATCTAATTTATTTTTATTTA
1 TAAAAT-TAATTTATTTTTATTTA
*
3431170 TAAAATTAATTTA-ATTTATTTTA
1 TAAAATTAATTTATTTTTA-TTTA
* *
3431193 CAAAATTTATTT-TATTTTATTATA
1 TAAAATTAATTTAT-TTTTATT-TA
3431217 TATAAATT
1 TA-AAATT
3431225 TAAAATATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
22 4 0.09
23 23 0.51
24 13 0.29
25 5 0.11
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (23 bp):
TAAAATTAATTTATTTTTATTTA
Found at i:3431210 original size:19 final size:20
Alignment explanation
Indices: 3431143--3431211 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 20
3431133 TTTAAAATTT
3431143 TTTTAAAATCTAATTTATTTTTA
1 TTTTAAAA--TAATTTA-TTTTA
*
3431166 TTTATAAAATTAATTTAATTTA
1 TTT-TAAAA-TAATTTATTTTA
*
3431188 TTTTACAA-AATTTATTTTA
1 TTTTAAAATAATTTATTTTA
3431207 TTTTA
1 TTTTA
3431212 TTATATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 15 0.37
21 4 0.10
22 7 0.17
23 10 0.24
24 5 0.12
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTAAAATAATTTATTTTA
Found at i:3431251 original size:22 final size:21
Alignment explanation
Indices: 3431226--3431270 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3431216 ATATAAATTT
*
3431226 AAAATATT-AATTATAAAAATAA
1 AAAAT-TTAAATTA-AAAAAGAA
3431248 AAAATTTAAATTAAAAAAGAA
1 AAAATTTAAATTAAAAAAGAA
3431269 AA
1 AA
3431271 GGTCATGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAATTTAAATTAAAAAAGAA
Found at i:3435086 original size:16 final size:15
Alignment explanation
Indices: 3435067--3435109 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
3435057 AAAAAAGAAA
3435067 AATTAAATAAAATTTT
1 AATTAAA-AAAATTTT
* *
3435083 AATTTAAAAATTTTT
1 AATTAAAAAAATTTT
*
3435098 ATTTAAAAAAAT
1 AATTAAAAAAAT
3435110 AAAATTACTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAAAAAATTTT
Found at i:3435107 original size:15 final size:14
Alignment explanation
Indices: 3435075--3435106 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3435065 AAAATTAAAT
3435075 AAAATTTTAATTTA
1 AAAATTTTAATTTA
*
3435089 AAAATTTTTATTTA
1 AAAATTTTAATTTA
3435103 AAAA
1 AAAA
3435107 AATAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAAATTTTAATTTA
Found at i:3435283 original size:6 final size:7
Alignment explanation
Indices: 3435267--3435293 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3435257 AAATAATCAC
3435267 TTTTTAT
1 TTTTTAT
3435274 TTTTTAT
1 TTTTTAT
3435281 TTTTTAT
1 TTTTTAT
3435288 TTTTTA
1 TTTTTA
3435294 AAAATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTAT
Found at i:3435524 original size:14 final size:15
Alignment explanation
Indices: 3435492--3435522 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3435482 ATGATTTTTT
3435492 AATAAATTTTAAAAA
1 AATAAATTTTAAAAA
*
3435507 AATACATTTTAAAAA
1 AATAAATTTTAAAAA
3435522 A
1 A
3435523 TATTTTCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAAATTTTAAAAA
Found at i:3438138 original size:15 final size:16
Alignment explanation
Indices: 3438109--3438140 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3438099 GTGCATTTTT
3438109 AAATATTTATATAAAA
1 AAATATTTATATAAAA
3438125 AAATATTT-TATAAAA
1 AAATATTTATATAAAA
3438140 A
1 A
3438141 TTAAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATATTTATATAAAA
Found at i:3438153 original size:2 final size:2
Alignment explanation
Indices: 3438146--3438170 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3438136 AAAAATTAAA
3438146 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
3438171 ACTCAACTAA
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:3438315 original size:20 final size:20
Alignment explanation
Indices: 3438276--3438316 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3438266 CAACGGAAAC
* * *
3438276 AAAAAAGAAAAATCATTAAA
1 AAAAAAAAAAAAACACTAAA
3438296 AAAAAAAAAAAAACACTAAA
1 AAAAAAAAAAAAACACTAAA
3438316 A
1 A
3438317 CTTGCCTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.80, C:0.07, G:0.02, T:0.10
Consensus pattern (20 bp):
AAAAAAAAAAAAACACTAAA
Found at i:3439527 original size:16 final size:16
Alignment explanation
Indices: 3439506--3439536 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3439496 TTTCTTTGAT
3439506 TTTGATTGCTATGGCC
1 TTTGATTGCTATGGCC
*
3439522 TTTGATTTCTATGGC
1 TTTGATTGCTATGGC
3439537 TTTAATTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.16, G:0.23, T:0.48
Consensus pattern (16 bp):
TTTGATTGCTATGGCC
Found at i:3440329 original size:97 final size:97
Alignment explanation
Indices: 3440163--3440355 Score: 341
Period size: 97 Copynumber: 2.0 Consensus size: 97
3440153 TTCTAGATGT
* * *
3440163 ACATGCATTCTGAAATTTATCAATGGCTAGATTGTTGTAACTCAGCAAGTTAGACATAATGCATA
1 ACATGCATTCTGAAACTTATCAATGGCTAGATTGTTGTAACTCAACAAGTTAGACATAATACATA
*
3440228 GTTTCCCAAGCATTCATGTCTCTGTTTTTGGG
66 GTTTCCCAAGCATTCATGGCTCTGTTTTTGGG
3440260 ACATGCATTCTGAAACTTATCAATGGCTAGATTGTTGTAACTCAACAAGTTAGACATAATACATA
1 ACATGCATTCTGAAACTTATCAATGGCTAGATTGTTGTAACTCAACAAGTTAGACATAATACATA
*
3440325 GTTTCCCAAGCCTTCATGGCTCTGTTTTTGG
66 GTTTCCCAAGCATTCATGGCTCTGTTTTTGG
3440356 AATGTATGCC
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
97 91 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (97 bp):
ACATGCATTCTGAAACTTATCAATGGCTAGATTGTTGTAACTCAACAAGTTAGACATAATACATA
GTTTCCCAAGCATTCATGGCTCTGTTTTTGGG
Found at i:3442602 original size:29 final size:31
Alignment explanation
Indices: 3442569--3442632 Score: 96
Period size: 29 Copynumber: 2.1 Consensus size: 31
3442559 TATATTAAGA
3442569 AATATTTTAATTTTTATATTATT-AAAT-TT
1 AATATTTTAATTTTTATATTATTAAAATATT
* *
3442598 AATATTTTAGTTTTTATATTTTTAAAATATT
1 AATATTTTAATTTTTATATTATTAAAATATT
3442629 AATA
1 AATA
3442633 AATAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 21 0.68
30 4 0.13
31 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (31 bp):
AATATTTTAATTTTTATATTATTAAAATATT
Found at i:3442616 original size:14 final size:14
Alignment explanation
Indices: 3442570--3442619 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
3442560 ATATTAAGAA
3442570 ATATTTTAATTTTT
1 ATATTTTAATTTTT
* *
3442584 ATATTATTAAATTTA
1 ATATT-TTAATTTTT
*
3442599 ATATTTTAGTTTTT
1 ATATTTTAATTTTT
3442613 ATATTTT
1 ATATTTT
3442620 TAAAATATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
ATATTTTAATTTTT
Done.