Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 14 of 150
Found at i:3879227 original size:19 final size:20
Alignment explanation
Indices: 3879205--3879256 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
3879195 AAAATAGTAC
*
3879205 AAAAATTATA-AAAAATTGT
1 AAAAATTATATAAAAATCGT
*
3879224 -AAAATTTTATAAAAATCGT
1 AAAAATTATATAAAAATCGT
*
3879243 AAAAA-AATATAAAA
1 AAAAATTATATAAAA
3879257 TATATAGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 8 0.30
19 15 0.56
20 4 0.15
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (20 bp):
AAAAATTATATAAAAATCGT
Found at i:3879276 original size:67 final size:67
Alignment explanation
Indices: 3879148--3879296 Score: 167
Period size: 70 Copynumber: 2.2 Consensus size: 67
3879138 AAAAATAAAT
* * *
3879148 AAAAATTATTAAATTTTAATAAAAATGTAAAAAATATAAATTTTATTAAAATAGTACAAAAATTA
1 AAAAATTATAAAATTTTAATAAAAATGTAAAAAATATAAAATATATTAAAATAGTACAAAAATTA
3879213 TA
66 TA
* * *
3879215 AAAAATTGTAAAATTTT-ATAAAAATCGTAAAAAAATATAAAATATA-TAGAAATGTAGAAAAAA
1 AAAAATTATAAAATTTTAATAAAAAT-GT-AAAAAATATAAAATATATTA-AAA--TAGTACAAA
3879278 AATTATA
61 AATTATA
**
3879285 AAATTTTATAAA
1 AAAAATTATAAA
3879297 GTCATAAGAA
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
66 8 0.12
67 19 0.28
68 18 0.26
70 23 0.34
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (67 bp):
AAAAATTATAAAATTTTAATAAAAATGTAAAAAATATAAAATATATTAAAATAGTACAAAAATTA
TA
Found at i:3879850 original size:88 final size:86
Alignment explanation
Indices: 3879700--3879975 Score: 254
Period size: 88 Copynumber: 3.1 Consensus size: 86
3879690 CACCCATAGC
3879700 CTTTTTGATGCATTTTGGCAA-TTCAAGTATCCAATT-AAGTGCAAAAAAAAAG-GGGGACTTAA
1 CTTTTTGATGCATTTTGG-AAGTTCAAGTA-CCAATTGAA-TGCAAAAAAAAAGAGGGG-CTTAA
3879762 TTGCTTTTTTTGAAAAGTTTGAGGG
62 TTGCTTTTTTTGAAAAGTTTGAGGG
* *
3879787 CATTTTTGATGCATTTTGGTAGTTCAAGCACCTAATTGAATG-AAAAAAAAAGCAGGGGCTTAAT
1 C-TTTTTGATGCATTTTGGAAGTTCAAGTACC-AATTGAATGCAAAAAAAAAG-AGGGGCTTAAT
****** *
3879851 TGCTTCTTTTTTTTTTTTTTGAAAAAGGT
63 TGCTT-TTTTTGAAAAGTTTG----AGGG
* * * *
3879880 CTTTTTTATGCATATTGAAAGTTCAAGTACCCAATTGAATGCAACAAAAAAAATAGGGGCTTAAT
1 CTTTTTGATGCATTTTGGAAGTTCAAGTA-CCAATTGAATGC-A-AAAAAAAAGAGGGGCTTAAT
*
3879945 TGCTTTTTTTGAAAAAGTTTGAAGG
63 TGCTTTTTTTG-AAAAGTTTGAGGG
3879970 CTTTTT
1 CTTTTT
3879976 ACACCCTCAA
Statistics
Matches: 150, Mismatches: 23, Indels: 29
0.74 0.11 0.14
Matches are distributed among these distances:
87 14 0.09
88 41 0.27
89 15 0.10
90 8 0.05
92 32 0.21
93 11 0.07
94 21 0.14
95 8 0.05
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (86 bp):
CTTTTTGATGCATTTTGGAAGTTCAAGTACCAATTGAATGCAAAAAAAAAGAGGGGCTTAATTGC
TTTTTTTGAAAAGTTTGAGGG
Found at i:3881638 original size:2 final size:2
Alignment explanation
Indices: 3881631--3881669 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3881621 GGTTGATTTT
3881631 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3881670 TTTAAATAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3882912 original size:200 final size:189
Alignment explanation
Indices: 3882540--3882936 Score: 584
Period size: 189 Copynumber: 2.0 Consensus size: 189
3882530 AGTGTTAAGG
3882540 AAGGTGAAAGGTTGATTATAATAAACATCTACTTAATAACATTCATAACACTTCCCCTTGGATGT
1 AAGGTGAAAGGTTGATTATAATAAACATCTACTTAATAACATTCATAACACTTCCCCTTGGATGT
*
3882605 TCATTGTATAAAGGATATGCTTCATTAAAAATCATCATCATTAGTAGTATATTCCTATATATATA
66 TCATTGTATAAAGGATATGCTTCATTAAAAATAATCATCATTAGTAGTATATTCCTATATATATA
*
3882670 GGGAGTTAGACTCCTCATTTTTCTAATACATAAATAGTAAAAGAGTTACAAGAAGATGA
131 GGGAGTTAGACTCCTCATTTTTCTAATACATAAATAGTAAAAGAGTTACAAGAAGACGA
* *
3882729 AAGGTGAAAGGTTGATTATAATGAACATAC-ACTTAATAGCATTCATAACAC-TCCCCTTTGGAT
1 AAGGTGAAAGGTTGATTATAATAAACAT-CTACTTAATAACATTCATAACACTTCCCC-TTGGAT
*
3882792 GTTCATTGTATAAATGATATG-TCTCATTAAAAATAATCATCATTAGTAGTATATTCCTATATAT
64 GTTCATTGTATAAAGGATATGCT-TCATTAAAAATAATCATCATTAGTAGTATATTCC-------
*
3882856 ATATATATATATAGGGAGATTAGACTCCTTATTTTTCTAATACATAAATAGTAAAAGAGTTACAA
121 ---TATATATATAGGGAG-TTAGACTCCTCATTTTTCTAATACATAAATAGTAAAAGAGTTACAA
*
3882921 GGAGACGA
182 GAAGACGA
3882929 AAGGTGAA
1 AAGGTGAA
3882937 GAGTTAATGA
Statistics
Matches: 187, Mismatches: 7, Indels: 17
0.89 0.03 0.08
Matches are distributed among these distances:
188 6 0.03
189 106 0.57
190 1 0.01
199 15 0.08
200 59 0.32
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (189 bp):
AAGGTGAAAGGTTGATTATAATAAACATCTACTTAATAACATTCATAACACTTCCCCTTGGATGT
TCATTGTATAAAGGATATGCTTCATTAAAAATAATCATCATTAGTAGTATATTCCTATATATATA
GGGAGTTAGACTCCTCATTTTTCTAATACATAAATAGTAAAAGAGTTACAAGAAGACGA
Found at i:3888555 original size:3 final size:3
Alignment explanation
Indices: 3888547--3888605 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
3888537 ATTCATAACA
3888547 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3888595 ATT ATT ATT AT
1 ATT ATT ATT AT
3888606 ATTTGACATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3890322 original size:9 final size:9
Alignment explanation
Indices: 3890319--3890343 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3890309 ATTTTTAATT
3890319 TTTTTTTTA
1 TTTTTTTTA
3890328 TTTTTTTTA
1 TTTTTTTTA
3890337 TTTTTTT
1 TTTTTTT
3890344 AATAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:3906527 original size:4 final size:4
Alignment explanation
Indices: 3906518--3906548 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3906508 TATAAAAACA
3906518 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
3906549 CAATTTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:3914189 original size:38 final size:38
Alignment explanation
Indices: 3914122--3914207 Score: 100
Period size: 38 Copynumber: 2.3 Consensus size: 38
3914112 TTAAAATTAT
* * * *
3914122 TTATATTAAAAACACTACCAAAAAAAATAAATGTTTTA
1 TTATATTAAAAACACAAACAAAAAAAATAAATATGTTA
* * *
3914160 TTATATTAAAAACACAAATAAATATAATAAATATGTTA
1 TTATATTAAAAACACAAACAAAAAAAATAAATATGTTA
*
3914198 TTGTATTAAA
1 TTATATTAAA
3914208 TATATTTATT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (38 bp):
TTATATTAAAAACACAAACAAAAAAAATAAATATGTTA
Found at i:3915266 original size:12 final size:12
Alignment explanation
Indices: 3915246--3915279 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3915236 ACGAATAAAT
3915246 AATAAATTTTAA
1 AATAAATTTTAA
*
3915258 AATATATTTTAA
1 AATAAATTTTAA
*
3915270 AAGAAATTTT
1 AATAAATTTT
3915280 TTTAGTACTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (12 bp):
AATAAATTTTAA
Found at i:3916205 original size:26 final size:27
Alignment explanation
Indices: 3916150--3916207 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 27
3916140 ATATGTTATA
3916150 AAATAATATTATATTAATTATATATGTT
1 AAATAATATTATATTAATTATATA-GTT
3916178 AAATAATTATTAT-TTATATT-TATA-TT
1 AAATAA-TATTATATTA-ATTATATAGTT
3916204 AAAT
1 AAAT
3916208 CACTAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
26 6 0.21
28 13 0.46
29 9 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
AAATAATATTATATTAATTATATAGTT
Found at i:3916359 original size:39 final size:39
Alignment explanation
Indices: 3916305--3916393 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 39
3916295 AAAATTTATA
* * * *
3916305 TTTAACATAATAAAACATTTATTATATTTAT-TTGTGTTT
1 TTTAATATAACAAAACATTCATTATATTTATATAGTG-TT
3916344 TTTAATATAACAAAACATTCATTATATTTATGATAGTGTT
1 TTTAATATAACAAAACATTCATTATATTTAT-ATAGTGTT
3916384 TTTAATATAA
1 TTTAATATAA
3916394 ATATATTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
39 28 0.64
40 12 0.27
41 4 0.09
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (39 bp):
TTTAATATAACAAAACATTCATTATATTTATATAGTGTT
Found at i:3916466 original size:16 final size:16
Alignment explanation
Indices: 3916446--3916478 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3916436 AATGTATTAT
3916446 ATTTTTAA-AAAAATA
1 ATTTTTAATAAAAATA
3916461 ATTTTTAATAAAAATA
1 ATTTTTAATAAAAATA
3916477 AT
1 AT
3916479 CTAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTTTAATAAAAATA
Found at i:3929529 original size:29 final size:27
Alignment explanation
Indices: 3929489--3929542 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
3929479 TATCTTAAAA
*
3929489 AATATATCATTTTTATAAATAATTTAT
1 AATATATCATTTTCATAAATAATTTAT
*
3929516 AATATATCCTATTTTCATAATTAATTT
1 AATATAT-C-ATTTTCATAAATAATTT
3929543 TTTATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 1 0.04
29 15 0.65
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (27 bp):
AATATATCATTTTCATAAATAATTTAT
Found at i:3939769 original size:28 final size:28
Alignment explanation
Indices: 3939737--3939791 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
3939727 AAAAATATAT
3939737 AAATTTTGAAATTT-TTATAAATATTTTA
1 AAATTTT-AAATTTATTATAAATATTTTA
* *
3939765 AAATTTTAAATTTATTTTAAATTTTTT
1 AAATTTTAAATTTATTATAAATATTTT
3939792 GTTGAGAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
AAATTTTAAATTTATTATAAATATTTTA
Found at i:3939790 original size:19 final size:19
Alignment explanation
Indices: 3939734--3939790 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
3939724 TTAAAAAATA
*
3939734 TATAAAT-TTTGAAATTTT
1 TATAAATATTTTAAATTTT
*
3939752 TATAAATATTTTAAAATTT
1 TATAAATATTTTAAATTTT
*
3939771 TA-AATTTATTTTAAATTTT
1 TATAA-ATATTTTAAATTTT
3939790 T
1 T
3939791 TGTTGAGAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 9 0.27
19 24 0.73
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TATAAATATTTTAAATTTT
Found at i:3940212 original size:22 final size:23
Alignment explanation
Indices: 3940150--3940215 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 23
3940140 ATTTAAATTA
* *
3940150 TAAAATTATTTGATATAT-TATT
1 TAAAATTATTTGATAAATATAAT
* * **
3940172 TAAAATTAATTAAGGAATATAAT
1 TAAAATTATTTGATAAATATAAT
3940195 T-AAATTATTTGATAAATATAA
1 TAAAATTATTTGATAAATATAA
3940216 ATTTTGAAAT
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (23 bp):
TAAAATTATTTGATAAATATAAT
Found at i:3945434 original size:10 final size:9
Alignment explanation
Indices: 3945407--3945506 Score: 53
Period size: 9 Copynumber: 10.8 Consensus size: 9
3945397 TAAATTTATT
3945407 TTTTTAAT-
1 TTTTTAATA
**
3945415 TTTAAAATA
1 TTTTTAATA
3945424 TTTTTACATA
1 TTTTTA-ATA
*
3945434 TTTTTAATT
1 TTTTTAATA
3945443 TTTTTAAT-
1 TTTTTAATA
**
3945451 TTTAAAATA
1 TTTTTAATA
3945460 TTTTTAAAATA
1 TTTTT--AATA
*
3945471 CTTTTTTTAATT
1 ---TTTTTAATA
3945483 TTTTTAAT-
1 TTTTTAATA
**
3945491 TTTAAAATA
1 TTTTTAATA
3945500 TTTTTAA
1 TTTTTAA
3945507 AATCCTTTTT
Statistics
Matches: 69, Mismatches: 14, Indels: 17
0.69 0.14 0.17
Matches are distributed among these distances:
8 18 0.26
9 30 0.43
10 9 0.13
11 4 0.06
12 3 0.04
14 5 0.07
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTTAATA
Found at i:3945466 original size:11 final size:11
Alignment explanation
Indices: 3945450--3945590 Score: 62
Period size: 11 Copynumber: 13.9 Consensus size: 11
3945440 ATTTTTTTAA
3945450 TTTTAAAATAT
1 TTTTAAAATAT
3945461 TTTTAAAATACT
1 TTTTAAAATA-T
**
3945473 TTTTTTAAT-T
1 TTTTAAAATAT
*
3945483 TTTT----TAA
1 TTTTAAAATAT
3945490 TTTTAAAATAT
1 TTTTAAAATAT
*
3945501 TTTTAAAATCCT
1 TTTTAAAAT-AT
*
3945513 TTTT---TTAT
1 TTTTAAAATAT
*
3945521 TTTT---TTAT
1 TTTTAAAATAT
3945529 -TTTAAAATAT
1 TTTTAAAATAT
3945539 TTTTAAAATA-
1 TTTTAAAATAT
*
3945549 TTTTAAAATGCTT
1 TTTTAAAAT--AT
*
3945562 TTTTTAAAT-T
1 TTTTAAAATAT
3945572 TTTT-AAA-AT
1 TTTTAAAATAT
3945581 TTTTAAAATA
1 TTTTAAAATA
3945591 AAAATAGGCC
Statistics
Matches: 103, Mismatches: 10, Indels: 34
0.70 0.07 0.23
Matches are distributed among these distances:
6 1 0.01
7 7 0.07
8 9 0.09
9 9 0.09
10 25 0.24
11 31 0.30
12 13 0.13
13 8 0.08
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:3945478 original size:40 final size:39
Alignment explanation
Indices: 3945404--3945552 Score: 227
Period size: 40 Copynumber: 3.9 Consensus size: 39
3945394 TAATAAATTT
*
3945404 ATTTTTTTAATTTTAAAATATTTTT-ACATA--TTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTTA
3945440 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATA-TTTTTTTA
*
3945480 ATTTTTTTAATTTTAAAATATTTTTAAAATCCTTTTTTT-
1 ATTTTTTTAATTTTAAAATATTTTTAAAAT-ATTTTTTTA
3945519 ATTTTTTT-ATTTTAAAATATTTTTAAAATATTTT
1 ATTTTTTTAATTTTAAAATATTTTTAAAATATTTT
3945553 AAAATGCTTT
Statistics
Matches: 105, Mismatches: 3, Indels: 9
0.90 0.03 0.08
Matches are distributed among these distances:
36 25 0.24
37 8 0.08
38 21 0.20
39 8 0.08
40 43 0.41
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.64
Consensus pattern (39 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTTA
Found at i:3945515 original size:29 final size:29
Alignment explanation
Indices: 3945461--3945516 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
3945451 TTTAAAATAT
** *
3945461 TTTTAAAATACTTTTTTTAATTTTTTTAA
1 TTTTAAAATACTTTTTAAAATCTTTTTAA
3945490 TTTTAAAATA-TTTTTAAAATCCTTTTT
1 TTTTAAAATACTTTTTAAAAT-CTTTTT
3945517 TTATTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTTAAAATACTTTTTAAAATCTTTTTAA
Found at i:3945539 original size:10 final size:10
Alignment explanation
Indices: 3945526--3945590 Score: 60
Period size: 10 Copynumber: 6.2 Consensus size: 10
3945516 TTTATTTTTT
3945526 TATTTTAAAA
1 TATTTTAAAA
3945536 TATTTTTAAAA
1 TA-TTTTAAAA
3945547 TATTTTAAAA
1 TATTTTAAAA
* *
3945557 TGCTTTTTTTAAA
1 ---TATTTTAAAA
*
3945570 TTTTTTAAAA
1 TATTTTAAAA
3945580 T-TTTTAAAA
1 TATTTTAAAA
3945589 TA
1 TA
3945591 AAAATAGGCC
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
9 9 0.19
10 20 0.43
11 10 0.21
13 8 0.17
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:3946263 original size:23 final size:22
Alignment explanation
Indices: 3946230--3946292 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
3946220 GGCCCGGCCC
*
3946230 ATTTTTAATTAAAATTAAAATTA
1 ATTTTT-ATTAAAATTAAAACTA
3946253 TATTTTTATTAAAATTAAAACTA
1 -ATTTTTATTAAAATTAAAACTA
* *
3946276 ATTGTTATCAAAATTAA
1 ATTTTTATTAAAATTAA
3946293 TTGTTATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 15 0.42
23 15 0.42
24 6 0.17
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTTTTATTAAAATTAAAACTA
Found at i:3946293 original size:16 final size:16
Alignment explanation
Indices: 3946269--3946306 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3946259 TATTAAAATT
*
3946269 AAAACTAATTGTTATC
1 AAAATTAATTGTTATC
*
3946285 AAAATTAATTGTTATT
1 AAAATTAATTGTTATC
3946301 AAAATT
1 AAAATT
3946307 GTATCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (16 bp):
AAAATTAATTGTTATC
Found at i:3946456 original size:93 final size:93
Alignment explanation
Indices: 3946351--3946534 Score: 332
Period size: 93 Copynumber: 2.0 Consensus size: 93
3946341 TTTATAAAAT
*
3946351 CTAACATTTTGTTAGTAAAATTATTAATTTTTAATTATATTAATTGTTACTAAAATTATCAAATT
1 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTATATTAATTGTTACTAAAATTATCAAATT
3946416 ATATCAAATTATTAATTATTAATTGTTA
66 ATATCAAATTATTAATTATTAATTGTTA
* *
3946444 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATT
1 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTATATTAATTGTTACTAAAATTATCAAATT
*
3946509 ATATCAAATTATTAATTGTTAATTGT
66 ATATCAAATTATTAATTATTAATTGT
3946535 ATTAATTGTT
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 87 1.00
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.49
Consensus pattern (93 bp):
CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTATATTAATTGTTACTAAAATTATCAAATT
ATATCAAATTATTAATTATTAATTGTTA
Found at i:3946607 original size:22 final size:20
Alignment explanation
Indices: 3946576--3946615 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
3946566 TAACTTAAAA
*
3946576 TAAAACTAAAACTAGTATATTT
1 TAAAAATAAAA-TA-TATATTT
3946598 TAAAAATAAAATATATAT
1 TAAAAATAAAATATATAT
3946616 ATATTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 2 0.12
22 10 0.59
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (20 bp):
TAAAAATAAAATATATATTT
Found at i:3947216 original size:2 final size:2
Alignment explanation
Indices: 3947209--3947233 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3947199 AATTAAGTAG
3947209 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 T
3947234 GGAAAATGCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3948583 original size:19 final size:19
Alignment explanation
Indices: 3948537--3948588 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
3948527 CCATTTAATG
* * *
3948537 ATTATATTTAAATATTTAA
1 ATTAAATTTATATATTCAA
*
3948556 AATATAATTTATATATTCAA
1 ATTA-AATTTATATATTCAA
3948576 ATTAAATTT-TATA
1 ATTAAATTTATATA
3948589 AATAATTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 4 0.15
19 8 0.30
20 15 0.56
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTAAATTTATATATTCAA
Found at i:3950127 original size:2 final size:2
Alignment explanation
Indices: 3950120--3950152 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3950110 TTGATTTACC
3950120 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3950153 CCAAAATGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3950941 original size:26 final size:26
Alignment explanation
Indices: 3950912--3951075 Score: 85
Period size: 26 Copynumber: 6.5 Consensus size: 26
3950902 CTCTCTCAAG
3950912 CCATATAA-CAGGAAGCTCACAAAGAA
1 CCAT-TAATCAGGAAGCTCACAAAGAA
*
3950938 CCATTAATCGGGAAGCTCACAAAG-A
1 CCATTAATCAGGAAGCTCACAAAGAA
* * * **
3950963 GC-TT-ATCAGGAAGCTTATC--CGGG
1 CCATTAATCAGGAAGCTCA-CAAAGAA
* * *
3950986 CTATATAAT-AGGAAGCTCA-TAAGAG
1 CCAT-TAATCAGGAAGCTCACAAAGAA
* *
3951011 TCA-TAATCAGGAAGTTCACAAAGAA
1 CCATTAATCAGGAAGCTCACAAAGAA
** * * *
3951036 CTTTTAATTAGGAAGCTCACGAAGAG
1 CCATTAATCAGGAAGCTCACAAAGAA
*
3951062 CCTTTAATCAGGAA
1 CCATTAATCAGGAA
3951076 CCCCGGATAG
Statistics
Matches: 102, Mismatches: 25, Indels: 22
0.68 0.17 0.15
Matches are distributed among these distances:
22 1 0.01
23 15 0.15
24 13 0.13
25 22 0.22
26 51 0.50
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (26 bp):
CCATTAATCAGGAAGCTCACAAAGAA
Found at i:3952374 original size:41 final size:40
Alignment explanation
Indices: 3952255--3952389 Score: 127
Period size: 41 Copynumber: 3.5 Consensus size: 40
3952245 ACCAGTTTGG
* * *
3952255 CACCCAGTGCCTCATCGGA-TAATTCGAAGTAATAATTTGA
1 CACCCAGTGCCTCATCGAATTAATTC-AAGTAGTAAATTGA
* * * *
3952295 CACCCAGTGTCTCATTG--TTAAATC--GAAGTAAATTGA
1 CACCCAGTGCCTCATCGAATTAATTCAAGTAGTAAATTGA
*
3952331 CACTCAGTGCCTCATCGAATTAATTCAAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAATTAATTC-AAGTAGTAAATTGA
* *
3952372 CACCCAGCGTCTCATCGA
1 CACCCAGTGCCTCATCGA
3952390 CTCGAAGTCG
Statistics
Matches: 75, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
36 23 0.31
38 6 0.08
39 5 0.07
40 15 0.20
41 26 0.35
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGAATTAATTCAAGTAGTAAATTGA
Found at i:3953272 original size:4 final size:4
Alignment explanation
Indices: 3953265--3953347 Score: 50
Period size: 4 Copynumber: 20.5 Consensus size: 4
3953255 TTTCTCCTTC
* *
3953265 CTTT CTTT CCTT -TTT C-TT -TTT CTTT CTGTTT CATTT ATTT CTTT C-TT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT C--TTT C-TTT CTTT CTTT CTTT
*
3953312 -TTT CTTT CTGTTT CGTTT CTAT CTTT CTTT CTTT CT
1 CTTT CTTT C--TTT C-TTT CTTT CTTT CTTT CTTT CT
3953348 ATTTATTCTT
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
3 10 0.16
4 37 0.59
5 8 0.13
6 8 0.13
ACGTcount: A:0.04, C:0.22, G:0.04, T:0.71
Consensus pattern (4 bp):
CTTT
Found at i:3953296 original size:10 final size:10
Alignment explanation
Indices: 3953277--3953331 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
3953267 TTCTTTCCTT
*
3953277 TTTCTTTTTC
1 TTTCTGTTTC
3953287 TTTCTGTTTC
1 TTTCTGTTTC
* *
3953297 ATT-TATTTC
1 TTTCTGTTTC
*
3953306 TTTCTTTTTC
1 TTTCTGTTTC
3953316 TTTCTGTTTC
1 TTTCTGTTTC
3953326 GTTTCT
1 -TTTCT
3953332 ATCTTTCTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
9 7 0.19
10 25 0.68
11 5 0.14
ACGTcount: A:0.04, C:0.18, G:0.05, T:0.73
Consensus pattern (10 bp):
TTTCTGTTTC
Found at i:3953311 original size:29 final size:29
Alignment explanation
Indices: 3953277--3953341 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
3953267 TTCTTTCCTT
*
3953277 TTTCTTTTTCTTTCTGTTTCATTTATTTC
1 TTTCTTTTTCTTTCTGTTTCATTTATATC
* *
3953306 TTTCTTTTTCTTTCTGTTTCGTTTCTATC
1 TTTCTTTTTCTTTCTGTTTCATTTATATC
3953335 TTTCTTT
1 TTTCTTT
3953342 CTTTCTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.05, C:0.18, G:0.05, T:0.72
Consensus pattern (29 bp):
TTTCTTTTTCTTTCTGTTTCATTTATATC
Found at i:3953356 original size:17 final size:16
Alignment explanation
Indices: 3953302--3953363 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
3953292 GTTTCATTTA
3953302 TTTCTTTCTTT-T-TC
1 TTTCTTTCTTTCTATC
3953316 TTTCTGTTTCGTTTCTATC
1 TTTC--TTTC-TTTCTATC
*
3953335 TTTCTTTCTTTCTATT
1 TTTCTTTCTTTCTATC
*
3953351 TATTCTTTATTTC
1 T-TTCTTTCTTTC
3953364 ATAATTATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 4 0.10
16 12 0.30
17 17 0.43
18 1 0.03
19 6 0.15
ACGTcount: A:0.06, C:0.19, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTCTTTCTTTCTATC
Found at i:3953385 original size:5 final size:5
Alignment explanation
Indices: 3953364--3953441 Score: 56
Period size: 5 Copynumber: 15.6 Consensus size: 5
3953354 TCTTTATTTC
* *
3953364 ATAATT ATAATT ATAAT ATAAT ATAAT ATAAT AT-AT ATACT -TAAT A-ATT
1 ATAA-T ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* *
3953413 A-AGAT ATAAT ATTAT AATATT ATAAT ATA
1 ATA-AT ATAAT ATAAT -ATAAT ATAAT ATA
3953442 TATTTTAAGT
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
4 11 0.19
5 34 0.58
6 14 0.24
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (5 bp):
ATAAT
Found at i:3957872 original size:78 final size:78
Alignment explanation
Indices: 3957743--3957899 Score: 296
Period size: 78 Copynumber: 2.0 Consensus size: 78
3957733 TCCTTTTATT
*
3957743 TTTCAAATTTTGAAATTTAGTTCTAATCCAAATAGTAGTAATTAAATTAGTTTGGTTAGATTCAG
1 TTTCAAATTTTGAAATTTAGTTCTAACCCAAATAGTAGTAATTAAATTAGTTTGGTTAGATTCAG
*
3957808 TTACTAGTCTATG
66 TTACTAGCCTATG
3957821 TTTCAAATTTTGAAATTTAGTTCTAACCCAAATAGTAGTAATTAAATTAGTTTGGTTAGATTCAG
1 TTTCAAATTTTGAAATTTAGTTCTAACCCAAATAGTAGTAATTAAATTAGTTTGGTTAGATTCAG
3957886 TTACTAGCCTATG
66 TTACTAGCCTATG
3957899 T
1 T
3957900 CGTGTGCTCG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (78 bp):
TTTCAAATTTTGAAATTTAGTTCTAACCCAAATAGTAGTAATTAAATTAGTTTGGTTAGATTCAG
TTACTAGCCTATG
Found at i:3964443 original size:29 final size:29
Alignment explanation
Indices: 3964411--3964468 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
3964401 ACAATTGGAC
*
3964411 CTAAATT-TT-GAAATATGAAAGTATAGAGA
1 CTAAATTCTTGGAAATA--AAAGTAGAGAGA
3964440 CTAAATTCTTGGAAATAAAAGTAGAGAGA
1 CTAAATTCTTGGAAATAAAAGTAGAGAGA
3964469 TTACATTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 18 0.69
30 2 0.08
31 6 0.23
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.28
Consensus pattern (29 bp):
CTAAATTCTTGGAAATAAAAGTAGAGAGA
Found at i:3967816 original size:88 final size:88
Alignment explanation
Indices: 3967667--3967840 Score: 330
Period size: 88 Copynumber: 2.0 Consensus size: 88
3967657 ACCCTAGAAG
* *
3967667 AAACCCCGTTAGACTCAAATTGTGAGATTTTCCAGCTAATTTGGAAATTATTAGAATGCTCCTGA
1 AAACCCCATTAGACTCAAATTGTGAGATTTTCCAGCTAATTTGGAAATTATTAGAATGCTCCAGA
3967732 AATAAACCCCCAAAAACAAGGGA
66 AATAAACCCCCAAAAACAAGGGA
3967755 AAACCCCATTAGACTCAAATTGTGAGATTTTCCAGCTAATTTGGAAATTATTAGAATGCTCCAGA
1 AAACCCCATTAGACTCAAATTGTGAGATTTTCCAGCTAATTTGGAAATTATTAGAATGCTCCAGA
3967820 AATAAACCCCCAAAAACAAGG
66 AATAAACCCCCAAAAACAAGG
3967841 AAAGATACCT
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (88 bp):
AAACCCCATTAGACTCAAATTGTGAGATTTTCCAGCTAATTTGGAAATTATTAGAATGCTCCAGA
AATAAACCCCCAAAAACAAGGGA
Found at i:3969141 original size:14 final size:14
Alignment explanation
Indices: 3969122--3969149 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3969112 AAATTGAAGC
3969122 GACAAACTGTAGTA
1 GACAAACTGTAGTA
3969136 GACAAACTGTAGTA
1 GACAAACTGTAGTA
3969150 AAGCATGCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
GACAAACTGTAGTA
Found at i:3976438 original size:47 final size:43
Alignment explanation
Indices: 3976387--3976475 Score: 115
Period size: 47 Copynumber: 2.0 Consensus size: 43
3976377 TAAATGTAAC
* *
3976387 TAAATTATAAGTATTTTTAAATATGTAATAATTATCACAATATTTTT
1 TAAATTATAAGTATTGTTAAAT-T-T-ATAATTATAACAA-ATTTTT
*
3976434 TAAATTATAATTATTGTTAAATTTATAATTATAACAAATTTT
1 TAAATTATAAGTATTGTTAAATTTATAATTATAACAAATTTT
3976476 ATTTTATGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
43 5 0.13
44 12 0.31
45 1 0.03
46 1 0.03
47 20 0.51
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (43 bp):
TAAATTATAAGTATTGTTAAATTTATAATTATAACAAATTTTT
Found at i:3976823 original size:4 final size:4
Alignment explanation
Indices: 3976814--3976926 Score: 65
Period size: 4 Copynumber: 27.5 Consensus size: 4
3976804 GCAGAAGGAG
* * *
3976814 AGAA AGAA AGAA AGAA AGGAGA GGAA AGAA AGGGGA GGAA AGAA AGAAA
1 AGAA AGAA AGAA AGAA A-GA-A AGAA AGAA A--GAA AGAA AGAA AG-AA
*
3976863 AGGAA AG-G AGAA GAGAA A-AA AGGAA AGAA AG-A AG-A AGAA A-AA AGAA
1 A-GAA AGAA AGAA -AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AGAA AGAA
* *
3976909 AGAA GGAA GGAA AGAA AG
1 AGAA AGAA AGAA AGAA AG
3976927 GGAAAGGAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
3 14 0.16
4 52 0.60
5 17 0.20
6 4 0.05
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:3976902 original size:14 final size:14
Alignment explanation
Indices: 3976821--3976970 Score: 73
Period size: 14 Copynumber: 10.8 Consensus size: 14
3976811 GAGAGAAAGA
*
3976821 AAGAAAGAAAGGAG
1 AAGAAAGAAAGAAG
* **
3976835 AGGAAAGAAAGGGG
1 AAGAAAGAAAGAAG
*
3976849 AGGAAAGAAAGAA-
1 AAGAAAGAAAGAAG
*
3976862 AAGGAAAG-GAGAAG
1 AA-GAAAGAAAGAAG
*
3976876 -AGAAA-AAAGGA-
1 AAGAAAGAAAGAAG
3976887 AAGAAAG-AAGAAG
1 AAGAAAGAAAGAAG
*
3976900 AAAAAAGAAAGAAGG
1 AAGAAAGAAAGAA-G
3976915 AAGGAAAGAAAGGGAAAG
1 AA-GAAAGAAA--G-AAG
* *
3976933 GAGAAGAGAAAAAAG
1 AAGAA-AGAAAGAAG
3976948 AAG-AAG-AAGAAG
1 AAGAAAGAAAGAAG
* *
3976960 AGGGAAGAAAG
1 AAGAAAGAAAG
3976971 GAAAAAAAAG
Statistics
Matches: 105, Mismatches: 16, Indels: 30
0.70 0.11 0.20
Matches are distributed among these distances:
12 23 0.22
13 17 0.16
14 37 0.35
15 8 0.08
16 7 0.07
17 3 0.03
18 8 0.08
19 2 0.02
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (14 bp):
AAGAAAGAAAGAAG
Found at i:3976937 original size:29 final size:30
Alignment explanation
Indices: 3976849--3976942 Score: 91
Period size: 33 Copynumber: 3.0 Consensus size: 30
3976839 AAGAAAGGGG
* *
3976849 AGGAAAGAAAGAAAAGGAAAGGAGAAGAGA
1 AGGAAGGAAAGAAAGGGAAAGGAGAAGAGA
** **
3976879 AAAAAGGAAAGAAAGAAGAAGAAAAAAGAA-AGA
1 AGGAAGGAAAGAAAG--G--GAAAGGAGAAGAGA
3976912 AGGAAGGAAAGAAAGGGAAAGGAGAAGAGA
1 AGGAAGGAAAGAAAGGGAAAGGAGAAGAGA
3976942 A
1 A
3976943 AAAAGAAGAA
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
29 8 0.16
30 15 0.31
31 1 0.02
32 1 0.02
33 16 0.33
34 8 0.16
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (30 bp):
AGGAAGGAAAGAAAGGGAAAGGAGAAGAGA
Found at i:3976961 original size:21 final size:19
Alignment explanation
Indices: 3976860--3976957 Score: 92
Period size: 21 Copynumber: 4.9 Consensus size: 19
3976850 GGAAAGAAAG
* *
3976860 AAAAGGAAAGGAGAAGAGA
1 AAAAAGAAAGAAGAAGAGA
3976879 AAAAAGGAAAGAAAGAAGAAGA
1 AAAAA-GAAAG-AAGAAG-AGA
3976901 AAAAAGAAAGAAGGAAG-GA
1 AAAAAGAAAGAA-GAAGAGA
*
3976920 AAGAAAGGGAAAGGAGAAGAGA
1 AA-AAA--GAAAGAAGAAGAGA
3976942 AAAAAG-AAGAAGAAGA
1 AAAAAGAAAGAAGAAGA
3976958 AGAGGGAAGA
Statistics
Matches: 67, Mismatches: 4, Indels: 17
0.76 0.05 0.19
Matches are distributed among these distances:
18 9 0.13
19 9 0.13
20 10 0.15
21 21 0.31
22 18 0.27
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAGAAGAAGAGA
Found at i:3976990 original size:63 final size:62
Alignment explanation
Indices: 3976812--3976990 Score: 154
Period size: 63 Copynumber: 2.9 Consensus size: 62
3976802 GGGCAGAAGG
* * ** * *
3976812 AGAGAAAGAAAG-AAAGAAAGGAGAGGAAAGAAAG-GGGAGGAAA-GAAAGAAAAGGAAAGGAGA
1 AGAGAAA-AAAGAAAAGAAAGAAGAAGAAA-AAAGAAAGAAGAAAGGAAA-AAAGGGAAAGGAGA
* *
3976874 AGAGAAAAAAGGAAAGAAAGAAGAAGAAAAAAGAAAGAAGGAAGGAAAGAAAGGGAAAGGAGA
1 AGAGAAAAAAGAAAAGAAAGAAGAAGAAAAAAGAAAGAAGAAAGGAAA-AAAGGGAAAGGAGA
* *
3976937 AGAGAAAAAAGAAGAAG-AAGAAGAGGGAAGAAAGGAAA-AA-AAAGGGAAAAAAGG
1 AGAGAAAAAAGAA-AAGAAAGAAGA-AGAA-AAAAGAAAGAAGAAA-GGAAAAAAGG
3976991 TAATTTTATT
Statistics
Matches: 99, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
61 8 0.08
62 27 0.27
63 44 0.44
64 13 0.13
65 7 0.07
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (62 bp):
AGAGAAAAAAGAAAAGAAAGAAGAAGAAAAAAGAAAGAAGAAAGGAAAAAAGGGAAAGGAGA
Found at i:3977319 original size:13 final size:13
Alignment explanation
Indices: 3977301--3977325 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3977291 GAAAATAAAT
3977301 AAATGCGAAAAAG
1 AAATGCGAAAAAG
3977314 AAATGCGAAAAA
1 AAATGCGAAAAA
3977326 TGTACATGAA
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:0.64, C:0.08, G:0.20, T:0.08
Consensus pattern (13 bp):
AAATGCGAAAAAG
Found at i:3982216 original size:26 final size:26
Alignment explanation
Indices: 3982167--3982219 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
3982157 TACACACTAA
*
3982167 ATTATTAATTTTATACTACGAATAAT
1 ATTATTAATTTTATACTACAAATAAT
3982193 ATTATTAATTTTATACT-CAAAATAAT
1 ATTATTAATTTTATACTAC-AAATAAT
3982219 A
1 A
3982220 CACACTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (26 bp):
ATTATTAATTTTATACTACAAATAAT
Found at i:3982409 original size:3 final size:3
Alignment explanation
Indices: 3982401--3982465 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
3982391 TCTTCATACT
3982401 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
3982449 AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AA
3982466 TAATAATAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:3982470 original size:3 final size:3
Alignment explanation
Indices: 3982464--3982498 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
3982454 CAACAACAAC
*
3982464 AAT AAT AAT AAT AAT AAT AAT AAT ACT AACT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT A
3982499 CTTTTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3982756 original size:27 final size:27
Alignment explanation
Indices: 3982718--3982793 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
3982708 ATAATACGAG
3982718 TGGTGCCGCCAATGGCATTGGCACCAT
1 TGGTGCCGCCAATGGCATTGGCACCAT
** * *
3982745 TGGTGCCGCCAATGGTTTTGACACCTT
1 TGGTGCCGCCAATGGCATTGGCACCAT
**
3982772 TGGTGCCGCCAATACCATTGGC
1 TGGTGCCGCCAATGGCATTGGC
3982794 GTGACCAGTG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.17, C:0.29, G:0.28, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCAATGGCATTGGCACCAT
Found at i:3982869 original size:19 final size:18
Alignment explanation
Indices: 3982834--3982873 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3982824 TTTTTTGTCA
**
3982834 GGTTTTTTTTTTAATTTT
1 GGTTTTTTTGATAATTTT
3982852 GGTTTTTTTGATATATTTT
1 GGTTTTTTTGATA-ATTTT
3982871 GGT
1 GGT
3982874 AAATAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.12, C:0.00, G:0.17, T:0.70
Consensus pattern (18 bp):
GGTTTTTTTGATAATTTT
Found at i:3986231 original size:2 final size:2
Alignment explanation
Indices: 3986224--3986263 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3986214 GATATTGGAA
*
3986224 AT AT AT AT AT AT AT AT AT GT 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
3986264 GCAAAGCTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3987737 original size:31 final size:31
Alignment explanation
Indices: 3987691--3987772 Score: 112
Period size: 31 Copynumber: 2.6 Consensus size: 31
3987681 AACAATCGAG
* *
3987691 TGACTTAAATAAAAACTTTCGAATAGT-TCAA
1 TGACTTAAATGAAAACTTTCGAATAATGT-AA
* *
3987722 TGACTCAAATGAAAACTTTTGAATAATGTAA
1 TGACTTAAATGAAAACTTTCGAATAATGTAA
3987753 TGACTTAAATGAAAACTTTC
1 TGACTTAAATGAAAACTTTC
3987773 AAAAAAATCA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
31 43 0.98
32 1 0.02
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTCGAATAATGTAA
Found at i:3989631 original size:24 final size:24
Alignment explanation
Indices: 3989616--3989667 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3989606 AATCAAAGTC
3989616 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
3989640 AAATATATTATACTTATAAATACT
1 AAATATATTATGCTAATAAATGCT
3989664 AAAT
1 AAAT
3989668 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:3990412 original size:24 final size:24
Alignment explanation
Indices: 3990361--3990412 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
3990351 AATCAAAGTC
* * *
3990361 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACA
*
3990385 AAATATATTATACTCATAAATACA
1 AAATATATTATACTAATAAATACA
3990409 AAAT
1 AAAT
3990413 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACA
Found at i:3995893 original size:132 final size:132
Alignment explanation
Indices: 3995670--3996462 Score: 937
Period size: 132 Copynumber: 6.0 Consensus size: 132
3995660 CATCAGTCTA
* * * * * *
3995670 CTCCACTACTGCTTAGGGAGATAAGATCTGTTATTCTTCGATCGATTCCACTGTCGA-CCA-GGA
1 CTCCACTACTGCTTAGGGAAATAAGATCTG-AAATCTTCAATCTATTCCACTG-CTACCCAGGGA
* *
3995733 AGATAGAATTACTGGCTTCAATGTACTCCACTGTAACC-CCAGGGAGGTAAAATCCGCCATCTTC
64 AG-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGA-GGAGGTAAAATCTGCCATCTTC
*
3995797 AATCTG
127 GATCTG
* * * *
3995803 CTCTACTACCGCTTAGGGAAATAAGATCCGAAATCTTTAATCTATTCCACTGCTACCCAGGGAAG
1 CTCCACTACTGCTTAGGGAAATAAGATCTGAAATCTTCAATCTATTCCACTGCTACCCAGGGAAG
* * * *
3995868 TAGAATTATTGGCTTCAATGCACTCCACTGTAACCAC-AGGGAGGTAAAATCTGCCATTTTTGAT
66 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGA-GGAGGTAAAATCTGCCATCTTCGAT
3995932 CTG
130 CTG
* * * *
3995935 CTCCACTATTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAG
1 CTCCACTACTGCTTAGGGAAATAAGATCTGAAATCTTCAATCTATTCCACTGCTACCCAGGGAAG
*
3996000 TAGAATTATTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCTGCCATCTTCGATC
66 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCTGCCATCTTCGATC
3996065 TG
131 TG
* * * * * * *
3996067 CTTCGCTGTCTA-TGC--A-GGAAGGTAAGATCTAAAATCTTCAATCTATTCCGCTACTGCCTAG
1 C-TC-C--ACTACTGCTTAGGGAA-ATAAGATCTGAAATCTTCAATCTATTCCACTGCTACCCAG
* *
3996128 GGAAGTAGAATTACCGGCTTCAATGTACTCCACTGTAACCAC-AGGGAGGTAAAATTTGCCATCT
61 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGA-GGAGGTAAAATCTGCCATCT
*
3996192 TCGATCTA
125 TCGATCTG
* * * * *
3996200 CTCCACTACTGCCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCCAACCAGGG-AG
1 CTCCACTACTGCTTAGGGAAATAAGATCTGAAATCTTCAATCTATTCCACTGCTACCCAGGGAAG
3996264 ATAGAATTAC-GGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCTGCCATCTTCGAT
66 -TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCTGCCATCTTCGAT
3996328 CTG
130 CTG
* * * * ** * *
3996331 CTTCGCTGTCT-ATGTA-GGAAGGCAAGATCTGAAATCTTTAATCTATTCCACTGCTGCCCAGGG
1 CTCCACT-ACTGCT-TAGGGAA-ATAAGATCTGAAATCTTCAATCTATTCCACTGCTACCCAGGG
* *
3996394 AAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTTG
63 AAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCTGCCATCTTCG
3996459 ATCT
128 ATCT
3996463 ACTCAACTGC
Statistics
Matches: 572, Mismatches: 67, Indels: 42
0.84 0.10 0.06
Matches are distributed among these distances:
129 3 0.01
130 3 0.01
131 66 0.12
132 297 0.52
133 196 0.34
134 1 0.00
135 3 0.01
136 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (132 bp):
CTCCACTACTGCTTAGGGAAATAAGATCTGAAATCTTCAATCTATTCCACTGCTACCCAGGGAAG
TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCTGCCATCTTCGATC
TG
Found at i:3996047 original size:264 final size:263
Alignment explanation
Indices: 3995666--3996466 Score: 1091
Period size: 264 Copynumber: 3.0 Consensus size: 263
3995656 CCGTCATCAG
* * *
3995666 TCTACTCCACTACTGCTTAGGGAGATAAGATCTGTTATTCTTCGATCGATTCCACTG-TCGACCA
1 TCTACTCCACTACTGCTTAGGGAGATAAGATCTG-TAATCTTCAATCTATTCCACTGCT-GACCA
* *
3995730 -GGAAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACC-CCAGGGAGGTAAAATCCGCCAT
64 GGGAAGATAGAATTA-TGGCTTCAATGTACTCCACTGTAACCACGA-GGAGGTAAAATCTGCCAT
* * * *
3995793 CTTCAATCTGCTCTACTACCG-CTTAGGGAA-ATAAGATCCGAAATCTTTAATCTATTCCACTGC
127 CTTCGATCTGCT-T-CTGCCGTC-TAGGGAAGGTAAGATCTGAAATCTTTAATCTATTCCACTGC
* * *
3995856 TACCCAGGGAAGTAGAATTATTGGCTTCAATGCACTCCACTGTAACCACAGGGAGGTAAAATCTG
189 TGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTG
*
3995921 CCATTTTTGA
254 CCATCTTTGA
* * * * *
3995931 TCTGCTCCACTATTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGG
1 TCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGACCAGG
3995996 GAAG-TAGAATTATTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCTGCCATCTT
66 GAAGATAGAATTA-TGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCTGCCATCTT
* * * * *
3996060 CGATCTGCTTC-GCTGTCTATGCAGGAAGGTAAGATCTAAAATCTTCAATCTATTCCGCTACTGC
130 CGATCTGCTTCTGCCGTCTA-G--GGAAGGTAAGATCTGAAATCTTTAATCTATTCCACTGCTGC
* * *
3996124 CTAGGGAAGTAGAATTACCGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTTGCCA
192 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCA
*
3996189 TCTTCGA
257 TCTTTGA
* **
3996196 TCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCCAACCAGG
1 TCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGACCAGG
*
3996261 G-AGATAGAATTACGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCTGCCATCTTC
66 GAAGATAGAATTATGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCTGCCATCTTC
* *
3996325 GATCTGCTTC-GCTGTCTATGTAGGAAGGCAAGATCTGAAATCTTTAATCTATTCCACTGCTGCC
131 GATCTGCTTCTGCCGTCTA-G--GGAAGGTAAGATCTGAAATCTTTAATCTATTCCACTGCTGCC
*
3996389 CAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCAC-GAGGAGGTAAAATCCGCCA
193 CAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAG-GGAGGTAAAATCTGCCA
3996453 TCTTTGA
257 TCTTTGA
3996460 TCTACTC
1 TCTACTC
3996467 AACTGCCCAA
Statistics
Matches: 478, Mismatches: 48, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
261 4 0.01
262 3 0.01
263 2 0.00
264 270 0.56
265 199 0.42
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (263 bp):
TCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGACCAGG
GAAGATAGAATTATGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCTGCCATCTTC
GATCTGCTTCTGCCGTCTAGGGAAGGTAAGATCTGAAATCTTTAATCTATTCCACTGCTGCCCAG
GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTT
TGA
Found at i:3996359 original size:397 final size:398
Alignment explanation
Indices: 3995730--3996462 Score: 1134
Period size: 397 Copynumber: 1.8 Consensus size: 398
3995720 CTGTCGACCA
* *
3995730 GGAAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCCCAGGGAGGTAAAATCCGCCATCT
1 GGAAGATAGAATTACCGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCT
* * * * * *
3995795 TCAATCTGCTCTACTACCGCTTAGGGAAATAAGATCCGAAATCTTTAATCTATTCCACTGCTACC
66 TCAATCTACTCCACTACCGCCTAGGGAAATAAGATCCGAAATCTTCAATCTATTCCACTGCCAAC
*
3995860 CAGGGAAGTAGAATTATTGGCTTCAATGCACTCCACTGTAACCACAGGGAGGTAAAATCTGCCAT
131 CAGGGAAGTAGAATTATCGGCTTCAATGCACTCCACTGTAACCACAGGGAGGTAAAATCTGCCAT
* * * *
3995925 TTTTGATCTGCTCCACTATTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTG
196 CTTCGATCTGCTCCACTATTGATTAGGAAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTG
* *
3995990 CCCAGGGAAGTAGAATTATTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCTGCC
261 CCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCC
3996055 ATCTTCGATCTGCTTCGCTGTCTATGCAGGAAGGTAAGATCTAAAATCTTCAATCTATTCCGCTA
326 ATCTTCGATCTGCTTCGCTGTCTATGCAGGAAGGTAAGATCTAAAATCTTCAATCTATTCCGCTA
3996120 CTGCCTAG
391 CTGCCTAG
**
3996128 GGAAG-TAGAATTACCGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTTGCCATCT
1 GGAAGATAGAATTACCGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCT
* * * * *
3996192 TCGATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCCAAC
66 TCAATCTACTCCACTACCGCCTAGGGAAATAAGATCCGAAATCTTCAATCTATTCCACTGCCAAC
*
3996257 CAGGG-AGATAGAATTA-CGGCTTCAATGTACTCCACTGTAACCAC-GAGGAGGTAAAATCTGCC
131 CAGGGAAG-TAGAATTATCGGCTTCAATGCACTCCACTGTAACCACAG-GGAGGTAAAATCTGCC
* * * * *
3996319 ATCTTCGATCTGCTTCGCTGTCT-ATGTAGGAAGGCAAGATCTGAAATCTTTAATCTATTCCACT
194 ATCTTCGATCTGCTCCACTAT-TGAT-TAGGAAGACAAGATCTGAAATCTTCAATCTATTCCACT
3996383 GCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATC
257 GCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATC
*
3996448 CGCCATCTTTGATCT
322 CGCCATCTTCGATCT
3996463 ACTCAACTGC
Statistics
Matches: 302, Mismatches: 29, Indels: 9
0.89 0.09 0.03
Matches are distributed among these distances:
395 1 0.00
396 61 0.20
397 235 0.78
398 5 0.02
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (398 bp):
GGAAGATAGAATTACCGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCT
TCAATCTACTCCACTACCGCCTAGGGAAATAAGATCCGAAATCTTCAATCTATTCCACTGCCAAC
CAGGGAAGTAGAATTATCGGCTTCAATGCACTCCACTGTAACCACAGGGAGGTAAAATCTGCCAT
CTTCGATCTGCTCCACTATTGATTAGGAAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTG
CCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCC
ATCTTCGATCTGCTTCGCTGTCTATGCAGGAAGGTAAGATCTAAAATCTTCAATCTATTCCGCTA
CTGCCTAG
Found at i:3996676 original size:89 final size:88
Alignment explanation
Indices: 3996472--3997294 Score: 888
Period size: 89 Copynumber: 9.3 Consensus size: 88
3996462 TACTCAACTG
* * * * * * *
3996472 CCCAAGGAGACAAGGCTGGTCTCTTCGATCTGCTTCTCTGTTAGTACAAGAAGGCAGGATCTGTT
1 CCCAGGGAGACAAGGCTGGTGTTTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCT
* * ** * *
3996537 ATTTTTAACCTACTCCACTACTA
66 ATATTCAGTCTGCTCCGCTACTA
* * * *
3996560 CCCAGGGAGACAAGGCTGGTATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGTAAGATCTGCC
1 CCCAGGGAGACAAGGCTGGTGTTTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCT
* * ** * * *
3996625 ATTTTTTAACCTACTCCACTACTG
66 A-TATTCAGTCTGCTCCGCTACTA
* *
3996649 CCCAGGGAGACAAGGCTGGTCTTTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCC
1 CCCAGGGAGACAAGGCTGGTGTTTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCT
* * *
3996714 ATATTCAGTCTGCTCTGCTGCAAA
66 ATATTCAGTCTGCTCCGCTAC-TA
* * *
3996738 CCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGT-TGTCAGTACAAGAAGGCAAGATCTGC
1 CCCAGGGAGACAAGGCTGGTGTTTTCGATCTGCTTC-TCTGTCAGTACAGGAAGGCAAGATCTGC
* *
3996802 TATATTCAGTCTGCTCCGCTGCAA
65 TATATTCAGTCTGCTCCGCTACTA
* * *
3996826 CCCAGGGAGGCAAGGCTGGTGTCTTT-GATCTGCTTCGCTGTTAGTACAGGAAGGCAAGATCTGC
1 CCCAGGGAGACAAGGCTGGTGT-TTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGC
*
3996890 TATATTCAGTCTGCTCCGCT-GTAA
65 TATATTCAGTCTGCTCCGCTACT-A
** *
3996914 CCCAATGATG-CAAGGCTGGTGTCTTT-GATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTG
1 CCCAGGGA-GACAAGGCTGGTGT-TTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTG
* *
3996977 CTATATTCAGTCTGCTCCGCTGCAAA
64 CTATATTCAGTCTGCTCCGCTAC-TA
* *
3997003 CCCAGGGAGGCAAGGCTGGTGTCTTT-GATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGC
1 CCCAGGGAGACAAGGCTGGTGT-TTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGC
* * *
3997067 TATATTCAGTTTGCTCCGCTGCAAA
65 TATATTCAGTCTGCTCCGCTAC-TA
* * * * *
3997092 TCCAGGGAGGCAAGGTTGGTGTCTTT-GATCTACTTCGCTGTCAGTACAGGAAGGCAAGATCTGC
1 CCCAGGGAGACAAGGCTGGTGT-TTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGC
* *
3997156 TATATTCAGTCTGCTCCGCTGCAAA
65 TATATTCAGTCTGCTCCGCTAC-TA
* * *
3997181 CCCAGGGAGGCAAGGCTGGTGACTTT-GATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGC
1 CCCAGGGAGACAAGGCTGGTG-TTTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGC
* * * *
3997245 TATATTTAGTCTACTCCGCTGCAAA
65 TATATTCAGTCTGCTCCGCTAC-TA
*
3997270 CCCAGGGAGGCAAGGCTGGTTGTTT
1 CCCAGGGAGACAAGGCTGG-TGTTT
3997295 CACCGATCAG
Statistics
Matches: 670, Mismatches: 53, Indels: 23
0.90 0.07 0.03
Matches are distributed among these distances:
88 229 0.34
89 438 0.65
90 3 0.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (88 bp):
CCCAGGGAGACAAGGCTGGTGTTTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCT
ATATTCAGTCTGCTCCGCTACTA
Found at i:3996799 original size:178 final size:176
Alignment explanation
Indices: 3996472--3997289 Score: 1075
Period size: 178 Copynumber: 4.6 Consensus size: 176
3996462 TACTCAACTG
* * * * * * * *
3996472 CCCAAGGAGACAAGGCTGGTCTCTTCGATCTGCTTCTCTGTTAGTACAAGAAGGCAGGATCTGTT
1 CCCAGGGAGGCAAGGCTGGTCT-TTTGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCT
* * ** * * * * * * *
3996537 ATTTTTAACCTACTCCACTAC-TACCCAGGGAGACAAGGCTGGTATCTTCGATCTGCTTCTCTGT
65 ATATTCAGTCTGCTCCGCTGCAAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGT
* * * * ** * * * **
3996601 CAGTACAGGAAGGTAAGATCTGCCATTTTTTAACCTACTCCACTACTG
130 CAGTACAGGAAGGCAAGATCTGCTA-TATTCAGTCTGCTCCGCTGCAA
* * *
3996649 CCCAGGGAGACAAGGCTGGTCTTTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCC
1 CCCAGGGAGGCAAGGCTGGTCTTTT-GATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCT
* *
3996714 ATATTCAGTCTGCTCTGCTGCAAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGTTGT
65 ATATTCAGTCTGCTCCGCTGCAAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGT
*
3996779 CAGTACAAGAAGGCAAGATCTGCTATATTCAGTCTGCTCCGCTGCAA
130 CAGTACAGGAAGGCAAGATCTGCTATATTCAGTCTGCTCCGCTGCAA
* *
3996826 CCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTTAGTACAGGAAGGCAAGATCTGCT
1 CCCAGGGAGGCAAGGCTGGTCT-TTTGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCT
* ** * *
3996891 ATATTCAGTCTGCTCCGCTG-TAACCCAATGATGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGT
65 ATATTCAGTCTGCTCCGCTGCAAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGT
3996955 CAGTACAGGAAGGCAAGATCTGCTATATTCAGTCTGCTCCGCTGCAAA
130 CAGTACAGGAAGGCAAGATCTGCTATATTCAGTCTGCTCCGCTGC-AA
*
3997003 CCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCT
1 CCCAGGGAGGCAAGGCTGGTCT-TTTGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCT
* * * * *
3997068 ATATTCAGTTTGCTCCGCTGCAAATCCAGGGAGGCAAGGTTGGTGTCTTTGATCTACTTCGCTGT
65 ATATTCAGTCTGCTCCGCTGCAAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGT
3997133 CAGTACAGGAAGGCAAGATCTGCTATATTCAGTCTGCTCCGCTGCAAA
130 CAGTACAGGAAGGCAAGATCTGCTATATTCAGTCTGCTCCGCTGC-AA
3997181 CCCAGGGAGGCAAGGCTGGTGAC-TTTGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGC
1 CCCAGGGAGGCAAGGCTGGT--CTTTTGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGC
* *
3997245 TATATTTAGTCTACTCCGCTGCAAACCCAGGGAGGCAAGGCTGGT
64 TATATTCAGTCTGCTCCGCTGCAAACCCAGGGAGGCAAGGCTGGT
3997290 TGTTTCACCG
Statistics
Matches: 574, Mismatches: 60, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
176 84 0.15
177 241 0.42
178 249 0.43
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.27
Consensus pattern (176 bp):
CCCAGGGAGGCAAGGCTGGTCTTTTGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
TATTCAGTCTGCTCCGCTGCAAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTC
AGTACAGGAAGGCAAGATCTGCTATATTCAGTCTGCTCCGCTGCAA
Found at i:3996967 original size:354 final size:354
Alignment explanation
Indices: 3996472--3997289 Score: 1131
Period size: 354 Copynumber: 2.3 Consensus size: 354
3996462 TACTCAACTG
* * * * * * * *
3996472 CCCAAGGAGACAAGGCTGGTCTCTTCGATCTGCTTCTCTGTTAGTACAAGAAGGCAGGATCTGTT
1 CCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTTAGTACAGGAAGGCAAGATCTGCT
* ** * * *
3996537 ATTTTTAACCTACTCCACTACT-ACCCAGGGAGACAAGGCTGGTATCTTCGATCTGCTTCTCTGT
66 ATATTTAGTCTACTCCGCT-GTAACCCAGGGAG-CAAGGCTGGTATCTTCGATCTGCTTCGCTGT
* * * **
3996601 CAGTACAGGAAGGTAAGATCTGCCATTTTTTAACCTACTCCACTAC-TGCCCAGGGAGACAAGGC
129 CAGTACAGGAAGGCAAGATCTGCCA-TATTCAACCTACTCCACTACAAACCCAGGGAGACAAGGC
*
3996665 TGGTCT-TTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCCATATTCAGTCTGCTC
193 TGGTCTCTTT-GATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCCATATTCAGTCTGCTC
* * *
3996729 TGCTGCAAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGTTGTCAGTACAAGAAGGCA
257 CGCTGCAAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTCGCTGTCAGTACAAGAAGGCA
3996794 AGATCTGCTATATTCAGTCTGCTCCGCTGC-AA
322 AGATCTGCTATATTCAGTCTGCTCCGCTGCAAA
3996826 CCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTTAGTACAGGAAGGCAAGATCTGCT
1 CCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTTAGTACAGGAAGGCAAGATCTGCT
* * ** * *
3996891 ATATTCAGTCTGCTCCGCTGTAACCCAATGATGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTC
66 ATATTTAGTCTACTCCGCTGTAACCCAGGGA-GCAAGGCTGGTATCTTCGATCTGCTTCGCTGTC
* ** * * * *
3996956 AGTACAGGAAGGCAAGATCTGCTATATTCAGTCTGCTCCGCTGCAAACCCAGGGAGGCAAGGCTG
130 AGTACAGGAAGGCAAGATCTGCCATATTCAACCTACTCCACTACAAACCCAGGGAGACAAGGCTG
* * *
3997021 GTGTCTTTGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATATTCAGTTTGCTCCGC
195 GTCTCTTTGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCCATATTCAGTCTGCTCCGC
* * * *
3997086 TGCAAATCCAGGGAGGCAAGGTTGGTGTCTTTGATCTACTTCGCTGTCAGTACAGGAAGGCAAGA
260 TGCAAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTCGCTGTCAGTACAAGAAGGCAAGA
3997151 TCTGCTATATTCAGTCTGCTCCGCTGCAAA
325 TCTGCTATATTCAGTCTGCTCCGCTGCAAA
* *
3997181 CCCAGGGAGGCAAGGCTGGTGACTTTGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCT
1 CCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTTAGTACAGGAAGGCAAGATCTGCT
*
3997246 ATATTTAGTCTACTCCGCTGCAAACCCAGGGAGGCAAGGCTGGT
66 ATATTTAGTCTACTCCGCTG-TAACCCAGGGA-GCAAGGCTGGT
3997290 TGTTTCACCG
Statistics
Matches: 407, Mismatches: 51, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
353 14 0.03
354 287 0.71
355 87 0.21
356 19 0.05
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.27
Consensus pattern (354 bp):
CCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTTAGTACAGGAAGGCAAGATCTGCT
ATATTTAGTCTACTCCGCTGTAACCCAGGGAGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCA
GTACAGGAAGGCAAGATCTGCCATATTCAACCTACTCCACTACAAACCCAGGGAGACAAGGCTGG
TCTCTTTGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCCATATTCAGTCTGCTCCGCT
GCAAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTCGCTGTCAGTACAAGAAGGCAAGAT
CTGCTATATTCAGTCTGCTCCGCTGCAAA
Found at i:3997149 original size:44 final size:44
Alignment explanation
Indices: 3996740--3997238 Score: 232
Period size: 44 Copynumber: 11.3 Consensus size: 44
3996730 GCTGCAAACC
* * * *
3996740 CAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGTTGTCAGTA
1 CAGGAAGGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGTCAGTA
* * * * * * * ***
3996784 CAAGAAGGCAAGATCTGCTAT-ATTCAGTCTGCTCCGCTG-CAACC
1 CAGGAAGGCAAGGT-TGGTGTCTTTGA-TCTGCTTCGCTGTCAGTA
* * *
3996828 CAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTTAGTA
1 CAGGAAGGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGTCAGTA
* * * * * * ***
3996872 CAGGAAGGCAAGATCTGCTAT-ATTCAGTCTGCTCCGCTGT-AACC
1 CAGGAAGGCAAGGT-TGGTGTCTTTGA-TCTGCTTCGCTGTCAGTA
* * *
3996916 CAATG-ATGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTCAGTA
1 C-AGGAAGGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGTCAGTA
* * * * * * *
3996960 CAGGAAGGCAAGATCTGCTAT-ATTCAGTCTGCTCCGCTG-CA-AA
1 CAGGAAGGCAAGGT-TGGTGTCTTTGA-TCTGCTTCGCTGTCAGTA
* *
3997003 CCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTCAGTA
1 --CAGGAAGGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGTCAGTA
* * * * * * * * *
3997049 CAGGAAGGCAAGATCTGCTAT-ATTCAGTTTGCTCCGCTG-CAAATC
1 CAGGAAGGCAAGGT-TGGTGTCTTTGA-TCTGCTTCGCTGTC-AGTA
* *
3997094 CAGGGAGGCAAGGTTGGTGTCTTTGATCTACTTCGCTGTCAGTA
1 CAGGAAGGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGTCAGTA
* * * * * * *
3997138 CAGGAAGGCAAGATCTGCTAT-ATTCAGTCTGCTCCGCTG-CA-AA
1 CAGGAAGGCAAGGT-TGGTGTCTTTGA-TCTGCTTCGCTGTCAGTA
* * *
3997181 CCCAGGGAGGCAAGGCTGGTGACTTTGATCTGCTTCGCTGTCAGTA
1 --CAGGAAGGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGTCAGTA
3997227 CAGGAAGGCAAG
1 CAGGAAGGCAAG
3997239 ATCTGCTATA
Statistics
Matches: 315, Mismatches: 111, Indels: 58
0.65 0.23 0.12
Matches are distributed among these distances:
43 35 0.11
44 153 0.49
45 125 0.40
46 2 0.01
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.27
Consensus pattern (44 bp):
CAGGAAGGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGTCAGTA
Found at i:3998499 original size:14 final size:14
Alignment explanation
Indices: 3998468--3998498 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
3998458 GCCTCTCCAC
3998468 TTTTACTTTTTCAT
1 TTTTACTTTTTCAT
3998482 TTTTAC-TTTTCAT
1 TTTTACTTTTTCAT
3998495 TTTT
1 TTTT
3998499 TCGTCATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTACTTTTTCAT
Found at i:3998995 original size:1 final size:1
Alignment explanation
Indices: 3998989--3999113 Score: 79
Period size: 1 Copynumber: 125.0 Consensus size: 1
3998979 TCGGTAGAGG
* * * * * * * * * * * *
3998989 TTTTTTTGTTTCTTTTTGTTTTTTATTCTTTTTTGTTCTCTTTTTTCTTTTTTCTATTTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * *
3999054 TTTTTTGTTTTTTTTTTGTTTTTTTGTTTTTTTGTTTTTGTTTTTGTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3999114 GAACTGAATC
Statistics
Matches: 86, Mismatches: 38, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 86 1.00
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.85
Consensus pattern (1 bp):
T
Found at i:3999006 original size:10 final size:9
Alignment explanation
Indices: 3998989--3999113 Score: 103
Period size: 10 Copynumber: 13.3 Consensus size: 9
3998979 TCGGTAGAGG
3998989 TTTTTTTGT
1 TTTTTTTGT
3998998 TTCTTTTTGT
1 TT-TTTTTGT
*
3999008 TTTTTAT-T
1 TTTTTTTGT
*
3999016 CTTTTTTGT
1 TTTTTTTGT
3999025 TCTCTTTTT-T
1 T-T-TTTTTGT
* *
3999035 CTTTTTTCT
1 TTTTTTTGT
3999044 ATTTTTTTG-
1 -TTTTTTTGT
3999053 TTTTTTTGT
1 TTTTTTTGT
*
3999062 TTTTTTTTT
1 TTTTTTTGT
3999071 GTTTTTTTGT
1 -TTTTTTTGT
*
3999081 TTTTTTGTTT
1 TTTTTT-TGT
3999091 TTGTTTTTGTT
1 TT-TTTTTG-T
3999102 TTTTTTTGT
1 TTTTTTTGT
3999111 TTT
1 TTT
3999114 GAACTGAATC
Statistics
Matches: 94, Mismatches: 11, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
8 19 0.20
9 27 0.29
10 36 0.38
11 12 0.13
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.85
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:3999017 original size:16 final size:14
Alignment explanation
Indices: 3998989--3999113 Score: 103
Period size: 14 Copynumber: 8.9 Consensus size: 14
3998979 TCGGTAGAGG
*
3998989 TTTTTTTGTTTCTT
1 TTTTTTTGTTTTTT
* *
3999003 TTTGTTT-TTTATT
1 TTTTTTTGTTTTTT
*
3999016 CTTTTTTGTTCTCTTT
1 TTTTTTTGTT-T-TTT
* * *
3999032 TTTCTTT-TTTCTA
1 TTTTTTTGTTTTTT
3999045 TTTTTTTGTTTTTT
1 TTTTTTTGTTTTTT
* *
3999059 TGTTTTT-TTTTTG
1 TTTTTTTGTTTTTT
3999072 TTTTTTTGTTTTTT
1 TTTTTTTGTTTTTT
*
3999086 TGTTTTTGTTTTTGTT
1 TTTTTTTG-TTTT-TT
3999102 TTTTTTTGTTTT
1 TTTTTTTGTTTT
3999114 GAACTGAATC
Statistics
Matches: 86, Mismatches: 18, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
13 28 0.33
14 31 0.36
15 11 0.13
16 16 0.19
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.85
Consensus pattern (14 bp):
TTTTTTTGTTTTTT
Found at i:3999086 original size:27 final size:27
Alignment explanation
Indices: 3998988--3999114 Score: 127
Period size: 27 Copynumber: 4.6 Consensus size: 27
3998978 CTCGGTAGAG
*
3998988 GTTTTTTTGTTTCTTTT-TGTTTTTTATT
1 GTTTTTTTGTTT-TTTTGT-TTTTTTTTT
* *
3999016 -CTTTTTTGTTCTCTTTT-TTCTTTTTTCT
1 GTTTTTTTGTT-T-TTTTGTT-TTTTTTTT
*
3999044 ATTTTTTTGTTTTTTTGTTTTTTTTTT
1 GTTTTTTTGTTTTTTTGTTTTTTTTTT
3999071 GTTTTTTTGTTTTTTTGTTTTTGTTTTT
1 GTTTTTTTGTTTTTTTGTTTTT-TTTTT
*
3999099 GTTTTTTT-TTGTTTTG
1 GTTTTTTTGTTTTTTTG
3999115 AACTGAATCT
Statistics
Matches: 87, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
27 49 0.56
28 29 0.33
29 9 0.10
ACGTcount: A:0.02, C:0.05, G:0.10, T:0.83
Consensus pattern (27 bp):
GTTTTTTTGTTTTTTTGTTTTTTTTTT
Found at i:4004089 original size:3 final size:3
Alignment explanation
Indices: 4004081--4004140 Score: 52
Period size: 3 Copynumber: 19.7 Consensus size: 3
4004071 TGCGGTAAGT
* * *
4004081 ATA ATA ATA AAA ATA TATA AT- ATA ATG ATA ATA A-A CTA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4004125 ATA CAGTA ATA ATA AT
1 ATA -A-TA ATA ATA AT
4004141 GTAATATATA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
2 3 0.07
3 36 0.78
4 5 0.11
5 2 0.04
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4008696 original size:22 final size:22
Alignment explanation
Indices: 4008670--4008822 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
4008660 TGTATCCACT
*
4008670 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
4008692 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
4008714 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
4008736 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
4008758 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
4008780 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
4008802 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
4008823 GAACAATACT
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:4023169 original size:18 final size:17
Alignment explanation
Indices: 4023139--4023175 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
4023129 ATATAATATA
4023139 ATATGTTTATATTAACT
1 ATATGTTTATATTAACT
*
4023156 ATATGTTATGTATTAACT
1 ATATGTT-TATATTAACT
4023174 AT
1 AT
4023176 TATAATAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.51
Consensus pattern (17 bp):
ATATGTTTATATTAACT
Found at i:4023352 original size:30 final size:26
Alignment explanation
Indices: 4023299--4023357 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 26
4023289 TAAATGATAT
4023299 TAATTTTATATTTATAATATAAAATA
1 TAATTTTATATTTATAATATAAAATA
4023325 TAATTTTATTATTTATTAAATTATAAAATA
1 TAATTTTA-TATTTA-T-AA-TATAAAATA
4023355 TAA
1 TAA
4023358 ATACATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 8 0.28
27 6 0.21
28 1 0.03
29 2 0.07
30 12 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TAATTTTATATTTATAATATAAAATA
Found at i:4025471 original size:2 final size:2
Alignment explanation
Indices: 4025464--4025500 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4025454 GGCCACAAAA
4025464 AG AG AG 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 AG AG AG A
4025501 TTTTTCAGAT
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4027656 original size:3 final size:3
Alignment explanation
Indices: 4027648--4027687 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
4027638 AATACCAGTA
4027648 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4027688 TCTCTTCAAA
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:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:4029043 original size:41 final size:41
Alignment explanation
Indices: 4028997--4029080 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
4028987 GTCAGTGGTC
4028997 TTATGTTCAAATCTCTACGTGTGCATTAAGGAATATTATTT
1 TTATGTTCAAATCTCTACGTGTGCATTAAGGAATATTATTT
* *
4029038 TTATGTTCGAATCTCTACGTGTGCATTGAGGAATATTATTT
1 TTATGTTCAAATCTCTACGTGTGCATTAAGGAATATTATTT
4029079 TT
1 TT
4029081 TCACTTCTCC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (41 bp):
TTATGTTCAAATCTCTACGTGTGCATTAAGGAATATTATTT
Found at i:4029170 original size:22 final size:22
Alignment explanation
Indices: 4029140--4029197 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 22
4029130 TGACTCATTC
*
4029140 TTTCCTTCTTCCTTTTTTTTAT
1 TTTCTTTCTTCCTTTTTTTTAT
* *
4029162 TTTCTTTC-T--TTTCTTTTCT
1 TTTCTTTCTTCCTTTTTTTTAT
4029181 TTT-TTTCTTCCTTTTTT
1 TTTCTTTCTTCCTTTTTT
4029198 CCTTTTGGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
18 4 0.14
19 12 0.41
21 6 0.21
22 7 0.24
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTCTTTCTTCCTTTTTTTTAT
Found at i:4029172 original size:18 final size:19
Alignment explanation
Indices: 4029145--4029189 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
4029135 CATTCTTTCC
*
4029145 TTCTTCCTTTT-TTTTATT
1 TTCTTTCTTTTCTTTTATT
*
4029163 TTCTTTCTTTTCTTTTCTT
1 TTCTTTCTTTTCTTTTATT
4029182 TT-TTTCTT
1 TTCTTTCTT
4029190 CCTTTTTTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (19 bp):
TTCTTTCTTTTCTTTTATT
Found at i:4029173 original size:14 final size:13
Alignment explanation
Indices: 4029153--4029186 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
4029143 CCTTCTTCCT
4029153 TTTTTTTATTTTC
1 TTTTTTTATTTTC
*
4029166 TTTCTTTTCTTTTC
1 TTT-TTTTATTTTC
4029180 TTTTTTT
1 TTTTTTT
4029187 CTTCCTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTATTTTC
Found at i:4045621 original size:114 final size:114
Alignment explanation
Indices: 4045431--4046130 Score: 1048
Period size: 114 Copynumber: 6.2 Consensus size: 114
4045421 CGCAACCGAT
* *
4045431 TGAGTATTAGCGGCGTTTCTATAAAAACGCAGCAAAAACT-AAACCCAGACGACGACGTTTGGAG
1 TGAGTATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGAG
* *
4045495 AAACTTCGGTGACATTACTGGCGTTTTTCGAATAGCGCCGCTAATAATA
66 ACACTTCGGTGACATTAGTGGCGTTTTTCGAATAGCGCCGCTAATAATA
* * * * *
4045544 TGAGTATTAGCGGCTTTTCTGTAAAAATGCTGTAAAAACTAAAACCCAGACGACGTCGTTTGGAG
1 TGAGTATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGAG
*
4045609 ACACTTCGGTGACATTAGTGGCGTTTTTTGAATAGCGCCGCTAAT-ATA
66 ACACTTCGGTGACATTAGTGGCGTTTTTCGAATAGCGCCGCTAATAATA
* * *
4045657 TGAGTATTAGCGGCGTTTTTATAAAAATGCCGCAAAAACTAAACCCCAGACGACGTCGTTTGGAG
1 TGAGTATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGAG
* *
4045722 ACACTTCGGTGACTTTAGTGGCGTTTTTCAAATAGCGCCGCTAATAATA
66 ACACTTCGGTGACATTAGTGGCGTTTTTCGAATAGCGCCGCTAATAATA
* * * * *
4045771 TGAGTATTAGCGGCGTTTCTACAAAAACGCTGGAAAAACTAAAACCCAAACGACTTCGTTTGGAG
1 TGAGTATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGAG
* *
4045836 ACACTTCGGTGACATTAGTGGCGTTTTCCGAGTAGCGCCGCTAATAATA
66 ACACTTCGGTGACATTAGTGGCGTTTTTCGAATAGCGCCGCTAATAATA
* * *
4045885 TGAGTATTAGCGGCGTTT-TGTTTAAAACGCCGCAAAAACTAAAACCCAGACGACATCGTTTGGA
1 TGAGTATTAGCGGCGTTTCT-ATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGA
*
4045949 GACACTTCGGTGACATTAGTGGCGTTTTTTGAATAGCGCCGCTAATAATA
65 GACACTTCGGTGACATTAGTGGCGTTTTTCGAATAGCGCCGCTAATAATA
* *
4045999 TGAGTATTAGCGGCGTTTCTATAAAAATGCCGCAAAAACTAAACCCCAGACGACGTCGTTTGGAG
1 TGAGTATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGAG
* * * * *
4046064 ACACTTCGGTGACTTTAGTGGCGCTTTTAGATTAGCGCCGCGAATAATA
66 ACACTTCGGTGACATTAGTGGCGTTTTTCGAATAGCGCCGCTAATAATA
*
4046113 T-AGGTTTTAGCGGCGTTT
1 TGA-GTATTAGCGGCGTTT
4046131 TTGTTAAAGC
Statistics
Matches: 531, Mismatches: 51, Indels: 9
0.90 0.09 0.02
Matches are distributed among these distances:
113 141 0.27
114 389 0.73
115 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (114 bp):
TGAGTATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGAG
ACACTTCGGTGACATTAGTGGCGTTTTTCGAATAGCGCCGCTAATAATA
Found at i:4049233 original size:11 final size:11
Alignment explanation
Indices: 4049213--4049245 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
4049203 ATTTATTGAC
*
4049213 TGTCAGTGAAT
1 TGTCAATGAAT
4049224 TGTCAATGAA-
1 TGTCAATGAAT
4049234 TGTCAATGAAT
1 TGTCAATGAAT
4049245 T
1 T
4049246 ATTAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.36
Consensus pattern (11 bp):
TGTCAATGAAT
Found at i:4049336 original size:13 final size:13
Alignment explanation
Indices: 4049290--4049381 Score: 73
Period size: 13 Copynumber: 6.9 Consensus size: 13
4049280 TATAACTTAC
4049290 ATTACTTAAATAT
1 ATTACTTAAATAT
* *
4049303 ATTAATTACTAAAAT
1 ATTACTTA--AATAT
4049318 -TTACTTAAATAT
1 ATTACTTAAATAT
*
4049330 ATTACTTAAATAC
1 ATTACTTAAATAT
* *
4049343 ATTACTT-ACTAGA
1 ATTACTTAAATA-T
4049356 ATTGGA-TTAAATAT
1 ATT--ACTTAAATAT
4049370 ATTACTTAAATA
1 ATTACTTAAATA
4049382 CATGACTTAC
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
12 8 0.13
13 35 0.56
14 11 0.18
15 8 0.13
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (13 bp):
ATTACTTAAATAT
Found at i:4049352 original size:40 final size:40
Alignment explanation
Indices: 4049290--4049398 Score: 157
Period size: 40 Copynumber: 2.7 Consensus size: 40
4049280 TATAACTTAC
* * *
4049290 ATTACTTAAATATATTAATTACTAAAATT-TACTTAAATAT
1 ATTACTTAAATACATTACTTACTAAAATTGGA-TTAAATAT
*
4049330 ATTACTTAAATACATTACTTACTAGAATTGGATTAAATAT
1 ATTACTTAAATACATTACTTACTAAAATTGGATTAAATAT
*
4049370 ATTACTTAAATACATGACTTACTAAAATT
1 ATTACTTAAATACATTACTTACTAAAATT
4049399 AAAGTATATA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
40 61 0.98
41 1 0.02
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (40 bp):
ATTACTTAAATACATTACTTACTAAAATTGGATTAAATAT
Found at i:4049433 original size:17 final size:17
Alignment explanation
Indices: 4049413--4049473 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
4049403 TATATATTAC
4049413 ATTACTTACTAAAATAT
1 ATTACTTACTAAAATAT
*
4049430 ATTACATTACTTAAATAT
1 ATTAC-TTACTAAAATAT
* *
4049448 ATTACTTACAAAAATTT
1 ATTACTTACTAAAATAT
*
4049465 ATAACTTAC
1 ATTACTTAC
4049474 ACTACTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
17 22 0.58
18 16 0.42
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTACTTACTAAAATAT
Found at i:4049445 original size:18 final size:18
Alignment explanation
Indices: 4049413--4049501 Score: 92
Period size: 18 Copynumber: 4.8 Consensus size: 18
4049403 TATATATTAC
*
4049413 ATTAC-TTACTAAAATAT
1 ATTACATTACTTAAATAT
4049430 ATTACATTACTTAAATAT
1 ATTACATTACTTAAATAT
**
4049448 ATTAC-TTACAAAAATTTAT
1 ATTACATTACTTAAA--TAT
*
4049467 AACTTACACTACTTAAATAT
1 -A-TTACATTACTTAAATAT
4049487 ATTACATTACTTAAA
1 ATTACATTACTTAAA
4049502 CTTTATATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
17 12 0.20
18 29 0.49
19 4 0.07
20 4 0.07
21 4 0.07
22 6 0.10
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTACATTACTTAAATAT
Found at i:4049456 original size:22 final size:21
Alignment explanation
Indices: 4049404--4049496 Score: 67
Period size: 17 Copynumber: 4.6 Consensus size: 21
4049394 AAATTAAAGT
4049404 ATATATTACATTAC-TTACTAA
1 ATATATTAC-TTACATTACTAA
4049425 A-ATA-TA-TTACATTACTTAA
1 ATATATTACTTACATTAC-TAA
4049444 ATATATTACTTACA--A--AA
1 ATATATTACTTACATTACTAA
* * *
4049461 ATTTATAACTTACACTACTTAA
1 ATATATTACTTACATTAC-TAA
4049483 ATATATTACATTAC
1 ATATATTAC-TTAC
4049497 TTAAACTTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
17 18 0.32
18 4 0.07
19 7 0.12
20 7 0.12
21 3 0.05
22 14 0.25
23 4 0.07
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATATTACTTACATTACTAA
Found at i:4049462 original size:35 final size:38
Alignment explanation
Indices: 4049413--4049496 Score: 111
Period size: 39 Copynumber: 2.2 Consensus size: 38
4049403 TATATATTAC
* *
4049413 ATTACTTACTAAAA-TAT-A-TTACATTACTTAAATAT
1 ATTACTTACAAAAATTATAACTTACACTACTTAAATAT
4049448 ATTACTTACAAAAATTTATAACTTACACTACTTAAATAT
1 ATTACTTACAAAAA-TTATAACTTACACTACTTAAATAT
4049487 ATTACATTAC
1 ATTAC-TTAC
4049497 TTAAACTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
35 13 0.31
37 3 0.07
38 1 0.02
39 21 0.50
40 4 0.10
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.40
Consensus pattern (38 bp):
ATTACTTACAAAAATTATAACTTACACTACTTAAATAT
Found at i:4050122 original size:16 final size:16
Alignment explanation
Indices: 4050084--4050114 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4050074 TAACTTTGAT
*
4050084 AACTAACATAATACAC
1 AACTTACATAATACAC
4050100 AACTTACATAATACA
1 AACTTACATAATACA
4050115 TTACTTACTT
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:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (16 bp):
AACTTACATAATACAC
Found at i:4050132 original size:25 final size:25
Alignment explanation
Indices: 4050022--4050378 Score: 247
Period size: 25 Copynumber: 14.2 Consensus size: 25
4050012 TCAATTTTTA
*
4050022 ATAACTTACATAATACACAACTTAC
1 ATAACTTACATAATACATAACTTAC
* *
4050047 ATAACTTAAATAGAAACACATAA--TAC
1 ATAACTTACAT---AATACATAACTTAC
**
4050073 ATAACTTTGATAACTAACATAA--TAC
1 ATAACTTACATAA-T-ACATAACTTAC
* *
4050098 ACAACTTACATAATACATTACTTAC
1 ATAACTTACATAATACATAACTTAC
* * *
4050123 TTAACATACATAGCCTACATAACTTAC
1 ATAACTTACATA--ATACATAACTTAC
* ** *
4050150 ATAATTTACATGTTACATAACTTAA
1 ATAACTTACATAATACATAACTTAC
**
4050175 ATAACTTACATAATACATAACTTTG
1 ATAACTTACATAATACATAACTTAC
* * *
4050200 ATAACTAACATTATACACAACTTAC
1 ATAACTTACATAATACATAACTTAC
* ** *
4050225 ATAA-TTGTCATGTTACATAACTTAA
1 ATAACTT-ACATAATACATAACTTAC
* **
4050250 ATAACTTACATAAAACATAACTTTG
1 ATAACTTACATAATACATAACTTAC
* * * *
4050275 ATAACTAACATTATTCACAACTTAC
1 ATAACTTACATAATACATAACTTAC
* * ** *
4050300 ATGATTTACATGTTACATAACTTAA
1 ATAACTTACATAATACATAACTTAC
**
4050325 ATAACTTACATAATACATAACTTTG
1 ATAACTTACATAATACATAACTTAC
* * *
4050350 ATAACTAACATTATACACAACTTAC
1 ATAACTTACATAATACATAACTTAC
4050375 ATAA
1 ATAA
4050379 TACACAACTT
Statistics
Matches: 252, Mismatches: 69, Indels: 22
0.73 0.20 0.06
Matches are distributed among these distances:
23 7 0.03
24 2 0.01
25 203 0.81
26 14 0.06
27 19 0.08
28 7 0.03
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.32
Consensus pattern (25 bp):
ATAACTTACATAATACATAACTTAC
Found at i:4050150 original size:9 final size:9
Alignment explanation
Indices: 4050022--4050415 Score: 166
Period size: 9 Copynumber: 47.0 Consensus size: 9
4050012 TCAATTTTTA
4050022 ATAACTTAC
1 ATAACTTAC
4050031 ATAA--TAC
1 ATAACTTAC
*
4050038 ACAACTTAC
1 ATAACTTAC
*
4050047 ATAACTTAA
1 ATAACTTAC
***
4050056 ATAGAAACAC
1 ATA-ACTTAC
4050066 ATAA--TAC
1 ATAACTTAC
**
4050073 ATAACTTTG
1 ATAACTTAC
*
4050082 ATAACTAAC
1 ATAACTTAC
4050091 ATAA--TAC
1 ATAACTTAC
*
4050098 ACAACTTAC
1 ATAACTTAC
4050107 ATAA--TAC
1 ATAACTTAC
*
4050114 ATTACTTAC
1 ATAACTTAC
* *
4050123 TTAACATAC
1 ATAACTTAC
* *
4050132 ATAGCCTAC
1 ATAACTTAC
4050141 ATAACTTAC
1 ATAACTTAC
*
4050150 ATAATTTAC
1 ATAACTTAC
*
4050159 AT--GTTAC
1 ATAACTTAC
*
4050166 ATAACTTAA
1 ATAACTTAC
4050175 ATAACTTAC
1 ATAACTTAC
4050184 ATAA--TAC
1 ATAACTTAC
**
4050191 ATAACTTTG
1 ATAACTTAC
*
4050200 ATAACTAAC
1 ATAACTTAC
*
4050209 ATTA--TAC
1 ATAACTTAC
*
4050216 ACAACTTAC
1 ATAACTTAC
*
4050225 ATAA-TTGTC
1 ATAACTT-AC
*
4050234 AT--GTTAC
1 ATAACTTAC
*
4050241 ATAACTTAA
1 ATAACTTAC
4050250 ATAACTTAC
1 ATAACTTAC
*
4050259 ATAA--AAC
1 ATAACTTAC
**
4050266 ATAACTTTG
1 ATAACTTAC
*
4050275 ATAACTAAC
1 ATAACTTAC
*
4050284 ATTA-TT-C
1 ATAACTTAC
*
4050291 ACAACTTAC
1 ATAACTTAC
* *
4050300 ATGATTTAC
1 ATAACTTAC
*
4050309 AT--GTTAC
1 ATAACTTAC
*
4050316 ATAACTTAA
1 ATAACTTAC
4050325 ATAACTTAC
1 ATAACTTAC
4050334 ATAA--TAC
1 ATAACTTAC
**
4050341 ATAACTTTG
1 ATAACTTAC
*
4050350 ATAACTAAC
1 ATAACTTAC
*
4050359 ATTA--TAC
1 ATAACTTAC
*
4050366 ACAACTTAC
1 ATAACTTAC
4050375 ATAA--TAC
1 ATAACTTAC
*
4050382 ACAACTTAC
1 ATAACTTAC
*
4050391 ATAGCTTAC
1 ATAACTTAC
*
4050400 ACAA--TAC
1 ATAACTTAC
4050407 ATAACTTAC
1 ATAACTTAC
4050416 CCGTGCAATT
Statistics
Matches: 273, Mismatches: 79, Indels: 66
0.65 0.19 0.16
Matches are distributed among these distances:
7 81 0.30
8 7 0.03
9 180 0.66
10 5 0.02
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (9 bp):
ATAACTTAC
Found at i:4050391 original size:25 final size:25
Alignment explanation
Indices: 4050363--4050415 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
4050353 ACTAACATTA
*
4050363 TACACAACTTACATAATACACAACT
1 TACACAACTTACACAATACACAACT
* * *
4050388 TACATAGCTTACACAATACATAACT
1 TACACAACTTACACAATACACAACT
4050413 TAC
1 TAC
4050416 CCGTGCAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.26
Consensus pattern (25 bp):
TACACAACTTACACAATACACAACT
Found at i:4050393 original size:75 final size:75
Alignment explanation
Indices: 4050138--4050379 Score: 432
Period size: 75 Copynumber: 3.2 Consensus size: 75
4050128 ATACATAGCC
*
4050138 TACATAACTTACATAATTTACATGTTACATAACTTAAATAACTTACATAATACATAACTTTGATA
1 TACACAACTTACATAATTTACATGTTACATAACTTAAATAACTTACATAATACATAACTTTGATA
4050203 ACTAACATTA
66 ACTAACATTA
*
4050213 TACACAACTTACATAATTGT-CATGTTACATAACTTAAATAACTTACATAAAACATAACTTTGAT
1 TACACAACTTACATAATT-TACATGTTACATAACTTAAATAACTTACATAATACATAACTTTGAT
4050277 AACTAACATTA
65 AACTAACATTA
* *
4050288 TTCACAACTTACATGATTTACATGTTACATAACTTAAATAACTTACATAATACATAACTTTGATA
1 TACACAACTTACATAATTTACATGTTACATAACTTAAATAACTTACATAATACATAACTTTGATA
4050353 ACTAACATTA
66 ACTAACATTA
4050363 TACACAACTTACATAAT
1 TACACAACTTACATAAT
4050380 ACACAACTTA
Statistics
Matches: 158, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
74 1 0.01
75 156 0.99
76 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (75 bp):
TACACAACTTACATAATTTACATGTTACATAACTTAAATAACTTACATAATACATAACTTTGATA
ACTAACATTA
Found at i:4050407 original size:41 final size:41
Alignment explanation
Indices: 4050327--4050415 Score: 106
Period size: 41 Copynumber: 2.2 Consensus size: 41
4050317 TAACTTAAAT
* ** **
4050327 AACTTACATAATACATAACTTTGATAACTAACATTATACAC
1 AACTTACATAATACACAACTTACATAACTAACACAATACAC
* * *
4050368 AACTTACATAATACACAACTTACATAGCTTACACAATACAT
1 AACTTACATAATACACAACTTACATAACTAACACAATACAC
4050409 AACTTAC
1 AACTTAC
4050416 CCGTGCAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.29
Consensus pattern (41 bp):
AACTTACATAATACACAACTTACATAACTAACACAATACAC
Found at i:4052253 original size:14 final size:15
Alignment explanation
Indices: 4052227--4052257 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4052217 ACTATATATA
4052227 TATGGATTTAGGGAT
1 TATGGATTTAGGGAT
4052242 TATGGA-TTAGGGAT
1 TATGGATTTAGGGAT
4052256 TA
1 TA
4052258 AGGGTTGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (15 bp):
TATGGATTTAGGGAT
Found at i:4052340 original size:15 final size:16
Alignment explanation
Indices: 4052320--4052358 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
4052310 ACGTTAGTGG
4052320 TTAAGAG-TTAGGGAT
1 TTAAGAGTTTAGGGAT
*
4052335 TTAAGAGGTTTAGGGTT
1 TTAAGA-GTTTAGGGAT
4052352 TTAAGAG
1 TTAAGAG
4052359 GGTCGGGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 2 0.10
17 13 0.62
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (16 bp):
TTAAGAGTTTAGGGAT
Found at i:4052349 original size:17 final size:17
Alignment explanation
Indices: 4052327--4052359 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4052317 TGGTTAAGAG
4052327 TTAGGGATTTAAGAGGT
1 TTAGGGATTTAAGAGGT
*
4052344 TTAGGGTTTTAAGAGG
1 TTAGGGATTTAAGAGG
4052360 GTCGGGTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.36, T:0.36
Consensus pattern (17 bp):
TTAGGGATTTAAGAGGT
Found at i:4052707 original size:12 final size:12
Alignment explanation
Indices: 4052685--4052715 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
4052675 TAGATATTAC
4052685 TTAAGAAATAAAA
1 TTAA-AAATAAAA
4052698 TTAAAAATAAAA
1 TTAAAAATAAAA
4052710 TTAAAA
1 TTAAAA
4052716 TACAAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (12 bp):
TTAAAAATAAAA
Found at i:4052729 original size:20 final size:20
Alignment explanation
Indices: 4052700--4052752 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
4052690 AAATAAAATT
4052700 AAAAAT-AAAATTAAA-ATA
1 AAAAATCAAAATTAAATATA
*
4052718 CAAAAATCAAAATGAAATATA
1 -AAAAATCAAAATTAAATATA
*
4052739 AAAACTCTAAAATT
1 AAAAATC-AAAATT
4052753 TTTAATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 6 0.21
20 14 0.50
21 8 0.29
ACGTcount: A:0.68, C:0.08, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAAATCAAAATTAAATATA
Found at i:4052741 original size:19 final size:18
Alignment explanation
Indices: 4052690--4052742 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
4052680 ATTACTTAAG
4052690 AAATAAAAT-TAAAAATA
1 AAATAAAATATAAAAATA
*
4052707 AAATTAAAATACAAAAATCA
1 AAA-TAAAATATAAAAAT-A
*
4052727 AAATGAAATATAAAAA
1 AAATAAAATATAAAAA
4052743 CTCTAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 3 0.10
18 6 0.20
19 17 0.57
20 4 0.13
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.21
Consensus pattern (18 bp):
AAATAAAATATAAAAATA
Found at i:4053168 original size:84 final size:81
Alignment explanation
Indices: 4053044--4053321 Score: 315
Period size: 84 Copynumber: 3.3 Consensus size: 81
4053034 AATTTTATCA
* * ** *
4053044 TTTTTGTAAACAAAACGGTGTCGTTTTGCCTGGCATATTAACGGCATTAGTGGCATTACGCCGAA
1 TTTTT-TAAACAAAACGGTGTCGTTTTACCTGGCACATTAACGGCATTAGTGGCGCTATG--GAA
4053109 AACGCCGCAAA-TTGTCGGGG
63 AACGCCGCAAAGTT-TC-GGG
* ** * * * *
4053129 TTTTTTTAATGAAACGGTGGCGTTTTAACTAGCACATTAAGGGCATTAGTGGCGCTATGGTAAAA
1 TTTTTTAAACAAAACGGTGTCGTTTTACCTGGCACATTAACGGCATTAGTGGCGCTATGG-AAAA
4053194 GCGCCGCAAAGTTTTCGGG
65 -CGCCGCAAAG-TTTCGGG
* * *
4053213 TTTTTTAAACCAAACGGTGTCGTTTTCCCTGGCACATTAACGACATTAGTGGCGCTATGGTGAAA
1 TTTTTTAAACAAAACGGTGTCGTTTTACCTGGCACATTAACGGCATTAGTGGCGCTAT-G-GAAA
4053278 ACGCCGCAAAGTTTCGGG
64 ACGCCGCAAAGTTTCGGG
*
4053296 TTTTTTAAACAAAACGGTGCCGTTTT
1 TTTTTTAAACAAAACGGTGTCGTTTT
4053322 GCCTTTACGG
Statistics
Matches: 164, Mismatches: 23, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
82 1 0.01
83 35 0.21
84 113 0.69
85 12 0.07
86 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (81 bp):
TTTTTTAAACAAAACGGTGTCGTTTTACCTGGCACATTAACGGCATTAGTGGCGCTATGGAAAAC
GCCGCAAAGTTTCGGG
Found at i:4055646 original size:9 final size:9
Alignment explanation
Indices: 4055632--4055790 Score: 51
Period size: 9 Copynumber: 16.8 Consensus size: 9
4055622 TTAATTAATA
4055632 TACATAAAT
1 TACATAAAT
*
4055641 TACATAAGT
1 TACATAAAT
4055650 TACATTAATATT
1 TACA-TAA-A-T
4055662 ATACATAAAT
1 -TACATAAAT
*
4055672 TACATAACT
1 TACATAAAT
*
4055681 TA-ATTAAT
1 TACATAAAT
*
4055689 TA-AT-ATT
1 TACATAAAT
*
4055696 ATACATAACT
1 -TACATAAAT
*
4055706 TGCATTAATATT
1 TACA-TAA-A-T
4055718 ATACATAAAT
1 -TACATAAAT
*
4055728 TACATAACT
1 TACATAAAT
*
4055737 TA-ATTAAT
1 TACATAAAT
*
4055745 TA-AT-ATT
1 TACATAAAT
*
4055752 ATACATAACT
1 -TACATAAAT
*
4055762 TACATTAGTATT
1 TACA-TA--AAT
4055774 ATACATAAAT
1 -TACATAAAT
4055784 TACATAA
1 TACATAA
4055791 CTTAATTAAT
Statistics
Matches: 115, Mismatches: 17, Indels: 36
0.68 0.10 0.21
Matches are distributed among these distances:
7 4 0.03
8 20 0.17
9 50 0.43
10 16 0.14
11 2 0.02
12 12 0.10
13 11 0.10
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.40
Consensus pattern (9 bp):
TACATAAAT
Found at i:4055712 original size:56 final size:56
Alignment explanation
Indices: 4055641--4056118 Score: 495
Period size: 56 Copynumber: 8.2 Consensus size: 56
4055631 ATACATAAAT
*
4055641 TACATAAGTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTA
1 TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTA
*
4055697 TACATAACTTGCATTAATATTATACATAAATTACATAACTTAATTAATTAATATTA
1 TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTA
*
4055753 TACATAACTTACATTAGTATTATACATAAATTACATAACTTAATTAA-T--TATTA
1 TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTA
* * * *
4055806 CACATAAATTACATTGCTTACAGTAATA-ACTTACAACTTACATAACTTAATTAATTAATATTA
1 TACATAACTTACA----TTA-A-TATTATACATA-AA-TTACATAACTTAATTAATTAATATTA
* * *** * *
4055869 TACATAACTTACATAGCTTACA-ACT-TACATAACTTACATTTTTATAATT-ATTCATA-AA
1 TACATAACTTAC--A--TTA-ATATTATACATAAATTACATAACT-TAATTAATTAATATTA
*
4055927 TTGCATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATACATAAA
1 -TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATAT---T--A
* **
4055989 TTACATAACTAATTAGATTAATATTATACATAAATTACATAACTTTGTTAATTAATATTA
1 -TACATAAC---TTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTA
* * *
4056049 TACATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTA
1 TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTA
4056105 TACATAACTTACAT
1 TACATAACTTACAT
4056119 AACTTACAAC
Statistics
Matches: 359, Mismatches: 35, Indels: 56
0.80 0.08 0.12
Matches are distributed among these distances:
53 16 0.04
54 1 0.00
55 11 0.03
56 177 0.49
57 4 0.01
58 5 0.01
59 38 0.11
60 24 0.07
61 7 0.02
62 10 0.03
63 22 0.06
65 44 0.12
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.40
Consensus pattern (56 bp):
TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTA
Found at i:4055773 original size:22 final size:22
Alignment explanation
Indices: 4055738--4055788 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
4055728 TACATAACTT
4055738 AATTA-ATTAATATTATACATA
1 AATTACATTAATATTATACATA
* *
4055759 ACTTACATTAGTATTATACATA
1 AATTACATTAATATTATACATA
4055781 AATTACAT
1 AATTACAT
4055789 AACTTAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (22 bp):
AATTACATTAATATTATACATA
Found at i:4055852 original size:16 final size:16
Alignment explanation
Indices: 4055831--4055906 Score: 59
Period size: 16 Copynumber: 4.6 Consensus size: 16
4055821 GCTTACAGTA
4055831 ATAACTTACAACTTAC
1 ATAACTTACAACTTAC
*
4055847 ATAACTTA-ATTAATTA-
1 ATAACTTACA--ACTTAC
*
4055863 AT-ATTATACATAACTTAC
1 ATAACT-TAC--AACTTAC
*
4055881 ATAGCTTACAACTTAC
1 ATAACTTACAACTTAC
4055897 ATAACTTACA
1 ATAACTTACA
4055907 TTTTTATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 16
0.68 0.09 0.24
Matches are distributed among these distances:
15 3 0.07
16 28 0.61
17 8 0.17
18 5 0.11
19 2 0.04
ACGTcount: A:0.45, C:0.18, G:0.01, T:0.36
Consensus pattern (16 bp):
ATAACTTACAACTTAC
Found at i:4055854 original size:9 final size:9
Alignment explanation
Indices: 4055831--4055907 Score: 62
Period size: 9 Copynumber: 9.2 Consensus size: 9
4055821 GCTTACAGTA
4055831 ATAACTTAC
1 ATAACTTAC
4055840 --AACTTAC
1 ATAACTTAC
4055847 ATAACTTA-
1 ATAACTTAC
4055855 ATTAA-TTA-
1 A-TAACTTAC
*
4055863 AT-ATTATAC
1 ATAACT-TAC
4055872 ATAACTTAC
1 ATAACTTAC
*
4055881 ATAGCTTAC
1 ATAACTTAC
4055890 --AACTTAC
1 ATAACTTAC
4055897 ATAACTTAC
1 ATAACTTAC
4055906 AT
1 AT
4055908 TTTTATAATT
Statistics
Matches: 56, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
6 1 0.02
7 15 0.27
8 7 0.12
9 31 0.55
10 2 0.04
ACGTcount: A:0.44, C:0.18, G:0.01, T:0.36
Consensus pattern (9 bp):
ATAACTTAC
Found at i:4055856 original size:112 final size:109
Alignment explanation
Indices: 4055641--4056118 Score: 347
Period size: 121 Copynumber: 4.1 Consensus size: 109
4055631 ATACATAAAT
* ** *
4055641 TACATAAGTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACT
1 TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATAACATAAATAACT
*
4055706 TGCATTAATATTATACATAAATTACATAACTTAATTAATTAATATTA
66 TGCATTAATAATATACATAAATTACATAAC---ATTAATTAATATTA
* * *
4055753 TACATAACTTACATTAGTATTATACATAAATTACATAACTTAATTAATTATTACACATAAATTAC
1 TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATA-ACATAAATAAC
*
4055818 ATTGC-TTACAGTAATA-ACTTACAACTTACATAACTTAATTAATTAATATTA
65 -TTGCATTA-A-TAATATACATA-AA-TTACATAAC---ATTAATTAATATTA
* * *** * *
4055869 TACATAACTTACATAGCTTACA-ACT-TACATAACTTACATTTTTATAATT-ATTCATAA-ATTG
1 TACATAACTTAC--A--TTA-ATATTATACATAAATTACATAACT-TAATTAATTAATAACA-TA
* * *
4055930 CATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATACATAAA
59 AATAACTTGCATTAATAATATACATAAATTACATAAC---ATTAATTAATAT---T--A
* ** ** *
4055989 TTACATAACTAATTAGATTAATATTATACATAAATTACATAACTTTGTTAATTAATATTATACAT
1 -TACATAAC---TTACATTAATATTATACATAAATTACATAACTTAATTAATTAATAACATAAAT
* * * *
4056054 AACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTA
62 AACTTGCATTAATAATATACATAAATTACATAA--CA-TTAATTAATATTA
4056105 TACATAACTTACAT
1 TACATAACTTACAT
4056119 AACTTACAAC
Statistics
Matches: 298, Mismatches: 37, Indels: 62
0.75 0.09 0.16
Matches are distributed among these distances:
112 55 0.18
113 10 0.03
114 9 0.03
115 38 0.13
116 45 0.15
117 9 0.03
118 12 0.04
119 20 0.07
120 20 0.07
121 75 0.25
122 2 0.01
124 3 0.01
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.40
Consensus pattern (109 bp):
TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATAACATAAATAACT
TGCATTAATAATATACATAAATTACATAACATTAATTAATATTA
Found at i:4055897 original size:25 final size:24
Alignment explanation
Indices: 4055834--4055907 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 24
4055824 TACAGTAATA
4055834 ACTTACAACTTACATAACTTA-ATT
1 ACTTACAACTTACATAACTTACA-T
* *
4055858 AATTA-ATATTATACATAACTTACAT
1 ACTTACA-ACT-TACATAACTTACAT
4055883 AGCTTACAACTTACATAACTTACAT
1 A-CTTACAACTTACATAACTTACAT
4055908 TTTTATAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
23 1 0.02
24 6 0.15
25 27 0.66
26 6 0.15
27 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.01, T:0.36
Consensus pattern (24 bp):
ACTTACAACTTACATAACTTACAT
Found at i:4055919 original size:50 final size:50
Alignment explanation
Indices: 4055831--4056033 Score: 160
Period size: 50 Copynumber: 4.1 Consensus size: 50
4055821 GCTTACAGTA
*
4055831 ATAACTTACAACTTACATAACTTAATTAATTAATATTATACATAACTTAC
1 ATAACTTACAACTTACATAACTTAATTAATTAATATTATACATAAATTAC
* * * *
4055881 ATAGCTTACAACTTACATAACTTACATT--TTTATAATTATTCATAAATTGC
1 ATAACTTACAACTTACATAACTTA-ATTAATTAAT-ATTATACATAAATTAC
* * * *
4055931 ATAACTTAC-A-TTA-AT-ATTATACATAAATTACATAACT-TA-ATTAATTA-
1 ATAACTTACAACTTACATAACT-TA-ATTAATTA-AT-ATTATACATAAATTAC
*
4055978 ATATACATA-AA-TTACATAAC-TAATTAGATTAATATTATACATAAATTAC
1 ATA-ACTTACAACTTACATAACTTAATTA-ATTAATATTATACATAAATTAC
4056027 ATAACTT
1 ATAACTT
4056034 TGTTAATTAA
Statistics
Matches: 120, Mismatches: 19, Indels: 30
0.71 0.11 0.18
Matches are distributed among these distances:
46 4 0.03
47 17 0.14
48 33 0.28
49 13 0.11
50 50 0.42
51 3 0.03
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.39
Consensus pattern (50 bp):
ATAACTTACAACTTACATAACTTAATTAATTAATATTATACATAAATTAC
Found at i:4056001 original size:22 final size:22
Alignment explanation
Indices: 4055959--4056001 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
4055949 ATACATAAAT
* *
4055959 TACATAACTTAATTAATTAATA
1 TACATAAATTAATTAACTAATA
4055981 TACATAAATTACA-TAACTAAT
1 TACATAAATTA-ATTAACTAAT
4056002 TAGATTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TACATAAATTAATTAACTAATA
Found at i:4056018 original size:34 final size:34
Alignment explanation
Indices: 4055893--4056062 Score: 187
Period size: 34 Copynumber: 5.2 Consensus size: 34
4055883 AGCTTACAAC
* *
4055893 TTACATAACTTACATT--TTTATAATTATTCATAAA
1 TTACATAACTTA-ATTAATTAAT-ATTATACATAAA
* *
4055927 TTGCATAACTT-A--CATTAATATTATACATAAA
1 TTACATAACTTAATTAATTAATATTATACATAAA
4055958 TTACATAACTTAATTAATT-A-A-TATACATAAA
1 TTACATAACTTAATTAATTAATATTATACATAAA
4055989 TTACATAAC-TAATTAGATTAATATTATACATAAA
1 TTACATAACTTAATTA-ATTAATATTATACATAAA
** *
4056023 TTACATAACTTTGTTAATTAATATTATACATAAC
1 TTACATAACTTAATTAATTAATATTATACATAAA
4056057 TTACAT
1 TTACAT
4056063 TAATATTATA
Statistics
Matches: 118, Mismatches: 8, Indels: 20
0.81 0.05 0.14
Matches are distributed among these distances:
30 6 0.05
31 43 0.36
32 8 0.07
33 2 0.02
34 55 0.47
35 4 0.03
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (34 bp):
TTACATAACTTAATTAATTAATATTATACATAAA
Found at i:4056067 original size:22 final size:22
Alignment explanation
Indices: 4056039--4056084 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
4056029 AACTTTGTTA
*
4056039 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTAC
*
4056061 ATTAATATTATACTTAAATTAC
1 ATTAATATTATACATAAATTAC
4056083 AT
1 AT
4056085 AAGTTAGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTAATATTATACATAAATTAC
Found at i:4056099 original size:90 final size:90
Alignment explanation
Indices: 4055959--4056123 Score: 253
Period size: 90 Copynumber: 1.8 Consensus size: 90
4055949 ATACATAAAT
4055959 TACATAACTTAATTAATTAATATACATAAATTACATAACTAATTAGATTAATATTATACATAAAT
1 TACATAACTTAATTAATTAATATACATAAATTACATAACTAATTAGATTAATATTATACATAAAT
4056024 TACATAACTTTGTTAATTAATATTA
66 TACATAACTTTGTTAATTAATATTA
* * * *
4056049 TACATAACTTACATTAA-TATTATACTTAAATTACATAAGTTAGTTA-ATTAATATTATACATAA
1 TACATAACTTA-ATTAATTAATATACATAAATTACATAA-CTAATTAGATTAATATTATACATAA
*
4056112 CTTACATAACTT
64 ATTACATAACTT
4056124 ACAACTTACA
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
90 58 0.85
91 10 0.15
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.41
Consensus pattern (90 bp):
TACATAACTTAATTAATTAATATACATAAATTACATAACTAATTAGATTAATATTATACATAAAT
TACATAACTTTGTTAATTAATATTA
Found at i:4056119 original size:9 final size:9
Alignment explanation
Indices: 4056105--4056322 Score: 96
Period size: 9 Copynumber: 26.2 Consensus size: 9
4056095 ATTAATATTA
4056105 TACATAACT
1 TACATAACT
4056114 TACATAACT
1 TACATAACT
4056123 TAC--AACT
1 TACATAACT
4056130 TACATAACT
1 TACATAACT
* ***
4056139 TACGTTTTTT
1 TAC-ATAACT
*
4056149 TA-ATTA-T
1 TACATAACT
* *
4056156 T-CGTAAAT
1 TACATAACT
4056164 TACATAACT
1 TACATAACT
* *
4056173 TACTTAATT
1 TACATAACT
*
4056182 TTCATAA--
1 TACATAACT
*
4056189 TAAATAACT
1 TACATAACT
4056198 TACATAACT
1 TACATAACT
4056207 TAC--AACT
1 TACATAACT
4056214 TACATAACT
1 TACATAACT
* *
4056223 TATATGACT
1 TACATAACT
4056232 TACATAACT
1 TACATAACT
4056241 TACAT-A--
1 TACATAACT
* *
4056247 -GCATAATT
1 TACATAACT
*
4056255 TTCATAA--
1 TACATAACT
*
4056262 TACACAACT
1 TACATAACT
*
4056271 TACATAATT
1 TACATAACT
***
4056280 TGGGTAA-T
1 TACATAACT
*
4056288 GA-ATAACT
1 TACATAACT
4056296 TACATAA--
1 TACATAACT
4056303 TACATAACT
1 TACATAACT
4056312 TACATAACT
1 TACATAACT
4056321 TA
1 TA
4056323 ACTATACTTA
Statistics
Matches: 155, Mismatches: 34, Indels: 40
0.68 0.15 0.17
Matches are distributed among these distances:
5 3 0.02
6 1 0.01
7 38 0.25
8 8 0.05
9 101 0.65
10 4 0.03
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.38
Consensus pattern (9 bp):
TACATAACT
Found at i:4056131 original size:16 final size:16
Alignment explanation
Indices: 4056110--4056141 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4056100 TATTATACAT
4056110 AACTTACATAACTTAC
1 AACTTACATAACTTAC
4056126 AACTTACATAACTTAC
1 AACTTACATAACTTAC
4056142 GTTTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:4056201 original size:34 final size:34
Alignment explanation
Indices: 4056163--4056277 Score: 99
Period size: 34 Copynumber: 3.2 Consensus size: 34
4056153 TATTCGTAAA
4056163 TTACATAACTTACTTAATTTTCATAATAAATAAC
1 TTACATAACTTACTTAATTTTCATAATAAATAAC
* * * *
4056197 TTACATAACTTAC--AACTTACATAACTTATATGAC
1 TTACATAACTTACTTAATTTTCATAA--TAAATAAC
* *
4056231 TTACATAACTTACATAGCATAATTTTCATAATACACAAC
1 TTACATAACTTAC-T----TAATTTTCATAATAAATAAC
4056270 TTACATAA
1 TTACATAA
4056278 TTTGGGTAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
32 9 0.14
34 32 0.51
39 13 0.21
41 9 0.14
ACGTcount: A:0.43, C:0.18, G:0.02, T:0.37
Consensus pattern (34 bp):
TTACATAACTTACTTAATTTTCATAATAAATAAC
Found at i:4056234 original size:18 final size:16
Alignment explanation
Indices: 4056194--4056244 Score: 75
Period size: 16 Copynumber: 3.1 Consensus size: 16
4056184 CATAATAAAT
4056194 AACTTACATAACTTAC
1 AACTTACATAACTTAC
*
4056210 AACTTACATAACTTAT
1 AACTTACATAACTTAC
4056226 ATGACTTACATAACTTAC
1 A--ACTTACATAACTTAC
4056244 A
1 A
4056245 TAGCATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 16 0.52
18 15 0.48
ACGTcount: A:0.43, C:0.22, G:0.02, T:0.33
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:4063522 original size:43 final size:42
Alignment explanation
Indices: 4063459--4063672 Score: 194
Period size: 43 Copynumber: 5.0 Consensus size: 42
4063449 GCCAAATTTA
* * * *
4063459 GTGGCGTTTTTGGTCAAAGCGTCGCTAAAGATTAGGTTCTTT
1 GTGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGTCTTT
** *
4063501 AGTGGCGTTTGTGGTTGAAGCGCCGCTATAGATCAGGGTCTATT
1 -GTGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGTCT-TT
* * ** * * *
4063545 GCGGCGTTTGAGGGGAAAGCGCCGCTAAAAATTAGGTTCTTT
1 GTGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGTCTTT
* *
4063587 CGTGGCATTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTATT
1 -GTGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGTCT-TT
* *** **
4063631 GTGGCGTTTGAGAAAAAAATGCCGCTAAAGATCAGGGTCTTT
1 GTGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGTCTTT
4063673 AGCGGCGCTT
Statistics
Matches: 135, Mismatches: 33, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
42 4 0.03
43 127 0.94
44 4 0.03
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.30
Consensus pattern (42 bp):
GTGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGTCTTT
Found at i:4063608 original size:86 final size:86
Alignment explanation
Indices: 4063474--4063642 Score: 275
Period size: 86 Copynumber: 2.0 Consensus size: 86
4063464 GTTTTTGGTC
* * * **
4063474 AAAGCGTCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTTGAAGCGCCGCTATAGATCAGGG
1 AAAGCGCCGCTAAAAATTAGGTTCTTTAGTGGCATTTGTGGTCAAAGCGCCGCTATAGATCAGGG
4063539 TCTATTGCGGCGTTTGAGGGG
66 TCTATTGCGGCGTTTGAGGGG
*
4063560 AAAGCGCCGCTAAAAATTAGGTTCTTTCGTGGCATTTGTGGTCAAAGCGCCGCTATAGATCAGGG
1 AAAGCGCCGCTAAAAATTAGGTTCTTTAGTGGCATTTGTGGTCAAAGCGCCGCTATAGATCAGGG
*
4063625 TCTATTGTGGCGTTTGAG
66 TCTATTGCGGCGTTTGAG
4063643 AAAAAAATGC
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 76 1.00
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (86 bp):
AAAGCGCCGCTAAAAATTAGGTTCTTTAGTGGCATTTGTGGTCAAAGCGCCGCTATAGATCAGGG
TCTATTGCGGCGTTTGAGGGG
Found at i:4063655 original size:86 final size:86
Alignment explanation
Indices: 4063481--4063674 Score: 262
Period size: 86 Copynumber: 2.3 Consensus size: 86
4063471 GTCAAAGCGT
* * **
4063481 CGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTTGAAGCGCCGCTATAGATCAGGGTCTATTG
1 CGCTAAAAATTAGGTTCTTTAGTGGCATTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTATTG
*** *
4063546 CGGCGTTTGAGGGGAAAGCGC
66 CGGCGTTTGAGAAAAAAACGC
*
4063567 CGCTAAAAATTAGGTTCTTTCGTGGCATTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTATTG
1 CGCTAAAAATTAGGTTCTTTAGTGGCATTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTATTG
* *
4063632 TGGCGTTTGAGAAAAAAATGC
66 CGGCGTTTGAGAAAAAAACGC
* * *
4063653 CGCTAAAGATCAGGGTCTTTAG
1 CGCTAAAAATTAGGTTCTTTAG
4063675 CGGCGCTTTC
Statistics
Matches: 93, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
86 93 1.00
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.29
Consensus pattern (86 bp):
CGCTAAAAATTAGGTTCTTTAGTGGCATTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTATTG
CGGCGTTTGAGAAAAAAACGC
Found at i:4063858 original size:22 final size:21
Alignment explanation
Indices: 4063825--4063869 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
4063815 ATCTGCGGCG
*
4063825 CTAAAAAACGCCGCTAAAGGC
1 CTAAAAAACGCCGCTAAAAGC
4063846 CTAAAAAAGCGCCGCTAAAAGC
1 CTAAAAAA-CGCCGCTAAAAGC
4063868 CT
1 CT
4063870 GTTTTGGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.42, C:0.29, G:0.18, T:0.11
Consensus pattern (21 bp):
CTAAAAAACGCCGCTAAAAGC
Found at i:4064447 original size:25 final size:25
Alignment explanation
Indices: 4064419--4064527 Score: 89
Period size: 25 Copynumber: 4.4 Consensus size: 25
4064409 CAAACATGTG
*
4064419 AACGGGAAGCTC-TTTCGAGCCATAT
1 AACGGGAAGCTCATGT-GAGCCATAT
* *
4064444 AACGAGAAGCTCATGTGAGCCATGT
1 AACGGGAAGCTCATGTGAGCCATAT
***
4064469 AACGGGAAGCTCATCCAAGCCATA-
1 AACGGGAAGCTCATGTGAGCCATAT
* * * *
4064493 ATCGGGAAGTTCAAGCGAGCCA-AT
1 AACGGGAAGCTCATGTGAGCCATAT
*
4064517 ATCGGGAAGCT
1 AACGGGAAGCT
4064528 TCGGAGAGAA
Statistics
Matches: 68, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
23 1 0.01
24 27 0.40
25 38 0.56
26 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.18
Consensus pattern (25 bp):
AACGGGAAGCTCATGTGAGCCATAT
Done.