Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007993.1 Hibiscus syriacus cultivar Beakdansim tig00110443_pilon, whole genome shotgun sequence
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: 2245901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 12
Found at i:236945 original size:20 final size:22
Alignment explanation
Indices: 236909--236949 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
236899 TTTATAACGG
236909 TTATAGATGTATTTAAATGAAT
1 TTATAGATGTATTTAAATGAAT
236931 TTAT-GATGT-TTTAAATGAA
1 TTATAGATGTATTTAAATGAA
236950 AATGAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 5 0.26
22 4 0.21
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (22 bp):
TTATAGATGTATTTAAATGAAT
Found at i:241310 original size:21 final size:20
Alignment explanation
Indices: 241280--241354 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
241270 TGAATACTTT
*
241280 TATCAATACCGGATAAACTGG
1 TATCCATACCGGA-AAACTGG
* **
241301 TATCCGTACCGGAAGGCTGG
1 TATCCATACCGGAAAACTGG
** *
241321 TATCCATACCGGAGGATTGG
1 TATCCATACCGGAAAACTGG
241341 TATCCATA-CGGAAA
1 TATCCATACCGGAAA
241355 GGTTCAGTAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
19 4 0.09
20 29 0.66
21 11 0.25
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (20 bp):
TATCCATACCGGAAAACTGG
Found at i:241341 original size:20 final size:20
Alignment explanation
Indices: 241297--241353 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
241287 ACCGGATAAA
*
241297 CTGGTATCCGTACCGGAAGG
1 CTGGTATCCATACCGGAAGG
241317 CTGGTATCCATACCGG-AGG
1 CTGGTATCCATACCGGAAGG
*
241336 ATTGGTATCCATA-CGGAA
1 -CTGGTATCCATACCGGAA
241354 AGGTTCAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.18
20 27 0.82
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (20 bp):
CTGGTATCCATACCGGAAGG
Found at i:241541 original size:79 final size:79
Alignment explanation
Indices: 241410--241585 Score: 334
Period size: 79 Copynumber: 2.2 Consensus size: 79
241400 TTAAAGGACA
241410 AGAAATACCCTTAAAGGGTATCCATAATACCCTTATATGATAGAAATTACCAAAATATCCTCACT
1 AGAAATACCCTTAAAGGGTATCCATAATACCCTTATATGATAGAAATTACCAAAATATCCTCACT
241475 GAGTTAGAAACTTT
66 GAGTTAGAAACTTT
*
241489 AGAAATACCCTTAAAGGGTATCCATAATACCCTTATATGATAGAAATTACCAAAATATCCTCATT
1 AGAAATACCCTTAAAGGGTATCCATAATACCCTTATATGATAGAAATTACCAAAATATCCTCACT
*
241554 GAGTTAGACACTTT
66 GAGTTAGAAACTTT
241568 AGAAATACCCTTAAAGGG
1 AGAAATACCCTTAAAGGG
241586 ATATATATTG
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 95 1.00
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (79 bp):
AGAAATACCCTTAAAGGGTATCCATAATACCCTTATATGATAGAAATTACCAAAATATCCTCACT
GAGTTAGAAACTTT
Found at i:243699 original size:34 final size:34
Alignment explanation
Indices: 243656--243726 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
243646 TTCAAAATGC
* *
243656 ATTGGAAATCTAAGAGGAAAATGAATAATGTCCA
1 ATTGGAAATCTAAGAGGAAAAGGAATAATGCCCA
243690 ATTGGAAATCTAAGAGGAAAAGGAATAATGCCCA
1 ATTGGAAATCTAAGAGGAAAAGGAATAATGCCCA
243724 ATT
1 ATT
243727 AATGTCCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (34 bp):
ATTGGAAATCTAAGAGGAAAAGGAATAATGCCCA
Found at i:243907 original size:17 final size:17
Alignment explanation
Indices: 243885--243991 Score: 81
Period size: 17 Copynumber: 6.2 Consensus size: 17
243875 CAATTAAAAG
243885 CTAGTTTAATTAATGAA
1 CTAGTTTAATTAATGAA
* * *
243902 CTAGTTAAATGAATGGA
1 CTAGTTTAATTAATGAA
*
243919 CTAATTTAATTAATGAA
1 CTAGTTTAATTAATGAA
*
243936 CTAACTTT-ATTCAATGAA
1 CT-AGTTTAATT-AATGAA
* ** *
243954 CTTGTAGACTTGAATGAA
1 CTAGTTTAATT-AATGAA
* *
243972 CTAGTTTGATGAATGAA
1 CTAGTTTAATTAATGAA
243989 CTA
1 CTA
243992 CTTAGTTAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
17 42 0.63
18 25 0.37
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (17 bp):
CTAGTTTAATTAATGAA
Found at i:244036 original size:17 final size:17
Alignment explanation
Indices: 243983--244028 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
243973 TAGTTTGATG
*
243983 AATGAACTACTTAGTTA
1 AATGAACTACATAGTTA
* *
244000 AATGAAGTGCATAGTTA
1 AATGAACTACATAGTTA
244017 AATGAACTACAT
1 AATGAACTACAT
244029 GTTTAAATAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (17 bp):
AATGAACTACATAGTTA
Found at i:250246 original size:17 final size:18
Alignment explanation
Indices: 250211--250248 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
250201 ATTAGTAATA
*
250211 AAAAGAAAAAAACTTACC
1 AAAAGAAAAAAACTCACC
*
250229 AAAAG-AAAAACCTCACC
1 AAAAGAAAAAAACTCACC
250246 AAA
1 AAA
250249 CACTCCAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.66, C:0.21, G:0.05, T:0.08
Consensus pattern (18 bp):
AAAAGAAAAAAACTCACC
Found at i:252096 original size:17 final size:17
Alignment explanation
Indices: 251993--252099 Score: 63
Period size: 17 Copynumber: 6.2 Consensus size: 17
251983 CAATTAAAAG
*
251993 CTAGTTTAATTAATGAA
1 CTAGTTTAATCAATGAA
* * *
252010 CTAATTAAATGAATGAA
1 CTAGTTTAATCAATGAA
* *
252027 CTATTTTAA-CTAAAGAA
1 CTAGTTTAATC-AATGAA
* *
252044 CTAACTTTATTCAATGAA
1 CT-AGTTTAATCAATGAA
* ** * *
252062 CTTGTAGACTTGAATGAA
1 CTAGTTTA-ATCAATGAA
252080 CTAGTTTAATCAATGAA
1 CTAGTTTAATCAATGAA
252097 CTA
1 CTA
252100 CTTTGTTAAA
Statistics
Matches: 66, Mismatches: 20, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
17 40 0.61
18 25 0.38
19 1 0.02
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (17 bp):
CTAGTTTAATCAATGAA
Found at i:252934 original size:16 final size:16
Alignment explanation
Indices: 252913--252944 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
252903 TCAGGGGTGT
252913 GAGCGTTAAATGTCAA
1 GAGCGTTAAATGTCAA
252929 GAGCGTTAAATGTCAA
1 GAGCGTTAAATGTCAA
252945 ATGGTTGAGA
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:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (16 bp):
GAGCGTTAAATGTCAA
Found at i:253701 original size:11 final size:13
Alignment explanation
Indices: 253675--253706 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
253665 TTGCTTCCGC
253675 TTAGTATGCATGT
1 TTAGTATGCATGT
253688 TTAGTAT-C-TGT
1 TTAGTATGCATGT
253699 TTAGTATG
1 TTAGTATG
253707 ATTCACTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.56
12 1 0.06
13 7 0.39
ACGTcount: A:0.22, C:0.06, G:0.22, T:0.50
Consensus pattern (13 bp):
TTAGTATGCATGT
Found at i:256325 original size:30 final size:31
Alignment explanation
Indices: 256271--256341 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
256261 GAGCTTTTCA
256271 TTTCTTTCATATCATATCATATCATAGCATG
1 TTTCTTTCATATCATATCATATCATAGCATG
* *
256302 TTTCTTTCACT-TCAT-TTATATCATAGTATG
1 TTTCTTTCA-TATCATATCATATCATAGCATG
* *
256332 TGTCATTCAT
1 TTTCTTTCAT
256342 TTAATTCATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 1 0.03
30 20 0.57
31 13 0.37
32 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.49
Consensus pattern (31 bp):
TTTCTTTCATATCATATCATATCATAGCATG
Found at i:259535 original size:10 final size:9
Alignment explanation
Indices: 259512--259555 Score: 65
Period size: 8 Copynumber: 5.0 Consensus size: 9
259502 TTGTCAAGAA
259512 TAAA-AATG
1 TAAAGAATG
259520 TAAAGAATG
1 TAAAGAATG
259529 ATAAAGAATG
1 -TAAAGAATG
259539 TAAA-AATG
1 TAAAGAATG
259547 TAAAGAATG
1 TAAAGAATG
259556 ATTCTCAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
8 12 0.36
9 12 0.36
10 9 0.27
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.23
Consensus pattern (9 bp):
TAAAGAATG
Found at i:259552 original size:17 final size:19
Alignment explanation
Indices: 259511--259555 Score: 69
Period size: 17 Copynumber: 2.5 Consensus size: 19
259501 ATTGTCAAGA
259511 ATAAA-AATGTAAAGAATG
1 ATAAAGAATGTAAAGAATG
259529 ATAAAGAATGTAAA-AATG
1 ATAAAGAATGTAAAGAATG
259547 -TAAAGAATG
1 ATAAAGAATG
259556 ATTCTCAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.35
18 9 0.35
19 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.18, T:0.22
Consensus pattern (19 bp):
ATAAAGAATGTAAAGAATG
Found at i:260435 original size:26 final size:25
Alignment explanation
Indices: 260398--260447 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
260388 AATAATAAAT
**
260398 AAAACAAGAAAAAATGGAAAATAAC
1 AAAACAAGAAAAAATAAAAAATAAC
*
260423 AAAACATGTAAAAAATAAAAAATAA
1 AAAACAAG-AAAAAATAAAAAATAA
260448 AATAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.12
Consensus pattern (25 bp):
AAAACAAGAAAAAATAAAAAATAAC
Found at i:260469 original size:18 final size:18
Alignment explanation
Indices: 260415--260472 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
260405 GAAAAAATGG
*
260415 AAAATAACAAAACATGTA-A
1 AAAATAA-AAAA-ATGAATA
*
260434 AAAAT-AAAAAATAAAATA
1 AAAATAAAAAAAT-GAATA
260452 AAAATAAAAAAATGAATA
1 AAAATAAAAAAATGAATA
260470 AAA
1 AAA
260473 TGTTAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 2 0.06
17 5 0.15
18 14 0.42
19 12 0.36
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (18 bp):
AAAATAAAAAAATGAATA
Found at i:260549 original size:18 final size:17
Alignment explanation
Indices: 260517--260563 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
260507 TATTAATGGA
260517 GTAAAAAAATAAAAAAG
1 GTAAAAAAATAAAAAAG
*
260534 GTAAAAGAAATTAAAAAG
1 GTAAAA-AAATAAAAAAG
260552 G-AATAAAAATAA
1 GTAA-AAAAATAA
260564 TGTGTACATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (17 bp):
GTAAAAAAATAAAAAAG
Found at i:260606 original size:22 final size:23
Alignment explanation
Indices: 260580--260628 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
260570 CATATCAAAT
* * *
260580 AATATTTACTAAAA-AAATAATA
1 AATATATAATAAAACAAATAAAA
260602 AATATATAATAAAACAAATAAAA
1 AATATATAATAAAACAAATAAAA
260625 AATA
1 AATA
260629 AAGATATACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (23 bp):
AATATATAATAAAACAAATAAAA
Found at i:260680 original size:13 final size:15
Alignment explanation
Indices: 260647--260702 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
260637 CATGATATTA
260647 AGAAAAAATAATAAT
1 AGAAAAAATAATAAT
*
260662 AGAAAAAATAA-AGT
1 AGAAAAAATAATAAT
*
260676 A-AAAATATAATATAT
1 AGAAAAAATAATA-AT
*
260691 ATAAATAAATAA
1 AGAAA-AAATAA
260703 AAACAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 8 0.24
14 4 0.12
15 13 0.39
16 3 0.09
17 5 0.15
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.23
Consensus pattern (15 bp):
AGAAAAAATAATAAT
Found at i:260696 original size:26 final size:25
Alignment explanation
Indices: 260650--260716 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
260640 GATATTAAGA
260650 AAAAATAATAATAGAAAAAATAAAGT
1 AAAAATAATAATAGAAAAAATAAA-T
* *
260676 AAAAAT-ATAATATATATAAATAAAT
1 AAAAATAATAATAGA-AAAAATAAAT
* *
260701 AAAAACAAAAATAGAA
1 AAAAATAATAATAGAA
260717 TATTAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
25 14 0.41
26 20 0.59
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.21
Consensus pattern (25 bp):
AAAAATAATAATAGAAAAAATAAAT
Found at i:260766 original size:16 final size:16
Alignment explanation
Indices: 260676--260755 Score: 60
Period size: 16 Copynumber: 5.1 Consensus size: 16
260666 AAAATAAAGT
260676 AAAAATATAATATAT-
1 AAAAATATAATATATA
* * *
260691 ATAAATA-AATAAAAA
1 AAAAATATAATATATA
*
260706 CAAAAATAGAATAT-TA
1 -AAAAATATAATATATA
260722 AGAAAATAT-ATATATA
1 A-AAAATATAATATATA
*
260738 AAAACATATAAAATATA
1 AAAA-ATATAATATATA
260755 A
1 A
260756 TATTAAGAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
14 5 0.10
15 14 0.28
16 20 0.40
17 11 0.22
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAAATATAATATATA
Found at i:263376 original size:65 final size:65
Alignment explanation
Indices: 263207--263523 Score: 258
Period size: 65 Copynumber: 4.7 Consensus size: 65
263197 AAGATATCTG
* * * * * * **
263207 TTGTTTCACGAGAAACGGTCTCAGGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGAGAAATAAATTCAAAGA-
263272 TT
64 TT
* * * *
263274 TGTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTGTTTTAGGATAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAATAAATTCAAAGAT
263339 T
65 T
* * * *
263340 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAA-----T--A-A-AT
* *
263405 ACAAA-ACT
57 TCAAAGATT
* * * * *** *
263413 TAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGAGAAACGTATTCAAATATT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAATAAATTCAAAGATT
* * *
263478 TTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAG
263524 GGAAGCTGTC
Statistics
Matches: 201, Mismatches: 38, Indels: 24
0.76 0.14 0.09
Matches are distributed among these distances:
64 5 0.02
65 84 0.42
66 3 0.01
67 24 0.12
68 29 0.14
70 1 0.00
72 1 0.00
73 49 0.24
74 5 0.02
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAATAAATTCAAAGATT
Found at i:263391 original size:36 final size:36
Alignment explanation
Indices: 263339--263564 Score: 243
Period size: 36 Copynumber: 6.4 Consensus size: 36
263329 ATTCAAAGAT
263339 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
* *
263375 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
* * ** *
263411 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
* * * *
263448 TTTGTTTCAAGAGAAAC-GTATTC---A-A-A--TAT
1 TTTGTTTCAAGGGAAACTGT-CTCAAGAGAGACGAAA
**
263477 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
*
263513 TTTGTTTCAAGGGAAGCTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
*
263549 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGGGAAA
263565 TGTTTTCAAA
Statistics
Matches: 157, Mismatches: 23, Indels: 20
0.79 0.12 0.10
Matches are distributed among these distances:
29 19 0.12
30 2 0.01
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 2 0.01
36 98 0.62
37 31 0.20
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
Found at i:263449 original size:138 final size:138
Alignment explanation
Indices: 263285--263544 Score: 403
Period size: 138 Copynumber: 1.9 Consensus size: 138
263275 GTGTTTCAAG
* * * * *
263285 AGAAATTGTCTCAAGGGAGACAAAATTTGTTTTAGGATAAATAAATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACAAATTCAAAGATTTTGTTTCAAG
*
263350 GGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
263415 GTTCCAAA
131 GTTCCAAA
* ** *
263423 AGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGAGAAACGTATTCAAATATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACAAATTCAAAGATTTTGTTTCAAG
* * *
263488 GGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAGCTGTCTCAAGAGAGAC
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
263545 GAAATTTATT
Statistics
Matches: 109, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
138 109 1.00
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (138 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACAAATTCAAAGATTTTGTTTCAAG
GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
GTTCCAAA
Found at i:263499 original size:102 final size:102
Alignment explanation
Indices: 263375--263901 Score: 569
Period size: 102 Copynumber: 5.2 Consensus size: 102
263365 AGAGACGAAA
* * * * ** *
263375 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAG
** * * *
263440 AGACGAAATTTGTTTCAAGAGAAACGTATTCAAATAT
66 AGACGAAATTCATTTCAAGGGAAATGTTTTCAAATAT
* * * *
263477 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAA-TTTGTTTCAAGGGAAGCTGTCTCAAGAG
1 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAG
*
263541 AGACGAAATTTATTTCAAGGGAAATGTTTTCAAAGT-T
66 AGACGAAATTCATTTCAAGGGAAATGTTTTCAAA-TAT
* * * * * *
263578 TATGTTTCAAGAGAAACTGTCTCAAGGGAGGCAAAATTTTGTTTCAAGGGAAACTATCTTAATAT
1 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAG
* * *
263643 AGACAAAATTCATTTCAAGGGAAATATTTTC-AATGT
66 AGACGAAATTCATTTCAAGGGAAATGTTTTCAAATAT
* * **
263679 TTATGTTTTAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAATC
1 TT-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTGTCTCAAGA
** *
263744 GAGATAAAATTCATTTCAAGGGAAATGTTTTC-AATGTT
65 GAGACGAAATTCATTTCAAGGGAAATGTTTTCAAAT-AT
* * ** * *
263782 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAAGAAAATGTCTCAAGGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAG
* * ** *
263847 AGACGAAATT-AGTTTCAATGAAAACATATTCAAATAT
66 AGACGAAATTCA-TTTCAAGGGAAATGTTTTCAAATAT
* *
263884 TTTATTTCAAGGGAAACT
1 TTTGTTTCAAGAGAAACT
263902 TGGAAACTGT
Statistics
Matches: 365, Mismatches: 53, Indels: 14
0.84 0.12 0.03
Matches are distributed among these distances:
100 1 0.00
101 89 0.24
102 269 0.74
103 6 0.02
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (102 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAG
AGACGAAATTCATTTCAAGGGAAATGTTTTCAAATAT
Found at i:263733 original size:37 final size:37
Alignment explanation
Indices: 263682--263864 Score: 118
Period size: 37 Copynumber: 5.2 Consensus size: 37
263672 TCAATGTTTA
*
263682 TGTTTTAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * ** *
263719 TGTTTCAAGGGAAACTATCTCAATCGAGATAAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
** * * * *
263755 CATTTCAAGGGAAA-TGTTTTCAA---TG-----TTTT
1 TGTTTCAAGAGAAACTG-TCTCAAGGGAGACAAAATTT
263784 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * * * *
263821 AGTTCCAAAAGAAAATGTCTCAAGGGAGACGAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
263857 AGTTTCAA
1 TGTTTCAA
263865 TGAAAACATA
Statistics
Matches: 111, Mismatches: 24, Indels: 23
0.70 0.15 0.15
Matches are distributed among these distances:
29 18 0.16
30 2 0.02
32 1 0.01
33 1 0.01
35 1 0.01
36 28 0.25
37 60 0.54
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:264362 original size:106 final size:105
Alignment explanation
Indices: 264049--264367 Score: 415
Period size: 106 Copynumber: 3.0 Consensus size: 105
264039 TGTATCGTTC
* * * * **
264049 CGAGTCCAATATCCTCAGTCGTGAAGTTAAAATTGGCTCTGGAACTAAGAAATTGTTTGTTGACA
1 CGAGTCCAATATCTTC-GTTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * * * * *
264114 GCCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTATAT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
264155 CGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCCGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATAT-CTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
264220 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTCGTGTTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
264261 CGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTTTTTGTTGACA
1 CGAGTCCAATATC-TTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
264326 ACCAGCCGTGCCTTCGTTGTGGAA-TTGAACTTGTGTTGTCT
65 ACCAGCCGTCCCTTCGTTGT-GAAGTTGAACTTGTGTTGTCT
264367 C
1 C
264368 AAGTGGCACG
Statistics
Matches: 186, Mismatches: 24, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
105 1 0.01
106 179 0.96
107 6 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (105 bp):
CGAGTCCAATATCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:265002 original size:32 final size:32
Alignment explanation
Indices: 264949--265035 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
264939 TTGCATCAGA
* *
264949 ATGTTGAAT-TCCCAAAGATGCCCCAATATTCG
1 ATGTTGAATCT-CAAAAAATGCCCCAATATTCG
* *
264981 ATGTTGAATCTCAAAAAATGCCTCAATATTTG
1 ATGTTGAATCTCAAAAAATGCCCCAATATTCG
*
265013 ATGTTAAATCT-AAAAAATGCCCC
1 ATGTTGAATCTCAAAAAATGCCCC
265036 GGCATTTGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 11 0.23
32 36 0.75
33 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.30
Consensus pattern (32 bp):
ATGTTGAATCTCAAAAAATGCCCCAATATTCG
Found at i:265043 original size:31 final size:32
Alignment explanation
Indices: 264966--265059 Score: 100
Period size: 31 Copynumber: 2.9 Consensus size: 32
264956 ATTCCCAAAG
* * *
264966 ATGCCCCAATATTCGATGTTGAATCTCAAAAA
1 ATGCCCCAACATTTGATGTTAAATCTCAAAAA
* *
264998 ATGCCTCAATATTTGATGTTAAATCT-AAAAA
1 ATGCCCCAACATTTGATGTTAAATCTCAAAAA
** *
265029 ATGCCCCGGCATTTGATGTTAATTCTTCAAA
1 ATGCCCCAACATTTGATGTTAAATC-TCAAA
265060 GATGTCCTCA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
31 25 0.48
32 24 0.46
33 3 0.06
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (32 bp):
ATGCCCCAACATTTGATGTTAAATCTCAAAAA
Found at i:266107 original size:69 final size:69
Alignment explanation
Indices: 265977--266114 Score: 231
Period size: 69 Copynumber: 2.0 Consensus size: 69
265967 TGTGTCTCTC
* *
265977 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCATAAATGATTGTGCTCGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTATGCTCGATCAATC
266042 TCAT
66 TCAT
* * *
266046 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGAAATTATTATGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTATGCTCGATCAATC
266111 TCAT
66 TCAT
266115 AGTTTGAATA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.38
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTATGCTCGATCAATC
TCAT
Found at i:266186 original size:11 final size:11
Alignment explanation
Indices: 266172--266255 Score: 64
Period size: 12 Copynumber: 7.4 Consensus size: 11
266162 GCATCTTGTC
266172 TTCTTCTTTTT
1 TTCTTCTTTTT
**
266183 TTCTTCAATTT
1 TTCTTCTTTTT
* *
266194 TCCTTTGTTTTT
1 TTC-TTCTTTTT
266206 TTCTCTCTTTTT
1 TTCT-TCTTTTT
266218 TTC-TCTTTGTT
1 TTCTTCTTT-TT
*
266229 TTTTCTCTTTTT
1 TTCT-TCTTTTT
266241 TTC-TCTTTTT
1 TTCTTCTTTTT
266251 GTTCT
1 -TTCT
266256 GATTTAATCT
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
10 12 0.21
11 19 0.34
12 20 0.36
13 5 0.09
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.75
Consensus pattern (11 bp):
TTCTTCTTTTT
Found at i:266206 original size:12 final size:12
Alignment explanation
Indices: 266201--266250 Score: 68
Period size: 12 Copynumber: 4.2 Consensus size: 12
266191 TTTTCCTTTG
*
266201 TTTTTTTCTCTC
1 TTTTTTTCTCTT
266213 TTTTTTTCTCTT
1 TTTTTTTCTCTT
266225 TGTTTTTTCTC--
1 T-TTTTTTCTCTT
266236 TTTTTTTCTCTT
1 TTTTTTTCTCTT
266248 TTT
1 TTT
266251 GTTCTGATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
12 15 0.44
13 9 0.26
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (12 bp):
TTTTTTTCTCTT
Found at i:266208 original size:23 final size:25
Alignment explanation
Indices: 266178--266248 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 25
266168 TGTCTTCTTC
266178 TTTTTTTCTTC-AATTTTC-CTTTG
1 TTTTTTTCTTCTAATTTTCTCTTTG
**
266201 TTTTTTTCTCTCTTTTTTTCTCTTTG
1 TTTTTTTCT-TCTAATTTTCTCTTTG
266227 TTTTTTCTCTT-T--TTTTCTCTTT
1 TTTTTT-TCTTCTAATTTTCTCTTT
266249 TTGTTCTGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
23 19 0.45
24 2 0.05
25 6 0.14
26 12 0.29
27 3 0.07
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (25 bp):
TTTTTTTCTTCTAATTTTCTCTTTG
Found at i:266219 original size:25 final size:24
Alignment explanation
Indices: 266191--266248 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 24
266181 TTTTCTTCAA
266191 TTTTC-CTTTGTTTTTTTCTCTCTTT
1 TTTTCTCTTTG-TTTTTTCTCT-TTT
266216 TTTTCTCTTTGTTTTTTCTC-TTT
1 TTTTCTCTTTGTTTTTTCTCTTTT
266239 TTTTCTCTTT
1 TTTTCTCTTT
266249 TTGTTCTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 13 0.41
25 14 0.44
26 5 0.16
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (24 bp):
TTTTCTCTTTGTTTTTTCTCTTTT
Found at i:266253 original size:25 final size:25
Alignment explanation
Indices: 266191--266248 Score: 86
Period size: 23 Copynumber: 2.4 Consensus size: 25
266181 TTTTCTTCAA
266191 TTTTC-CTTTGTTTTTTTCTCTCTTT
1 TTTTCTCTTTG-TTTTTTCTCTCTTT
266216 TTTTCTCTTTG-TTTTT-TCTCTTT
1 TTTTCTCTTTGTTTTTTCTCTCTTT
266239 TTTTCTCTTT
1 TTTTCTCTTT
266249 TTGTTCTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 17 0.53
24 5 0.16
25 5 0.16
26 5 0.16
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (25 bp):
TTTTCTCTTTGTTTTTTCTCTCTTT
Found at i:269591 original size:26 final size:26
Alignment explanation
Indices: 269562--269611 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
269552 AATAAAAACA
269562 AAAATAGAATATTAAGAAAAAAATAT
1 AAAATAGAATATTAAGAAAAAAATAT
*
269588 AAAATATAATATTAAGAAAAAAAT
1 AAAATAGAATATTAAGAAAAAAAT
269612 GTATATACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (26 bp):
AAAATAGAATATTAAGAAAAAAATAT
Found at i:269704 original size:23 final size:22
Alignment explanation
Indices: 269655--269747 Score: 64
Period size: 23 Copynumber: 4.1 Consensus size: 22
269645 ATCTATACAT
**
269655 ATATATATATATAATGATATA-A
1 ATATATATA-ATAAAAATATATA
269677 GATATATATAATAAAAATAGTATA
1 -ATATATATAATAAAAATA-TATA
* * *
269701 ATATAAATAAAAAAAAGGAATATA
1 ATATATATAATAAAAA--TATATA
* *
269725 GTAAATA-AATAAAAATATATA
1 ATATATATAATAAAAATATATA
269746 AT
1 AT
269748 TAAAAATATA
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
21 6 0.11
22 7 0.13
23 32 0.58
24 9 0.16
25 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (22 bp):
ATATATATAATAAAAATATATA
Found at i:269751 original size:14 final size:14
Alignment explanation
Indices: 269729--269759 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
269719 AATATAGTAA
269729 ATAAATAAAAATAT
1 ATAAATAAAAATAT
*
269743 ATAATTAAAAATAT
1 ATAAATAAAAATAT
269757 ATA
1 ATA
269760 TATAGGGGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAAATAAAAATAT
Found at i:269751 original size:22 final size:22
Alignment explanation
Indices: 269686--269751 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 22
269676 AGATATATAT
269686 AATAAAAATAGTATAATATAAATA
1 AATAAAAATA-TATAAT-TAAATA
* *
269710 AA-AAAAAGGA-ATATAGTAAATA
1 AATAAAAA-TATATA-ATTAAATA
269732 AATAAAAATATATAATTAAA
1 AATAAAAATATATAATTAAA
269752 AATATATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
22 17 0.50
23 14 0.41
24 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (22 bp):
AATAAAAATATATAATTAAATA
Found at i:270197 original size:17 final size:17
Alignment explanation
Indices: 270160--270202 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
270150 TAACTATTTT
*
270160 TAGAATCCTATTAACAA
1 TAGAATCCTAATAACAA
270177 TAGAATCCTAAT-ACAA
1 TAGAATCCTAATAACAA
*
270193 GTAGACTCCT
1 -TAGAATCCT
270203 TGCTCGGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (17 bp):
TAGAATCCTAATAACAA
Found at i:276405 original size:20 final size:20
Alignment explanation
Indices: 276380--276420 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
276370 TACGCGTCAT
276380 GGGCCTGTATGTTGAAGGTA
1 GGGCCTGTATGTTGAAGGTA
276400 GGGCCTGTATGTTGAAGGTA
1 GGGCCTGTATGTTGAAGGTA
276420 G
1 G
276421 AAGTGTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.41, T:0.29
Consensus pattern (20 bp):
GGGCCTGTATGTTGAAGGTA
Found at i:279671 original size:19 final size:20
Alignment explanation
Indices: 279638--279677 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
279628 CTAGGCATTT
279638 TATAAGGGTGGTATCGATAC
1 TATAAGGGTGGTATCGATAC
279658 TATAAGGG-GGTATCGATAC
1 TATAAGGGTGGTATCGATAC
279677 T
1 T
279678 GCTTCTCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (20 bp):
TATAAGGGTGGTATCGATAC
Found at i:280919 original size:17 final size:17
Alignment explanation
Indices: 280893--280966 Score: 112
Period size: 17 Copynumber: 4.4 Consensus size: 17
280883 AATACTAAGG
* *
280893 TGACCAAGATTACATCA
1 TGACCCAGATTATATCA
280910 TGACCCAGATTATATCA
1 TGACCCAGATTATATCA
*
280927 TGACCCATATTATATCA
1 TGACCCAGATTATATCA
*
280944 TGACCCATATTATATCA
1 TGACCCAGATTATATCA
280961 TGACCC
1 TGACCC
280967 TTGCTTGTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (17 bp):
TGACCCAGATTATATCA
Found at i:281951 original size:20 final size:21
Alignment explanation
Indices: 281905--281951 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 21
281895 CTTGTAGCGT
*
281905 TAATAATTCATTTTCAACATA
1 TAATAAATCATTTTCAACATA
281926 -AA-AAATCA-TTTCAACATA
1 TAATAAATCATTTTCAACATA
281944 TAATAAAT
1 TAATAAAT
281952 TAAATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 10 0.43
19 7 0.30
20 6 0.26
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (21 bp):
TAATAAATCATTTTCAACATA
Found at i:291109 original size:20 final size:19
Alignment explanation
Indices: 291066--291110 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
291056 ATTAACATTA
291066 ATATTTTTTATATTTATAT
1 ATATTTTTTATATTTATAT
*
291085 TTATTTTTTA-ATATTATCAT
1 ATATTTTTTATAT-TTAT-AT
291105 ATATTT
1 ATATTT
291111 AGTATTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 13 0.59
20 7 0.32
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
ATATTTTTTATATTTATAT
Found at i:291250 original size:13 final size:13
Alignment explanation
Indices: 291234--291271 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
291224 AACGTAAAAA
291234 TAAAATTTGAATT
1 TAAAATTTGAATT
*
291247 TAAAATTTGAAAT
1 TAAAATTTGAATT
*
291260 T-GAATTTGAATT
1 TAAAATTTGAATT
291272 AGAGTTAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (13 bp):
TAAAATTTGAATT
Found at i:297254 original size:14 final size:14
Alignment explanation
Indices: 297235--297264 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
297225 TTATTTTTGC
*
297235 TTTAATTACTTTTA
1 TTTAATCACTTTTA
297249 TTTAATCACTTTTA
1 TTTAATCACTTTTA
297263 TT
1 TT
297265 ATCTTTTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTAATCACTTTTA
Found at i:306775 original size:17 final size:17
Alignment explanation
Indices: 306753--306793 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
306743 CACACCAAAA
*
306753 ATGCACTTACATGCTTC
1 ATGCACTTACATGCCTC
306770 ATGCACTTACATGCCTC
1 ATGCACTTACATGCCTC
306787 ATGCACT
1 ATGCACT
306794 CATACAAGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.24, C:0.32, G:0.12, T:0.32
Consensus pattern (17 bp):
ATGCACTTACATGCCTC
Found at i:333886 original size:29 final size:29
Alignment explanation
Indices: 333836--333891 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
333826 TCTCCATTTT
* *
333836 TAAATAATAATTGTTGTTTTAAATAAATA
1 TAAAAAATAATTGTTGTGTTAAATAAATA
333865 TAAAAAATAA-TGTTGTAGTTAAATAAA
1 TAAAAAATAATTGTTGT-GTTAAATAAA
333892 AATGATTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (29 bp):
TAAAAAATAATTGTTGTGTTAAATAAATA
Found at i:351285 original size:30 final size:30
Alignment explanation
Indices: 351249--351311 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
351239 AGCACACCAT
351249 TTGCCTTGCTTCCCATGTGTTATATGATAC
1 TTGCCTTGCTTCCCATGTGTTATATGATAC
351279 TTGCCTTGCTTCCCATGTGTTATATGATAC
1 TTGCCTTGCTTCCCATGTGTTATATGATAC
351309 TTG
1 TTG
351312 TCAAAGGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.44
Consensus pattern (30 bp):
TTGCCTTGCTTCCCATGTGTTATATGATAC
Found at i:354504 original size:25 final size:24
Alignment explanation
Indices: 354476--354524 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
354466 AAACAAACTT
*
354476 TTTTAAAAAATAATAATAAATGTTG
1 TTTTAAAAAAT-ATAAAAAATGTTG
**
354501 TTTTAAGTAATATAAAAAATGTTG
1 TTTTAAAAAATATAAAAAATGTTG
354525 CAGTAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (24 bp):
TTTTAAAAAATATAAAAAATGTTG
Found at i:359353 original size:45 final size:45
Alignment explanation
Indices: 359280--359498 Score: 295
Period size: 45 Copynumber: 4.9 Consensus size: 45
359270 TCAAAAATAT
*
359280 AATATCTTACCATTTAAATTCCATAAGCTCGTAATCTTATTTTTCA
1 AATA-CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCA
* *
359326 AATACTTACCATTTAAATTCCACAAGCTCGTAAGCTTATTTTTCC
1 AATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCA
*
359371 AATACTTACCATTT-AATTCCATAATCTCGTAAGCTTATTTTTCTA
1 AATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTC-A
*
359416 ATATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTCCA
1 A-ATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCA
* * *
359462 ATATACTTGCCA-TT--ATTCCGTAAG-TCATAAGCTTATT
1 A-ATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATT
359499 GCATGGTTAC
Statistics
Matches: 159, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
42 12 0.08
43 9 0.06
44 27 0.17
45 55 0.35
46 29 0.18
47 27 0.17
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (45 bp):
AATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCA
Found at i:359445 original size:91 final size:90
Alignment explanation
Indices: 359280--359498 Score: 306
Period size: 91 Copynumber: 2.5 Consensus size: 90
359270 TCAAAAATAT
*
359280 AATATCTTACCATTTAAATTCCATAAGCTCGTAATCTTATTTTTCAAATACTTACCATTTAAATT
1 AATATCTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCAAATACTTACCATTTAAATT
359345 CCACAAGCTCGTAAGCTTATTTTTCC
66 CCACAAGCTCGTAAGCTTA-TTTTCC
*
359371 AATA-CTTACCATTT-AATTCCATAATCTCGTAAGCTTATTTTTCTAATATACTTACCATTTAAA
1 AATATCTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTC-AA-ATACTTACCATTTAAA
*
359434 TTCCATAAGCTCGTAAGCTTATTTTCC
64 TTCCACAAGCTCGTAAGCTTATTTTCC
* * *
359461 AATATACTTGCCA-TT--ATTCCGTAAG-TCATAAGCTTATT
1 AATAT-CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATT
359499 GCATGGTTAC
Statistics
Matches: 117, Mismatches: 7, Indels: 10
0.87 0.05 0.07
Matches are distributed among these distances:
89 39 0.33
90 30 0.26
91 42 0.36
92 6 0.05
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (90 bp):
AATATCTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCAAATACTTACCATTTAAATT
CCACAAGCTCGTAAGCTTATTTTCC
Found at i:368380 original size:18 final size:18
Alignment explanation
Indices: 368354--368417 Score: 119
Period size: 18 Copynumber: 3.6 Consensus size: 18
368344 ACCGGTCACA
368354 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
368372 ACTCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
368390 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
368408 ACCCGACCCG
1 ACCCGACCCG
368418 TTGACCGTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.17, C:0.50, G:0.22, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:368392 original size:13 final size:13
Alignment explanation
Indices: 368376--368423 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 13
368366 CCGTTGACTC
368376 GACCCGACCCGTT
1 GACCCGACCCGTT
368389 GACCCGACCCGACCCGTT
1 GA--C--CC-GACCCGTT
368407 GACCCGACCCGTT
1 GACCCGACCCGTT
368420 GACC
1 GACC
368424 GTTGACCGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 14 0.47
14 2 0.07
15 1 0.03
16 1 0.03
17 2 0.07
18 10 0.33
ACGTcount: A:0.17, C:0.48, G:0.23, T:0.12
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:370944 original size:24 final size:24
Alignment explanation
Indices: 370908--370998 Score: 94
Period size: 24 Copynumber: 3.8 Consensus size: 24
370898 TCAAATTTGA
* * *
370908 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACTTGACATGG
* *
370932 ATTCTGATCTGATA-TTGAGATGG
1 ATTCTGATATGATACTTGACATGG
* * * *
370955 ATTCTAATCTGATACATGATATGG
1 ATTCTGATATGATACTTGACATGG
370979 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
370999 TTGAATTATG
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 19 0.35
24 35 0.65
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:370959 original size:23 final size:24
Alignment explanation
Indices: 370929--370997 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
370919 ATACCTGACC
370929 TGGATTCTGATCTGATA-TTGAGA
1 TGGATTCTGATCTGATACTTGAGA
* * *
370952 TGGATTCTAATCTGATACATGATA
1 TGGATTCTGATCTGATACTTGAGA
*
370976 TGGATTCTGATATGATACTTGA
1 TGGATTCTGATCTGATACTTGA
370998 CTTGAATTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 16 0.41
24 23 0.59
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (24 bp):
TGGATTCTGATCTGATACTTGAGA
Found at i:371123 original size:35 final size:35
Alignment explanation
Indices: 371076--371150 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
371066 TGGAGGAAGA
*
371076 TTACTTGGAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
371111 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
371146 TTACT
1 TTACT
371151 GTTCGTGACG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.09, C:0.29, G:0.28, T:0.33
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
Found at i:374231 original size:18 final size:18
Alignment explanation
Indices: 374208--374258 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
374198 ACCGGTCACA
*
374208 ACCTGACCCAACCCGTTG
1 ACCTGACCCGACCCGTTG
374226 ACCTGACCCGACCCGTTG
1 ACCTGACCCGACCCGTTG
*
374244 ACCCGACCCGACCCG
1 ACCTGACCCGACCCG
374259 ACCCGATTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.20, C:0.49, G:0.20, T:0.12
Consensus pattern (18 bp):
ACCTGACCCGACCCGTTG
Found at i:374245 original size:13 final size:13
Alignment explanation
Indices: 374229--374285 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
374219 CCCGTTGACC
374229 TGACCCGACCCGT
1 TGACCCGACCCGT
374242 TGACCCGACCC--
1 TGACCCGACCCGT
374253 -GACCCGACCCGAT
1 TGACCCGACCCG-T
*
374266 TGACCCGACCCAT
1 TGACCCGACCCGT
374279 TGACCCG
1 TGACCCG
374286 TTGACCGGCG
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
10 10 0.26
13 19 0.49
14 10 0.26
ACGTcount: A:0.19, C:0.47, G:0.21, T:0.12
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:374251 original size:23 final size:24
Alignment explanation
Indices: 374225--374276 Score: 88
Period size: 23 Copynumber: 2.2 Consensus size: 24
374215 CCAACCCGTT
*
374225 GACCTGACCCGACCCG-TTGACCC
1 GACCCGACCCGACCCGATTGACCC
374248 GACCCGACCCGACCCGATTGACCC
1 GACCCGACCCGACCCGATTGACCC
374272 GACCC
1 GACCC
374277 ATTGACCCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.19, C:0.50, G:0.21, T:0.10
Consensus pattern (24 bp):
GACCCGACCCGACCCGATTGACCC
Found at i:376814 original size:24 final size:24
Alignment explanation
Indices: 376787--376905 Score: 159
Period size: 24 Copynumber: 5.0 Consensus size: 24
376777 TTCGATTTGA
*
376787 ATTCTGATATGATATTTGACATGG
1 ATTCTGATATGATACTTGACATGG
376811 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
* *
376835 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
* *
376859 ATTCTGATATAATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
* *
376883 ATTTTGATACGATACTTGACATG
1 ATTCTGATATGATACTTGACATG
376906 AATTATGTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.01
24 82 0.98
25 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:376840 original size:12 final size:12
Alignment explanation
Indices: 376803--376841 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
376793 ATATGATATT
376803 TGACATGGATTC
1 TGACATGGATTC
*
376815 TGATAT-GATATC
1 TGACATGGAT-TC
376827 TGACATGGATTC
1 TGACATGGATTC
376839 TGA
1 TGA
376842 TCTGATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:377069 original size:43 final size:43
Alignment explanation
Indices: 377021--377108 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
377011 GGGCCTTACT
*
377021 TGGTGTGTTGGTGGGTGTATGGTTATGGGGAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTATGGGAAACCTACACATTA
*
377064 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTATGGGAAACCTACACATTA
377107 TG
1 TG
377109 ATACGTTCGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.18, C:0.10, G:0.36, T:0.35
Consensus pattern (43 bp):
TGGTGTGTTGGTGGGTGTATGGTTATGGGAAACCTACACATTA
Found at i:379266 original size:13 final size:13
Alignment explanation
Indices: 379249--379285 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
379239 CCGTAGACCC
*
379249 GACCCGACTCGTT
1 GACCCGACCCGTT
*
379262 TACCCGACCCGTT
1 GACCCGACCCGTT
379275 GACCCGACCCG
1 GACCCGACCCG
379286 ACCCGATTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:379272 original size:31 final size:32
Alignment explanation
Indices: 379231--379312 Score: 112
Period size: 31 Copynumber: 2.6 Consensus size: 32
379221 GTCACAACCC
* * *
379231 GACCCCACCCGTAGACCCGACCCGACTCG-TT
1 GACCCGACCCGTTGACCCGACCCGACCCGATT
*
379262 TACCCGACCCGTTGACCCGACCCGACCCGATT
1 GACCCGACCCGTTGACCCGACCCGACCCGATT
*
379294 GACCCGACCCATTGACCCG
1 GACCCGACCCGTTGACCCG
379313 TTGACCGTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 25 0.57
32 19 0.43
ACGTcount: A:0.20, C:0.48, G:0.20, T:0.13
Consensus pattern (32 bp):
GACCCGACCCGTTGACCCGACCCGACCCGATT
Found at i:379297 original size:19 final size:18
Alignment explanation
Indices: 379227--379318 Score: 77
Period size: 18 Copynumber: 5.2 Consensus size: 18
379217 ACCGGTCACA
* *
379227 ACCCGACCCCACCCGTAG
1 ACCCGACCCGACCCGTTG
*
379245 ACCCGACCCGACTCGTT-
1 ACCCGACCCGACCCGTTG
*
379262 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
379276 ACCCGACCCGACCCGATTG
1 ACCCGACCCGACCCG-TTG
379295 ACCCGACCCATTGACCCGTTG
1 ACCCGACCC---GACCCGTTG
379316 ACC
1 ACC
379319 GTTAACCGGC
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
13 11 0.19
18 24 0.41
19 12 0.20
21 6 0.10
22 6 0.10
ACGTcount: A:0.20, C:0.48, G:0.18, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:379309 original size:13 final size:14
Alignment explanation
Indices: 379280--379312 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
379270 CCGTTGACCC
379280 GACCCGACCCGATT
1 GACCCGACCCGATT
379294 GACCCGACCC-ATT
1 GACCCGACCCGATT
379307 GACCCG
1 GACCCG
379313 TTGACCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.21, C:0.45, G:0.21, T:0.12
Consensus pattern (14 bp):
GACCCGACCCGATT
Found at i:381885 original size:12 final size:12
Alignment explanation
Indices: 381848--381886 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
381838 ATCTGATATT
381848 TGACATGGATTC
1 TGACATGGATTC
*
381860 TGATAT-GATATC
1 TGACATGGAT-TC
381872 TGACATGGATTC
1 TGACATGGATTC
381884 TGA
1 TGA
381887 TCTGATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:381891 original size:48 final size:48
Alignment explanation
Indices: 381832--381950 Score: 161
Period size: 48 Copynumber: 2.5 Consensus size: 48
381822 TTCGATTTGA
* *
381832 ATTCTGATCTGATATTTGACATGGATTCTGATATGATATC-TGACATGG
1 ATTCTGATCTGATACTTGACATGGATTCTGATATAATA-CATGACATGG
* *
381880 ATTCTGATCTGATACTTGACTTGGATTCTGATATAATACATGACCTGG
1 ATTCTGATCTGATACTTGACATGGATTCTGATATAATACATGACATGG
*
381928 ATTTTGATAC-GATACTTGACATG
1 ATTCTGAT-CTGATACTTGACATG
381951 AATTATGTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
47 1 0.02
48 61 0.97
49 1 0.02
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (48 bp):
ATTCTGATCTGATACTTGACATGGATTCTGATATAATACATGACATGG
Found at i:381918 original size:24 final size:24
Alignment explanation
Indices: 381832--381950 Score: 141
Period size: 24 Copynumber: 5.0 Consensus size: 24
381822 TTCGATTTGA
* *
381832 ATTCTGATCTGATATTTGACATGG
1 ATTCTGATATGATACTTGACATGG
381856 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
* *
381880 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
* * *
381904 ATTCTGATATAATACATGACCTGG
1 ATTCTGATATGATACTTGACATGG
* *
381928 ATTTTGATACGATACTTGACATG
1 ATTCTGATATGATACTTGACATG
381951 AATTATGTTT
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
23 1 0.01
24 79 0.98
25 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:382127 original size:43 final size:43
Alignment explanation
Indices: 382066--382153 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
382056 GGGCCTTACT
*
382066 TGGTGTGTTGGTGGGTGTATGGTTCTGGGGAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
382109 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
382152 TG
1 TG
382154 ATACGTTCGG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.17, C:0.11, G:0.36, T:0.35
Consensus pattern (43 bp):
TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
Found at i:385126 original size:32 final size:31
Alignment explanation
Indices: 385090--385166 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
385080 CGGGGCCGTG
*
385090 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
385122 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
385153 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
385167 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:385149 original size:63 final size:63
Alignment explanation
Indices: 385043--385166 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
385033 CCCTAAGGGA
* * ** *
385043 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
385106 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
385167 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:386064 original size:5 final size:5
Alignment explanation
Indices: 386054--386128 Score: 69
Period size: 5 Copynumber: 13.8 Consensus size: 5
386044 AACGGTCAAC
* *
386054 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC--G GGTCG GGTCG
*
386103 GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTC--G GGTCG GGTCG GGTC
386129 AGACCGGTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
5 46 0.79
7 12 0.21
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:386075 original size:22 final size:22
Alignment explanation
Indices: 386047--386128 Score: 129
Period size: 22 Copynumber: 4.0 Consensus size: 22
386037 AACGGTCAAC
386047 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
386069 GGTCAA----C-GGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
386086 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
386108 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
386129 AGACCGGTCA
Statistics
Matches: 55, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
17 16 0.29
18 1 0.02
21 1 0.02
22 37 0.67
ACGTcount: A:0.10, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:386079 original size:17 final size:17
Alignment explanation
Indices: 386059--386129 Score: 97
Period size: 17 Copynumber: 3.9 Consensus size: 17
386049 TCAACGGTCG
386059 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
386076 GGTCGGGTCGGGTCAACGGTC
1 GGTCGGGTCGGGTCAA----C
386097 GGGTCGGGTCGGGTCAAC
1 -GGTCGGGTCGGGTCAAC
386115 GGTCGGGTCGGGTCA
1 GGTCGGGTCGGGTCA
386130 GACCGGTCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
17 31 0.63
18 1 0.02
21 1 0.02
22 16 0.33
ACGTcount: A:0.10, C:0.23, G:0.49, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:386095 original size:39 final size:39
Alignment explanation
Indices: 386047--386129 Score: 166
Period size: 39 Copynumber: 2.1 Consensus size: 39
386037 AACGGTCAAC
386047 GGTCAACGGTCGGGTCGGGTCGGGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCGGGTCAACGGTCGGGTCG
386086 GGTCAACGGTCGGGTCGGGTCGGGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCGGGTCAACGGTCGGGTCG
386125 GGTCA
1 GGTCA
386130 GACCGGTCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (39 bp):
GGTCAACGGTCGGGTCGGGTCGGGTCAACGGTCGGGTCG
Found at i:386174 original size:19 final size:19
Alignment explanation
Indices: 386131--386194 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
386121 GTCGGGTCAG
*
386131 ACCGGTCAAACCGATTC-A
1 ACCGGTCAAACCGGTTCGA
*
386149 GATCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTCGA
*
386169 ACCGGTTGAAACCGG-TCAGA
1 ACCGG-TCAAACCGGTTC-GA
386189 ACCGGT
1 ACCGGT
386195 TGAAAACCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
19 22 0.58
20 16 0.42
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.17
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:386182 original size:20 final size:20
Alignment explanation
Indices: 386157--386215 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 20
386147 CAGATCGGTC
386157 AAACCGGTTCGAACCGGTTG-
1 AAACCGG-TCGAACCGGTTGA
386177 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTC-GAACCGGTTGA
*
386198 AAACCGGTCAAACCGGTT
1 AAACCGGTCGAACCGGTT
386216 TCCAGTAGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 2 0.06
20 25 0.69
21 9 0.25
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.17
Consensus pattern (20 bp):
AAACCGGTCGAACCGGTTGA
Found at i:392500 original size:63 final size:63
Alignment explanation
Indices: 392394--392517 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
392384 CCCTAAGGGA
* * ** *
392394 ACATCTTAGGGCCTGAGCGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGCGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
392457 ACATCTTAGGGCC-GTAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGCGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
392518 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGCGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:393421 original size:17 final size:17
Alignment explanation
Indices: 393399--393476 Score: 102
Period size: 17 Copynumber: 4.3 Consensus size: 17
393389 AACGGTCAAC
*
393399 GGTCAACGGTCGAGTCG
1 GGTCAACGGTCGGGTCG
393416 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
393433 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAA----C-GGTCGGGTCG
393455 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
393472 GGTCA
1 GGTCA
393477 GACCGGTCAA
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
17 37 0.67
18 1 0.02
21 1 0.02
22 16 0.29
ACGTcount: A:0.13, C:0.23, G:0.46, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:393431 original size:5 final size:5
Alignment explanation
Indices: 393423--393475 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
393413 TCGGGTCAAC
* *
393423 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
393472 GGTC
1 GGTC
393476 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:393448 original size:22 final size:22
Alignment explanation
Indices: 393426--393475 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
393416 GGTCAACGGT
393426 CGGGTCGGGTCAACGGTCGGGT
1 CGGGTCGGGTCAACGGTCGGGT
393448 CGGGTCGGGTCAACGGTCGGGT
1 CGGGTCGGGTCAACGGTCGGGT
393470 CGGGTC
1 CGGGTC
393476 AGACCGGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.08, C:0.24, G:0.50, T:0.18
Consensus pattern (22 bp):
CGGGTCGGGTCAACGGTCGGGT
Found at i:393460 original size:39 final size:40
Alignment explanation
Indices: 393392--393485 Score: 136
Period size: 39 Copynumber: 2.3 Consensus size: 40
393382 GAAAGTCAAC
393392 GGTCAACGGTCAACGGTCGAGTCGGGTCAACGGTCGGGTCG
1 GGTCAACGGTC-ACGGTCGAGTCGGGTCAACGGTCGGGTCG
* *
393433 GGTCAACGGTC-GGGTCGGGTCGGGTCAACGGTCGGGTCG
1 GGTCAACGGTCACGGTCGAGTCGGGTCAACGGTCGGGTCG
393472 GGTCAGACCGGTCA
1 GGTCA-A-CGGTCA
393486 AACCGATTCA
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
39 31 0.65
40 1 0.02
41 16 0.33
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.17
Consensus pattern (40 bp):
GGTCAACGGTCACGGTCGAGTCGGGTCAACGGTCGGGTCG
Found at i:393490 original size:9 final size:9
Alignment explanation
Indices: 393472--393570 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
393462 GGTCGGGTCG
*
393472 GGTCAGACC
1 GGTCAAACC
393481 GGTCAAACC
1 GGTCAAACC
* *
393490 GATTCAGACC
1 G-GTCAAACC
393500 GGTCAAACC
1 GGTCAAACC
*
393509 GGTTCGAACC
1 GG-TCAAACC
*
393519 GGTTGAAACC
1 GG-TCAAACC
393529 GGTCAAACC
1 GGTCAAACC
393538 GGTCAGAACC
1 GGTCA-AACC
*
393548 GGTTGAAAACC
1 GG-T-CAAACC
393559 GGTCAAACC
1 GGTCAAACC
393568 GGT
1 GGT
393571 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:393496 original size:19 final size:19
Alignment explanation
Indices: 393474--393571 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
393464 TCGGGTCGGG
*
393474 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGGT
393493 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
393512 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
393531 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* *
393551 TGAAAACCGGTCAAACCGGT
1 T-CAGACCGGTCAAACCGGT
393571 T
1 T
393572 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.04
19 38 0.56
20 17 0.25
21 10 0.15
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:393529 original size:29 final size:31
Alignment explanation
Indices: 393497--393571 Score: 129
Period size: 29 Copynumber: 2.5 Consensus size: 31
393487 ACCGATTCAG
393497 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
393526 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
393556 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
393572 TCCAGCAGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.56
30 16 0.37
31 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:408607 original size:10 final size:10
Alignment explanation
Indices: 408594--408646 Score: 65
Period size: 10 Copynumber: 5.5 Consensus size: 10
408584 TTTGACCAGT
408594 TTTGAACCGG
1 TTTGAACCGG
408604 TTTG-ACCGG
1 TTTGAACCGG
*
408613 TCTGAACCGG
1 TTTGAACCGG
408623 TTTG-ACCGG
1 TTTGAACCGG
*
408632 TCTGAACCGG
1 TTTGAACCGG
*
408642 GTTGA
1 TTTGA
408647 CCCGACCCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 16 0.44
10 20 0.56
ACGTcount: A:0.17, C:0.23, G:0.32, T:0.28
Consensus pattern (10 bp):
TTTGAACCGG
Found at i:408611 original size:9 final size:9
Alignment explanation
Indices: 408582--408648 Score: 62
Period size: 10 Copynumber: 7.0 Consensus size: 9
408572 CTGGAAAACA
408582 GGTTTGACC
1 GGTTTGACC
*
408591 AGTTTTGAACC
1 -GGTTTG-ACC
408602 GGTTTGACC
1 GGTTTGACC
*
408611 GGTCTGAACC
1 GGTTTG-ACC
408621 GGTTTGACC
1 GGTTTGACC
*
408630 GGTCTGAACC
1 GGTTTG-ACC
*
408640 GGGTTGACC
1 GGTTTGACC
408649 CGACCCGACT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
9 19 0.40
10 25 0.53
11 3 0.06
ACGTcount: A:0.16, C:0.24, G:0.31, T:0.28
Consensus pattern (9 bp):
GGTTTGACC
Found at i:408620 original size:19 final size:19
Alignment explanation
Indices: 408582--408648 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
408572 CTGGAAAACA
* *
408582 GGTTTGACCAGTTTTGAACC
1 GGTTTGACC-GGTCTGAACC
408602 GGTTTGACCGGTCTGAACC
1 GGTTTGACCGGTCTGAACC
408621 GGTTTGACCGGTCTGAACC
1 GGTTTGACCGGTCTGAACC
*
408640 GGGTTGACC
1 GGTTTGACC
408649 CGACCCGACT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 35 0.80
20 9 0.20
ACGTcount: A:0.16, C:0.24, G:0.31, T:0.28
Consensus pattern (19 bp):
GGTTTGACCGGTCTGAACC
Found at i:408664 original size:17 final size:17
Alignment explanation
Indices: 408642--408682 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
408632 TCTGAACCGG
*
408642 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
408659 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
408676 GTTGACC
1 GTTGACC
408683 GTTGACCGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:408684 original size:7 final size:7
Alignment explanation
Indices: 408672--408708 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
408662 GACCCGACCC
408672 GACCGTT
1 GACCGTT
408679 GACCGTT
1 GACCGTT
408686 GACCG-T
1 GACCGTT
408692 GACCGTT
1 GACCGTT
408699 GACCGTT
1 GACCGTT
408706 GAC
1 GAC
408709 TTTCTTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:408696 original size:13 final size:13
Alignment explanation
Indices: 408672--408704 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
408662 GACCCGACCC
408672 GACCGTTGACCGTT
1 GACCG-TGACCGTT
408686 GACCGTGACCGTT
1 GACCGTGACCGTT
408699 GACCGT
1 GACCGT
408705 TGACTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:414729 original size:9 final size:9
Alignment explanation
Indices: 414715--414783 Score: 75
Period size: 9 Copynumber: 7.3 Consensus size: 9
414705 TTGCTGGAAA
414715 ACCGGTTTG
1 ACCGGTTTG
*
414724 ACCGGTTCG
1 ACCGGTTTG
414733 AACCGGTTTG
1 -ACCGGTTTG
*
414743 ACCGGTCTG
1 ACCGGTTTG
414752 AACCGGTTTG
1 -ACCGGTTTG
*
414762 ACCGGTCTG
1 ACCGGTTTG
*
414771 AACCGGGTTG
1 -ACCGGTTTG
414781 ACC
1 ACC
414784 CGACCCGACT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
9 27 0.54
10 23 0.46
ACGTcount: A:0.16, C:0.28, G:0.32, T:0.25
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:414738 original size:19 final size:19
Alignment explanation
Indices: 414714--414783 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
414704 GTTGCTGGAA
414714 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
414733 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
414752 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
414771 AACCGGGTTGACC
1 AACCGGTTTGACC
414784 CGACCCGACT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 48 0.98
20 1 0.02
ACGTcount: A:0.17, C:0.27, G:0.31, T:0.24
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:414799 original size:17 final size:17
Alignment explanation
Indices: 414777--414834 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
414767 TCTGAACCGG
*
414777 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
*
414794 GTTGACCCGACCTGACC
1 GTTGACCCGACCCGACC
414811 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
414828 GTTGACC
1 GTTGACC
414835 GTTGACCGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:414816 original size:34 final size:36
Alignment explanation
Indices: 414777--414854 Score: 115
Period size: 34 Copynumber: 2.2 Consensus size: 36
414767 TCTGAACCGG
*
414777 GTTGACCCGACCCGACTGTTGACC-CGACC-TGACC
1 GTTGACCCGACCCGACCGTTGACCGCGACCGTGACC
*
414811 GTTGACCCGACCCGACCGTTGACCGTTGACCGTGACC
1 GTTGACCCGACCCGACCGTTGACCG-CGACCGTGACC
414848 GTTGACC
1 GTTGACC
414855 GTGACCGTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
34 23 0.59
36 4 0.10
37 12 0.31
ACGTcount: A:0.17, C:0.38, G:0.26, T:0.19
Consensus pattern (36 bp):
GTTGACCCGACCCGACCGTTGACCGCGACCGTGACC
Found at i:414834 original size:7 final size:7
Alignment explanation
Indices: 414824--414873 Score: 86
Period size: 7 Copynumber: 7.4 Consensus size: 7
414814 GACCCGACCC
414824 GACCGTT
1 GACCGTT
414831 GACCGTT
1 GACCGTT
414838 GACCG-T
1 GACCGTT
414844 GACCGTT
1 GACCGTT
414851 GACCG-T
1 GACCGTT
414857 GACCGTT
1 GACCGTT
414864 GACCGTT
1 GACCGTT
414871 GAC
1 GAC
414874 TTTCTTTGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.29
7 29 0.71
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:414848 original size:13 final size:13
Alignment explanation
Indices: 414824--414869 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
414814 GACCCGACCC
414824 GACCGTTGACCGTT
1 GACCG-TGACCGTT
414838 GACCGTGACCGTT
1 GACCGTGACCGTT
414851 GACCGTGACCGTT
1 GACCGTGACCGTT
414864 GACCGT
1 GACCGT
414870 TGACTTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 27 0.84
14 5 0.16
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:414849 original size:20 final size:20
Alignment explanation
Indices: 414824--414873 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
414814 GACCCGACCC
414824 GACCGTTGACCGTTGACCG-T
1 GACCGTTGACCG-TGACCGTT
414844 GACCGTTGACCGTGACCGTT
1 GACCGTTGACCGTGACCGTT
414864 GACCGTTGAC
1 GACCGTTGAC
414874 TTTCTTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (20 bp):
GACCGTTGACCGTGACCGTT
Found at i:433428 original size:28 final size:27
Alignment explanation
Indices: 433396--433463 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
433386 AATTTCAGGG
433396 TTTAGAGGAACTTTAGGCCATTCTACAC
1 TTTAGAGGAA-TTTAGGCCATTCTACAC
* * * * *
433424 TTTAGGGGTATTTTGGTCATTTTACAC
1 TTTAGAGGAATTTAGGCCATTCTACAC
*
433451 TTTAGAGGTATTT
1 TTTAGAGGAATTT
433464 TTATAATTCT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 26 0.76
28 8 0.24
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.43
Consensus pattern (27 bp):
TTTAGAGGAATTTAGGCCATTCTACAC
Found at i:433871 original size:12 final size:13
Alignment explanation
Indices: 433854--433882 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
433844 CTGAGATTAC
433854 TTGATTCATTG-A
1 TTGATTCATTGAA
433866 TTGATTCATTGAA
1 TTGATTCATTGAA
433879 TTGA
1 TTGA
433883 GATTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (13 bp):
TTGATTCATTGAA
Found at i:445674 original size:81 final size:81
Alignment explanation
Indices: 445588--446402 Score: 1038
Period size: 81 Copynumber: 10.1 Consensus size: 81
445578 TATTCTAAAA
* * * * * * * *
445588 TAAAAGATTAATGACTTAGTTGTGTATTTGAAAGAAAGGTATCAATTATGTCAGTTACATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
445653 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * ** **
445669 TAAAAGCTTAATGGACTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGGTAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
445734 GTTAAATATCTTTTAG
66 GTTAAATACCTTTGAG
* ** * * *
445750 TAAAAGATTAATGGCCTAACTGTGCATTTGGGAGAAATGTGTCAATTATGCCTGTTAGATGAAAT
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
445815 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
445831 TAAAATATTAATGGTCTAGCTGTGCATTTGGTAGAAAGATGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
445896 GTTAAATACTTTTGAG
66 GTTAAATACCTTTGAG
* * * * * *
445912 TAAAAGATTAATGTCCTAGCTATGCATTTGATAGAAATGTGTCAATTATACTAGTTAGATGAAAT
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
445977 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
*
445993 TAAAAGATTAGTGGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
446058 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
446074 TAAAAGATTAATGGCCTAGGTGTGTATTTGATAGAAATGTGTCAATTATGCCAGATAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
446139 GTTAAGTACCTTTGAC
66 GTTAAATACCTTTGAG
* * * *
446155 TAAAAGATTAATGGCATAGTTGTGCATTTGGA-AGAAATGTGTCAATTATGCCATTTAGATGAAA
1 TAAAAGATTAATGGCCTAGCTGTGCATTT-GATAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
*
446219 GGTTAAATACCTTTAAG
65 GGTTAAATACCTTTGAG
* * * * *
446236 TAAAAGATTAATGGACTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCCAATTTGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
446301 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * ** * * * * *
446317 TAAAAGAATAATGGCCTAGTTGTGTATTTGGCAGGAAGGTGTCAATCATGCAAGTTAGATGGAAT
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* * *
446382 GCTAAATGCCTTTGGG
66 GTTAAATACCTTTGAG
446398 TAAAA
1 TAAAA
446403 TACTAAATGC
Statistics
Matches: 643, Mismatches: 89, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
80 2 0.00
81 639 0.99
82 2 0.00
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.33
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:451756 original size:161 final size:162
Alignment explanation
Indices: 451491--451944 Score: 631
Period size: 161 Copynumber: 2.8 Consensus size: 162
451481 GGCCCAGCTT
* * *
451491 TGCATTTGACAGAAATGTGTCATTTATGCTAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAG
1 TGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
* * *
451556 ATTAATTGCCTAGCTGTGCATTTGATAGAAATGTGTCAATTATGCCAGTTAAATGAAAGGTTAAA
66 ATTAATGGCCTAGCTGTGCATTTGGTAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA
*
451621 TACCTTTGAGTAAAAGACTAATGGTCTAG-CG
131 TACCTTTGAGTAAAAGACTAATGGCCTAGTCG
* *
451652 TGCATTTGGCAAAAAGGTGTCAATTATGCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
1 TGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
* * * *
451717 AGTAATGGTCTAGCTGTGCATTTGGTATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA
66 ATTAATGGCCTAGCTGTGCATTTGGTAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA
* * * *
451782 TACCTTTGTGTAAAATATTAATGGCCTAGTTG
131 TACCTTTGAGTAAAAGACTAATGGCCTAGTCG
* * * * * * *
451814 TTCATTTAACAGAAAGGTATCAATTATGCCATTTAAATGAAAGGTTAAATACCTTTGAGTAAAAT
1 TGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
* * * * * *
451879 ATTAATGGCCTAGCTGTGTATTTGGCAGAAATGTGTCAATCATGCAAGTTAGATGGAAGGCTAAA
66 ATTAATGGCCTAGCTGTGCATTTGGTAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA
451944 T
131 T
451945 GTCTTTGGGT
Statistics
Matches: 256, Mismatches: 36, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
161 143 0.56
162 113 0.44
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.33
Consensus pattern (162 bp):
TGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
ATTAATGGCCTAGCTGTGCATTTGGTAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA
TACCTTTGAGTAAAAGACTAATGGCCTAGTCG
Found at i:451951 original size:81 final size:81
Alignment explanation
Indices: 451469--451944 Score: 612
Period size: 81 Copynumber: 5.9 Consensus size: 81
451459 TATTCTAAAA
* * * * * *
451469 TAAAATATTAATGGCCCAGCTTTGCATTTGACAGAAATGTGTCATTTATGCTAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
451534 GTTAAATACATTTGAG
66 GTTAAATACCTTTGAG
* * * *
451550 TAAAAGATTAATTGCCTAGCTGTGCATTTGATAGAAATGTGTCAATTATGCCAGTTAAATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
451615 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
451631 TAAAAGACTAATGGTCTAGC-GTGCATTTGGCAAAAAGGTGTCAATTATGCTAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
451695 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * ** *
451711 TAAAAGAGTAATGGTCTAGCTGTGCATTTGGTATAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
451776 GTTAAATACCTTTGTG
66 GTTAAATACCTTTGAG
* * * * * * *
451792 TAAAATATTAATGGCCTAGTTGTTCATTTAACAGAAAGGTATCAATTATGCCATTTAAATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
451857 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * * * *
451873 TAAAATATTAATGGCCTAGCTGTGTATTTGGCAGAAATGTGTCAATCATGCAAGTTAGATGGAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
451938 GCTAAAT
66 GTTAAAT
451945 GTCTTTGGGT
Statistics
Matches: 345, Mismatches: 49, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
80 73 0.21
81 272 0.79
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:455284 original size:55 final size:54
Alignment explanation
Indices: 455239--455850 Score: 756
Period size: 55 Copynumber: 11.3 Consensus size: 54
455229 CCCATTACCG
* * *
455239 ATACAGAAATTTATAAACTCATTATGAATTTTGTGAGGTTGCACACATTGTGCCA
1 ATAC-GAAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCA
* *
455294 ATACAGAAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACAAATAGTGCTA
1 ATAC-GAAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCA
* * * *
455349 ATACGAAAATTCATAAACTCATTATAAATTTCTTGAGGCTGCATACATAGTGCCA
1 ATACG-AAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCA
* * * *
455404 ATACGAAAATCCATAAACTCATTATAAATTTCGTGAGGTTACACACATAGTGCTA
1 ATACG-AAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCA
* *
455459 ATACGAAAATTCATAAACTCATTATGAATTTCATGAGGTTGCACATATAGTGCCA
1 ATACG-AAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCA
*
455514 ATACAGAAATTCATAAACACATTATGAATTTCGTGAGGTTGCACACATAGTGCCA
1 ATAC-GAAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCA
* *
455569 ATACAAAAATTCAT--A---A--A-GAATTTCGTGAGGTTGCACACATAGTGCTA
1 ATAC-GAAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCA
* * * *
455616 ATATGGAAATTCATAAACTCATTATGAATTTTGTGAGGCTGCATACATAGTGCCA
1 ATA-CGAAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCA
* **
455671 ATACAGAAATCCATAAACTCATTACAAATTTCGTGAGGTTGCACACATAGTG-CA
1 ATAC-GAAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCA
* * * *
455725 ATACCTAATTTCATAAACTCATTATTAATTTCGTGAGGTTGAACACATAGTGCCA
1 ATA-CGAAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCA
* * *
455780 ATACGAAAATTCATAAACTCATTATGAATTTCGTGAGGTTGTACACATAGCGTCA
1 ATACG-AAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCA
*
455835 ATATGGAAATTCATAA
1 ATA-CGAAATTCATAA
455851 CATATATATG
Statistics
Matches: 487, Mismatches: 54, Indels: 32
0.85 0.09 0.06
Matches are distributed among these distances:
47 40 0.08
48 1 0.00
49 1 0.00
50 1 0.00
52 1 0.00
53 1 0.00
54 49 0.10
55 391 0.80
56 2 0.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.31
Consensus pattern (54 bp):
ATACGAAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCA
Found at i:455608 original size:47 final size:47
Alignment explanation
Indices: 455539--455632 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
455529 AACACATTAT
455539 GAATTTCGTGAGGTTGCACACATAGTGCCAATACAAAAATTCATAAA
1 GAATTTCGTGAGGTTGCACACATAGTGCCAATACAAAAATTCATAAA
* ***
455586 GAATTTCGTGAGGTTGCACACATAGTGCTAATATGGAAATTCATAAA
1 GAATTTCGTGAGGTTGCACACATAGTGCCAATACAAAAATTCATAAA
455633 CTCATTATGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (47 bp):
GAATTTCGTGAGGTTGCACACATAGTGCCAATACAAAAATTCATAAA
Found at i:455664 original size:102 final size:102
Alignment explanation
Indices: 455484--455796 Score: 387
Period size: 102 Copynumber: 3.0 Consensus size: 102
455474 AACTCATTAT
* * * * *
455484 GAATTTCATGAGGTTGCACATATAGTGCCAATACAGAAATTCATAAACACATTATGAATTTCGTG
1 GAATTTCGTGAGGTTGCACACATAGTGCTAATACGGAAATTCATAAACTCATTATGAATTTCGTG
455549 AGGTTGCACACATAGTGCCAATACAAAAATTCATAAA
66 AGGTTGCACACATAGTGCCAATACAAAAATTCATAAA
* *
455586 GAATTTCGTGAGGTTGCACACATAGTGCTAATATGGAAATTCATAAACTCATTATGAATTTTGTG
1 GAATTTCGTGAGGTTGCACACATAGTGCTAATACGGAAATTCATAAACTCATTATGAATTTCGTG
* * *
455651 AGGCTGCATACATAGTGCCAATACAGAAATCCATAAACTCATTACA
66 AGGTTGCACACATAGTGCCAATACA-AAA---AT----TCA-TAAA
** * *
455697 -AATTTCGTGAGGTTGCACACATAGTGC-AATACCTAATTTCATAAACTCATTATTAATTTCGTG
1 GAATTTCGTGAGGTTGCACACATAGTGCTAATACGGAAATTCATAAACTCATTATGAATTTCGTG
* *
455760 AGGTTGAACACATAGTGCCAATACGAAAATTCATAAA
66 AGGTTGCACACATAGTGCCAATACAAAAATTCATAAA
455797 CTCATTATGA
Statistics
Matches: 181, Mismatches: 21, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
100 3 0.02
101 3 0.02
102 81 0.45
103 3 0.02
105 2 0.01
106 2 0.01
108 3 0.02
109 51 0.28
110 30 0.17
111 3 0.02
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (102 bp):
GAATTTCGTGAGGTTGCACACATAGTGCTAATACGGAAATTCATAAACTCATTATGAATTTCGTG
AGGTTGCACACATAGTGCCAATACAAAAATTCATAAA
Found at i:473327 original size:18 final size:18
Alignment explanation
Indices: 473300--473358 Score: 91
Period size: 18 Copynumber: 3.3 Consensus size: 18
473290 TGGCTCAGAT
*
473300 CGGTCAGCTCGATCCAGC
1 CGGTCGGCTCGATCCAGC
*
473318 TGGTCGGCTCGATCCAGC
1 CGGTCGGCTCGATCCAGC
*
473336 CGGTCGGCTCGATCTAGC
1 CGGTCGGCTCGATCCAGC
473354 CGGTC
1 CGGTC
473359 AATCGGTTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.12, C:0.36, G:0.32, T:0.20
Consensus pattern (18 bp):
CGGTCGGCTCGATCCAGC
Found at i:474262 original size:90 final size:90
Alignment explanation
Indices: 474109--474290 Score: 310
Period size: 90 Copynumber: 2.0 Consensus size: 90
474099 AAAAGAATTT
* ** *
474109 TGTCCTCAAAATTTTTTCATGTTACAAAATTAAAGACATGAAACTTTCATCAGTTTTTCCATGTC
1 TGTCCACAAAATTCATTCATGTTACAAAATTAAAGACATGAAACTTCCATCAGTTTTTCCATGTC
474174 TTCTAGTAGCTTTTACAGAAGTACA
66 TTCTAGTAGCTTTTACAGAAGTACA
*
474199 TGTCCACAAAATTCATTCATGTTACAAAATTAAAGACATGAAACTTCCATTAGTTTTTCCATGTC
1 TGTCCACAAAATTCATTCATGTTACAAAATTAAAGACATGAAACTTCCATCAGTTTTTCCATGTC
*
474264 TTCTAGTAGCTTTTACCGAAGTACA
66 TTCTAGTAGCTTTTACAGAAGTACA
474289 TG
1 TG
474291 CCCTCTATTA
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (90 bp):
TGTCCACAAAATTCATTCATGTTACAAAATTAAAGACATGAAACTTCCATCAGTTTTTCCATGTC
TTCTAGTAGCTTTTACAGAAGTACA
Found at i:476627 original size:211 final size:207
Alignment explanation
Indices: 476253--476655 Score: 567
Period size: 211 Copynumber: 1.9 Consensus size: 207
476243 CTTATTTTTA
* *
476253 TTTATCAAAACTTGAAAAAGAATTGAAACAAAAGGATTAAGCTATTCATTTTTCCCAAAAAAGAC
1 TTTATCAAAACTTGAAAAAGAAGTGAAACAAAAGGATTAAGCTATACATTTTTCCCAAAAAAGAC
*
476318 AAACTTTAAAATAATAATAATAATTCTTTTAAATAAATATAAAAATATTATTTTTATAGAAATAG
66 AAACTTTAAAATAATAATAATAATTCTTGTAAATAAATATAAAAATATTATTTTTATAGAAATAG
476383 GGGCCTCATTAAAAATCCCCTCATACAAAAGTCGTATCGAAATACAACTGCTAGTACTGGAAGGA
131 GGGCCTCATTAAAAATCCCCTCATACAAAAGTCGTATCGAAATACAACTGCTAGTACTGGAAGGA
476448 AAAACGACTTCT
196 AAAACGACTTCT
* ** * *
476460 TTTATCAAAACTTTAAAATTAAGTGAAACAAAAGTATTAAGCTATACATTCTTTCCCAAAAATGA
1 TTTATCAAAACTTGAAAAAGAAGTGAAACAAAAGGATTAAGCTATACATT-TTTCCCAAAAAAGA
* * * * *
476525 TAAACTTTTAAAAATAATGATAACT-TTTCTTGTAAATAAATATAAAAATATTCTTTTTTATTGA
65 CAAAC-TTT-AAAATAATAATAA-TAATTCTTGTAAATAAATATAAAAATATT-ATTTTTATAGA
* * * * * *
476589 AGTGGGGGCCTCATTAGAAA-CCTCCTCATACCAAAGTCGTATCGAAATAGAACTGCTAGTAGTG
126 AATAGGGGCCTCATTAAAAATCC-CCTCATACAAAAGTCGTATCGAAATACAACTGCTAGTACTG
476653 GAA
190 GAA
476656 TGAGGAAAAT
Statistics
Matches: 171, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
207 44 0.26
208 17 0.10
209 3 0.02
210 39 0.23
211 68 0.40
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.31
Consensus pattern (207 bp):
TTTATCAAAACTTGAAAAAGAAGTGAAACAAAAGGATTAAGCTATACATTTTTCCCAAAAAAGAC
AAACTTTAAAATAATAATAATAATTCTTGTAAATAAATATAAAAATATTATTTTTATAGAAATAG
GGGCCTCATTAAAAATCCCCTCATACAAAAGTCGTATCGAAATACAACTGCTAGTACTGGAAGGA
AAAACGACTTCT
Found at i:480982 original size:17 final size:17
Alignment explanation
Indices: 480960--480999 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
480950 AAAATATGTG
480960 TTTAAACTATTACTGTT
1 TTTAAACTATTACTGTT
*
480977 TTTAAACTATTATTGTT
1 TTTAAACTATTACTGTT
480994 TTTAAA
1 TTTAAA
481000 TGACATGTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTAAACTATTACTGTT
Found at i:491250 original size:22 final size:21
Alignment explanation
Indices: 491208--491247 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
491198 GAGTTTATTT
*
491208 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
491229 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
491248 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:492303 original size:14 final size:14
Alignment explanation
Indices: 492284--492311 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
492274 CATCATCCTA
492284 TTTTTCCAATAGGC
1 TTTTTCCAATAGGC
492298 TTTTTCCAATAGGC
1 TTTTTCCAATAGGC
492312 ATAATTAGCC
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:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (14 bp):
TTTTTCCAATAGGC
Found at i:494087 original size:17 final size:17
Alignment explanation
Indices: 494065--494105 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
494055 ATTACTGTTG
494065 TTTTAAACTATTATTGT
1 TTTTAAACTATTATTGT
494082 TTTTAAACTATTATTGT
1 TTTTAAACTATTATTGT
494099 TTTTAAA
1 TTTTAAA
494106 TGATATGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (17 bp):
TTTTAAACTATTATTGT
Found at i:517055 original size:46 final size:45
Alignment explanation
Indices: 516959--517063 Score: 147
Period size: 45 Copynumber: 2.3 Consensus size: 45
516949 TGCACCAAGT
* * *
516959 GTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGC
1 GTGCATCGATGCATCAAATGCATTCGATGTTTGAAAATAGCCAGA
* **
517004 GTGCATTGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTGAAAATAGCCAGA
517050 GTGCATCGATGCAT
1 GTGCATCGATGCAT
517064 GGAGAATGCA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
45 27 0.52
46 25 0.48
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (45 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTGAAAATAGCCAGA
Found at i:517082 original size:65 final size:65
Alignment explanation
Indices: 517013--517149 Score: 163
Period size: 65 Copynumber: 2.1 Consensus size: 65
517003 CGTGCATTGA
*
517013 TGCATCAAATGCATTCGATGTTTTGAAAAT-ATTCA-GAGTGCATCGATGCATGG-AGAATGCAT
1 TGCATCAAATGCATTCGATG-TTT-AAAATAATTCACGAATGCATCGATGCATGGTAG-ATGCAT
517075 CGG
63 CGG
** * * * *
517078 TGCATGGAATGCATTCGATGTTTCAATTAATTCACTAATGCATCGATGCATGGTTGATGCATCGG
1 TGCATCAAATGCATTCGATGTTTAAAATAATTCACGAATGCATCGATGCATGGTAGATGCATCGG
517143 TGCATCA
1 TGCATCA
517150 CCTCAAATAA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
63 3 0.05
64 8 0.13
65 48 0.80
66 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.31
Consensus pattern (65 bp):
TGCATCAAATGCATTCGATGTTTAAAATAATTCACGAATGCATCGATGCATGGTAGATGCATCGG
Found at i:517089 original size:17 final size:19
Alignment explanation
Indices: 517051--517097 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
517041 ATATTCAGAG
517051 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
517070 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
517087 TGCATTCGATG
1 TGCA-TCGATG
517098 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:518145 original size:21 final size:21
Alignment explanation
Indices: 518111--518154 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
518101 CAGGAGCTGG
*
518111 AGGAGGAGCACGAGAATAACT
1 AGGAGGAGCACGAGAAGAACT
* *
518132 AGGAGTAGCTCGAGAAGAACT
1 AGGAGGAGCACGAGAAGAACT
518153 AG
1 AG
518155 CTCCCGAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.14, G:0.34, T:0.11
Consensus pattern (21 bp):
AGGAGGAGCACGAGAAGAACT
Done.