Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002905.1 Hibiscus syriacus cultivar Beakdansim tig00006001_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: 233955
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:1446 original size:24 final size:25
Alignment explanation
Indices: 1400--1454 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
1390 AACAGTTATG
*
1400 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
1424 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
1449 CA-TTGA
1 CACTTGA
1455 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:5382 original size:11 final size:10
Alignment explanation
Indices: 5367--5410 Score: 52
Period size: 11 Copynumber: 4.1 Consensus size: 10
5357 TTGCAATTCC
5367 TTTATCTTTT
1 TTTATCTTTT
5377 CTTTATCTTTT
1 -TTTATCTTTT
*
5388 TTAATCTTATT
1 TTTATCTT-TT
5399 TTTAATCTTTT
1 TTT-ATCTTTT
5410 T
1 T
5411 ACTAAAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 7 0.24
11 17 0.59
12 5 0.17
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTATCTTTT
Found at i:10028 original size:12 final size:12
Alignment explanation
Indices: 10013--10042 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
10003 TTTCTTTATC
10013 TTTTTAATCTTA
1 TTTTTAATCTTA
10025 TTTTTAATCTTA
1 TTTTTAATCTTA
10037 TTTTTA
1 TTTTTA
10043 GCACTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTAATCTTA
Found at i:10335 original size:12 final size:12
Alignment explanation
Indices: 10318--10357 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
10308 TTTTGGTGCT
10318 GAAATAAGATAA
1 GAAATAAGATAA
*
10330 GAAATAAGATTA
1 GAAATAAGATAA
10342 -AAATAAGATAAA
1 GAAATAAGAT-AA
10354 GAAA
1 GAAA
10358 AGATTAAGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 9 0.38
12 12 0.50
13 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (12 bp):
GAAATAAGATAA
Found at i:10349 original size:23 final size:22
Alignment explanation
Indices: 10319--10364 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
10309 TTTGGTGCTG
10319 AAATAAGAT-AAGAAATAAGATTA
1 AAATAAGATAAAG-AA-AAGATTA
10342 AAATAAGATAAAGAAAAGATTA
1 AAATAAGATAAAGAAAAGATTA
10364 A
1 A
10365 GGAATTGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.36
23 11 0.50
24 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (22 bp):
AAATAAGATAAAGAAAAGATTA
Found at i:13670 original size:16 final size:16
Alignment explanation
Indices: 13649--13681 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
13639 TAGTTAGCTC
13649 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
13665 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
13681 A
1 A
13682 GGTGGCAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:19153 original size:24 final size:25
Alignment explanation
Indices: 19107--19161 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
19097 ACAGTTATGC
*
19107 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
19131 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
19156 CA-TTGA
1 CACTTGA
19162 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:24281 original size:14 final size:15
Alignment explanation
Indices: 24262--24305 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
24252 CAAAGTGCTA
24262 CAACAAAAA-AAAAG
1 CAACAAAAAGAAAAG
24276 CAACAAGAAAGAAAA-
1 CAACAA-AAAGAAAAG
*
24291 AAACAAAAAGAAAAG
1 CAACAAAAAGAAAAG
24306 AAAAAGACTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 14 0.54
15 8 0.31
16 4 0.15
ACGTcount: A:0.77, C:0.11, G:0.11, T:0.00
Consensus pattern (15 bp):
CAACAAAAAGAAAAG
Found at i:24292 original size:18 final size:19
Alignment explanation
Indices: 24268--24310 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
24258 GCTACAACAA
*
24268 AAAAAAAGCAACAAG-AAAG
1 AAAAAAA-CAAAAAGAAAAG
24287 AAAAAAACAAAAAGAAAAG
1 AAAAAAACAAAAAGAAAAG
24306 AAAAA
1 AAAAA
24311 GACTCCTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (19 bp):
AAAAAAACAAAAAGAAAAG
Found at i:24524 original size:16 final size:15
Alignment explanation
Indices: 24493--24545 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
24483 GAGTTGTAAG
24493 TTATC-TTCATTTTTT
1 TTATCTTTCA-TTTTT
24508 TTATCATTTCATTTTT
1 TTATC-TTTCATTTTT
24524 TTATTCTTTCATCTTTT
1 TTA-TCTTTCAT-TTTT
24541 CTTAT
1 -TTAT
24546 TTCATTACCA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.15
16 14 0.42
17 11 0.33
18 3 0.09
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATCTTTCATTTTT
Found at i:24540 original size:17 final size:17
Alignment explanation
Indices: 24498--24551 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
24488 GTAAGTTATC
24498 TTCATTTTTTT-TATCAT
1 TTCATTTTTTTAT-TCAT
24515 TTCATTTTTTTATTC-T
1 TTCATTTTTTTATTCAT
24531 TTCATCTTTTCTTATTTCAT
1 TTCAT-TTTT-TTA-TTCAT
24551 T
1 T
24552 ACCATATCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.19
17 17 0.53
18 4 0.12
19 3 0.09
20 2 0.06
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (17 bp):
TTCATTTTTTTATTCAT
Found at i:28945 original size:18 final size:17
Alignment explanation
Indices: 28901--28946 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
28891 GTGCTACAAC
* *
28901 AAAAAAAAAGCAATAAG
1 AAAAAAAAAACAAAAAG
28918 AAATAAAAAAACAAAAAG
1 AAA-AAAAAAACAAAAAG
28936 AAAAAGAAAAA
1 AAAAA-AAAAA
28947 GACTCCTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.83, C:0.04, G:0.09, T:0.04
Consensus pattern (17 bp):
AAAAAAAAAACAAAAAG
Found at i:35219 original size:7 final size:6
Alignment explanation
Indices: 35200--35243 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
35190 TAAAAGCAAC
*
35200 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG AGAAAA- AAAAAG A
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG A-AAAAG AAAAAG A
35244 CTCCTACAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 4 0.12
6 19 0.58
7 10 0.30
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:35225 original size:25 final size:24
Alignment explanation
Indices: 35197--35243 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
35187 CAATAAAAGC
35197 AACAAAAAGA-AAAAGAAAGAAGAAA
1 AACAAAAAGAGAAAA-AAA-AAGAAA
35222 AACAAAAAGAGAAAAAAAAAGA
1 AACAAAAAGAGAAAAAAAAAGA
35244 CTCCTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.19
25 13 0.62
26 4 0.19
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (24 bp):
AACAAAAAGAGAAAAAAAAAGAAA
Found at i:35231 original size:12 final size:12
Alignment explanation
Indices: 35197--35243 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
35187 CAATAAAAGC
35197 AACAAAAAGAAA
1 AACAAAAAGAAA
*
35209 AAGAAAGAAGAAA
1 AACAAA-AAGAAA
35222 AACAAAAAGAGAA
1 AACAAAAAGA-AA
35235 AA-AAAAAGA
1 AACAAAAAGA
35244 CTCCTACAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 16 0.52
13 15 0.48
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (12 bp):
AACAAAAAGAAA
Found at i:35241 original size:19 final size:19
Alignment explanation
Indices: 35200--35240 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
35190 TAAAAGCAAC
* *
35200 AAAAAGAAAAAGAAAGAAG
1 AAAAACAAAAAGAAAGAAA
35219 AAAAACAAAAAG--AGAAA
1 AAAAACAAAAAGAAAGAAA
35236 AAAAA
1 AAAAA
35241 AGACTCCTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 9 0.45
19 11 0.55
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAAACAAAAAGAAAGAAA
Found at i:37760 original size:21 final size:20
Alignment explanation
Indices: 37717--37761 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
37707 TCATTTGCAT
*
37717 TCATATATCTATTTTATAGC
1 TCATATATCTATTTTAAAGC
* *
37737 TCATATATGTTTTCTTAAAGC
1 TCATATATCTATT-TTAAAGC
37758 TCAT
1 TCAT
37762 GAACGTCCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.49
Consensus pattern (20 bp):
TCATATATCTATTTTAAAGC
Found at i:39452 original size:17 final size:16
Alignment explanation
Indices: 39425--39467 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
39415 AATTCAAAAC
*
39425 AAAAG-AGAAAAGCATA
1 AAAAGAAGAAAAGC-CA
39441 AAAAGAAGAAAAGCCA
1 AAAAGAAGAAAAGCCA
39457 AAAAGAA-AAAA
1 AAAAGAAGAAAA
39468 ATTTCCAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 4 0.16
16 13 0.52
17 8 0.32
ACGTcount: A:0.74, C:0.07, G:0.16, T:0.02
Consensus pattern (16 bp):
AAAAGAAGAAAAGCCA
Found at i:41293 original size:36 final size:36
Alignment explanation
Indices: 41253--41357 Score: 156
Period size: 36 Copynumber: 2.9 Consensus size: 36
41243 AACACCATCT
41253 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCTCCATTATCACGCCTATATCATCACCATAG
* * * **
41289 TCCATCACCATTATCACCCCTTTATCATCATTATAG
1 TCCATCTCCATTATCACGCCTATATCATCACCATAG
*
41325 TCCATCTCCATTATCACGCCTATATTATCACCA
1 TCCATCTCCATTATCACGCCTATATCATCACCA
41358 ACTTATAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.28, C:0.35, G:0.04, T:0.33
Consensus pattern (36 bp):
TCCATCTCCATTATCACGCCTATATCATCACCATAG
Found at i:41777 original size:24 final size:24
Alignment explanation
Indices: 41737--41783 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
41727 AAAGTGCTAC
41737 AACAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAGCAACAAGAAA-AAGAA
41762 AACAAAAGAG-AA-AAGAAAAAGA
1 AACAAAA-AGCAACAAGAAAAAGA
41784 CTCCTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGCAACAAGAAAAAGAA
Found at i:45818 original size:36 final size:36
Alignment explanation
Indices: 45778--45883 Score: 158
Period size: 37 Copynumber: 2.9 Consensus size: 36
45768 AACACCATCT
45778 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCTCCATTATCACGCCTATATCATCACCATAG
* * * *
45814 TCCATCACCATTATCACCCCCTTTATCATCACTATAG
1 TCCATCTCCATTATCA-CGCCTATATCATCACCATAG
*
45851 TCCATCTCCATTATCACGCCTATATTATCACCA
1 TCCATCTCCATTATCACGCCTATATCATCACCA
45884 ACTTATAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
36 28 0.47
37 32 0.53
ACGTcount: A:0.27, C:0.37, G:0.04, T:0.32
Consensus pattern (36 bp):
TCCATCTCCATTATCACGCCTATATCATCACCATAG
Found at i:54559 original size:33 final size:33
Alignment explanation
Indices: 54500--54564 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
54490 TGATGAATGA
*
54500 AGGATGATTTAATGGTGATGAAATGGTAATGGT
1 AGGATGATTTAATGGCGATGAAATGGTAATGGT
* * *
54533 AGGATGATGTTATTGGCG-TGATATGGTGATGG
1 AGGATGAT-TTAATGGCGATGAAATGGTAATGG
54565 AATATGGTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 20 0.74
34 7 0.26
ACGTcount: A:0.28, C:0.02, G:0.37, T:0.34
Consensus pattern (33 bp):
AGGATGATTTAATGGCGATGAAATGGTAATGGT
Found at i:54596 original size:36 final size:36
Alignment explanation
Indices: 54537--54649 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
54527 AATGGTAGGA
* *
54537 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* * *
54572 TGATTATATAGGTGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
54608 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
54644 TGATGA
1 TGATGA
54650 AAATAGTATC
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 14 0.21
36 54 0.79
ACGTcount: A:0.27, C:0.03, G:0.35, T:0.35
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:54648 original size:13 final size:12
Alignment explanation
Indices: 54554--54649 Score: 56
Period size: 13 Copynumber: 7.9 Consensus size: 12
54544 ATTGGCGTGA
*
54554 TATGGTGATGGAA
1 TATGGTGAT-GAT
*
54567 TATGGTGATTA-
1 TATGGTGATGAT
54578 TATAGGTG-TGAT
1 TAT-GGTGATGAT
* *
54590 AATGGTGATGGAC
1 TATGGTGAT-GAT
54603 TATGGTGATGA-
1 TATGGTGATGAT
*
54614 TATAGGCG-TGAT
1 TAT-GGTGATGAT
* *
54626 AATGGAGATGGAT
1 TATGGTGAT-GAT
54639 TATGGTGATGA
1 TATGGTGATGA
54650 AAATAGTATC
Statistics
Matches: 65, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
11 18 0.28
12 18 0.28
13 29 0.45
ACGTcount: A:0.29, C:0.02, G:0.35, T:0.33
Consensus pattern (12 bp):
TATGGTGATGAT
Found at i:64549 original size:13 final size:13
Alignment explanation
Indices: 64531--64560 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
64521 AATCTGGACC
*
64531 GAATGATGAATTT
1 GAATGATGAATAT
64544 GAATGATGAATAT
1 GAATGATGAATAT
64557 GAAT
1 GAAT
64561 CGAATCTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (13 bp):
GAATGATGAATAT
Found at i:64718 original size:17 final size:17
Alignment explanation
Indices: 64698--64738 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
64688 TCATTTACAT
64698 TTTTTTTGAATTTTTTG
1 TTTTTTTGAATTTTTTG
**
64715 TTTTTTTGCCTTTTTTG
1 TTTTTTTGAATTTTTTG
64732 TTTTTTT
1 TTTTTTT
64739 AAAAAAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.05, C:0.05, G:0.10, T:0.80
Consensus pattern (17 bp):
TTTTTTTGAATTTTTTG
Found at i:69493 original size:15 final size:16
Alignment explanation
Indices: 69465--69495 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
69455 CATTTCTATC
69465 CATTTCCTTTTCTTAT
1 CATTTCCTTTTCTTAT
69481 CATTTCC-TTTCTTAT
1 CATTTCCTTTTCTTAT
69496 TTCATATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTCCTTTTCTTAT
Found at i:69822 original size:17 final size:16
Alignment explanation
Indices: 69795--69837 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
69785 AGTTCAAAAC
*
69795 AAAAG-AGAAAAGCATA
1 AAAAGAAGAAAAGC-CA
69811 AAAAGAAGAAAAGCCA
1 AAAAGAAGAAAAGCCA
69827 AAAAGAA-AAAA
1 AAAAGAAGAAAA
69838 ATTTCTAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 4 0.16
16 13 0.52
17 8 0.32
ACGTcount: A:0.74, C:0.07, G:0.16, T:0.02
Consensus pattern (16 bp):
AAAAGAAGAAAAGCCA
Found at i:78516 original size:8 final size:8
Alignment explanation
Indices: 78503--78573 Score: 76
Period size: 8 Copynumber: 9.0 Consensus size: 8
78493 TATTTTTTTT
78503 CAAAAAAA
1 CAAAAAAA
78511 CAAAAAAA
1 CAAAAAAA
78519 C-AAAAAA
1 CAAAAAAA
78526 CAAAAAAA
1 CAAAAAAA
78534 GGCAAAAAAA
1 --CAAAAAAA
*
78544 -ACAAAAA
1 CAAAAAAA
**
78551 -AAAAAGG
1 CAAAAAAA
78558 CAAAAAAA
1 CAAAAAAA
78566 CAAAAAAA
1 CAAAAAAA
78574 GAGCCAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
7 17 0.32
8 28 0.53
10 8 0.15
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:78523 original size:6 final size:7
Alignment explanation
Indices: 78505--78572 Score: 52
Period size: 7 Copynumber: 9.9 Consensus size: 7
78495 TTTTTTTTCA
78505 AAAAAAC
1 AAAAAAC
78512 AAAAAAAC
1 -AAAAAAC
78520 AAAAAAC
1 AAAAAAC
78527 AAAAAA-
1 AAAAAAC
***
78533 AGGCAA-
1 AAAAAAC
78539 AAAAAAC
1 AAAAAAC
78546 AAAAAA-
1 AAAAAAC
**
78552 AAAAGGC
1 AAAAAAC
78559 AAAAAAAC
1 -AAAAAAC
78567 AAAAAA
1 AAAAAA
78573 AGAGCCAAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
6 10 0.21
7 25 0.53
8 12 0.26
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:78532 original size:22 final size:22
Alignment explanation
Indices: 78504--78573 Score: 79
Period size: 22 Copynumber: 3.0 Consensus size: 22
78494 ATTTTTTTTC
78504 AAAAAAACAAAAAAACAAAAAA
1 AAAAAAACAAAAAAACAAAAAA
78526 CAAAAAAAGGCAAAAAAA-ACAAAAA
1 -AAAAAAA--CAAAAAAACA-AAAAA
**
78551 AAAAAGGCAAAAAAACAAAAAA
1 AAAAAAACAAAAAAACAAAAAA
78573 A
1 A
78574 GAGCCAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
22 14 0.34
23 8 0.20
24 6 0.15
25 13 0.32
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (22 bp):
AAAAAAACAAAAAAACAAAAAA
Found at i:78543 original size:11 final size:11
Alignment explanation
Indices: 78527--78565 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
78517 AACAAAAAAC
78527 AAAAAAAGGCA
1 AAAAAAAGGCA
***
78538 AAAAAAACAAA
1 AAAAAAAGGCA
78549 AAAAAAAGGCA
1 AAAAAAAGGCA
78560 AAAAAA
1 AAAAAA
78566 CAAAAAAAGA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAGGCA
Found at i:78572 original size:21 final size:22
Alignment explanation
Indices: 78513--78573 Score: 88
Period size: 21 Copynumber: 2.7 Consensus size: 22
78503 CAAAAAAACA
*
78513 AAAAAACAAAAAACAAAAAAAGGC
1 AAAAAA-AACAAA-AAAAAAAGGC
78537 AAAAAAAACAAAAAAAAAAGGC
1 AAAAAAAACAAAAAAAAAAGGC
78559 -AAAAAAACAAAAAAA
1 AAAAAAAACAAAAAAA
78574 GAGCCAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
21 15 0.42
22 10 0.28
23 5 0.14
24 6 0.17
ACGTcount: A:0.84, C:0.10, G:0.07, T:0.00
Consensus pattern (22 bp):
AAAAAAAACAAAAAAAAAAGGC
Found at i:78591 original size:20 final size:20
Alignment explanation
Indices: 78520--78584 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
78510 ACAAAAAAAC
* *
78520 AAAAAAC-AAAAAAAGGCAA
1 AAAAAACAAAAAAAAAGCCA
*
78539 AAAAAACAAAAAAAAAAGGCA
1 AAAAAAC-AAAAAAAAAGCCA
*
78560 AAAAAACAAAAAAAGAGCCA
1 AAAAAACAAAAAAAAAGCCA
78580 AAAAA
1 AAAAA
78585 GCCAAAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 7 0.18
20 16 0.41
21 16 0.41
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (20 bp):
AAAAAACAAAAAAAAAGCCA
Found at i:86015 original size:33 final size:33
Alignment explanation
Indices: 85973--86041 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
85963 GTTGATGAAT
*
85973 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
86006 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
86039 GAA
1 GAA
86042 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:97568 original size:33 final size:33
Alignment explanation
Indices: 97509--97573 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
97499 TGATGAATGA
*
97509 AGGATGATTTAATGGTGATGAAATGGTAATGGT
1 AGGATGATTTAATGGCGATGAAATGGTAATGGT
* * *
97542 AGGATGATGTTATTGGCG-TGATATGGTGATGG
1 AGGATGAT-TTAATGGCGATGAAATGGTAATGG
97574 AATATGGTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 20 0.74
34 7 0.26
ACGTcount: A:0.28, C:0.02, G:0.37, T:0.34
Consensus pattern (33 bp):
AGGATGATTTAATGGCGATGAAATGGTAATGGT
Found at i:97605 original size:36 final size:36
Alignment explanation
Indices: 97546--97658 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
97536 AATGGTAGGA
* *
97546 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* * *
97581 TGATTATATAGGTGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
97617 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
97653 TGATGA
1 TGATGA
97659 AAATAGTATC
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 14 0.21
36 54 0.79
ACGTcount: A:0.27, C:0.03, G:0.35, T:0.35
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:97657 original size:13 final size:12
Alignment explanation
Indices: 97563--97658 Score: 56
Period size: 13 Copynumber: 7.9 Consensus size: 12
97553 ATTGGCGTGA
*
97563 TATGGTGATGGAA
1 TATGGTGAT-GAT
*
97576 TATGGTGATTA-
1 TATGGTGATGAT
97587 TATAGGTG-TGAT
1 TAT-GGTGATGAT
* *
97599 AATGGTGATGGAC
1 TATGGTGAT-GAT
97612 TATGGTGATGA-
1 TATGGTGATGAT
*
97623 TATAGGCG-TGAT
1 TAT-GGTGATGAT
* *
97635 AATGGAGATGGAT
1 TATGGTGAT-GAT
97648 TATGGTGATGA
1 TATGGTGATGA
97659 AAATAGTATC
Statistics
Matches: 65, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
11 18 0.28
12 18 0.28
13 29 0.45
ACGTcount: A:0.29, C:0.02, G:0.35, T:0.33
Consensus pattern (12 bp):
TATGGTGATGAT
Found at i:109667 original size:11 final size:11
Alignment explanation
Indices: 109651--109681 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
109641 CCTAATTCCT
109651 TCATTTCTTTA
1 TCATTTCTTTA
109662 TCATTTCTTTA
1 TCATTTCTTTA
109673 TCATTTCTT
1 TCATTTCTT
109682 AGCCATTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.65
Consensus pattern (11 bp):
TCATTTCTTTA
Found at i:112606 original size:33 final size:33
Alignment explanation
Indices: 112527--112630 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
112517 ATACAATCTG
* *
112527 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
112563 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
112596 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
112629 TC
1 TC
112631 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:113059 original size:11 final size:11
Alignment explanation
Indices: 113043--113088 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
113033 TTTGTAGTGC
113043 AAAAGAAAAGA
1 AAAAGAAAAGA
113054 AAAAG--AAGA
1 AAAAGAAAAGA
**
113063 AAATCAAAAGA
1 AAAAGAAAAGA
113074 AAAAGAAAAGTA
1 AAAAGAAAAG-A
113086 AAA
1 AAA
113089 CAAAGTTGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
9 7 0.25
11 17 0.61
12 4 0.14
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.04
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:117078 original size:33 final size:33
Alignment explanation
Indices: 116999--117078 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 33
116989 ATACAATCTG
* *
116999 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCA-TATCACGCCAATAACATCACC--AT
117035 TCCATCACCATATCACGCCAATAACATCATCC-T
1 TCCATCACCATATCACGCCAATAACATCA-CCAT
*
117068 TCCATTACCAT
1 TCCATCACCAT
117079 TCCATCACCA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
33 11 0.28
35 17 0.43
36 12 0.30
ACGTcount: A:0.31, C:0.38, G:0.03, T:0.29
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCACCAT
Found at i:124283 original size:19 final size:20
Alignment explanation
Indices: 124259--124304 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
124249 CGGCCAAGAG
**
124259 CATGTATCTTCAT-TTAAAT
1 CATGTATCTTCATCAAAAAT
*
124278 CATGTATTTTCATCAAAAAT
1 CATGTATCTTCATCAAAAAT
124298 CATGTAT
1 CATGTAT
124305 TTTAAATGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (20 bp):
CATGTATCTTCATCAAAAAT
Found at i:128165 original size:20 final size:19
Alignment explanation
Indices: 128119--128165 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
128109 ACATGCCCAT
*
128119 TAATAT-TTAAGCATCTTA
1 TAATATATTAAGCATATTA
128137 TAATCATATTAAGCATGATTA
1 TAAT-ATATTAAGCAT-ATTA
*
128158 TCATATAT
1 TAATATAT
128166 ACATCAAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 4 0.17
19 2 0.08
20 12 0.50
21 6 0.25
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (19 bp):
TAATATATTAAGCATATTA
Found at i:129607 original size:12 final size:12
Alignment explanation
Indices: 129585--129611 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
129575 AATACAAAAA
129585 GAAGTGCAAAGT
1 GAAGTGCAAAGT
129597 GAAGTGCAAAGT
1 GAAGTGCAAAGT
129609 GAA
1 GAA
129612 AGAAATCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.07, G:0.33, T:0.15
Consensus pattern (12 bp):
GAAGTGCAAAGT
Found at i:129685 original size:21 final size:22
Alignment explanation
Indices: 129635--129685 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
129625 AAAATCTAGT
129635 AAAGAAAATCAAAGCACTCTAA
1 AAAGAAAATCAAAGCACTCTAA
* *
129657 AGAAGAAATTGAAAGCACTC-AA
1 A-AAGAAAATCAAAGCACTCTAA
129679 AAAGAAA
1 AAAGAAA
129686 GAAAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 6 0.23
22 4 0.15
23 16 0.62
ACGTcount: A:0.61, C:0.14, G:0.14, T:0.12
Consensus pattern (22 bp):
AAAGAAAATCAAAGCACTCTAA
Found at i:129692 original size:10 final size:10
Alignment explanation
Indices: 129677--129710 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
129667 GAAAGCACTC
129677 AAAAAGAAAG
1 AAAAAGAAAG
129687 AAAAAGAAAAG
1 AAAAAG-AAAG
129698 AAAAAGAAAG
1 AAAAAGAAAG
129708 AAA
1 AAA
129711 GTTGAAGCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:129692 original size:21 final size:21
Alignment explanation
Indices: 129645--129710 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
129635 AAAGAAAATC
***
129645 AAAGCACTCTAAAGAAGAAATTG
1 AAAGCACTC-AAA-AAGAAAGAA
129668 AAAGCACTCAAAAAGAAAGAA
1 AAAGCACTCAAAAAGAAAGAA
* ***
129689 AAAGAAAAGAAAAAGAAAGAA
1 AAAGCACTCAAAAAGAAAGAA
129710 A
1 A
129711 GTTGAAGCAC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 24 0.67
22 3 0.08
23 9 0.25
ACGTcount: A:0.67, C:0.09, G:0.17, T:0.08
Consensus pattern (21 bp):
AAAGCACTCAAAAAGAAAGAA
Found at i:134995 original size:20 final size:19
Alignment explanation
Indices: 134972--135013 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
134962 AAATTTTGGC
134972 TTTTTGGCTCTTTTTTTTGTT
1 TTTTTGGC-CTTTTTTTT-TT
*
134993 TTTTTTGCCTTTTTTTTTT
1 TTTTTGGCCTTTTTTTTTT
135012 TT
1 TT
135014 GCCTTTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.81
Consensus pattern (19 bp):
TTTTTGGCCTTTTTTTTTT
Found at i:135012 original size:36 final size:34
Alignment explanation
Indices: 134972--135045 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 34
134962 AAATTTTGGC
134972 TTTTTGGCTCTTTTTT-TTGTTT-TTTTTGCCTTTTTT
1 TTTTTGGC-CTTTTTTGTT-TTTGTTTTTG--TTTTTT
*
135008 TTTTTTGCCTTTTTTGTTTTTGTTTTTGTTTTTT
1 TTTTTGGCCTTTTTTGTTTTTGTTTTTGTTTTTT
135042 TTTT
1 TTTT
135046 GAAAAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
34 10 0.29
35 10 0.29
36 15 0.43
ACGTcount: A:0.00, C:0.08, G:0.11, T:0.81
Consensus pattern (34 bp):
TTTTTGGCCTTTTTTGTTTTTGTTTTTGTTTTTT
Found at i:135043 original size:15 final size:15
Alignment explanation
Indices: 134986--135042 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
134976 TGGCTCTTTT
134986 TTTTGTTTTTTTTGCC
1 TTTT-TTTTTTTTGCC
135002 TTTTTTTTTTTTGCC
1 TTTTTTTTTTTTGCC
*
135017 TTTTTTGTTTTTG--
1 TTTTTTTTTTTTGCC
135030 TTTTTGTTTTTTT
1 TTTTT-TTTTTTT
135043 TTTGAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
13 5 0.13
14 6 0.16
15 23 0.61
16 4 0.11
ACGTcount: A:0.00, C:0.07, G:0.11, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTTTTGCC
Found at i:141881 original size:36 final size:35
Alignment explanation
Indices: 141830--141941 Score: 127
Period size: 36 Copynumber: 3.2 Consensus size: 35
141820 TAAGATACTA
141830 CCTA-AACATCACCATCTTCCATTACTATTTTCACG
1 CCTATAACATCACCATCTTCCATTACTA-TTTCACG
* *
141865 CCTATAACATCACCATCTGCCATTACTATTGCACG
1 CCTATAACATCACCATCTTCCATTACTATTTCACG
* * * ** *
141900 CCTATATCCTAACCATCTTTTTATCACTATTTCACG
1 CCTATAACATCACCATC-TTCCATTACTATTTCACG
141936 CCTATA
1 CCTATA
141942 TAACCACCAA
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
35 24 0.37
36 41 0.63
ACGTcount: A:0.28, C:0.33, G:0.04, T:0.35
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATTACTATTTCACG
Found at i:141915 original size:35 final size:36
Alignment explanation
Indices: 141830--141917 Score: 108
Period size: 35 Copynumber: 2.5 Consensus size: 36
141820 TAAGATACTA
* * *
141830 CCTA-AACATCACCATCTTCCATTACTATTTTCACG
1 CCTATAACATAACCATCTGCCATTACTATTTGCACG
*
141865 CCTATAACATCACCATCTGCCATTACTA-TTGCACG
1 CCTATAACATAACCATCTGCCATTACTATTTGCACG
* *
141900 CCTATATCCTAACCATCT
1 CCTATAACATAACCATCT
141918 TTTTATCACT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 25 0.53
36 22 0.47
ACGTcount: A:0.28, C:0.35, G:0.05, T:0.32
Consensus pattern (36 bp):
CCTATAACATAACCATCTGCCATTACTATTTGCACG
Found at i:142358 original size:13 final size:12
Alignment explanation
Indices: 142334--142374 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
142324 CAAAAGCAAC
142334 AAAAAGAGAAAA
1 AAAAAGAGAAAA
*
142346 AGAAAGAAGAAAA
1 AAAAAG-AGAAAA
142359 AAAAAGAGAAAGA
1 AAAAAGAGAAA-A
142372 AAA
1 AAA
142375 GACTCCTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAAAA
Found at i:144382 original size:36 final size:36
Alignment explanation
Indices: 144330--144442 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
144320 GATACTATTT
*
144330 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
144366 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
144402 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
144437 ACATCA
1 TCATCA
144443 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:144385 original size:13 final size:11
Alignment explanation
Indices: 144330--144428 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
144320 GATACTATTT
144330 TCATCACCATAA
1 TCATCACCAT-A
*
144342 TCCATCTCCATTA
1 T-CATCACCA-TA
*
144355 TCA-CGCCTATA
1 TCATCACC-ATA
144366 TCATCACCATA
1 TCATCACCATA
144377 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
144391 TCA-CGCCTATA
1 TCATCACC-ATA
144402 TCATCACCATA
1 TCATCACCATA
144413 TTCCATCACCATA
1 -T-CATCACCATA
144426 TCA
1 TCA
144429 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:144457 original size:33 final size:33
Alignment explanation
Indices: 144342--144481 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
144332 ATCACCATAA
* * *
144342 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
144376 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
144414 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
144447 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
144480 TC
1 TC
144482 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:152504 original size:36 final size:35
Alignment explanation
Indices: 152453--152528 Score: 118
Period size: 36 Copynumber: 2.2 Consensus size: 35
152443 TAAGATACTA
* *
152453 CCTA-AACATCACCATCTTCCATTACTATTTTCACG
1 CCTATAACATCACCATCTGCCATTACTA-TTGCACG
152488 CCTATAACATCACCATCTGCCATTACTATTGCACG
1 CCTATAACATCACCATCTGCCATTACTATTGCACG
152523 CCTATA
1 CCTATA
152529 TCCTAACCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 16 0.42
36 22 0.58
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (35 bp):
CCTATAACATCACCATCTGCCATTACTATTGCACG
Found at i:152538 original size:35 final size:36
Alignment explanation
Indices: 152453--152540 Score: 108
Period size: 35 Copynumber: 2.5 Consensus size: 36
152443 TAAGATACTA
* * *
152453 CCTA-AACATCACCATCTTCCATTACTATTTTCACG
1 CCTATAACATAACCATCTGCCATTACTATTTGCACG
*
152488 CCTATAACATCACCATCTGCCATTACTA-TTGCACG
1 CCTATAACATAACCATCTGCCATTACTATTTGCACG
* *
152523 CCTATATCCTAACCATCT
1 CCTATAACATAACCATCT
152541 TTTTATCACC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 25 0.53
36 22 0.47
ACGTcount: A:0.28, C:0.35, G:0.05, T:0.32
Consensus pattern (36 bp):
CCTATAACATAACCATCTGCCATTACTATTTGCACG
Found at i:152979 original size:22 final size:22
Alignment explanation
Indices: 152946--152992 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
152936 TGCTACAACA
*
152946 AAAGCAAGAAAAAGAGAAAAAG
1 AAAGCAAGAAAAAAAGAAAAAG
*
152968 AAAG-AAGAAAAAAAAGAGAAAG
1 AAAGCAAG-AAAAAAAGAAAAAG
152990 AAA
1 AAA
152993 AGACTCCTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (22 bp):
AAAGCAAGAAAAAAAGAAAAAG
Found at i:152993 original size:12 final size:11
Alignment explanation
Indices: 152954--152995 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
152944 CAAAAGCAAG
152954 AAAAAGAGAAA
1 AAAAAGAGAAA
152965 AAGAAAGAAGAAA
1 AA-AAAG-AGAAA
152978 AAAAAGAGAAA
1 AAAAAGAGAAA
*
152989 GAAAAGA
1 AAAAAGA
152996 CTCCTACAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 13 0.46
12 8 0.29
13 7 0.25
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAAGAGAAA
Found at i:155639 original size:13 final size:13
Alignment explanation
Indices: 155601--155639 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
155591 AAGAAAAATC
155601 AGAAAAAGAAGAAA
1 AGAAAAAG-AGAAA
155615 AGAAGAAA-AGAAA
1 AGAA-AAAGAGAAA
155628 AGAAAAAGAGAA
1 AGAAAAAGAGAA
155640 GTTCAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 3 0.13
13 13 0.57
14 4 0.17
15 3 0.13
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AGAAAAAGAGAAA
Found at i:161511 original size:17 final size:16
Alignment explanation
Indices: 161442--161513 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 16
161432 ATTCATGCAT
161442 CTAGTTCATTGAATAAA
1 CTAGTTCATT-AATAAA
* *
161459 GTTGGTTCATTAATTAAA
1 -CTAGTTCATTAA-TAAA
* * *
161477 GTAGTTCAATCATCAAA
1 CTAGTTCATTAAT-AAA
161494 CTAGTTCATTTAATAAA
1 CTAGTTCA-TTAATAAA
161511 CTA
1 CTA
161514 ACTCTTAATT
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
16 1 0.02
17 26 0.62
18 15 0.36
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (16 bp):
CTAGTTCATTAATAAA
Found at i:169677 original size:15 final size:15
Alignment explanation
Indices: 169659--169694 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
169649 ATGAATAATT
169659 AAGAATTGAAATGGA
1 AAGAATTGAAATGGA
169674 AAGAATTGAAATGGA
1 AAGAATTGAAATGGA
*
169689 TAGAAT
1 AAGAAT
169695 AGTTATCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.25, T:0.22
Consensus pattern (15 bp):
AAGAATTGAAATGGA
Found at i:169874 original size:13 final size:12
Alignment explanation
Indices: 169855--169940 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
169845 ATATAGGCGT
169855 GATATGGTGATG
1 GATATGGTGATG
169867 GAATATGGTGAT-
1 G-ATATGGTGATG
*
169879 GATATAGGCG-T-
1 GATAT-GGTGATG
169890 GATAATGGTGATG
1 GAT-ATGGTGATG
169903 GACTATGGTGAT-
1 GA-TATGGTGATG
*
169915 GATATAGGCG-T-
1 GATAT-GGTGATG
169926 GATAATGGTGATG
1 GAT-ATGGTGATG
169939 GA
1 GA
169941 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:169910 original size:36 final size:36
Alignment explanation
Indices: 169837--169941 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
169827 ATTTATAAGT
* *
169837 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
169872 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
169908 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
169942 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:173981 original size:18 final size:20
Alignment explanation
Indices: 173946--173988 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
173936 TGTAGGAGTC
173946 TTTTTCTTTCCTTTTTGTT-
1 TTTTTCTTTCCTTTTTGTTG
173965 TTTTTC-TT-CTTTCTTGTTG
1 TTTTTCTTTCCTTT-TTGTTG
173984 TTTTT
1 TTTTT
173989 TTGTTGTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.18
18 7 0.32
19 11 0.50
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTCCTTTTTGTTG
Found at i:173986 original size:21 final size:22
Alignment explanation
Indices: 173949--173990 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
173939 AGGAGTCTTT
*
173949 TTCTTTCCTTTTTGTTTTTTTC
1 TTCTTTCCTTGTTGTTTTTTTC
173971 TTCTTT-CTTGTTGTTTTTTT
1 TTCTTTCCTTGTTGTTTTTTT
173991 GTTGTAGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (22 bp):
TTCTTTCCTTGTTGTTTTTTTC
Found at i:174439 original size:36 final size:36
Alignment explanation
Indices: 174364--174466 Score: 163
Period size: 36 Copynumber: 2.9 Consensus size: 36
174354 TTATAAGTTG
* * * *
174364 GTGATAATATAGGCGTGAT-ATGGTGATGTAATATG
1 GTGATGATATAGGCGTGATAATGGTGATGGACTATA
174399 GTGATGATATAGGCGTGATAATGGTGATGGACTATA
1 GTGATGATATAGGCGTGATAATGGTGATGGACTATA
174435 GTGATGATATAGGCGTGATAATGGTGATGGAC
1 GTGATGATATAGGCGTGATAATGGTGATGGAC
174467 ATATTGTATC
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 18 0.29
36 45 0.71
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.31
Consensus pattern (36 bp):
GTGATGATATAGGCGTGATAATGGTGATGGACTATA
Found at i:175608 original size:560 final size:560
Alignment explanation
Indices: 174549--175677 Score: 2141
Period size: 560 Copynumber: 2.0 Consensus size: 560
174539 TAAGGGATGG
* *
174549 TATGAAATGACTTTGACCCACTAGTTATTTAAACTAGGAACCATAAGTATCAAGGTGAAGGAATG
1 TATGAAAGGACTTTGACCCACTAGTTATTTAAACTAGGAACCAGAAGTATCAAGGTGAAGGAATG
174614 ACGCCACAAGCTTTAGAAAGGCTTGTTTAATCGATATAGTTCTAAAAAGAACTTGAAGAGAGAAT
66 ACGCCACAAGCTTTAGAAAGGCTTGTTTAATCGATATAGTTCTAAAAAGAACTTGAAGAGAGAAT
*
174679 AATCTCACAAAGGATTTTTAATTGATCAAAGGGTTCATTACAAATGAGTGCCAAACCCTATTTAT
131 AATCTCACAAAGGATTTTTAATTGATCAAAGGGTTCATTACAAATGAATGCCAAACCCTATTTAT
174744 AGATTTGTAAAGGCTTGGCCGAATAGATATATGCCTTTTCGGCAAAGTACATGTCTTAAACGAAA
196 AGATTTGTAAAGGCTTGGCCGAATAGATATATGCCTTTTCGGCAAAGTACATGTCTTAAACGAAA
* *
174809 ATAAATGATGCTTGGATGAGGGGAGATGTCTTTGGTCGAATGGTTCCCTTATCACTTCATCTTGG
261 ATAAACGATGCTTGGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTATCACTTCATCTTGG
*
174874 CGCCAATTTGAAACAAGATGATACTTTGGCCGAATGGTTAGAAGCCTCTTCATTTTGGCGCCCAT
326 CGCCAATTTGAAACAAGATGATACTTTGACCGAATGGTTAGAAGCCTCTTCATTTTGGCGCCCAT
174939 TTCATCCACATGCATGGAACATGTGTGGGCTGTTCATGAGGCACTCACATGGGTGGCATAGGGGC
391 TTCATCCACATGCATGGAACATGTGTGGGCTGTTCATGAGGCACTCACATGGGTGGCATAGGGGC
175004 TTATGGTGTGGCTTCTTCTTGGCGTGAATTTGAGCAGCAACTTAGGCATGACTTGGCATCAAACT
456 TTATGGTGTGGCTTCTTCTTGGCGTGAATTTGAGCAGCAACTTAGGCATGACTTGGCATCAAACT
* *
175069 TGCATCTAGGTGACATGGTATTAATGGGACAGCAACTATT
521 TGCATCTAGGTGACATGGCATTAATGGGACAACAACTATT
175109 TATGAAAGGACTTTGACCCACTAGTTATTTAAACTAGGAACCAGAAGTATCAAGGTGAAGGAATG
1 TATGAAAGGACTTTGACCCACTAGTTATTTAAACTAGGAACCAGAAGTATCAAGGTGAAGGAATG
175174 ACGCCACAAGCTTTAGAAAGGCTTGTTTAATCGATATAGTTCTAAAAAGAACTTGAAGAGAGAAT
66 ACGCCACAAGCTTTAGAAAGGCTTGTTTAATCGATATAGTTCTAAAAAGAACTTGAAGAGAGAAT
175239 AATCTCACAAAGGATTTTTAATTGATCAAAGGGTTCATTACAAATGAATGCCAAACCCTATTTAT
131 AATCTCACAAAGGATTTTTAATTGATCAAAGGGTTCATTACAAATGAATGCCAAACCCTATTTAT
* *
175304 AGATTTGTAAAGGCTTGGCCGAATAGATATATGCTTTTTTGGCAAAGTACATGTCTTAAACGAAA
196 AGATTTGTAAAGGCTTGGCCGAATAGATATATGCCTTTTCGGCAAAGTACATGTCTTAAACGAAA
*
175369 ATAAACGATGCTTGGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTATCTCTTCATCTTGG
261 ATAAACGATGCTTGGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTATCACTTCATCTTGG
*
175434 CGCCAATTTGAAACAAGATGATGCTTTGACCGAATGGTTAGAAGCCTCTTCATTTTGGCGCCCAT
326 CGCCAATTTGAAACAAGATGATACTTTGACCGAATGGTTAGAAGCCTCTTCATTTTGGCGCCCAT
*
175499 TTCATCCACATGCATGGAACATGTGTGGGCTGTTCATGAGGCACTCACATGGGTGGCATAGGGGT
391 TTCATCCACATGCATGGAACATGTGTGGGCTGTTCATGAGGCACTCACATGGGTGGCATAGGGGC
175564 TTATGGTGTGGCTTCTTCTTGGCGTGAATTTGAGCAGCAACTTAGGCATGACTTGGCATCAAACT
456 TTATGGTGTGGCTTCTTCTTGGCGTGAATTTGAGCAGCAACTTAGGCATGACTTGGCATCAAACT
175629 TGCATCTAGGTGACATGGCATTAATGGGACAACAACTATT
521 TGCATCTAGGTGACATGGCATTAATGGGACAACAACTATT
175669 TATGAAAGG
1 TATGAAAGG
175678 TAACATTTGT
Statistics
Matches: 556, Mismatches: 13, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
560 556 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (560 bp):
TATGAAAGGACTTTGACCCACTAGTTATTTAAACTAGGAACCAGAAGTATCAAGGTGAAGGAATG
ACGCCACAAGCTTTAGAAAGGCTTGTTTAATCGATATAGTTCTAAAAAGAACTTGAAGAGAGAAT
AATCTCACAAAGGATTTTTAATTGATCAAAGGGTTCATTACAAATGAATGCCAAACCCTATTTAT
AGATTTGTAAAGGCTTGGCCGAATAGATATATGCCTTTTCGGCAAAGTACATGTCTTAAACGAAA
ATAAACGATGCTTGGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTATCACTTCATCTTGG
CGCCAATTTGAAACAAGATGATACTTTGACCGAATGGTTAGAAGCCTCTTCATTTTGGCGCCCAT
TTCATCCACATGCATGGAACATGTGTGGGCTGTTCATGAGGCACTCACATGGGTGGCATAGGGGC
TTATGGTGTGGCTTCTTCTTGGCGTGAATTTGAGCAGCAACTTAGGCATGACTTGGCATCAAACT
TGCATCTAGGTGACATGGCATTAATGGGACAACAACTATT
Found at i:178014 original size:16 final size:16
Alignment explanation
Indices: 177980--178028 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
177970 GTAAGTTATC
* * *
177980 TTCACTTTCTTACTAT
1 TTCATTTTCTTATTCT
177996 TTCATTTTCTTATTCT
1 TTCATTTTCTTATTCT
178012 TTCATCTATTCTTATTC
1 TTCAT-T-TTCTTATTC
178029 CATTACCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.61
Consensus pattern (16 bp):
TTCATTTTCTTATTCT
Found at i:181045 original size:19 final size:20
Alignment explanation
Indices: 181021--181063 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
181011 AGCATTTATC
*
181021 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
181040 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
181060 TTCA
1 TTCA
181064 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:182637 original size:22 final size:24
Alignment explanation
Indices: 182610--182661 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
182600 AAATCCAGCA
182610 AAGAAATCG-AAGCACTC-AAAAG
1 AAGAAATCGAAAGCACTCAAAAAG
*
182632 AAGAAATTGAAAGCACTCAAAAAG
1 AAGAAATCGAAAGCACTCAAAAAG
182656 AAGAAA
1 AAGAAA
182662 AAGAAAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 8 0.30
23 8 0.30
24 11 0.41
ACGTcount: A:0.60, C:0.13, G:0.17, T:0.10
Consensus pattern (24 bp):
AAGAAATCGAAAGCACTCAAAAAG
Found at i:182667 original size:24 final size:23
Alignment explanation
Indices: 182619--182667 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
182609 AAAGAAATCG
**
182619 AAGCACTCAAAAGAAGAAATTGA
1 AAGCACTCAAAAGAAGAAAAAGA
182642 AAGCACTCAAAAAGAAGAAAAAGA
1 AAGCACTC-AAAAGAAGAAAAAGA
182666 AA
1 AA
182668 AGAAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.63, C:0.12, G:0.16, T:0.08
Consensus pattern (23 bp):
AAGCACTCAAAAGAAGAAAAAGA
Found at i:182670 original size:5 final size:5
Alignment explanation
Indices: 182651--182693 Score: 63
Period size: 5 Copynumber: 9.0 Consensus size: 5
182641 AAAGCACTCA
*
182651 AAAAG AAGA- AAAAG AAAAG AAAAG AAAAG AAAAG -AAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
182694 TTGAAGCACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 7 0.21
5 27 0.79
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:182693 original size:9 final size:10
Alignment explanation
Indices: 182651--182693 Score: 63
Period size: 9 Copynumber: 4.5 Consensus size: 10
182641 AAAGCACTCA
*
182651 AAAAGAAGA-
1 AAAAGAAAAG
182660 AAAAGAAAAG
1 AAAAGAAAAG
182670 AAAAGAAAAG
1 AAAAGAAAAG
182680 AAAAG-AAAG
1 AAAAGAAAAG
182689 AAAAG
1 AAAAG
182694 TTGAAGCACT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 17 0.53
10 15 0.47
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAG
Found at i:185234 original size:14 final size:14
Alignment explanation
Indices: 185215--185247 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
185205 AGAAAGATAA
185215 AAGAGAAGTCTTAC
1 AAGAGAAGTCTTAC
*
185229 AAGAGAAGTCTTGC
1 AAGAGAAGTCTTAC
185243 AAGAG
1 AAGAG
185248 TAGCAAGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.27, T:0.18
Consensus pattern (14 bp):
AAGAGAAGTCTTAC
Found at i:189082 original size:2 final size:2
Alignment explanation
Indices: 189075--189164 Score: 180
Period size: 2 Copynumber: 45.0 Consensus size: 2
189065 ATAAGATAGT
189075 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
189117 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
189159 TA TA TA
1 TA TA TA
189165 ACTATAGTTA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:190806 original size:24 final size:24
Alignment explanation
Indices: 190762--190807 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
190752 TGCAAAAAGA
**
190762 AAGAAAAGAAAAAAATCAGAATAG
1 AAGAAAAGAAAAAAAGAAGAATAG
190786 AAGAAAAGAAAAAAAGAAGAAT
1 AAGAAAAGAAAAAAAGAAGAAT
190808 TTCAAAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.74, C:0.02, G:0.17, T:0.07
Consensus pattern (24 bp):
AAGAAAAGAAAAAAAGAAGAATAG
Found at i:203832 original size:2 final size:2
Alignment explanation
Indices: 203825--203860 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
203815 AGTTATTTTC
203825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
203861 CCTATAGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:205510 original size:34 final size:31
Alignment explanation
Indices: 205468--205539 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 31
205458 GTACAAAAAG
*
205468 AAAGAAAAGACA-AAAAGAAGAAGAAAGTTCAGAA
1 AAAGAAAAGA-AGAAAAGAAAAAGAAA-TTC--AA
205502 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
1 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
205533 AAAGAAA
1 AAAGAAA
205540 TCAAGCCAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 9 0.25
33 4 0.11
34 23 0.64
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (31 bp):
AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
Found at i:208695 original size:24 final size:23
Alignment explanation
Indices: 208660--208713 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
208650 TTTCTTTTCT
* * *
208660 TTTTTTTTAATTTTCGGAATTTG
1 TTTTTTTAAATTTTCAGAATTCG
208683 TTTCTTTTAAATTTTCAGAATTCG
1 TTT-TTTTAAATTTTCAGAATTCG
208707 TTTTTTT
1 TTTTTTT
208714 CAAGATGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 7 0.26
24 20 0.74
ACGTcount: A:0.19, C:0.07, G:0.09, T:0.65
Consensus pattern (23 bp):
TTTTTTTAAATTTTCAGAATTCG
Found at i:209961 original size:11 final size:11
Alignment explanation
Indices: 209940--209981 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
209930 GTGCTGGAAT
209940 CAAGATAAAAA
1 CAAGATAAAAA
* *
209951 TAAGATTAAAA
1 CAAGATAAAAA
209962 CAAGATAAAGAA
1 CAAGATAAA-AA
209974 -AAGATAAA
1 CAAGATAAA
209982 TGAATTGCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 24 0.92
12 2 0.08
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (11 bp):
CAAGATAAAAA
Found at i:214285 original size:20 final size:20
Alignment explanation
Indices: 214262--214326 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
214252 TTTTTTGAAA
214262 TTTTGGCTTTTTTTTTGTTTT
1 TTTTGGCTTTTTTTTTG-TTT
*
214283 TTTTGTG-TTTTTTTGTGTTT
1 TTTTG-GCTTTTTTTTTGTTT
*
214303 TTTTGCCTTTTTTTTTGTTT
1 TTTTGGCTTTTTTTTTGTTT
214323 TTTT
1 TTTT
214327 TTTGTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
20 24 0.62
21 14 0.36
22 1 0.03
ACGTcount: A:0.00, C:0.05, G:0.14, T:0.82
Consensus pattern (20 bp):
TTTTGGCTTTTTTTTTGTTT
Found at i:214286 original size:21 final size:21
Alignment explanation
Indices: 214262--214327 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
214252 TTTTTTGAAA
214262 TTTTGGCTTTTTTTTTGTTTT
1 TTTTGGCTTTTTTTTTGTTTT
*
214283 TTTT-G-TGTTTTTTTGTGTTT
1 TTTTGGCTTTTTTTTTGT-TTT
*
214303 TTTTGCCTTTTTTTTTGTTTT
1 TTTTGGCTTTTTTTTTGTTTT
214324 TTTT
1 TTTT
214328 TTGTTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
19 10 0.26
20 8 0.21
21 11 0.28
22 10 0.26
ACGTcount: A:0.00, C:0.05, G:0.14, T:0.82
Consensus pattern (21 bp):
TTTTGGCTTTTTTTTTGTTTT
Found at i:214327 original size:10 final size:10
Alignment explanation
Indices: 214269--214337 Score: 86
Period size: 10 Copynumber: 6.7 Consensus size: 10
214259 AAATTTTGGC
214269 TTTTTTTTTG
1 TTTTTTTTTG
214279 -TTTTTTTTG
1 TTTTTTTTTG
*
214288 TGTTTTTTTG
1 TTTTTTTTTG
*
214298 TGTTTTTTTG
1 TTTTTTTTTG
214308 CCTTTTTTTTTG
1 --TTTTTTTTTG
214320 TTTTTTTTTTG
1 -TTTTTTTTTG
214331 TTTTTTT
1 TTTTTTT
214338 GAAAAAAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
9 9 0.17
10 25 0.47
11 10 0.19
12 9 0.17
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:214338 original size:31 final size:32
Alignment explanation
Indices: 214279--214338 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
214269 TTTTTTTTTG
214279 TTTTTTTTGTGTTTTTTTGTGTTTTTTTGCCT
1 TTTTTTTTGTGTTTTTTTGTGTTTTTTTGCCT
*
214311 TTTTTTTTGT-TTTTTTTTTGTTTTTTTG
1 TTTTTTTTGTGTTTTTTTGTGTTTTTTTG
214339 AAAAAAATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.83
Consensus pattern (32 bp):
TTTTTTTTGTGTTTTTTTGTGTTTTTTTGCCT
Found at i:214689 original size:11 final size:11
Alignment explanation
Indices: 214668--214709 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
214658 GTGCTGGAAT
214668 CAAGATAAAAA
1 CAAGATAAAAA
* *
214679 TAAGATTAAAA
1 CAAGATAAAAA
214690 CAAGATAAAGAA
1 CAAGATAAA-AA
214702 -AAGATAAA
1 CAAGATAAA
214710 TGAATTGCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 24 0.92
12 2 0.08
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (11 bp):
CAAGATAAAAA
Found at i:216001 original size:28 final size:28
Alignment explanation
Indices: 215961--216016 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
215951 CGTGAATTAA
*
215961 CAAAACAAATGATGAACATGCTGTTATG
1 CAAAACAAATGATGAACATGATGTTATG
215989 CAAAACAAATGATGAACATGATGTTATG
1 CAAAACAAATGATGAACATGATGTTATG
216017 TGAATGTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (28 bp):
CAAAACAAATGATGAACATGATGTTATG
Found at i:216342 original size:27 final size:27
Alignment explanation
Indices: 216287--216342 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
216277 ACCTTGTGGC
* * *
216287 ATGACTTCGGGATCTGATGTCGGCTTG
1 ATGACTTCGAGATCTGATATCGGCGTG
* *
216314 ATGACTTCGATATCTGATATGGGCGTG
1 ATGACTTCGAGATCTGATATCGGCGTG
216341 AT
1 AT
216343 CACATAATCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.34
Consensus pattern (27 bp):
ATGACTTCGAGATCTGATATCGGCGTG
Found at i:218718 original size:11 final size:11
Alignment explanation
Indices: 218694--218738 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
218684 TTGGTGCTGG
218694 AAACAAGATAA
1 AAACAAGATAA
* *
218705 AAATAAGATTA
1 AAACAAGATAA
218716 AAACAAGATAA
1 AAACAAGATAA
218727 AGAA-AAGATAA
1 A-AACAAGATAA
218738 A
1 A
218739 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:218722 original size:22 final size:22
Alignment explanation
Indices: 218694--218735 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
218684 TTGGTGCTGG
218694 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
218716 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
218736 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:231224 original size:17 final size:17
Alignment explanation
Indices: 231202--231234 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
231192 TAAGATTTGA
231202 TTTAATAAATGAACTAG
1 TTTAATAAATGAACTAG
*
231219 TTTAATTAATGAACTA
1 TTTAATAAATGAACTA
231235 TTTCCCTAAA
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:0.45, C:0.06, G:0.09, T:0.39
Consensus pattern (17 bp):
TTTAATAAATGAACTAG
Done.