Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004250.1 Hibiscus syriacus cultivar Beakdansim tig00009318_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: 394940
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
File 1 of 2
Found at i:2082 original size:25 final size:24
Alignment explanation
Indices: 2029--2083 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
2019 TCTTTTCTTG
*
2029 CTTTTTCTTCTTTTGAGTGCTGGA
1 CTTTTTCTTCTTTTGAGTGCTGCA
* *
2053 TTTTTTCTTTCTTTTGAGTGCTTCA
1 CTTTTTC-TTCTTTTGAGTGCTGCA
2078 CTTTTT
1 CTTTTT
2084 TTGATTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.07, C:0.16, G:0.15, T:0.62
Consensus pattern (24 bp):
CTTTTTCTTCTTTTGAGTGCTGCA
Found at i:13096 original size:35 final size:36
Alignment explanation
Indices: 13027--13106 Score: 135
Period size: 35 Copynumber: 2.2 Consensus size: 36
13017 TACTATCTGT
**
13027 TCATCACCATCTTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
13063 TCATCACCATAGTCCATCACCA-TATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
13098 TCATCACCA
1 TCATCACCA
13107 AATTCTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
35 22 0.52
36 20 0.48
ACGTcount: A:0.30, C:0.39, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAGTCCATCACCATTATCACGCCTATA
Found at i:15239 original size:21 final size:22
Alignment explanation
Indices: 15189--15240 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
15179 GGAAAGGAGC
15189 CAAAGGATGTGACTCTTCAAGAAT
1 CAAAGGATGTGACTCTTC-A-AAT
* *
15213 CTAAGGCTGTGACTCTTC-AAT
1 CAAAGGATGTGACTCTTCAAAT
15234 CAAAGGA
1 CAAAGGA
15241 CATGATCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 8 0.33
24 16 0.67
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (22 bp):
CAAAGGATGTGACTCTTCAAAT
Found at i:17230 original size:35 final size:36
Alignment explanation
Indices: 17161--17238 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
17151 TACTATCTGT
** *
17161 TCATCACCATCTTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACACCTATA
17197 TCATCACCATAGTCCATCACCA-TATCACACCTATA
1 TCATCACCATAGTCCATCACCATTATCACACCTATA
17232 TCATCAC
1 TCATCAC
17239 TAAATTCCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 19 0.49
36 20 0.51
ACGTcount: A:0.31, C:0.38, G:0.03, T:0.28
Consensus pattern (36 bp):
TCATCACCATAGTCCATCACCATTATCACACCTATA
Found at i:17234 original size:11 final size:11
Alignment explanation
Indices: 17161--17238 Score: 61
Period size: 11 Copynumber: 6.6 Consensus size: 11
17151 TACTATCTGT
*
17161 TCATCACCATCT
1 TCATCACCAT-A
17173 TCCATCACCATTA
1 T-CATCACCA-TA
*
17186 TCA-CGCCTATA
1 TCATCACC-ATA
17197 TCATCACCATA
1 TCATCACCATA
17208 GTCCATCACCATA
1 -T-CATCACCATA
17221 TCA-CACCTATA
1 TCATCACC-ATA
17232 TCATCAC
1 TCATCAC
17239 TAAATTCCAT
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
10 4 0.07
11 19 0.35
12 12 0.22
13 19 0.35
14 1 0.02
ACGTcount: A:0.31, C:0.38, G:0.03, T:0.28
Consensus pattern (11 bp):
TCATCACCATA
Found at i:17248 original size:35 final size:36
Alignment explanation
Indices: 17161--17248 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 36
17151 TACTATCTGT
** *
17161 TCATCACCATCTTCCATCACCATTATCACGCCTATA
1 TCATCACCAAATTCCATCACCATTATCACACCTATA
* *
17197 TCATCACCATAGTCCATCACCA-TATCACACCTATA
1 TCATCACCAAATTCCATCACCATTATCACACCTATA
*
17232 TCATCACTAAATTCCAT
1 TCATCACCAAATTCCAT
17249 TTCCATTTCT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 26 0.57
36 20 0.43
ACGTcount: A:0.32, C:0.36, G:0.02, T:0.30
Consensus pattern (36 bp):
TCATCACCAAATTCCATCACCATTATCACACCTATA
Found at i:18491 original size:11 final size:11
Alignment explanation
Indices: 18469--18515 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
18459 TTTGAGGATT
18469 TGGTGATGATA
1 TGGTGATGATA
18480 TAGGTG-TGATA
1 T-GGTGATGATA
18491 TGGTGATGGACTA
1 TGGTGAT-GA-TA
18504 TGGTGATGATA
1 TGGTGATGATA
18515 T
1 T
18516 AGGCGTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 11 0.34
12 8 0.25
13 9 0.28
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:18495 original size:22 final size:24
Alignment explanation
Indices: 18469--18515 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
18459 TTTGAGGATT
18469 TGGTGAT-GA-TATAGGTG-TGATA
1 TGGTGATGGACTAT-GGTGATGATA
18491 TGGTGATGGACTATGGTGATGATA
1 TGGTGATGGACTATGGTGATGATA
18515 T
1 T
18516 AGGCGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 6 0.27
24 9 0.41
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (24 bp):
TGGTGATGGACTATGGTGATGATA
Found at i:18508 original size:35 final size:37
Alignment explanation
Indices: 18469--18548 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
18459 TTTGAGGATT
* *
18469 TGGTGATGATATAGGTGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
18504 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
18541 TGGTGATG
1 TGGTGATG
18549 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.50
36 4 0.10
37 16 0.40
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:22401 original size:11 final size:11
Alignment explanation
Indices: 22379--22425 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
22369 TTTGAGAATT
22379 TGGTGATGATA
1 TGGTGATGATA
22390 TAGGTG-TGATA
1 T-GGTGATGATA
22401 TGGTGATGGACTA
1 TGGTGAT-GA-TA
*
22414 TGGTAATGATA
1 TGGTGATGATA
22425 T
1 T
22426 AGGCGTGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
10 4 0.13
11 11 0.35
12 8 0.26
13 8 0.26
ACGTcount: A:0.28, C:0.02, G:0.34, T:0.36
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:22434 original size:35 final size:37
Alignment explanation
Indices: 22379--22454 Score: 102
Period size: 35 Copynumber: 2.1 Consensus size: 37
22369 TTTGAGAATT
* * *
22379 TGGTGATGATATAGGTGTGAT-ATGG-TGATGGACTA
1 TGGTAATGATATAGGCGTGATAATGGAAGATGGACTA
*
22414 TGGTAATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTAATGATATAGGCGTGATAATGGAAGATGGACTA
22451 TGGT
1 TGGT
22455 GATAGAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 19 0.54
36 4 0.11
37 12 0.34
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.33
Consensus pattern (37 bp):
TGGTAATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:26475 original size:17 final size:18
Alignment explanation
Indices: 26453--26491 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
26443 TTGTTGGAAA
*
26453 TTTCTTTCTTTTTG-GCT
1 TTTCTTTCTTATTGTGCT
26470 TTTC-TTCTTATTGTGCT
1 TTTCTTTCTTATTGTGCT
26487 TTTCT
1 TTTCT
26492 CTTTTGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.03, C:0.18, G:0.10, T:0.69
Consensus pattern (18 bp):
TTTCTTTCTTATTGTGCT
Found at i:26494 original size:16 final size:16
Alignment explanation
Indices: 26453--26498 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
26443 TTGTTGGAAA
26453 TTTCTTTCTTTT-TGGCT
1 TTTC-TTCTTTTGT-GCT
26470 TTTCTTCTTATTGTGCT
1 TTTCTTCTT-TTGTGCT
26487 TTTC-TCTTTTGT
1 TTTCTTCTTTTGT
26499 TTTGAACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 4 0.15
16 9 0.33
17 13 0.48
18 1 0.04
ACGTcount: A:0.02, C:0.17, G:0.11, T:0.70
Consensus pattern (16 bp):
TTTCTTCTTTTGTGCT
Found at i:27032 original size:28 final size:25
Alignment explanation
Indices: 26971--27030 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
26961 TAGTCCACAT
26971 CTTTATAATATGCACATTATTATTA
1 CTTTATAATATGCACATTATTATTA
26996 CTTTATAATATGCACATTATTATTA
1 CTTTATAATATGCACATTATTATTA
27021 CTTTATAATA
1 CTTTATAATA
27031 ATTCCTATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.48
Consensus pattern (25 bp):
CTTTATAATATGCACATTATTATTA
Found at i:28652 original size:20 final size:22
Alignment explanation
Indices: 28627--28671 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
28617 GTGATTCGGC
*
28627 AAGTACATAAT-TTTTAA-TGA
1 AAGTACATAATGCTTTAATTGA
28647 AAGTACATAATGCTTTAATTGA
1 AAGTACATAATGCTTTAATTGA
28669 AAG
1 AAG
28672 AATGAGTCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
21 5 0.23
22 6 0.27
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (22 bp):
AAGTACATAATGCTTTAATTGA
Found at i:36792 original size:23 final size:23
Alignment explanation
Indices: 36766--36816 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
36756 TTTCATATTG
36766 CACTCCACTCACACTCGTGTTTA
1 CACTCCACTCACACTCGTGTTTA
*
36789 CACTCCACTCACACTCGTGTTTG
1 CACTCCACTCACACTCGTGTTTA
36812 CACTC
1 CACTC
36817 GGGGATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.20, C:0.41, G:0.10, T:0.29
Consensus pattern (23 bp):
CACTCCACTCACACTCGTGTTTA
Found at i:37969 original size:35 final size:36
Alignment explanation
Indices: 37923--38034 Score: 181
Period size: 36 Copynumber: 3.1 Consensus size: 36
37913 GAAATGGAAA
37923 ATGGAATTTGGTGATGATATAGGCGTGAT-ATGGTG
1 ATGGAATTTGGTGATGATATAGGCGTGATAATGGTG
*
37958 ATGGACTTTGGTGATGATATAGGCGTGATAATGGTG
1 ATGGAATTTGGTGATGATATAGGCGTGATAATGGTG
** *
37994 ATGGAAGATGGTGATGATATAGGTGTGATAATGGTG
1 ATGGAATTTGGTGATGATATAGGCGTGATAATGGTG
38030 ATGGA
1 ATGGA
38035 CAGATTGTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 28 0.39
36 43 0.61
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.32
Consensus pattern (36 bp):
ATGGAATTTGGTGATGATATAGGCGTGATAATGGTG
Found at i:47692 original size:15 final size:15
Alignment explanation
Indices: 47642--47693 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
47632 AAAATATGGT
* *
47642 AATGAAATAAGAAAA
1 AATGAAATGATAAAA
*
47657 GATGAAA-GAATAAAGA
1 AATGAAATG-ATAAA-A
47673 AATGAAATGATAAAA
1 AATGAAATGATAAAA
47688 AATGAA
1 AATGAA
47694 GATAACTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 17 0.57
16 12 0.40
17 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.15
Consensus pattern (15 bp):
AATGAAATGATAAAA
Found at i:48368 original size:11 final size:11
Alignment explanation
Indices: 48352--48389 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
48342 AATTTGGTGA
48352 TGATATAGGCG
1 TGATATAGGCG
*
48363 TGATAT-GGTG
1 TGATATAGGCG
48373 ATGATATAGGCG
1 -TGATATAGGCG
48385 TGATA
1 TGATA
48390 ATGGTGATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 3 0.13
11 17 0.74
12 3 0.13
ACGTcount: A:0.29, C:0.05, G:0.34, T:0.32
Consensus pattern (11 bp):
TGATATAGGCG
Found at i:48374 original size:22 final size:23
Alignment explanation
Indices: 48346--48398 Score: 99
Period size: 22 Copynumber: 2.3 Consensus size: 23
48336 AAATGGAATT
48346 TGGTGATGATATAGGCGTGAT-A
1 TGGTGATGATATAGGCGTGATAA
48368 TGGTGATGATATAGGCGTGATAA
1 TGGTGATGATATAGGCGTGATAA
48391 TGGTGATG
1 TGGTGATG
48399 GAAGATGGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 21 0.70
23 9 0.30
ACGTcount: A:0.26, C:0.04, G:0.38, T:0.32
Consensus pattern (23 bp):
TGGTGATGATATAGGCGTGATAA
Found at i:48407 original size:36 final size:36
Alignment explanation
Indices: 48367--48436 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
48357 TAGGCGTGAT
48367 ATGGTGATGATATAGGCGTGATAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGATAATGGTGATGGAAG
48403 ATGGTGATGATATAGGCGTGATAATGGTGATGGA
1 ATGGTGATGATATAGGCGTGATAATGGTGATGGA
48437 CAGTTTGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.30, C:0.03, G:0.39, T:0.29
Consensus pattern (36 bp):
ATGGTGATGATATAGGCGTGATAATGGTGATGGAAG
Found at i:51303 original size:22 final size:22
Alignment explanation
Indices: 51278--51348 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
51268 ATCTTCTATG
* *
51278 ACCATTTCACACCGATTTTATC
1 ACCATTTCACACCGATATCATC
** *
51300 ACCATTTCATGCCTATATCATC
1 ACCATTTCACACCGATATCATC
* *
51322 ACCATTTCACGCCTATATCATC
1 ACCATTTCACACCGATATCATC
51344 ACCAT
1 ACCAT
51349 CTTCCATCAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.28, C:0.34, G:0.04, T:0.34
Consensus pattern (22 bp):
ACCATTTCACACCGATATCATC
Found at i:51364 original size:35 final size:35
Alignment explanation
Indices: 51318--51384 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
51308 ATGCCTATAT
51318 CATCACCATTTCACGCCTATATCATCACCATCTTC
1 CATCACCATTTCACGCCTATATCATCACCATCTTC
*
51353 CATCACCATTTCACGCCTATATCATTACCATC
1 CATCACCATTTCACGCCTATATCATCACCATC
51385 CCTTAACCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.27, C:0.39, G:0.03, T:0.31
Consensus pattern (35 bp):
CATCACCATTTCACGCCTATATCATCACCATCTTC
Found at i:51557 original size:17 final size:16
Alignment explanation
Indices: 51511--51558 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
51501 TCTTTGATAA
*
51511 CAATTCTATCCATTT-
1 CAATTCTTTCCATTTC
51526 CAATTCTTTCCATTTC
1 CAATTCTTTCCATTTC
*
51542 CAATTCCTTTCTATTTC
1 CAATT-CTTTCCATTTC
51559 TTAATTATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 14 0.48
16 5 0.17
17 10 0.34
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (16 bp):
CAATTCTTTCCATTTC
Found at i:53248 original size:2 final size:2
Alignment explanation
Indices: 53241--53331 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
53231 ATCACCAACT
53241 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
53283 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
53325 TA TA TA T
1 TA TA TA T
53332 TCCACTGCCA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53512 original size:15 final size:15
Alignment explanation
Indices: 53492--53541 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
53482 GAACTATATC
53492 AAAAAGAAAGAAAAG
1 AAAAAGAAAGAAAAG
53507 AAAAAG-AAGAAAA-
1 AAAAAGAAAGAAAAG
*
53520 ATTCAAAGAAA-AAAAG
1 A--AAAAGAAAGAAAAG
53536 AAAAAG
1 AAAAAG
53542 TGAAGAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
13 1 0.03
14 11 0.38
15 14 0.48
16 3 0.10
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (15 bp):
AAAAAGAAAGAAAAG
Found at i:74919 original size:20 final size:19
Alignment explanation
Indices: 74879--74929 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
74869 TGGCCAAGAG
*
74879 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
74898 CATGTATTTTCATTAGAAAT
1 CATGTATTTTCATTA-AAAT
* *
74918 CAAGCATTTTCA
1 CATGTATTTTCA
74930 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:76639 original size:9 final size:9
Alignment explanation
Indices: 76625--76685 Score: 63
Period size: 9 Copynumber: 6.7 Consensus size: 9
76615 TTTTTTTTTC
76625 AAAAAAACA
1 AAAAAAACA
76634 AAAAAAAC-
1 AAAAAAACA
76642 -AAAAAACA
1 AAAAAAACA
**
76650 AAAAAGGCAA
1 AAAAAAAC-A
76660 AAAAAAAGGCA
1 AAAAAAA--CA
76671 AAAAAAACA
1 AAAAAAACA
76680 AAAAAA
1 AAAAAA
76686 GAGCCAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
7 7 0.16
9 21 0.49
10 6 0.14
11 8 0.19
12 1 0.02
ACGTcount: A:0.84, C:0.10, G:0.07, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:76664 original size:12 final size:12
Alignment explanation
Indices: 76649--76677 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
76639 AACAAAAAAC
76649 AAAAAAGGCAAA
1 AAAAAAGGCAAA
76661 AAAAAAGGCAAA
1 AAAAAAGGCAAA
76673 AAAAA
1 AAAAA
76678 CAAAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAGGCAAA
Found at i:76665 original size:13 final size:13
Alignment explanation
Indices: 76644--76677 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
76634 AAAAAAACAA
76644 AAAACAAAAAAGGC
1 AAAA-AAAAAAGGC
76658 -AAAAAAAAAGGC
1 AAAAAAAAAAGGC
76670 AAAAAAAA
1 AAAAAAAA
76678 CAAAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.79, C:0.09, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGGC
Found at i:76693 original size:12 final size:11
Alignment explanation
Indices: 76649--76697 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
76639 AACAAAAAAC
76649 AAAAAAG-GCA
1 AAAAAAGAGCA
*
76659 AAAAAAAAGGCA
1 AAAAAAGA-GCA
76671 AAAAAA-A-CA
1 AAAAAAGAGCA
*
76680 AAAAAAGAGCC
1 AAAAAAGAGCA
76691 AAAAAAG
1 AAAAAAG
76698 CCAAAATTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 8 0.24
10 7 0.21
11 9 0.27
12 9 0.27
ACGTcount: A:0.76, C:0.10, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAGAGCA
Found at i:76702 original size:21 final size:21
Alignment explanation
Indices: 76648--76703 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
76638 AAACAAAAAA
* *
76648 CAAAAAAGGCAAAAAAAAAGG
1 CAAAAAAGACAAAAAAAAAGC
* *
76669 CAAAAAAAACAAAAAAAGAGC
1 CAAAAAAGACAAAAAAAAAGC
*
76690 CAAAAAAGCCAAAA
1 CAAAAAAGACAAAA
76704 TTACAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.73, C:0.14, G:0.12, T:0.00
Consensus pattern (21 bp):
CAAAAAAGACAAAAAAAAAGC
Found at i:82893 original size:23 final size:24
Alignment explanation
Indices: 82867--82915 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
82857 AGGTACAAGT
*
82867 GCCTTACATCAAGTGGTA-TCAGA
1 GCCTTACATCAAGCGGTAGTCAGA
82890 GCCTTACATCAAGCGGTAGTCAGA
1 GCCTTACATCAAGCGGTAGTCAGA
82914 GC
1 GC
82916 TTTAGTGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.22
Consensus pattern (24 bp):
GCCTTACATCAAGCGGTAGTCAGA
Found at i:83055 original size:22 final size:23
Alignment explanation
Indices: 83010--83053 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
83000 AAATCCAGCA
83010 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAATCAAAGCACTCAAAAG
* *
83033 AAGAAATTGAAAGCACTCAAA
1 AAGAAAATCAAAGCACTCAAA
83054 GAGGAAGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.59, C:0.16, G:0.14, T:0.11
Consensus pattern (23 bp):
AAGAAAATCAAAGCACTCAAAAG
Found at i:83086 original size:15 final size:16
Alignment explanation
Indices: 83061--83090 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
83051 AAAGAGGAAG
83061 GAAAAATAAAAGAAAA
1 GAAAAATAAAAGAAAA
83077 GAAAAA-AAAAGAAA
1 GAAAAATAAAAGAAA
83091 GTTGAAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (16 bp):
GAAAAATAAAAGAAAA
Found at i:89092 original size:11 final size:11
Alignment explanation
Indices: 89078--89141 Score: 60
Period size: 11 Copynumber: 5.7 Consensus size: 11
89068 TCTTTTTGAA
89078 TTCTTTTTCTT
1 TTCTTTTTCTT
89089 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
* *
89102 TTCTTCTTCTC
1 TTCTTTTTCTT
89113 TTCTTCTTT-TT
1 TTCTT-TTTCTT
*
89124 GTCTTTTTC-T
1 TTCTTTTTCTT
89134 TTCTTTTT
1 TTCTTTTT
89142 GCACTCCAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
10 11 0.26
11 17 0.40
12 7 0.16
13 8 0.19
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.77
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:89102 original size:19 final size:20
Alignment explanation
Indices: 89078--89123 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
89068 TCTTTTTGAA
*
89078 TTCTTTTTCTT-TTCTTTTC
1 TTCTTTTTCTTCTTCTCTTC
89097 TTC-TTTTCTTCTTCTCTTC
1 TTCTTTTTCTTCTTCTCTTC
89116 TTCTTTTT
1 TTCTTTTT
89124 GTCTTTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 7 0.29
19 13 0.54
20 4 0.17
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (20 bp):
TTCTTTTTCTTCTTCTCTTC
Found at i:89128 original size:19 final size:18
Alignment explanation
Indices: 89078--89142 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 18
89068 TCTTTTTGAA
* *
89078 TTCTTTTTCTTTTCTTTTC
1 TTCTTTTTGTCTTC-TTTC
89097 TTCTTTTCT-TCTTCTCTTC
1 TTCTTTT-TGTCTTCT-TTC
89116 TTCTTTTTGTCTT-TTTC
1 TTCTTTTTGTCTTCTTTC
89133 TTTCTTTTTG
1 -TTCTTTTTG
89143 CACTCCAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
17 3 0.07
18 12 0.29
19 25 0.61
20 1 0.02
ACGTcount: A:0.00, C:0.22, G:0.03, T:0.75
Consensus pattern (18 bp):
TTCTTTTTGTCTTCTTTC
Found at i:89135 original size:14 final size:13
Alignment explanation
Indices: 89081--89135 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 13
89071 TTTTGAATTC
89081 TTTTTC-TTTTCT
1 TTTTTCTTTTTCT
89093 TTTCTTC-TTTTCT
1 TTT-TTCTTTTTCT
* *
89106 TCTTCTCTTCTTCT
1 T-TTTTCTTTTTCT
89120 TTTTGTCTTTTTCT
1 TTTT-TCTTTTTCT
89134 TT
1 TT
89136 CTTTTTGCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 3 0.09
13 14 0.40
14 18 0.51
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:94669 original size:11 final size:11
Alignment explanation
Indices: 94655--94718 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
94645 TCTTTTTGAA
94655 TTCTTTTTCTT
1 TTCTTTTTCTT
94666 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
* **
94679 TTCTTCTTCCC
1 TTCTTTTTCTT
94690 TTCTTCTTT-TT
1 TTCTT-TTTCTT
*
94701 GTCTTTTTC-T
1 TTCTTTTTCTT
94711 TTCTTTTT
1 TTCTTTTT
94719 GCACTCCAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
10 11 0.27
11 15 0.37
12 7 0.17
13 8 0.20
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:94679 original size:19 final size:20
Alignment explanation
Indices: 94655--94700 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
94645 TCTTTTTGAA
**
94655 TTCTTTTTCTT-TTCTTTTC
1 TTCTTTTTCTTCTTCCCTTC
94674 TTC-TTTTCTTCTTCCCTTC
1 TTCTTTTTCTTCTTCCCTTC
94693 TTCTTTTT
1 TTCTTTTT
94701 GTCTTTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 7 0.30
19 12 0.52
20 4 0.17
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (20 bp):
TTCTTTTTCTTCTTCCCTTC
Found at i:99400 original size:33 final size:33
Alignment explanation
Indices: 99321--99424 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
99311 ATACAATCTG
* *
99321 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
99357 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
99390 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
99423 TC
1 TC
99425 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:99850 original size:17 final size:18
Alignment explanation
Indices: 99828--99875 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
99818 TGGAGTGCAA
99828 AAGAAAGAAAA-AAAAAG
1 AAGAAAGAAAAGAAAAAG
*
99845 AAGAAAAGCAAAAGCAAAAG
1 AAG-AAAG-AAAAGAAAAAG
99865 AA-AAAGAAAAG
1 AAGAAAGAAAAG
99876 TGAAGCAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 8 0.30
18 8 0.30
19 4 0.15
20 7 0.26
ACGTcount: A:0.77, C:0.04, G:0.19, T:0.00
Consensus pattern (18 bp):
AAGAAAGAAAAGAAAAAG
Found at i:99863 original size:12 final size:11
Alignment explanation
Indices: 99826--99875 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
99816 TTTGGAGTGC
99826 AAAAGAAAGAA-
1 AAAAGAAA-AAG
99837 AAAA-AAAGAAG
1 AAAAGAAA-AAG
*
99848 AAAAGCAAAAG
1 AAAAGAAAAAG
99859 CAAAAGAAAAAG
1 -AAAAGAAAAAG
99871 AAAAG
1 AAAAG
99876 TGAAGCAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 6 0.18
11 16 0.47
12 12 0.35
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:103423 original size:35 final size:37
Alignment explanation
Indices: 103354--103423 Score: 108
Period size: 35 Copynumber: 1.9 Consensus size: 37
103344 ATAAGATACA
* *
103354 ATATGTCCATCACCATTATCACGCCTATATCATCACT
1 ATATGTCCATCACCATTATCACGCCAATAACATCACT
103391 ATAT-TCCATCACCA-TATCACGCCAATAACATCA
1 ATATGTCCATCACCATTATCACGCCAATAACATCA
103424 TCCTTCCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 17 0.55
36 10 0.32
37 4 0.13
ACGTcount: A:0.34, C:0.33, G:0.04, T:0.29
Consensus pattern (37 bp):
ATATGTCCATCACCATTATCACGCCAATAACATCACT
Found at i:103438 original size:33 final size:33
Alignment explanation
Indices: 103394--103462 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
103384 CATCACTATA
*
103394 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
103427 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
103460 TTC
1 TTC
103463 ATTCATCAAC
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:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:107558 original size:17 final size:19
Alignment explanation
Indices: 107524--107558 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
107514 GCTACAACAA
107524 AAACACAAAGAAAGAAGAG
1 AAACACAAAGAAAGAAGAG
107543 AAACA-AAAGAAA-AAGA
1 AAACACAAAGAAAGAAGA
107559 AAAGACTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 7 0.44
19 5 0.31
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (19 bp):
AAACACAAAGAAAGAAGAG
Found at i:110977 original size:19 final size:19
Alignment explanation
Indices: 110953--111021 Score: 120
Period size: 19 Copynumber: 3.6 Consensus size: 19
110943 CGGCCAAGAG
*
110953 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
110972 CATGTATTTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
*
110991 CATGTATTTTCATTAAATT
1 CATGTATTTTCATTAAAAT
111010 CATGTATTTTCA
1 CATGTATTTTCA
111022 AAGGGGTTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:116471 original size:35 final size:37
Alignment explanation
Indices: 116425--116504 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
116415 TTTGAGAATT
*
116425 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
116460 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
116497 TGGTGATG
1 TGGTGATG
116505 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:122492 original size:11 final size:10
Alignment explanation
Indices: 122433--122493 Score: 60
Period size: 9 Copynumber: 6.3 Consensus size: 10
122423 TTTTTTATTC
122433 AAAAAAAGCA
1 AAAAAAAGCA
122443 AAAAAAAGGC-
1 AAAAAAA-GCA
122453 -AAAAAA-CA
1 AAAAAAAGCA
122461 AAAAAAAGGC-
1 AAAAAAA-GCA
122471 AAAAAAA-CA
1 AAAAAAAGCA
122480 AAAAAAAGCCA
1 AAAAAAAG-CA
122491 AAA
1 AAA
122494 TTTCAAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 19 0.44
10 14 0.33
11 8 0.19
ACGTcount: A:0.79, C:0.11, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAAGCA
Found at i:122502 original size:19 final size:18
Alignment explanation
Indices: 122434--122493 Score: 93
Period size: 19 Copynumber: 3.2 Consensus size: 18
122424 TTTTTATTCA
122434 AAAAAAGCAAAAAAAAGGC
1 AAAAAA-CAAAAAAAAGGC
122453 AAAAAACAAAAAAAAGGC
1 AAAAAACAAAAAAAAGGC
*
122471 AAAAAAACAAAAAAAAGCC
1 -AAAAAACAAAAAAAAGGC
122490 AAAA
1 AAAA
122494 TTTCAAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
18 16 0.41
19 23 0.59
ACGTcount: A:0.78, C:0.12, G:0.10, T:0.00
Consensus pattern (18 bp):
AAAAAACAAAAAAAAGGC
Found at i:128575 original size:8 final size:8
Alignment explanation
Indices: 128564--128616 Score: 52
Period size: 8 Copynumber: 6.0 Consensus size: 8
128554 TATTATTTTT
128564 CAAAAAAA
1 CAAAAAAA
128572 CAAAAAAA
1 CAAAAAAA
*
128580 TAAAAAAA
1 CAAAAAAA
128588 GGCAAAAAAAA
1 --C-AAAAAAA
128599 GTCAAAAAAA
1 --CAAAAAAA
128609 CAAAAAAA
1 CAAAAAAA
128617 AGCCAAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
8 23 0.59
10 7 0.18
11 9 0.23
ACGTcount: A:0.81, C:0.09, G:0.06, T:0.04
Consensus pattern (8 bp):
CAAAAAAA
Found at i:128595 original size:19 final size:19
Alignment explanation
Indices: 128563--128624 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
128553 CTATTATTTT
128563 TCAAAAAAAC-AAAAAAA-
1 TCAAAAAAACAAAAAAAAG
128580 T-AAAAAAAGGCAAAAAAAAG
1 TCAAAAAAA--CAAAAAAAAG
128600 TCAAAAAAACAAAAAAAAG
1 TCAAAAAAACAAAAAAAAG
*
128619 CCAAAA
1 TCAAAA
128625 TTTCAAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
16 7 0.18
17 1 0.03
18 1 0.03
19 22 0.56
20 1 0.03
21 7 0.18
ACGTcount: A:0.77, C:0.11, G:0.06, T:0.05
Consensus pattern (19 bp):
TCAAAAAAACAAAAAAAAG
Found at i:134478 original size:11 final size:13
Alignment explanation
Indices: 134446--134475 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
134436 TGGCCAAAGA
134446 TGAAAAGGTATGT
1 TGAAAAGGTATGT
134459 TGAAAAGGTATG-
1 TGAAAAGGTATGT
134471 TGAAA
1 TGAAA
134476 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:139965 original size:35 final size:37
Alignment explanation
Indices: 139914--139998 Score: 129
Period size: 35 Copynumber: 2.4 Consensus size: 37
139904 GGAAATTTGA
* *
139914 GAATTTGGTGATGATATAGGCGTGAT-ATGG-TGATG
1 GAATATGGTGATGATATAGGCGTGATAATGGAAGATG
139949 GAATATGGTGATGATATAGGCGTGATAATGGAAGATG
1 GAATATGGTGATGATATAGGCGTGATAATGGAAGATG
*
139986 GATTATGGTGATG
1 GAATATGGTGATG
139999 GAAATAGTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
35 25 0.56
36 4 0.09
37 16 0.36
ACGTcount: A:0.29, C:0.02, G:0.36, T:0.32
Consensus pattern (37 bp):
GAATATGGTGATGATATAGGCGTGATAATGGAAGATG
Found at i:146328 original size:5 final size:5
Alignment explanation
Indices: 146318--146347 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
146308 TTTTAATTCT
146318 TTTTC TTTTC TTTTC TTTTC TTCTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TT-TTC TTTT
146348 TGTCTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:146328 original size:11 final size:11
Alignment explanation
Indices: 146314--146366 Score: 56
Period size: 10 Copynumber: 4.7 Consensus size: 11
146304 TCTTTTTTAA
146314 TTCTTTTTCTT
1 TTCTTTTTCTT
146325 TTC-TTTTCTT
1 TTCTTTTTCTT
*
146335 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
146348 TGTCTTTTTC-T
1 T-TCTTTTTCTT
146359 TTCTTTTT
1 TTCTTTTT
146367 GCACTCCAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
10 17 0.47
11 6 0.17
12 3 0.08
13 6 0.17
14 4 0.11
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:148485 original size:35 final size:37
Alignment explanation
Indices: 148439--148518 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
148429 TTTGAGAATT
*
148439 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
148474 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
148511 TGGTGATG
1 TGGTGATG
148519 GAAATAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:150636 original size:35 final size:36
Alignment explanation
Indices: 150594--150698 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
150584 AAATGGAATT
*
150594 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACGA
* *
150629 TGTTGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACGA
150665 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
150699 AGATTGTATC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 20 0.31
36 44 0.69
ACGTcount: A:0.28, C:0.05, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACGA
Found at i:157639 original size:12 final size:12
Alignment explanation
Indices: 157607--157645 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
157597 GATTAACTTG
157607 TTGATTTT-TTT
1 TTGATTTTCTTT
157618 TTGCACTTTTCTTT
1 TTG-A-TTTTCTTT
157632 TTGATTTTCTTT
1 TTGATTTTCTTT
157644 TT
1 TT
157646 ATTGAATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.12
12 11 0.44
13 5 0.20
14 6 0.24
ACGTcount: A:0.08, C:0.10, G:0.08, T:0.74
Consensus pattern (12 bp):
TTGATTTTCTTT
Found at i:160513 original size:28 final size:28
Alignment explanation
Indices: 160482--160542 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
160472 CAAAAGGAAA
*
160482 AGAAAAGGCA-AAAAGAAGAAAAAAAATC
1 AGAAAAGGAAGAAAAGAA-AAAAAAAATC
*
160510 AGAAAA-GAAGAAAAGAAAAAGAAAATC
1 AGAAAAGGAAGAAAAGAAAAAAAAAATC
160537 A-AAAAG
1 AGAAAAG
160543 AGAAAGCAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 4 0.14
27 12 0.41
28 13 0.45
ACGTcount: A:0.74, C:0.05, G:0.18, T:0.03
Consensus pattern (28 bp):
AGAAAAGGAAGAAAAGAAAAAAAAAATC
Found at i:160546 original size:28 final size:28
Alignment explanation
Indices: 160492--160546 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
160482 AGAAAAGGCA
*
160492 AAAAGAAGAAAAAAAATCAGAAAAGAAG
1 AAAAGAAGAAAAAAAATCAAAAAAGAAG
*
160520 AAAAGAA-AAAGAAAATCAAAAAGAGAA
1 AAAAGAAGAAAAAAAATCAAAAA-AGAA
160547 AGCAAGCCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (28 bp):
AAAAGAAGAAAAAAAATCAAAAAAGAAG
Found at i:174295 original size:33 final size:33
Alignment explanation
Indices: 174216--174319 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
174206 ATACAATCTG
* *
174216 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
174252 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
174285 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
174318 TC
1 TC
174320 ATTTATCAAC
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:178702 original size:33 final size:33
Alignment explanation
Indices: 178623--178726 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
178613 ATACAATCTG
* *
178623 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
178659 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
178692 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
178725 TC
1 TC
178727 ATTTATCAAC
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:181268 original size:91 final size:91
Alignment explanation
Indices: 181113--181295 Score: 294
Period size: 91 Copynumber: 2.0 Consensus size: 91
181103 CCTAGAACAC
* *
181113 CCATGTGCCTTGCATATGACCAGCTCCCATATGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATATGCCTTGCATATGGATCATTTAGGCGCCAAGATG
181178 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
** * * * *
181204 CCATGTGTTTTGCATGTGATCAGCCCCCATGTGCCTTGCATATGGTTCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATATGCCTTGCATATGGATCATTTAGGCGCCAAGATG
181269 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
181295 C
1 C
181296 ATCAACTACC
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATATGCCTTGCATATGGATCATTTAGGCGCCAAGATG
AAGAGTTCTCTCCCTATTCGGCCAAG
Found at i:188090 original size:15 final size:15
Alignment explanation
Indices: 188070--188102 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
188060 AAAGAAAGGA
188070 AATTGAAATGGAAAG
1 AATTGAAATGGAAAG
*
188085 AATTGAAATGGATAG
1 AATTGAAATGGAAAG
188100 AAT
1 AAT
188103 AGTTATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (15 bp):
AATTGAAATGGAAAG
Found at i:188267 original size:11 final size:11
Alignment explanation
Indices: 188245--188291 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
188235 TTTGAGAATT
188245 TGGTGATGATA
1 TGGTGATGATA
188256 TAGGTG-TGATA
1 T-GGTGATGATA
188267 TGGTGATGGACTA
1 TGGTGAT-GA-TA
188280 TGGTGATGATA
1 TGGTGATGATA
188291 T
1 T
188292 AGGCGTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 11 0.34
12 8 0.25
13 9 0.28
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:188273 original size:22 final size:24
Alignment explanation
Indices: 188245--188291 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
188235 TTTGAGAATT
188245 TGGTGAT-GA-TATAGGTG-TGATA
1 TGGTGATGGACTAT-GGTGATGATA
188267 TGGTGATGGACTATGGTGATGATA
1 TGGTGATGGACTATGGTGATGATA
188291 T
1 T
188292 AGGCGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 6 0.27
24 9 0.41
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (24 bp):
TGGTGATGGACTATGGTGATGATA
Found at i:188291 original size:35 final size:37
Alignment explanation
Indices: 188245--188324 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
188235 TTTGAGAATT
* *
188245 TGGTGATGATATAGGTGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
188280 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
188317 TGGTGATG
1 TGGTGATG
188325 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.50
36 4 0.10
37 16 0.40
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:188711 original size:19 final size:20
Alignment explanation
Indices: 188664--188714 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
188654 GAAACCCCTT
**
188664 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
188684 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
188703 TGAAGATACATG
1 TGAAAATACATG
188715 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:192414 original size:11 final size:11
Alignment explanation
Indices: 192392--192438 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
192382 TTTGAGAATT
192392 TGGTGATGATA
1 TGGTGATGATA
192403 TAGGTG-TGATA
1 T-GGTGATGATA
192414 TGGTGATGGACTA
1 TGGTGAT-GA-TA
192427 TGGTGATGATA
1 TGGTGATGATA
192438 T
1 T
192439 AGGCGTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 11 0.34
12 8 0.25
13 9 0.28
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:192420 original size:22 final size:24
Alignment explanation
Indices: 192392--192438 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
192382 TTTGAGAATT
192392 TGGTGAT-GA-TATAGGTG-TGATA
1 TGGTGATGGACTAT-GGTGATGATA
192414 TGGTGATGGACTATGGTGATGATA
1 TGGTGATGGACTATGGTGATGATA
192438 T
1 T
192439 AGGCGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 6 0.27
24 9 0.41
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (24 bp):
TGGTGATGGACTATGGTGATGATA
Found at i:192438 original size:35 final size:37
Alignment explanation
Indices: 192392--192471 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
192382 TTTGAGAATT
* *
192392 TGGTGATGATATAGGTGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
192427 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
192464 TGGTGATG
1 TGGTGATG
192472 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.50
36 4 0.10
37 16 0.40
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:192857 original size:19 final size:20
Alignment explanation
Indices: 192810--192860 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
192800 GAAACCCCTT
**
192810 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
192830 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
192849 TGAAGATACATG
1 TGAAAATACATG
192861 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:198674 original size:33 final size:33
Alignment explanation
Indices: 198632--198700 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
198622 GTTGATGAAT
*
198632 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* *
198665 GAAGGATGATGTTATTGGCGTGATATGGTAATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
198698 GAA
1 GAA
198701 TATGGTGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.33, C:0.01, G:0.35, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:198741 original size:36 final size:36
Alignment explanation
Indices: 198671--198783 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
198661 AATGGAAGGA
* * *
198671 TGATGTTATTGGCGTGAT-ATGGTAATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
198706 TGATGATATAGGCGTGATAATGGTGATAGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
198742 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
198778 TGATGA
1 TGATGA
198784 AAATAGTATC
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 16 0.23
36 53 0.77
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:200501 original size:23 final size:20
Alignment explanation
Indices: 200472--200514 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 20
200462 GTGCTACAAC
200472 AAAAAAAGTAACAAGAAAGAAGA
1 AAAAAAAG-AA-AAGAAA-AAGA
200495 AAAAAAAGAAAAGAAAAAGA
1 AAAAAAAGAAAAGAAAAAGA
200515 CTCCTACAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 6 0.30
22 2 0.10
23 8 0.40
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (20 bp):
AAAAAAAGAAAAGAAAAAGA
Found at i:204254 original size:35 final size:37
Alignment explanation
Indices: 204192--204262 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 37
204182 ATAAGATACA
*
204192 ATATGTCCATCACCATTATCATGCCTATATCATCACT
1 ATATGTCCATCACCATTATCACGCCTATATCATCACT
*
204229 ATAT-TCCATCACCA-TATCACGCCTATATTATCAC
1 ATATGTCCATCACCATTATCACGCCTATATCATCAC
204263 CAACTTCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 18 0.56
36 10 0.31
37 4 0.12
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.34
Consensus pattern (37 bp):
ATATGTCCATCACCATTATCACGCCTATATCATCACT
Found at i:206082 original size:185 final size:189
Alignment explanation
Indices: 205747--206119 Score: 691
Period size: 185 Copynumber: 2.0 Consensus size: 189
205737 ATGCATATAA
205747 TCTATAGTTGTAATAATAATATTCATTCATTATCGTATGATGCATGAGTTATTATTATAACCTAT
1 TCTATAGTTGTAATAATAATATTCATTCATTATCGTATGATGCATGAGTTATTATTATAACCTAT
205812 AGTTCACATCTTTATAATATGCACATTCTTATTACTTTATAATAATTCATATACTTAGCTTATAT
66 AGTTCACATCTTTATAATATGCACATTCTTATTACTTTATAATAATTCATATACTTAGCTTATAT
205877 TATGCTTTCTTTTATAGGTGCATATTCGGCCACATGTTGGGAACTGATTTAAAGCTAGG
131 TATGCTTTCTTTTATAGGTGCATATTCGGCCACATGTTGGGAACTGATTTAAAGCTAGG
205936 TCTATAGTTGTAATAAT-AT-TTCATTCATTATCGTATGATGCATGAGTTATTATTATAACCTAT
1 TCTATAGTTGTAATAATAATATTCATTCATTATCGTATGATGCATGAGTTATTATTATAACCTAT
*
205999 AGTTCACATCTTTAT-A-ATGCACATTCTTATTACTTTATAGTAATTCATATACTTAGCTTATAT
66 AGTTCACATCTTTATAATATGCACATTCTTATTACTTTATAATAATTCATATACTTAGCTTATAT
* *
206062 TATGCTTTCTTTTGTAGGTGCATGTTCGGCCACATGTTGGGAACTGATTTAAAGCTAG
131 TATGCTTTCTTTTATAGGTGCATATTCGGCCACATGTTGGGAACTGATTTAAAGCTAG
206120 CATGGGAGTC
Statistics
Matches: 181, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
185 102 0.56
186 1 0.01
187 59 0.33
188 2 0.01
189 17 0.09
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.43
Consensus pattern (189 bp):
TCTATAGTTGTAATAATAATATTCATTCATTATCGTATGATGCATGAGTTATTATTATAACCTAT
AGTTCACATCTTTATAATATGCACATTCTTATTACTTTATAATAATTCATATACTTAGCTTATAT
TATGCTTTCTTTTATAGGTGCATATTCGGCCACATGTTGGGAACTGATTTAAAGCTAGG
Found at i:207216 original size:35 final size:37
Alignment explanation
Indices: 207147--207226 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
207137 ATACTATTTC
*
207147 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
207184 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
207219 CATCACCA
1 CATCACCA
207227 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:212829 original size:12 final size:12
Alignment explanation
Indices: 212814--212863 Score: 52
Period size: 13 Copynumber: 4.3 Consensus size: 12
212804 AAAAAAAAAC
212814 AAAAAAGGCAAAA
1 AAAAAAGGC-AAA
212827 AAAAAAGGC-AA
1 AAAAAAGGCAAA
212838 AAAAAA--CAAA
1 AAAAAAGGCAAA
* *
212848 AAAAGAGCCAAA
1 AAAAAAGGCAAA
212860 AAAA
1 AAAA
212864 GCCAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
9 1 0.03
10 7 0.21
11 8 0.24
12 8 0.24
13 9 0.27
ACGTcount: A:0.78, C:0.10, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAGGCAAA
Found at i:212831 original size:14 final size:14
Alignment explanation
Indices: 212808--212843 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
212798 TTTTTCAAAA
212808 AAAAACAAAAAAGGC
1 AAAAA-AAAAAAGGC
212823 -AAAAAAAAAAGGC
1 AAAAAAAAAAAGGC
212836 AAAAAAAA
1 AAAAAAAA
212844 CAAAAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.81, C:0.08, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGGC
Found at i:212832 original size:13 final size:13
Alignment explanation
Indices: 212809--212843 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
212799 TTTTCAAAAA
212809 AAAACAAAAAAGGC
1 AAAA-AAAAAAGGC
212823 AAAAAAAAAAGGC
1 AAAAAAAAAAGGC
212836 AAAAAAAA
1 AAAAAAAA
212844 CAAAAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGGC
Found at i:212832 original size:22 final size:22
Alignment explanation
Indices: 212804--212851 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
212794 ATTTTTTTTC
**
212804 AAAAAAAAACAAAAAAGGCAAA
1 AAAAAAAAACAAAAAAAACAAA
**
212826 AAAAAAAGGCAAAAAAAACAAA
1 AAAAAAAAACAAAAAAAACAAA
212848 AAAA
1 AAAA
212852 GAGCCAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.83, C:0.08, G:0.08, T:0.00
Consensus pattern (22 bp):
AAAAAAAAACAAAAAAAACAAA
Found at i:212860 original size:10 final size:10
Alignment explanation
Indices: 212826--212870 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
212816 AAAAGGCAAA
*
212826 AAAAAAAGGC
1 AAAAAAAGCC
* *
212836 AAAAAAAACA
1 AAAAAAAGCC
212846 AAAAAAGAGCC
1 AAAAAA-AGCC
212857 AAAAAAAGCC
1 AAAAAAAGCC
212867 AAAA
1 AAAA
212871 TTTCAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
10 21 0.72
11 8 0.28
ACGTcount: A:0.76, C:0.13, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAGCC
Found at i:212861 original size:31 final size:30
Alignment explanation
Indices: 212805--212870 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 30
212795 TTTTTTTTCA
*
212805 AAAAAAAACAAAAAAGGCAAAAAAAAAAGGC
1 AAAAAAAACAAAAAAGGC-AAAAAAAAAGCC
*
212836 AAAAAAAACAAAAAAAGAGC-CAAAAAAAGCC
1 AAAAAAAAC-AAAAAAG-GCAAAAAAAAAGCC
212867 AAAA
1 AAAA
212871 TTTCAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 22 0.71
32 7 0.23
33 2 0.06
ACGTcount: A:0.77, C:0.12, G:0.11, T:0.00
Consensus pattern (30 bp):
AAAAAAAACAAAAAAGGCAAAAAAAAAGCC
Found at i:212869 original size:22 final size:22
Alignment explanation
Indices: 212803--212870 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 22
212793 TATTTTTTTT
*
212803 CAAAAAAAAA--CAAAAAAGGC
1 CAAAAAAAAAGCCAAAAAAAGC
* * *
212823 AAAAAAAAAAGGCAAAAAAA-A
1 CAAAAAAAAAGCCAAAAAAAGC
*
212844 CAAAAAAAGAGCCAAAAAAAGC
1 CAAAAAAAAAGCCAAAAAAAGC
212866 CAAAA
1 CAAAA
212871 TTTCAAAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 9 0.24
21 17 0.45
22 12 0.32
ACGTcount: A:0.76, C:0.13, G:0.10, T:0.00
Consensus pattern (22 bp):
CAAAAAAAAAGCCAAAAAAAGC
Found at i:218339 original size:35 final size:37
Alignment explanation
Indices: 218270--218349 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
218260 ATACTATTTC
*
218270 CATCACCATAATCCATCTTCCATTATCAAGCCTATAT
1 CATCACCATAATCCATCTACCATTATCAAGCCTATAT
* *
218307 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCAAGCCTATAT
218342 CATCACCA
1 CATCACCA
218350 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCAAGCCTATAT
Found at i:220234 original size:19 final size:20
Alignment explanation
Indices: 220187--220237 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
220177 GAAACCCCTT
**
220187 TGAAAATACATGATATTTTA
1 TGAAAATACATGATATTAAA
220207 TGAAAATACATGAT-TTAAA
1 TGAAAATACATGATATTAAA
*
220226 TGAAGATACATG
1 TGAAAATACATG
220238 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATATTAAA
Found at i:230732 original size:24 final size:21
Alignment explanation
Indices: 230698--230740 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
230688 TCCACAAGAT
*
230698 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
230720 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
230741 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:231523 original size:36 final size:36
Alignment explanation
Indices: 231450--231554 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
231440 ATTTATAAGT
* *
231450 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
231485 TGGTGATGATATAGGCGTGATAATAGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
231521 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
231555 AGATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:238100 original size:19 final size:18
Alignment explanation
Indices: 238078--238147 Score: 77
Period size: 19 Copynumber: 3.6 Consensus size: 18
238068 TCCAAAAAAA
238078 CAAAAAAAAACAAAAAAGG
1 CAAAAAAAAA-AAAAAAGG
238097 CAAAAAAACAAAAAAAAAACGG
1 C--AAAAA-AAAAAAAAAA-GG
*
238119 CAAAAAAACAAAAAAAGAG
1 CAAAAAAAAAAAAAAAG-G
238138 CAAAAAAAAA
1 CAAAAAAAAA
238148 GCCAAAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
18 1 0.02
19 20 0.45
20 5 0.11
21 11 0.25
22 7 0.16
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (18 bp):
CAAAAAAAAAAAAAAAGG
Found at i:238113 original size:21 final size:22
Alignment explanation
Indices: 238079--238134 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
238069 CCAAAAAAAC
*
238079 AAAAAA-AAACAAAAAA-GGCA
1 AAAAAACAAAAAAAAAACGGCA
238099 AAAAAACAAAAAAAAAACGGCA
1 AAAAAACAAAAAAAAAACGGCA
238121 AAAAAACAAAAAAA
1 AAAAAACAAAAAAA
238135 GAGCAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 6 0.18
21 9 0.27
22 18 0.55
ACGTcount: A:0.82, C:0.11, G:0.07, T:0.00
Consensus pattern (22 bp):
AAAAAACAAAAAAAAAACGGCA
Found at i:238153 original size:12 final size:11
Alignment explanation
Indices: 238071--238154 Score: 51
Period size: 10 Copynumber: 8.2 Consensus size: 11
238061 TTTTTTTTCC
238071 AAAAAAA-CAA
1 AAAAAAAGCAA
238081 AAAAAAA-C--
1 AAAAAAAGCAA
*
238089 AAAAAAGGCAA
1 AAAAAAAGCAA
238100 AAAAACAA--AA
1 AAAAA-AAGCAA
*
238110 AAAAAACGGC--
1 AAAAAA-AGCAA
238120 AAAAAAA-CAA
1 AAAAAAAGCAA
*
238130 AAAAAGAGCAA
1 AAAAAAAGCAA
238141 AAAAAAAGCCAA
1 AAAAAAAG-CAA
238153 AA
1 AA
238155 TTTCAAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
8 7 0.12
9 2 0.04
10 27 0.47
11 15 0.26
12 6 0.11
ACGTcount: A:0.80, C:0.12, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAGCAA
Found at i:238154 original size:22 final size:20
Alignment explanation
Indices: 238069--238154 Score: 72
Period size: 19 Copynumber: 4.3 Consensus size: 20
238059 TATTTTTTTT
*
238069 CCAAAAAA-ACAAAAAAAAA
1 CCAAAAAAGGCAAAAAAAAA
238088 -CAAAAAAGGCAAAAAAACAA
1 CCAAAAAAGGCAAAAAAA-AA
**
238108 AAAAAAAACGGC--AAAAAAA
1 CCAAAAAA-GGCAAAAAAAAA
*
238127 CAAAAAAAGAGCAAAAAAAAA
1 CCAAAAAAG-GCAAAAAAAAA
238148 GCCAAAA
1 -CCAAAA
238155 TTTCAAAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
18 8 0.15
19 19 0.35
20 7 0.13
21 13 0.24
22 8 0.15
ACGTcount: A:0.78, C:0.14, G:0.08, T:0.00
Consensus pattern (20 bp):
CCAAAAAAGGCAAAAAAAAA
Found at i:242023 original size:40 final size:44
Alignment explanation
Indices: 241930--242025 Score: 119
Period size: 48 Copynumber: 2.2 Consensus size: 44
241920 TAGGATCAGA
*
241930 TTTATTATTTTATTAGGAATTAAGGTTGGGTTAAAACAATATTTTAG
1 TTTATTATTTTATTAGGAATTAA-G--GGGTTAAAACAATAGTTTAG
241977 TATTATTATTTTATTAGGAATT-A-GGGTTAAAAC-AT-GTTTAG
1 T-TTATTATTTTATTAGGAATTAAGGGGTTAAAACAATAGTTTAG
242018 TTTATTAT
1 TTTATTAT
242026 ATTTTATTCT
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
40 7 0.15
41 6 0.13
42 2 0.04
43 10 0.21
47 2 0.04
48 20 0.43
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (44 bp):
TTTATTATTTTATTAGGAATTAAGGGGTTAAAACAATAGTTTAG
Found at i:243031 original size:36 final size:36
Alignment explanation
Indices: 242958--243062 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
242948 ATTTATAAGT
* *
242958 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
242993 TGGTGATGATATAGGCGTGATAATAGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
243029 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
243063 AGATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:246494 original size:19 final size:21
Alignment explanation
Indices: 246472--246523 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 21
246462 AACAAGAAAG
246472 AAGAAAAA-AA-CAAAAAGAA
1 AAGAAAAAGAATCAAAAAGAA
246491 AAGAAAAATAAGAATCAAAAAGAA
1 AAG--AAA-AAGAATCAAAAAGAA
246515 AAGAAAAAG
1 AAGAAAAAG
246524 TGAAGCAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 3 0.11
21 6 0.21
22 5 0.18
23 2 0.07
24 12 0.43
ACGTcount: A:0.79, C:0.04, G:0.13, T:0.04
Consensus pattern (21 bp):
AAGAAAAAGAATCAAAAAGAA
Found at i:246497 original size:17 final size:18
Alignment explanation
Indices: 246462--246504 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
246452 AACAAAAAGC
246462 AACAAGAAAGAAGAAAAA
1 AACAAGAAAGAAGAAAAA
246480 AACAA-AAAGAA-AAGAAA
1 AACAAGAAAGAAGAA-AAA
*
246497 AATAAGAA
1 AACAAGAA
246505 TCAAAAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.09
17 13 0.59
18 7 0.32
ACGTcount: A:0.79, C:0.05, G:0.14, T:0.02
Consensus pattern (18 bp):
AACAAGAAAGAAGAAAAA
Found at i:252117 original size:7 final size:6
Alignment explanation
Indices: 252095--252166 Score: 51
Period size: 6 Copynumber: 12.0 Consensus size: 6
252085 GTGCTACAAC
* *
252095 AAAAAG CAACAAG AAAGAAG AAAAA- AACAA- AAAAAG AAAAAG AAAAAG
1 AAAAAG -AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
** *
252143 AAGAATC AAAAAG -AATAG AAAAAG
1 AA-AAAG AAAAAG AAAAAG AAAAAG
252167 TAAAGCAAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
5 12 0.24
6 24 0.47
7 15 0.29
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:252133 original size:16 final size:18
Alignment explanation
Indices: 252102--252135 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
252092 AACAAAAAGC
252102 AACAAGAAAGAAGAAAAA
1 AACAAGAAAGAAGAAAAA
252120 AACAA-AAA-AAGAAAAA
1 AACAAGAAAGAAGAAAAA
252136 GAAAAAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (18 bp):
AACAAGAAAGAAGAAAAA
Found at i:252153 original size:25 final size:23
Alignment explanation
Indices: 252105--252166 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
252095 AAAAAGCAAC
252105 AAGAAAGAAGAAAAA-AACAAAAA
1 AAGAAA-AAGAAAAAGAACAAAAA
*
252128 AAGAAAAAGAAAAAGAAGAATCAAA
1 AAGAAAAAGAAAAAGAACAA--AAA
*
252153 AAG-AATAGAAAAAG
1 AAGAAAAAGAAAAAG
252167 TAAAGCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 8 0.24
23 10 0.29
24 10 0.29
25 6 0.18
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.03
Consensus pattern (23 bp):
AAGAAAAAGAAAAAGAACAAAAA
Found at i:257795 original size:19 final size:18
Alignment explanation
Indices: 257771--257826 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
257761 TCTTTTTGAA
257771 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
257789 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
*
257808 TGTCTTTTT-ATTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
257826 T
1 T
257827 GCACTCCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
18 16 0.48
19 13 0.39
20 4 0.12
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:257813 original size:11 final size:10
Alignment explanation
Indices: 257774--257823 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 10
257764 TTTTGAATTC
257774 TTTTTCTT-T
1 TTTTTCTTCT
257783 TCTTTTCTTCT
1 T-TTTTCTTCT
257794 TTTCTTCTTCT
1 TTT-TTCTTCT
257805 TTTTGTCTT-T
1 TTTT-TCTTCT
257815 TTATTTCTT
1 TT-TTTCTT
257824 TTTGCACTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
9 1 0.03
10 17 0.47
11 18 0.50
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:257826 original size:11 final size:10
Alignment explanation
Indices: 257774--257826 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
257764 TTTTGAATTC
257774 TTTTTCTTTT
1 TTTTTCTTTT
*
257784 CTTTTCTTCTT
1 TTTTTCTT-TT
*
257795 TTCTTCTTCTT
1 TTTTTCTT-TT
*
257806 TTTGTCTTTT
1 TTTTTCTTTT
*
257816 TATTTCTTTT
1 TTTTTCTTTT
257826 T
1 T
257827 GCACTCCAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
10 18 0.51
11 17 0.49
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:262375 original size:21 final size:19
Alignment explanation
Indices: 262351--262425 Score: 73
Period size: 21 Copynumber: 3.8 Consensus size: 19
262341 TTTCCTTGGA
262351 TTTTCTTTCTTTTTGAATTCT
1 TTTTCTTTCTTTTTG--TTCT
*
262372 TTTTCTTT-TCTTTTCTTCTT
1 TTTTCTTTCT-TTTTGTTC-T
*
262392 TTCTTCTTCCTTTTTG-TCT
1 TT-TTCTTTCTTTTTGTTCT
262411 TTTTCTTTCTTTTTG
1 TTTTCTTTCTTTTTG
262426 CACTCCAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
18 12 0.26
19 6 0.13
20 6 0.13
21 21 0.46
22 1 0.02
ACGTcount: A:0.03, C:0.19, G:0.04, T:0.75
Consensus pattern (19 bp):
TTTTCTTTCTTTTTGTTCT
Found at i:262395 original size:18 final size:18
Alignment explanation
Indices: 262372--262425 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
262362 TTTGAATTCT
262372 TTTTCTTTTCTTTTCT-TC
1 TTTTCTTTTCTTTT-TGTC
262390 TTTTCTTCTTCCTTTTTGTC
1 TTTTCTT-TT-CTTTTTGTC
262410 TTTT-TCTTTCTTTTTG
1 TTTTCT-TTTCTTTTTG
262426 CACTCCAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 14 0.44
19 6 0.19
20 12 0.38
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (18 bp):
TTTTCTTTTCTTTTTGTC
Found at i:267233 original size:13 final size:13
Alignment explanation
Indices: 267217--267252 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
267207 AATACAAAAA
267217 GAAGTGCAAAAGT
1 GAAGTGCAAAAGT
267230 GAAGTGCAAAAGT
1 GAAGTGCAAAAGT
267243 GAAGTGCAAA
1 GAAGTGCAAA
267253 GTCAAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.47, C:0.08, G:0.31, T:0.14
Consensus pattern (13 bp):
GAAGTGCAAAAGT
Found at i:268705 original size:14 final size:14
Alignment explanation
Indices: 268686--268718 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
268676 GTGCTTCCAA
268686 CTTTTCTTTCTT-TT
1 CTTTTCTTT-TTCTT
268700 CTTTTCTTTTTCTT
1 CTTTTCTTTTTCTT
268714 CTTTT
1 CTTTT
268719 TGAGTGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTTCTTTTTCTT
Found at i:300032 original size:24 final size:21
Alignment explanation
Indices: 299997--300039 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
299987 GGCACATTCT
*
299997 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
300020 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
300040 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:310060 original size:33 final size:33
Alignment explanation
Indices: 309981--310084 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
309971 ATACAATCTA
* *
309981 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
310017 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
310050 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
310083 TC
1 TC
310085 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:310536 original size:11 final size:12
Alignment explanation
Indices: 310486--310536 Score: 54
Period size: 11 Copynumber: 4.4 Consensus size: 12
310476 TTTGGAGTGC
310486 AAAAGAAAGAA-
1 AAAAGAAAGAAG
*
310497 AAAAAAAAGAAG
1 AAAAGAAAGAAG
*
310509 AAAAGCAA-AAG
1 AAAAGAAAGAAG
310520 CAAAAGAAA-AAG
1 -AAAAGAAAGAAG
310532 AAAAG
1 AAAAG
310537 TGAAGCAAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
11 18 0.53
12 16 0.47
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAGAAAGAAG
Found at i:315091 original size:33 final size:33
Alignment explanation
Indices: 315012--315115 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
315002 ATACAATCTG
* *
315012 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
315048 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
315081 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
315114 TC
1 TC
315116 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:320476 original size:18 final size:18
Alignment explanation
Indices: 320435--320488 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
320425 CTTTAAAATT
320435 TCTTTTTTC-TCTTTTCTG
1 TCTTTTTTCTTCTTTT-TG
**
320453 AATTTTTTCTTCTTTTTG
1 TCTTTTTTCTTCTTTTTG
320471 TC-TTTTTCTTTCTTTTTG
1 TCTTTTTTC-TTCTTTTTG
320489 CACTCCAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 6 0.20
18 18 0.60
19 6 0.20
ACGTcount: A:0.04, C:0.17, G:0.06, T:0.74
Consensus pattern (18 bp):
TCTTTTTTCTTCTTTTTG
Found at i:320804 original size:20 final size:20
Alignment explanation
Indices: 320762--320806 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
320752 GGATATTAAT
320762 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
320782 ATAAG-AATG-AAATAAGATAA
1 ATAAGTAATGAAAATAA-AT-A
320802 ATAAG
1 ATAAG
320807 GATAGAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.26
19 6 0.26
20 11 0.48
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.22
Consensus pattern (20 bp):
ATAAGTAATGAAAATAAATA
Found at i:322795 original size:11 final size:10
Alignment explanation
Indices: 322772--322820 Score: 57
Period size: 11 Copynumber: 4.8 Consensus size: 10
322762 GGAGTGCAAA
322772 AAGAAAAAA-
1 AAGAAAAAAG
322781 AAGACAAAAAG
1 AAGA-AAAAAG
322792 AAGAAGAAAAG
1 AAGAA-AAAAG
322803 AAGAAAAGAA-
1 AAGAAAA-AAG
322813 AAGAAAAA
1 AAGAAAAA
322821 GAATTCAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
9 5 0.14
10 15 0.42
11 16 0.44
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAG
Found at i:322820 original size:19 final size:18
Alignment explanation
Indices: 322769--322823 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
322759 ATTGGAGTGC
322769 AAAAAG-AAA-AAAAAGA
1 AAAAAGAAAAGAAAAAGA
322785 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
322804 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
322823 A
1 A
322824 TTCAAAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.18
18 5 0.15
19 22 0.67
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:327033 original size:12 final size:12
Alignment explanation
Indices: 327001--327040 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
326991 TCATCATCAA
*
327001 CATCATCAACATC
1 CATCATCAAGA-C
*
327014 CTTCATCAAGAC
1 CATCATCAAGAC
327026 CATCATCAAGAC
1 CATCATCAAGAC
327038 CAT
1 CAT
327041 AATTCCGCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.38, C:0.35, G:0.05, T:0.23
Consensus pattern (12 bp):
CATCATCAAGAC
Found at i:331468 original size:11 final size:13
Alignment explanation
Indices: 331436--331465 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
331426 TGGCCAAAGA
331436 TGAAAAGGTATGT
1 TGAAAAGGTATGT
331449 TGAAAAGGTATG-
1 TGAAAAGGTATGT
331461 TGAAA
1 TGAAA
331466 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:335479 original size:28 final size:29
Alignment explanation
Indices: 335413--335479 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 29
335403 AAAGAAAATC
*
335413 AGAAAAG-AAATCGAAGCACTCCAAAAGA
1 AGAAAAGAAAATCGAAGCACTCAAAAAGA
*
335441 A-AGAAAGAAAATC-CAGCACTCAAAAAGA
1 AGA-AAAGAAAATCGAAGCACTCAAAAAGA
335469 AGAAAAGAAAA
1 AGAAAAGAAAA
335480 GAAAGAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 1 0.03
28 27 0.79
29 6 0.18
ACGTcount: A:0.63, C:0.15, G:0.16, T:0.06
Consensus pattern (29 bp):
AGAAAAGAAAATCGAAGCACTCAAAAAGA
Done.