Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008843.1 Hibiscus syriacus cultivar Beakdansim tig00112050_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: 173107
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6381 original size:21 final size:21
Alignment explanation
Indices: 6355--6400 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
6345 CTACAGTAAT
*
6355 GATACTCATGGTGTCAATATC
1 GATACTCAGGGTGTCAATATC
*
6376 GATACTCAGGGTGTCAGTATC
1 GATACTCAGGGTGTCAATATC
6397 GATA
1 GATA
6401 TTGAGGCCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (21 bp):
GATACTCAGGGTGTCAATATC
Found at i:8176 original size:17 final size:20
Alignment explanation
Indices: 8148--8188 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
8138 TTTTAGTACT
8148 GATACTCAA-GGG-AGTATC
1 GATACTCAAGGGGTAGTATC
8166 GATAC-CAAGGGGTAGTATC
1 GATACTCAAGGGGTAGTATC
8185 GATA
1 GATA
8189 ATCTATATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 8 0.38
19 10 0.48
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.22
Consensus pattern (20 bp):
GATACTCAAGGGGTAGTATC
Found at i:9540 original size:10 final size:10
Alignment explanation
Indices: 9525--9550 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
9515 ACTTAAAAGT
9525 TTTTTTTTCC
1 TTTTTTTTCC
9535 TTTTTTTTCC
1 TTTTTTTTCC
9545 TTTTTT
1 TTTTTT
9551 ATTTTGTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTTCC
Found at i:22900 original size:23 final size:23
Alignment explanation
Indices: 22874--22937 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
22864 CAGCTCGTAT
22874 AATTGCACCGAAGTGCCACATAG
1 AATTGCACCGAAGTGCCACATAG
* ***
22897 AATTGCACCGTAGTGCCGTGTAG
1 AATTGCACCGAAGTGCCACATAG
*
22920 AAATGCACCGAAGTGCCA
1 AATTGCACCGAAGTGCCA
22938 TATAAGGTTG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACATAG
Found at i:24544 original size:24 final size:20
Alignment explanation
Indices: 24487--24544 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
24477 TTATCCTTGA
*
24487 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
*
24507 AGTGTATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
24530 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
24545 CTACCCATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:24644 original size:64 final size:63
Alignment explanation
Indices: 24532--24691 Score: 160
Period size: 64 Copynumber: 2.5 Consensus size: 63
24522 TCTTTAACAT
** * * **
24532 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTTA-TTTTAAGGGG
1 GTGCATCGATGCACT-CATATGCATCGATGCACCAATCACATTCGATGTTTCCATTTTTAA-GGG
* ** * *
24596 GTGCATCGATGCACTCATTATGCATCGATGCACTAATTGCATTTGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCA-TATGCATCGATGCACCAATCACATTCGATGTTTCCATTTTTAAGGG
* *
24660 GTGCATCGATGCATTACATGTGCATCGATGCA
1 GTGCATCGATGCACT-CATATGCATCGATGCA
24692 TACTGAACAA
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 1 0.01
64 71 0.89
65 8 0.10
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (63 bp):
GTGCATCGATGCACTCATATGCATCGATGCACCAATCACATTCGATGTTTCCATTTTTAAGGG
Found at i:25520 original size:20 final size:20
Alignment explanation
Indices: 25495--25541 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
25485 ATGCGTAGAA
*
25495 ATCGATACTTATCATCCAAT
1 ATCGATACTGATCATCCAAT
*
25515 ATCGATACTGATCATCCAGT
1 ATCGATACTGATCATCCAAT
25535 ATCGATA
1 ATCGATA
25542 TTGTTCACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (20 bp):
ATCGATACTGATCATCCAAT
Found at i:26858 original size:2 final size:2
Alignment explanation
Indices: 26851--26884 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
26841 TGGATGCAAT
26851 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
26885 AATTAGAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28203 original size:13 final size:14
Alignment explanation
Indices: 28173--28205 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28163 CGCTCTCATT
*
28173 TTTTAGAAATATTA
1 TTTTAAAAATATTA
28187 TTTTAAAAATA-TA
1 TTTTAAAAATATTA
28200 TTTTAA
1 TTTTAA
28206 TTAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (14 bp):
TTTTAAAAATATTA
Found at i:29670 original size:2 final size:2
Alignment explanation
Indices: 29663--29700 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
29653 AATTAAAATG
29663 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
29701 ATTAATAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29874 original size:21 final size:21
Alignment explanation
Indices: 29835--29874 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29825 TAAAGTTAGT
**
29835 ATTTAAGGTTTAGGGTTTATG
1 ATTTAAGGTTTAGAATTTATG
29856 ATTTAAGGTTTAGAATTTA
1 ATTTAAGGTTTAGAATTTA
29875 ACGTTTAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (21 bp):
ATTTAAGGTTTAGAATTTATG
Found at i:38977 original size:21 final size:20
Alignment explanation
Indices: 38910--38979 Score: 58
Period size: 21 Copynumber: 3.6 Consensus size: 20
38900 CAGATTAAAT
*
38910 TTAAAAAAATTAATAATTTTA
1 TTAAAAAAATT-ATAATTCTA
*
38931 TTAAAAAAATTA-AATAC-A
1 TTAAAAAAATTATAATTCTA
**
38949 --AAGTAAATTAGTAATTCTA
1 TTAAAAAAATTA-TAATTCTA
38968 TTAAAAAAATTA
1 TTAAAAAAATTA
38980 CAAAGAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
16 8 0.22
18 5 0.14
19 4 0.11
20 1 0.03
21 19 0.51
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (20 bp):
TTAAAAAAATTATAATTCTA
Found at i:38990 original size:33 final size:35
Alignment explanation
Indices: 38915--38990 Score: 93
Period size: 37 Copynumber: 2.2 Consensus size: 35
38905 TAAATTTAAA
*
38915 AAAATTAATAATTTTATTAAAAAAATTAAATACAAAG
1 AAAATTAATAATTCTATTAAAAAAATT--ATACAAAG
* *
38952 TAAATTAGTAATTCTATTAAAAAAA-T-TACAAAG
1 AAAATTAATAATTCTATTAAAAAAATTATACAAAG
38985 AAAATT
1 AAAATT
38991 TATTTATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
33 12 0.34
36 1 0.03
37 22 0.63
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (35 bp):
AAAATTAATAATTCTATTAAAAAAATTATACAAAG
Found at i:39199 original size:34 final size:35
Alignment explanation
Indices: 39128--39218 Score: 148
Period size: 34 Copynumber: 2.6 Consensus size: 35
39118 TTCGTTGTTC
*
39128 AAAATTAATTACAAAGTAAATTAATAATTGTATTA
1 AAAATTAATTACAAAGAAAATTAATAATTGTATTA
39163 AAAATTAATTACAAAGAAAATTAATAA-TGTATTA
1 AAAATTAATTACAAAGAAAATTAATAATTGTATTA
**
39197 AAAATTGTTTACAAAGAAAATT
1 AAAATTAATTACAAAGAAAATT
39219 TATTTATATT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 27 0.51
35 26 0.49
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34
Consensus pattern (35 bp):
AAAATTAATTACAAAGAAAATTAATAATTGTATTA
Found at i:42500 original size:23 final size:22
Alignment explanation
Indices: 42464--42526 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 22
42454 GGAATTTGGT
42464 AATTTTTAAGTTTCATTAATGA
1 AATTTTTAAGTTTCATTAATGA
* * *
42486 TATTTTTGTAATTTCTCATTAATTA
1 -AATTTT-TAAGTT-TCATTAATGA
42511 AATTTTTAA-TTTCATT
1 AATTTTTAAGTTTCATT
42527 TAAATTAGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 5 0.15
22 2 0.06
23 8 0.24
24 10 0.29
25 9 0.26
ACGTcount: A:0.32, C:0.06, G:0.05, T:0.57
Consensus pattern (22 bp):
AATTTTTAAGTTTCATTAATGA
Found at i:42555 original size:12 final size:12
Alignment explanation
Indices: 42535--42564 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
42525 TTTAAATTAG
*
42535 GTTAAGACAAGT
1 GTTAGGACAAGT
42547 GTTAGGACAAGT
1 GTTAGGACAAGT
42559 GTTAGG
1 GTTAGG
42565 CATTTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.27
Consensus pattern (12 bp):
GTTAGGACAAGT
Found at i:48340 original size:17 final size:17
Alignment explanation
Indices: 48318--48351 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
48308 ATGATGAATA
48318 ATTGAATAAAGATATTC
1 ATTGAATAAAGATATTC
48335 ATTGAATAAAGATATTC
1 ATTGAATAAAGATATTC
48352 TTTTTTAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (17 bp):
ATTGAATAAAGATATTC
Found at i:49466 original size:53 final size:53
Alignment explanation
Indices: 49403--49510 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
49393 TGGTAAAAGT
49403 TCTTTGGCATAACCATAAAGTTGAGGAAGCCAATAAAGATACGTGTGGAAAAA
1 TCTTTGGCATAACCATAAAGTTGAGGAAGCCAATAAAGATACGTGTGGAAAAA
49456 TCTTTGGCATAACCATAAAGTTGAGGAAGCCAATAAAGATACGTGTGGAAAAA
1 TCTTTGGCATAACCATAAAGTTGAGGAAGCCAATAAAGATACGTGTGGAAAAA
49509 TC
1 TC
49511 GAGGATGAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.23
Consensus pattern (53 bp):
TCTTTGGCATAACCATAAAGTTGAGGAAGCCAATAAAGATACGTGTGGAAAAA
Found at i:50032 original size:23 final size:22
Alignment explanation
Indices: 50000--50064 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 22
49990 CAATGGCATT
*
50000 TGGTAATTTTTAAGTTTCATCAA
1 TGGTATTTTTTAA-TTTCATCAA
*
50023 TGGTATTTTTGTAATTTCTCATTAA
1 TGGTATTTTT-TAA-TT-TCATCAA
*
50048 TTG-ATTTTTTAATTTCA
1 TGGTATTTTTTAATTTCA
50065 ATTAAATTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 3 0.08
22 2 0.06
23 12 0.33
24 11 0.31
25 8 0.22
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (22 bp):
TGGTATTTTTTAATTTCATCAA
Found at i:52913 original size:44 final size:44
Alignment explanation
Indices: 52792--53007 Score: 249
Period size: 44 Copynumber: 4.9 Consensus size: 44
52782 GAGTGACACC
* *
52792 TTTCTGCCAA-AATGCACCGTTATGCATTTAAGTTTCATTTGTGGCACC
1 TTTCTGCCAATAATGCACCGTTATGCA--T---TTTCATTTATGGCACA
*
52840 TTTCTGTCAA-AATGCACCGTTATGCATTTTCATTTATGGCACA
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACA
* *
52883 TTTCTGCCAATAATGCACCGCTACGCATTTTCATTTATGGCACA
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACA
* * * *
52927 TTTCTTCCAATAATGCACCGTTATGTATTTTCATTTATGACACC
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACA
* * **
52971 TTTTTGCAAATAATGCATTGTTATGCA-TTTCATTTAT
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT
53008 TCATTCATTT
Statistics
Matches: 149, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
43 33 0.22
44 90 0.60
46 1 0.01
48 25 0.17
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (44 bp):
TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACA
Found at i:59948 original size:48 final size:43
Alignment explanation
Indices: 59872--60091 Score: 207
Period size: 44 Copynumber: 5.0 Consensus size: 43
59862 TCAGGAGTGA
* *
59872 CACCTTTCTGTCAAAATACACCGATATGCATTTAAGTTTCATTTGTGG
1 CACCTTTCTGTCAAAATGCACCGATATGCA--T---TTTCATTTATGG
*
59920 CACCTTTCTGTCAAAATGCACCGTTATGCATTTTCATTTATGG
1 CACCTTTCTGTCAAAATGCACCGATATGCATTTTCATTTATGG
* *
59963 CACATTTCTGTCAATAATGCA-CTACTATGCATTTTCATTTATGG
1 CACCTTTCTGTCAA-AATGCACCGA-TATGCATTTTCATTTATGG
*
60007 CACATTTCT-TCCAATAATGCACC-ATTATGCATTTTCATTTATGG
1 CACCTTTCTGT-CAA-AATGCACCGA-TATGCATTTTCATTTATGG
* ** *
60051 CACCTTTTTG-CAAATAATGCATTGTTATGCATTTT-ATTTAT
1 CACCTTTCTGTC-AA-AATGCACCGATATGCATTTTCATTTAT
60092 TCATTCATTT
Statistics
Matches: 153, Mismatches: 12, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
43 33 0.22
44 90 0.59
45 1 0.01
46 1 0.01
48 28 0.18
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.41
Consensus pattern (43 bp):
CACCTTTCTGTCAAAATGCACCGATATGCATTTTCATTTATGG
Found at i:59997 original size:44 final size:44
Alignment explanation
Indices: 59908--60091 Score: 232
Period size: 44 Copynumber: 4.2 Consensus size: 44
59898 TGCATTTAAG
* * *
59908 TTTCATTTGTGGCACCTTTCTGTCAA-AATGCACCGTTATGCAT
1 TTTCATTTATGGCACATTTCTGTCAATAATGCACCATTATGCAT
* *
59951 TTTCATTTATGGCACATTTCTGTCAATAATGCACTACTATGCAT
1 TTTCATTTATGGCACATTTCTGTCAATAATGCACCATTATGCAT
59995 TTTCATTTATGGCACATTTCT-TCCAATAATGCACCATTATGCAT
1 TTTCATTTATGGCACATTTCTGT-CAATAATGCACCATTATGCAT
* * ***
60039 TTTCATTTATGGCACCTTTTTG-CAAATAATGCATTGTTATGCAT
1 TTTCATTTATGGCACATTTCTGTC-AATAATGCACCATTATGCAT
60083 TTT-ATTTAT
1 TTTCATTTAT
60092 TCATTCATTT
Statistics
Matches: 125, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
43 32 0.26
44 93 0.74
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (44 bp):
TTTCATTTATGGCACATTTCTGTCAATAATGCACCATTATGCAT
Found at i:61260 original size:33 final size:33
Alignment explanation
Indices: 61218--61281 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
61208 TAGAATATTG
61218 TGAGGAGTATCCCGAGCATATTGTGAAGATCAT
1 TGAGGAGTATCCCGAGCATATTGTGAAGATCAT
* *
61251 TGAGGAGTATCCTGAGCATCTTGTGAAGATC
1 TGAGGAGTATCCCGAGCATATTGTGAAGATC
61282 TTGTGAAGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (33 bp):
TGAGGAGTATCCCGAGCATATTGTGAAGATCAT
Found at i:61943 original size:20 final size:19
Alignment explanation
Indices: 61902--61948 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
61892 AACCATTTTC
*
61902 TTTTGAAAGCAAAATTGGA
1 TTTTGAAAGCAAAATTGAA
61921 TTTTGAATAGCAAAA-TGAAA
1 TTTTGAA-AGCAAAATTG-AA
61941 TTTTGAAA
1 TTTTGAAA
61949 AATGATTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (19 bp):
TTTTGAAAGCAAAATTGAA
Found at i:63461 original size:20 final size:20
Alignment explanation
Indices: 63421--63472 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
63411 TGATACTTTT
*
63421 CAAGAGTTTCAAAACTATAC
1 CAAGAGTTTCGAAACTATAC
* *
63441 CAAGAGTTTCGAAGCTTTAC
1 CAAGAGTTTCGAAACTATAC
63461 CTAA-AGTTTCGA
1 C-AAGAGTTTCGA
63473 TACTTTGTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (20 bp):
CAAGAGTTTCGAAACTATAC
Found at i:66683 original size:38 final size:39
Alignment explanation
Indices: 66489--66797 Score: 277
Period size: 39 Copynumber: 7.7 Consensus size: 39
66479 CAAGATTCCC
* * * *
66489 AAAA-AAATCCAATGATTTATTTCCTTTCATAAAACAGG
1 AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGG
* *
66527 AAAATAAA-CTCAACGATTTATTTCCTTTCACAAAATAGA
1 AAAATAAATC-CAACGATTTATTTCCTTTTACAAAATAGG
* * *
66566 AAAATAAATCCAACAATTTATTTTCTTTTACAAAACAGG
1 AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGG
*
66605 AAAACAAATCAAACGATATGTTTCGATTTATTTCCTTTTACAAAATAGG
1 AAAATAAATC---C-A-A-----CGATTTATTTCCTTTTACAAAATAGG
* **
66654 AAACTAAATCCAACGATTT-TTTTTTTTTACAAAATAGG
1 AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGG
* **
66692 AAAATAAATCCAATGATTTATTTCCTTTTACAAACCAGG
1 AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGG
* * * * *
66731 AAATTAAATTCTATGGTTTATTTCCCTTTT-CAAAATAGG
1 AAAATAAATCCAACGATTTATTT-CCTTTTACAAAATAGG
*
66770 AAAATAAATCCAACAATTTA-TTCCTTTT
1 AAAATAAATCCAACGATTTATTTCCTTTT
66798 TACTTATTAG
Statistics
Matches: 221, Mismatches: 35, Indels: 31
0.77 0.12 0.11
Matches are distributed among these distances:
37 6 0.03
38 41 0.19
39 130 0.59
40 7 0.03
42 1 0.00
43 1 0.00
44 2 0.01
45 1 0.00
46 1 0.00
49 31 0.14
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.36
Consensus pattern (39 bp):
AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGG
Found at i:66731 original size:126 final size:127
Alignment explanation
Indices: 66502--66733 Score: 333
Period size: 126 Copynumber: 1.8 Consensus size: 127
66492 AAAATCCAAT
*
66502 GATTTATTTCCTTTCATAAAACAGGAAAATAAACTCAACGATTTATTTCCTTTCACAAAATAGAA
1 GATTTATTTCCTTTCACAAAACAGGAAAATAAACTCAACGATTTATTTCCTTTCACAAAATAGAA
*
66567 AAATAAATCCAACAATTTATTTTCTTTTACAAAACAGGAAAACAAATCAAACGATATGTTTC
66 AAATAAATCCAACAATTTATTTCCTTTTACAAAACAGGAAAACAAATCAAACGATATGTTTC
* * * ** * *
66629 GATTTATTTCCTTTTACAAAATAGGAAACTAAA-TCCAACGATTT-TTTTTTTTTACAAAATAGG
1 GATTTATTTCCTTTCACAAAACAGGAAAATAAACT-CAACGATTTATTTCCTTTCACAAAATAGA
** *
66692 AAAATAAATCCAATGATTTATTTCCTTTTACAAACCAGGAAA
65 AAAATAAATCCAACAATTTATTTCCTTTTACAAAACAGGAAA
66734 TTAAATTCTA
Statistics
Matches: 92, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
126 54 0.59
127 38 0.41
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (127 bp):
GATTTATTTCCTTTCACAAAACAGGAAAATAAACTCAACGATTTATTTCCTTTCACAAAATAGAA
AAATAAATCCAACAATTTATTTCCTTTTACAAAACAGGAAAACAAATCAAACGATATGTTTC
Found at i:67014 original size:39 final size:39
Alignment explanation
Indices: 66842--67019 Score: 189
Period size: 39 Copynumber: 4.5 Consensus size: 39
66832 TAAATTTATT
* *
66842 GATTTGTTTCCTTTTTTCAAAACAGGAAAAATAAATCC-AC
1 GATTTATTTCC-TTTTACAAAACAGG-AAAATAAATCCAAC
* * * *
66882 TTATTTATTTCCTTTCATAAAACGGGAAAATAAA-CTCAAC
1 -GATTTATTTCCTTTTACAAAACAGGAAAATAAATC-CAAC
** * * *
66922 GAGATATTTCCTTTAATAAAACAGGAAAATAAATCTAAC
1 GATTTATTTCCTTTTACAAAACAGGAAAATAAATCCAAC
* *
66961 GATTTATTTTCTTTTACAAAATAGGAAAATAAATCCAAC
1 GATTTATTTCCTTTTACAAAACAGGAAAATAAATCCAAC
67000 GATTTATTTCCTTTTACAAA
1 GATTTATTTCCTTTTACAAA
67020 TCAAAATCAT
Statistics
Matches: 114, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
38 1 0.01
39 91 0.80
40 13 0.11
41 9 0.08
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.35
Consensus pattern (39 bp):
GATTTATTTCCTTTTACAAAACAGGAAAATAAATCCAAC
Found at i:67140 original size:38 final size:39
Alignment explanation
Indices: 67040--67155 Score: 123
Period size: 39 Copynumber: 3.0 Consensus size: 39
67030 GTGAAATTCT
**
67040 CAGGAAAATAAATTCAACGGTTTATTT-TATTTTACAAGA
1 CAGGAAAATAAATTCAACAATTTATTTCT-TTTTACAAGA
*
67079 TAGGAAAATAAATTCAACAATTTATTTCTTTTTACAA-A
1 CAGGAAAATAAATTCAACAATTTATTTCTTTTTACAAGA
* * *
67117 CAGTAAAATAAA-TCAA-ATGATTTAGTTCTTTTTAAAAGA
1 CAGGAAAATAAATTCAACA--ATTTATTTCTTTTTACAAGA
67156 TAAATTCATA
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
36 1 0.02
37 4 0.06
38 27 0.41
39 33 0.50
40 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (39 bp):
CAGGAAAATAAATTCAACAATTTATTTCTTTTTACAAGA
Found at i:67265 original size:58 final size:57
Alignment explanation
Indices: 67197--67533 Score: 342
Period size: 58 Copynumber: 5.8 Consensus size: 57
67187 TTATTTCTTT
* * * *
67197 ATTCAAGATTCCCTAGAAAATAAATTTAACAATTTA-TTTCTTTTAACAAATTAGAATC
1 ATTCAAGATTCTCAAGAAAATAAATTCAACAATTTATTTTC-CTT-ACAAATTAGAATC
* * ** * * *
67255 ATTTAAGATTCTCAAGAAAATAAATTTAACAATTTATTTCTTTTTTAGAGGA-TAAAATC
1 ATTCAAGATTCTCAAGAAAATAAATTCAACAATTTA-TT-TTCCTTACA-AATTAGAATC
* * * *
67314 ATCCACA-ATTCTCAAGAAAATAAATTCGACAATTTATTTTCCTTACAAAATTAAAATA
1 ATTCA-AGATTCTCAAGAAAATAAATTCAACAATTTATTTTCCTTAC-AAATTAGAATC
* * *
67372 ATTCAAGATTTTCAAGGAAATAAATTCAACAATTTATTTTCCTTATAAAGTTAGAATC
1 ATTCAAGATTCTCAAGAAAATAAATTCAACAATTTATTTTCCTTACAAA-TTAGAATC
* *
67430 ATTTAAGATTCTCAAGAAAATAAATTCAACAATTTATTTTCCTTACAAAGTCAGAATC
1 ATTCAAGATTCTCAAGAAAATAAATTCAACAATTTATTTTCCTTACAAA-TTAGAATC
* *
67488 ATTAAAGATTCTCAACG-AAATAAA-TCTAACTATTTATTTTCCTTAC
1 ATTCAAGATTCTCAA-GAAAATAAATTC-AACAATTTATTTTCCTTAC
67534 GAAGATAGAA
Statistics
Matches: 238, Mismatches: 30, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
57 12 0.05
58 179 0.75
59 39 0.16
60 6 0.03
61 2 0.01
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (57 bp):
ATTCAAGATTCTCAAGAAAATAAATTCAACAATTTATTTTCCTTACAAATTAGAATC
Found at i:67556 original size:175 final size:178
Alignment explanation
Indices: 67214--67591 Score: 402
Period size: 175 Copynumber: 2.1 Consensus size: 178
67204 ATTCCCTAGA
* *
67214 AAATAAATTTAACAATTTATTT-CTTTTAACAAATTAGAATCATTTAAGATTCTCAAGAAAATAA
1 AAATAAATTCAACAATTTATTTCCTTATAACAAATTAGAATCATTTAAGATTCTCAAGAAAATAA
* ** * * * *
67278 ATTTAACAATTTATTTCTTTTTTAGAGGATAAAATCATCCACAATTCTCAAGAAAATAAATTCGA
66 ATTCAACAATTTATTTCTTCCTTAAAAGATAAAATCATCCAAAATTCTCAAGAAAATAAATTCAA
** *
67343 CAATTTATTTTCCTTACAAAATTAAAATAATTCAAGATT-T-TCAAGG
131 CAATTTATTTTCCTTACAAAATTAAAATAACACAAGATTCTAACAAGG
*
67389 AAATAAATTCAACAATTTATTTTCCTTAT-A-AAGTTAGAATCATTTAAGATTCTCAAGAAAATA
1 AAATAAATTCAACAATTTA-TTTCCTTATAACAAATTAGAATCATTTAAGATTCTCAAGAAAATA
* *
67452 AATTCAACAATTTA-TT-TTCCTTACAAAG-TCAGAATCAT-TAAAGATTCTCAACG-AAATAAA
65 AATTCAACAATTTATTTCTTCCTTA-AAAGAT-AAAATCATCCAAA-ATTCTCAA-GAAAATAAA
* * * *
67512 -TCTAACTATTTATTTTCCTTACGAAGA-TAGAATAAACACAAGATTCTAACAATG
126 TTC-AACAATTTATTTTCCTTAC-AAAATTAAAAT-AACACAAGATTCTAACAAGG
* **
67566 AAATAAATCCAATGATTTATTTCCTT
1 AAATAAATTCAACAATTTATTTCCTT
67592 TATGTTCTGT
Statistics
Matches: 170, Mismatches: 22, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
173 10 0.06
174 48 0.28
175 76 0.45
176 12 0.07
177 24 0.14
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (178 bp):
AAATAAATTCAACAATTTATTTCCTTATAACAAATTAGAATCATTTAAGATTCTCAAGAAAATAA
ATTCAACAATTTATTTCTTCCTTAAAAGATAAAATCATCCAAAATTCTCAAGAAAATAAATTCAA
CAATTTATTTTCCTTACAAAATTAAAATAACACAAGATTCTAACAAGG
Found at i:67803 original size:44 final size:45
Alignment explanation
Indices: 67706--67857 Score: 157
Period size: 45 Copynumber: 3.4 Consensus size: 45
67696 TTAATTTTAC
* * * * * *
67706 CAAC-CAATAATCAAAAGGAACTAATCATTTGATTTCAATATTCA
1 CAACACAATAATCAAAAGTAACTAATCCTTTGATTTTACTTTTGA
* * *
67750 CAATC-CAATAATCGAAAGTAACTAATTC-TTGATTTTACTTTTGG
1 CAA-CACAATAATCAAAAGTAACTAATCCTTTGATTTTACTTTTGA
* * *
67794 TAACACAATAATCAAAAGAAACTAATCCTTTTATTTTACTTTTGA
1 CAACACAATAATCAAAAGTAACTAATCCTTTGATTTTACTTTTGA
*
67839 CAACTCAATAATCAAAAGT
1 CAACACAATAATCAAAAGT
67858 CTTTGATTAA
Statistics
Matches: 87, Mismatches: 18, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
43 1 0.01
44 36 0.41
45 50 0.57
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34
Consensus pattern (45 bp):
CAACACAATAATCAAAAGTAACTAATCCTTTGATTTTACTTTTGA
Found at i:70784 original size:21 final size:21
Alignment explanation
Indices: 70754--70808 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
70744 TTTCCCAGTA
70754 ATGCAGAGAAAACTTCAGGAG
1 ATGCAGAGAAAACTTCAGGAG
*
70775 ATGGAGAGAAAACTTCAGGAG
1 ATGCAGAGAAAACTTCAGGAG
70796 ATGCAGAGAAAAC
1 ATGCAGAGAAAAC
70809 CAGAAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.45, C:0.13, G:0.29, T:0.13
Consensus pattern (21 bp):
ATGCAGAGAAAACTTCAGGAG
Found at i:73064 original size:27 final size:27
Alignment explanation
Indices: 73026--73106 Score: 162
Period size: 27 Copynumber: 3.0 Consensus size: 27
73016 AAGTTTAACC
73026 CTGTTATCACCGTTTTCCTTTTCAGCG
1 CTGTTATCACCGTTTTCCTTTTCAGCG
73053 CTGTTATCACCGTTTTCCTTTTCAGCG
1 CTGTTATCACCGTTTTCCTTTTCAGCG
73080 CTGTTATCACCGTTTTCCTTTTCAGCG
1 CTGTTATCACCGTTTTCCTTTTCAGCG
73107 TGGTAGCATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.11, C:0.30, G:0.15, T:0.44
Consensus pattern (27 bp):
CTGTTATCACCGTTTTCCTTTTCAGCG
Found at i:75959 original size:26 final size:25
Alignment explanation
Indices: 75923--75971 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 25
75913 TTTATAAAAG
75923 TTTTCTCTTTTATTTTTTAAGTTTTCA
1 TTTTCTCTTTTA--TTTTAAGTTTTCA
75950 TTTT-TCTTTTATTTTAAGTTTT
1 TTTTCTCTTTTATTTTAAGTTTT
75972 GTTTTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 11 0.50
26 7 0.32
27 4 0.18
ACGTcount: A:0.14, C:0.08, G:0.04, T:0.73
Consensus pattern (25 bp):
TTTTCTCTTTTATTTTAAGTTTTCA
Found at i:84667 original size:6 final size:6
Alignment explanation
Indices: 84656--84682 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
84646 GATATTATAA
84656 AATTTT AATTTT AATTTT AATTTT AAT
1 AATTTT AATTTT AATTTT AATTTT AAT
84683 AATGTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
AATTTT
Found at i:92311 original size:14 final size:14
Alignment explanation
Indices: 92294--92353 Score: 56
Period size: 13 Copynumber: 4.4 Consensus size: 14
92284 TTACCCTTTC
92294 TAATAAGTTATTTT
1 TAATAAGTTATTTT
92308 TAAT-AG-TATTTCT
1 TAATAAGTTATTT-T
*
92321 TAA-AA-TAATTTT
1 TAATAAGTTATTTT
*
92333 CTAATAAGGTATTTT
1 -TAATAAGTTATTTT
92348 TAATAA
1 TAATAA
92354 TATTTCTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
12 6 0.16
13 14 0.38
14 12 0.32
15 5 0.14
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (14 bp):
TAATAAGTTATTTT
Found at i:92346 original size:40 final size:40
Alignment explanation
Indices: 92290--92368 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
92280 TAATTTACCC
* *
92290 TTTCTAATAAGTTATTTTTAATAGTATTTCTTAAAATAAT
1 TTTCTAATAAGGTATTTTTAATAATATTTCTTAAAATAAT
92330 TTTCTAATAAGGTATTTTTAATAATATTTCTTAAAATAA
1 TTTCTAATAAGGTATTTTTAATAATATTTCTTAAAATAA
92369 ATTTATTGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (40 bp):
TTTCTAATAAGGTATTTTTAATAATATTTCTTAAAATAAT
Found at i:93142 original size:33 final size:33
Alignment explanation
Indices: 93083--93145 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
93073 ATATGCCTGC
* *
93083 TGAAGACGTATGGAAATCTTGTAGTCTTCACCT
1 TGAAGACGTATAGAAATCTAGTAGTCTTCACCT
*
93116 TGAAGACGTGTAGAAATCCTAG-AGTCTTCA
1 TGAAGACGTATAGAAAT-CTAGTAGTCTTCA
93146 AATTTCTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 23 0.88
34 3 0.12
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (33 bp):
TGAAGACGTATAGAAATCTAGTAGTCTTCACCT
Found at i:94150 original size:24 final size:23
Alignment explanation
Indices: 94123--94184 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
94113 TCATTCATAA
* * *
94123 TCACATATACATGTGCTCTCATTT
1 TCACATATACATATGAT-TCACTT
*
94147 TCACATAAACATATGATTCACTT
1 TCACATATACATATGATTCACTT
94170 TCACATATCACATAT
1 TCACATAT-ACATAT
94185 CCTTGTAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 12 0.38
24 20 0.62
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (23 bp):
TCACATATACATATGATTCACTT
Found at i:96307 original size:14 final size:14
Alignment explanation
Indices: 96288--96315 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
96278 AGCTTATACT
96288 AATATTAAATTTTA
1 AATATTAAATTTTA
96302 AATATTAAATTTTA
1 AATATTAAATTTTA
96316 TTTAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATATTAAATTTTA
Found at i:97368 original size:17 final size:18
Alignment explanation
Indices: 97346--97379 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
97336 TCTTTAAGGT
97346 ATATTTTATTA-TATTTA
1 ATATTTTATTATTATTTA
97363 ATATTTTATTATTATTT
1 ATATTTTATTATTATTT
97380 TATTTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATATTTTATTATTATTTA
Found at i:97377 original size:23 final size:23
Alignment explanation
Indices: 97347--97392 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
97337 CTTTAAGGTA
97347 TATTTTATTATATTTAA-TATTT
1 TATTTTATTATATTTAACTATTT
*
97369 TATTATTATTTTATTTAACTATTT
1 TATT-TTATTATATTTAACTATTT
97393 AAATTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 12 0.57
24 5 0.24
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TATTTTATTATATTTAACTATTT
Found at i:99456 original size:3 final size:3
Alignment explanation
Indices: 99443--99476 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
99433 GTAGCTGCTC
* *
99443 ACG ATG ACG ACG ACA ACG ACG ACG ACG ACG ACG A
1 ACG ACG ACG ACG ACG ACG ACG ACG ACG ACG ACG A
99477 TGATGATGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.29, G:0.29, T:0.03
Consensus pattern (3 bp):
ACG
Found at i:103437 original size:29 final size:29
Alignment explanation
Indices: 103378--103437 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
103368 TTTTTTTACT
* *
103378 GGTTGAGAGGATTATTGTAGTAGTTTCTA
1 GGTTGAGAGGAATATTGTAGGAGTTTCTA
103407 GGTTGAGAGGAAT-TTGTGAGAGAGTTT-TA
1 GGTTGAGAGGAATATTGT-AG-GAGTTTCTA
103436 GG
1 GG
103438 GGGAAGGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 4 0.15
29 18 0.67
30 5 0.19
ACGTcount: A:0.25, C:0.02, G:0.37, T:0.37
Consensus pattern (29 bp):
GGTTGAGAGGAATATTGTAGGAGTTTCTA
Found at i:104182 original size:18 final size:18
Alignment explanation
Indices: 104159--104200 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
104149 TTACAAAAAT
104159 AAATAAAAATGCAATAAA
1 AAATAAAAATGCAATAAA
*
104177 AAAT-AAAATTCAATAAA
1 AAATAAAAATGCAATAAA
104194 AATATAA
1 AA-ATAA
104201 TGTAAAGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 14 0.67
18 6 0.29
19 1 0.05
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (18 bp):
AAATAAAAATGCAATAAA
Found at i:104801 original size:26 final size:27
Alignment explanation
Indices: 104756--104811 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
104746 TTAAAAGTCA
104756 ATAATTTTTTCAAAAATATATAAA-ATTT
1 ATAATTTTTT-AAAAATATA-AAATATTT
*
104784 ATAATTTTTT-AAATTATAAAATATTT
1 ATAATTTTTTAAAAATATAAAATATTT
104810 AT
1 AT
104812 TATCATCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 3 0.12
26 13 0.50
28 10 0.38
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
ATAATTTTTTAAAAATATAAAATATTT
Found at i:112642 original size:19 final size:18
Alignment explanation
Indices: 112607--112645 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
112597 AAATATTCTT
**
112607 ATTAAAAAAAACTAAAAA
1 ATTAAAAAAAAAGAAAAA
112625 ATTAAAAAACAAAGAAAAA
1 ATTAAAAAA-AAAGAAAAA
112644 AT
1 AT
112646 ACAATCGACG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (18 bp):
ATTAAAAAAAAAGAAAAA
Found at i:113088 original size:12 final size:13
Alignment explanation
Indices: 113071--113099 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
113061 TTTATTTGCG
113071 AAAATTAAAA-TT
1 AAAATTAAAATTT
113083 AAAATTAAAATTT
1 AAAATTAAAATTT
113096 AAAA
1 AAAA
113100 AACTCGATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:113258 original size:8 final size:8
Alignment explanation
Indices: 113245--113285 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
113235 AAGGAAAAAG
113245 AAAATAAT
1 AAAATAAT
113253 AAAATAAT
1 AAAATAAT
113261 AAAATAA-
1 AAAATAAT
113268 AATAATAA-
1 AA-AATAAT
*
113276 AAAACAAT
1 AAAATAAT
113284 AA
1 AA
113286 TAAAAGATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (8 bp):
AAAATAAT
Found at i:113266 original size:13 final size:13
Alignment explanation
Indices: 113250--113290 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
113240 AAAAGAAAAT
113250 AATAAAATAATAA
1 AATAAAATAATAA
113263 AATAAAATAATAA
1 AATAAAATAATAA
113276 AA-AACAATAATAA
1 AATAA-AATAATAA
113289 AA
1 AA
113291 GATTAGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 2 0.07
13 25 0.93
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (13 bp):
AATAAAATAATAA
Found at i:113269 original size:21 final size:20
Alignment explanation
Indices: 113240--113290 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
113230 TGAAGAAGGA
* *
113240 AAAAGAAAATAATAAAATAAT
1 AAAATAAAATAATAAAA-AAC
113261 AAAATAAAATAATAAAAAAC
1 AAAATAAAATAATAAAAAAC
113281 AATAATAAAA
1 AA-AATAAAA
113291 GATTAGTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (20 bp):
AAAATAAAATAATAAAAAAC
Found at i:113284 original size:26 final size:27
Alignment explanation
Indices: 113254--113335 Score: 78
Period size: 26 Copynumber: 3.0 Consensus size: 27
113244 GAAAATAATA
113254 AAATAATAAAATAAAATAATAAAAAAC
1 AAATAATAAAATAAAATAATAAAAAAC
* * * *
113281 -AATAATAAAAGATTAGTTA-AAAAAAC
1 AAATAATAAAATA-AAATAATAAAAAAC
113307 AAATAAATAAGAATAAAAATAATAAAAAA
1 AAAT-AATAA-AAT-AAAATAATAAAAAA
113336 ATGTAGTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
26 18 0.44
27 6 0.15
28 5 0.12
29 5 0.12
30 7 0.17
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (27 bp):
AAATAATAAAATAAAATAATAAAAAAC
Found at i:114812 original size:71 final size:69
Alignment explanation
Indices: 114682--114831 Score: 156
Period size: 71 Copynumber: 2.0 Consensus size: 69
114672 TATATACTTT
* *
114682 AAAAAAGTTTTCAAAACTATATATTACATAGTTTCCAAAATGTTTTAAAAAATATTATATAAGTT
1 AAAAAAGTTTTCAAAACTATATATTACATAGTTTCAAAAATGTTTT-AAAAATACTATATAAGTT
114747 TTCAA
65 TTCAA
* * *
114752 AAAAAATGTTTTTAAAACTATATATTATATAATTTTACAAAAAATGTTTTTAAAACTATATACTA
1 AAAAAA-GTTTTCAAAACTATATATTACAT-AGTTT-C-AAAAATG-TTTT-AAA--A-ATACTA
*
114817 TATATGTTTTCAA
57 TATAAGTTTTCAA
114830 AA
1 AA
114832 TGTTTTAAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
70 6 0.09
71 21 0.32
72 4 0.06
73 1 0.02
74 6 0.09
75 8 0.12
77 1 0.02
78 19 0.29
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (69 bp):
AAAAAAGTTTTCAAAACTATATATTACATAGTTTCAAAAATGTTTTAAAAATACTATATAAGTTT
TCAA
Found at i:114832 original size:36 final size:36
Alignment explanation
Indices: 114683--114987 Score: 244
Period size: 38 Copynumber: 8.1 Consensus size: 36
114673 ATATACTTTA
* * *
114683 AAAAAGTTTTCAAAACTATATATTACATA-GTTTCC
1 AAAATGTTTTCAAAACTATATATTATATATGTTTTC
*
114718 AAAATGTTTT-AAAA--A-ATATTATATAAGTTTTC
1 AAAATGTTTTCAAAACTATATATTATATATGTTTTC
* *
114750 AAAAAAAATGTTTTTAAAACTATATATTATATAAT-TTTAC
1 ----AAAATGTTTTCAAAACTATATATTATAT-ATGTTTTC
* *
114790 AAAAAATGTTTTTAAAACTATATACTATATATGTTTTC
1 --AAAATGTTTTCAAAACTATATATTATATATGTTTTC
* * * *
114828 AAAATGTTTTAAAAACTATATAATATTTAAACGTTTTC
1 AAAATGTTTTCAAAACTATAT-AT-TATATATGTTTTC
* * *
114866 AAAATATTTTCAAAATTATATATTATATACGTATTTTC
1 AAAATGTTTTCAAAACTATATATTATATA--TGTTTTC
*
114904 AAAATGTTTTCAAAAAAAAACTATATAATATATAAATGTTTTC
1 AAAATGTTTTC-----AAAACTATAT-AT-TATATATGTTTTC
*
114947 AAACATGTTTTCAAAACTATATATTATATATATTTTC
1 AAA-ATGTTTTCAAAACTATATATTATATATGTTTTC
114984 AAAA
1 AAAA
114988 ACCATTTGCA
Statistics
Matches: 222, Mismatches: 25, Indels: 45
0.76 0.09 0.15
Matches are distributed among these distances:
31 9 0.04
32 6 0.03
34 4 0.02
35 9 0.04
36 35 0.16
37 23 0.10
38 78 0.35
39 11 0.05
40 13 0.06
41 1 0.00
43 18 0.08
44 10 0.05
45 5 0.02
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (36 bp):
AAAATGTTTTCAAAACTATATATTATATATGTTTTC
Found at i:115011 original size:81 final size:79
Alignment explanation
Indices: 114838--114999 Score: 200
Period size: 81 Copynumber: 2.0 Consensus size: 79
114828 AAAATGTTTT
* *
114838 AAAAACTATATAATATTTAAACGTTTTCAAAATATTTTCAAAATTATATATTATATACGTATTTT
1 AAAAAC-ATATAATATATAAACGTTTTCAAAATATTTTCAAAACTATATATTATATAC-TATTTT
** *
114903 CAAAATGTTTTCAAAA
64 CAAAACATTTGCAAAA
* *
114919 AAAAACTATATAATATATAAATGTTTTCAAACATGTTTTCAAAACTATATATTATATA-TATTTT
1 AAAAAC-ATATAATATATAAACGTTTTCAAA-ATATTTTCAAAACTATATATTATATACTATTTT
114983 CAAAAACCATTTGCAAA
64 C-AAAA-CATTTGCAAA
115000 CTATATAATA
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
80 7 0.10
81 33 0.46
82 31 0.44
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (79 bp):
AAAAACATATAATATATAAACGTTTTCAAAATATTTTCAAAACTATATATTATATACTATTTTCA
AAACATTTGCAAAA
Found at i:115287 original size:59 final size:60
Alignment explanation
Indices: 115164--115292 Score: 172
Period size: 60 Copynumber: 2.1 Consensus size: 60
115154 ATGAGTTAAG
*
115164 TACACAAATGAACCATTCACTATAGAGTATTGCTTTATTAAGTTCATCAACTATTAAAAGT
1 TACA-AAATGAACCATTCACTATAGAGTATTGCTTTATTAAGTCCATCAACTATTAAAAGT
* * ***
115225 TACAAAATGATCC-TTCGACTATAGAGTATTGCTTTATTGAGTCCAT-TGTTATTAAAAGT
1 TACAAAATGAACCATTC-ACTATAGAGTATTGCTTTATTAAGTCCATCAACTATTAAAAGT
115284 TACAAAATG
1 TACAAAATG
115293 GTCACCCGAT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
59 22 0.36
60 35 0.57
61 4 0.07
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (60 bp):
TACAAAATGAACCATTCACTATAGAGTATTGCTTTATTAAGTCCATCAACTATTAAAAGT
Found at i:116704 original size:11 final size:11
Alignment explanation
Indices: 116690--116720 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
116680 TATTATATAG
116690 TTTTGAAAACA
1 TTTTGAAAACA
116701 TTTTGAAAACA
1 TTTTGAAAACA
116712 TTTTGAAAA
1 TTTTGAAAA
116721 AATATATATT
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:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:116717 original size:47 final size:47
Alignment explanation
Indices: 116665--116756 Score: 175
Period size: 47 Copynumber: 2.0 Consensus size: 47
116655 AATATATAAT
*
116665 TTTTGAAAATATATATATTATATAGTTTTGAAAACATTTTGAAAACA
1 TTTTGAAAAAATATATATTATATAGTTTTGAAAACATTTTGAAAACA
116712 TTTTGAAAAAATATATATTATATAGTTTTGAAAACATTTTGAAAA
1 TTTTGAAAAAATATATATTATATAGTTTTGAAAACATTTTGAAAA
116757 ATATATATAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (47 bp):
TTTTGAAAAAATATATATTATATAGTTTTGAAAACATTTTGAAAACA
Found at i:116772 original size:37 final size:36
Alignment explanation
Indices: 116700--116782 Score: 139
Period size: 37 Copynumber: 2.3 Consensus size: 36
116690 TTTTGAAAAC
*
116700 ATTTTGAAAACATTTTGAAAAAATATATATTATATA
1 ATTTTGAAAACATTTTGAAAAAATATATAGTATATA
*
116736 GTTTTGAAAACATTTTGAAAAATATATATAGTATATA
1 ATTTTGAAAACATTTTGAAAAA-ATATATAGTATATA
116773 ATTTTGAAAA
1 ATTTTGAAAA
116783 ATATATATAC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
36 21 0.49
37 22 0.51
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.41
Consensus pattern (36 bp):
ATTTTGAAAACATTTTGAAAAAATATATAGTATATA
Found at i:116776 original size:26 final size:25
Alignment explanation
Indices: 116747--116805 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
116737 TTTTGAAAAC
*
116747 ATTTTGAAAAATATATATAGTATAT
1 ATTTTGAAAAATATATATACTATAT
116772 AATTTTGAAAAATATATATACTATAT
1 -ATTTTGAAAAATATATATACTATAT
*
116798 GTTTTGAA
1 ATTTTGAA
116806 TTTTTTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 7 0.23
26 24 0.77
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (25 bp):
ATTTTGAAAAATATATATACTATAT
Found at i:116802 original size:62 final size:62
Alignment explanation
Indices: 116711--116905 Score: 249
Period size: 62 Copynumber: 3.2 Consensus size: 62
116701 TTTTGAAAAC
****
116711 ATTTTGAAAAA-ATATATATTATATAGTTTTGAA-AACATTTTGAAAAATATATATAGTATATA
1 ATTTTGAAAAATATATATA-TATATAGTTTTGAATTTTTTTTTGAAAAATATATATA-TATATA
116773 ATTTTGAAAAATATATATACTATAT-GTTTTGAATTTTTTTTTGAAAAA-ATATATATTATATA
1 ATTTTGAAAAATATATATA-TATATAGTTTTGAATTTTTTTTTGAAAAATATATATA-TATATA
*
116835 GTTTTGAAAAATATATAT-TATATAGTTTTGAATTTTTTTTTGAAAACATATATA-ATATATA
1 ATTTTGAAAAATATATATATATATAGTTTTGAATTTTTTTTTGAAAA-ATATATATATATATA
*
116896 GTTTTGAAAA
1 ATTTTGAAAA
116906 TATTTTTGAA
Statistics
Matches: 121, Mismatches: 7, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
60 5 0.04
61 38 0.31
62 51 0.42
63 27 0.22
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (62 bp):
ATTTTGAAAAATATATATATATATAGTTTTGAATTTTTTTTTGAAAAATATATATATATATA
Found at i:116850 original size:26 final size:25
Alignment explanation
Indices: 116811--116866 Score: 105
Period size: 24 Copynumber: 2.3 Consensus size: 25
116801 TTGAATTTTT
116811 TTTTGAAAAAATATATATTATATAG
1 TTTTGAAAAAATATATATTATATAG
116836 TTTTG-AAAAATATATATTATATAG
1 TTTTGAAAAAATATATATTATATAG
116860 TTTTGAA
1 TTTTGAA
116867 TTTTTTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 24 0.80
25 6 0.20
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.46
Consensus pattern (25 bp):
TTTTGAAAAAATATATATTATATAG
Found at i:116894 original size:37 final size:36
Alignment explanation
Indices: 116836--116994 Score: 149
Period size: 37 Copynumber: 4.2 Consensus size: 36
116826 TATTATATAG
* ** *
116836 TTTTGAAAAATATATATTATATAGTTTTGAATTTTT
1 TTTTGAAAAATATATAATATATAGTTTTGAAAATAT
116872 TTTTGAAAACATATATAATATATAGTTTTGAAAATAT
1 TTTTGAAAA-ATATATAATATATAGTTTTGAAAATAT
* * *
116909 TTTTGAAAATATATATATATATATATATATATTTTAAAACAT
1 TTTTG-AAA-A-ATATATA-ATATATA-GT-TTTGAAAATAT
* * *
116951 TTTT-AAATATATATAATAAATAAGTTTTGAAAATGT
1 TTTTGAAAAATATATAATATAT-AGTTTTGAAAATAT
116987 TTTTGAAA
1 TTTTGAAA
116995 TTTTGAAAAC
Statistics
Matches: 101, Mismatches: 14, Indels: 15
0.78 0.11 0.12
Matches are distributed among these distances:
36 21 0.21
37 37 0.37
38 11 0.11
39 8 0.08
40 10 0.10
41 1 0.01
42 13 0.13
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (36 bp):
TTTTGAAAAATATATAATATATAGTTTTGAAAATAT
Found at i:116894 original size:61 final size:60
Alignment explanation
Indices: 116712--116905 Score: 257
Period size: 61 Copynumber: 3.1 Consensus size: 60
116702 TTTGAAAACA
**** *
116712 TTTTGAAAAAATATATATTATATAGTTTTGAA-AACATTTTGAAAAATATATATAGTATATAA
1 TTTTG-AAAAATATATATTATATAGTTTTGAATTTTTTTTTGAAAAATATATA-A-TATATAG
*
116774 TTTTGAAAAATATATA-TACTATATGTTTTGAATTTTTTTTTGAAAAAATATATATTATATAG
1 TTTTGAAAAATATATATTA-TATA-GTTTTGAATTTTTTTTTG-AAAAATATATAATATATAG
116836 TTTTGAAAAATATATATTATATAGTTTTGAATTTTTTTTTGAAAACATATATAATATATAG
1 TTTTGAAAAATATATATTATATAGTTTTGAATTTTTTTTTGAAAA-ATATATAATATATAG
116897 TTTTGAAAA
1 TTTTGAAAA
116906 TATTTTTGAA
Statistics
Matches: 119, Mismatches: 7, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
60 6 0.05
61 56 0.47
62 39 0.33
63 7 0.06
64 11 0.09
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (60 bp):
TTTTGAAAAATATATATTATATAGTTTTGAATTTTTTTTTGAAAAATATATAATATATAG
Found at i:117000 original size:20 final size:20
Alignment explanation
Indices: 116975--117014 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
116965 AATAAATAAG
* *
116975 TTTTGAAAATGTTTTTGAAA
1 TTTTGAAAACGTTTTAGAAA
116995 TTTTGAAAACGTTTTAGAAA
1 TTTTGAAAACGTTTTAGAAA
117015 ATATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.45
Consensus pattern (20 bp):
TTTTGAAAACGTTTTAGAAA
Found at i:118274 original size:5 final size:5
Alignment explanation
Indices: 118264--118324 Score: 61
Period size: 5 Copynumber: 11.4 Consensus size: 5
118254 TTTAGTATGC
*
118264 TTTTA TTTTA TTTTA TTTTTTA TTTTA TTTTA TTTTTA CTTCTTA TTAT-
1 TTTTA TTTTA TTTTA --TTTTA TTTTA TTTTA -TTTTA -TT-TTA TTTTA
118313 TTTTA TTTTA TT
1 TTTTA TTTTA TT
118325 ACTTTTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
4 3 0.06
5 28 0.58
6 9 0.19
7 8 0.17
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:118284 original size:17 final size:16
Alignment explanation
Indices: 118264--118324 Score: 81
Period size: 17 Copynumber: 3.8 Consensus size: 16
118254 TTTAGTATGC
118264 TTTTATTTTATTTTATT
1 TTTTATTTTATTTTA-T
118281 TTTTATTTTATTTTAT
1 TTTTATTTTATTTTAT
118297 TTTTACTTCTTA--TTAT
1 TTTTA-TT-TTATTTTAT
118313 TTTTATTTTATT
1 TTTTATTTTATT
118325 ACTTTTAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.08
15 2 0.05
16 15 0.38
17 17 0.43
18 3 0.08
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTATTTTATTTTAT
Found at i:118408 original size:35 final size:36
Alignment explanation
Indices: 118348--118430 Score: 107
Period size: 35 Copynumber: 2.3 Consensus size: 36
118338 AACATTGTTT
*
118348 TATTTTTATTTTGTTTTTTCCTTTGATTTATTTAATA
1 TATTTTTATTTTCTTTTTTCCTTTGATTT-TTTAATA
* *
118385 TATTTTT-TTTTCTTTTTT-CTTTGATTTTTTATTT
1 TATTTTTATTTTCTTTTTTCCTTTGATTTTTTAATA
*
118419 TTTTTTTATTTT
1 TATTTTTATTTT
118431 TTTATTATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
34 11 0.27
35 13 0.32
36 10 0.24
37 7 0.17
ACGTcount: A:0.13, C:0.05, G:0.04, T:0.78
Consensus pattern (36 bp):
TATTTTTATTTTCTTTTTTCCTTTGATTTTTTAATA
Found at i:118419 original size:18 final size:19
Alignment explanation
Indices: 118398--118443 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
118388 TTTTTTTTCT
118398 TTTTTCTTTGA-TTTTTTA
1 TTTTTCTTTGATTTTTTTA
* *
118416 TTTTTTTTTTATTTTTTTA
1 TTTTTCTTTGATTTTTTTA
118435 TTATTTCTT
1 TT-TTTCTT
118444 ATCTAACATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 9 0.39
19 9 0.39
20 5 0.22
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.83
Consensus pattern (19 bp):
TTTTTCTTTGATTTTTTTA
Found at i:118433 original size:19 final size:20
Alignment explanation
Indices: 118389--118443 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
118379 TTAATATATT
*
118389 TTTTTTTCTTTTTTCTTTGA
1 TTTTTTTATTTTTTCTTTGA
*
118409 -TTTTTTATTTTTT-TTTTA
1 TTTTTTTATTTTTTCTTTGA
*
118427 TTTTTTTATTATTTCTT
1 TTTTTTTATTTTTTCTT
118444 ATCTAACATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 4 0.13
19 24 0.80
20 2 0.07
ACGTcount: A:0.09, C:0.05, G:0.02, T:0.84
Consensus pattern (20 bp):
TTTTTTTATTTTTTCTTTGA
Found at i:118440 original size:29 final size:30
Alignment explanation
Indices: 118387--118445 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
118377 ATTTAATATA
* *
118387 TTTTTTTTTCTTTTTTCTTTGATTTTTTAT
1 TTTTTTTTTATTTTTTCTTTGATTTCTTAT
118417 TTTTTTTTTATTTTTT-TATT-ATTTCTTAT
1 TTTTTTTTTATTTTTTCT-TTGATTTCTTAT
118446 CTAACATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.10, C:0.05, G:0.02, T:0.83
Consensus pattern (30 bp):
TTTTTTTTTATTTTTTCTTTGATTTCTTAT
Found at i:121145 original size:18 final size:18
Alignment explanation
Indices: 121122--121156 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
121112 AGGGTTCTAC
*
121122 GTGGTCCTTCGGGACATA
1 GTGGTCATTCGGGACATA
121140 GTGGTCATTCGGGACAT
1 GTGGTCATTCGGGACAT
121157 TTCATAGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (18 bp):
GTGGTCATTCGGGACATA
Found at i:121183 original size:23 final size:23
Alignment explanation
Indices: 121136--121185 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
121126 TCCTTCGGGA
*
121136 CATAGTGGTCATTCGGGACATTT
1 CATAGTGGTCATTCGGGACAATT
121159 CATAGTGGTC-TTCGGGACAAATT
1 CATAGTGGTCATTCGGGAC-AATT
121182 CATA
1 CATA
121186 TGCCCCTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (23 bp):
CATAGTGGTCATTCGGGACAATT
Found at i:124886 original size:15 final size:15
Alignment explanation
Indices: 124853--124894 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
124843 TTAATATATA
*
124853 TATTCAATTTTTTAGT
1 TATTTAATTTTTTA-T
124869 TATTTAAATTTTTT-T
1 TATTT-AATTTTTTAT
124884 TATTTAATTTT
1 TATTTAATTTT
124895 AAAATATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 6 0.25
15 6 0.25
16 4 0.17
17 8 0.33
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (15 bp):
TATTTAATTTTTTAT
Found at i:124933 original size:16 final size:15
Alignment explanation
Indices: 124884--124944 Score: 52
Period size: 16 Copynumber: 4.0 Consensus size: 15
124874 AAATTTTTTT
124884 TATTTAATTTTAAAA
1 TATTTAATTTTAAAA
** **
124899 TATTTGAATAATATTA
1 TATTT-AATTTTAAAA
124915 TATTTAAATTTTAAAA
1 TATTT-AATTTTAAAA
*
124931 TATTT-TTTTTAAAA
1 TATTTAATTTTAAAA
124945 ATTAAATAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
14 8 0.23
15 5 0.14
16 22 0.63
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTTTAAAA
Found at i:129183 original size:55 final size:53
Alignment explanation
Indices: 129117--129311 Score: 198
Period size: 55 Copynumber: 3.6 Consensus size: 53
129107 AATGACGAGC
* * *
129117 CTGCTCCCTATTCCTTCAGGAAGTATAAGACTCGAGCAATCTTCATAAAATGTGT
1 CTGCTCTCTATTCCTTCA-GAAGTATAAGACTCGAACAATCTTCATAAAACG-GT
*
129172 CTGCTCTCTATTCATTCAG-AGTATAAGACT-GAACAATCTTCAATAAAACGGT
1 CTGCTCTCTATTCCTTCAGAAGTATAAGACTCGAACAATCTTC-ATAAAACGGT
* * * *
129224 CCGCTCTCTATTCCTTCAGAGAGTATAGGACTCGAAAAATCTTCA-ATGAACAGGT
1 CTGCTCTCTATTCCTTCAGA-AGTATAAGACTCGAACAATCTTCATA-AAAC-GGT
* * * *
129279 CCGCTCCCTATTCTTTCAGAGAGTATAGGACTC
1 CTGCTCTCTATTCCTTCAGA-AGTATAAGACTC
129312 AATCTTTAAC
Statistics
Matches: 123, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
52 29 0.24
53 19 0.15
54 15 0.12
55 60 0.49
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (53 bp):
CTGCTCTCTATTCCTTCAGAAGTATAAGACTCGAACAATCTTCATAAAACGGT
Found at i:129452 original size:51 final size:51
Alignment explanation
Indices: 129222--129670 Score: 621
Period size: 51 Copynumber: 8.9 Consensus size: 51
129212 CAATAAAACG
* * * **
129222 GTCCGCTCTCTATTCCTTCAGAGAGTATAGGACTCGAAAAATCTTCAATGAACAG
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTC----AATCTTCAACGAACTT
* * *
129277 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTTAAC-AAATGT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT-T
* * * * *
129328 GT-CGCTCCCTATCCGTTCAGGGAGTATAGAACTCGATCTTCAACGAAC-T
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
129377 -T--G-TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
* *
129424 GTCCGCTCTCTATTCATTCAGAGAGTATAGGACCCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
129475 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCCACGAACTTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAAC-TT
129527 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
129578 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAAC-T
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
129628 GTCCGCTCCCTATTCA-TCAGAGAGTATA-GACTCAATCTTCAAC
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
129671 AAAATGTTTG
Statistics
Matches: 360, Mismatches: 26, Indels: 23
0.88 0.06 0.06
Matches are distributed among these distances:
46 38 0.11
47 2 0.01
48 17 0.05
49 13 0.04
50 56 0.16
51 151 0.42
52 50 0.14
55 33 0.09
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.29
Consensus pattern (51 bp):
GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:129569 original size:103 final size:102
Alignment explanation
Indices: 129222--129670 Score: 621
Period size: 103 Copynumber: 4.4 Consensus size: 102
129212 CAATAAAACG
* * * **
129222 GTCCGCTCTCTATTCCTTCAGAGAGTATAGGACTCGAAAAATCTTCAATGAACAGGTCCGCTCCC
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTC----AATCTTCAACGAACTTGTCCGCTCCC
* * *
129287 TATTCTTTCAGAGAGTATAGGACTCAATCTTTAAC-AAATGT
62 TATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT-T
* * * * *
129328 GT-CGCTCCCTATCCGTTCAGGGAGTATAGAACTCGATCTTCAACGAAC-T-T--G-TCCCTATT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATT
*
129387 CCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
66 CATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
* *
129424 GTCCGCTCTCTATTCATTCAGAGAGTATAGGACCCAATCTTCAACGAACTTGTCCGCTCCCTATT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATT
*
129489 CATTCAGAGAGTATAGGACTCAATCTTCCACGAACTTT
66 CATTCAGAGAGTATAGGACTCAATCTTCAACGAAC-TT
129527 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATT
129592 CATTCAGAGAGTATAGGACTCAATCTTCAACGAAC-T
66 CATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
129628 GTCCGCTCCCTATTCA-TCAGAGAGTATA-GACTCAATCTTCAAC
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
129671 AAAATGTTTG
Statistics
Matches: 312, Mismatches: 23, Indels: 23
0.87 0.06 0.06
Matches are distributed among these distances:
96 40 0.13
97 43 0.14
98 1 0.00
99 17 0.05
100 12 0.04
101 30 0.10
102 41 0.13
103 99 0.32
105 27 0.09
106 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.29
Consensus pattern (102 bp):
GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATT
CATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:129571 original size:154 final size:152
Alignment explanation
Indices: 129169--129670 Score: 630
Period size: 154 Copynumber: 3.3 Consensus size: 152
129159 TCATAAAATG
* * * ** * *
129169 TGTCTGCTCTCTATTCATTC--AGAGTATAAGACTGAACAATCTTCAATAAAACGGTCCGCTCTC
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT---CAATCTTCAA-CGAACTGTCCGCTCCC
* ** *
129232 TATTCCTTCAGAGAGTATAGGACTCGAAAAATCTTCAATGAACAGGTCCGCTCCCTATTCTTTCA
62 TATTCCTTCAGAGAGTATAGGACTC----AATCTTCAACGAACTTGTCCGCTCCCTATTCATTCA
* *
129297 GAGAGTATAGGACTCAATCTTTAAC-AAAT
123 GAGAGTATAGGACTCAATCTTCAACGAACT
* * * * *
129326 GTGT-CGCTCCCTATCCGTTCAGGGAGTATAGAACTCGATCTTCAACGAACT-T--G-TCCCTAT
1 -TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTGTCCGCTCCCTAT
*
129386 TCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCTCTATTCATTCAGAGAGTA
65 TCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTA
*
129451 TAGGACCCAATCTTCAACGAACT
130 TAGGACTCAATCTTCAACGAACT
*
129474 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCCACGAACTTTGTCCGCTCCCTA
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAAC--TGTCCGCTCCCTA
*
129539 TTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGT
64 TTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGT
129604 ATAGGACTCAATCTTCAACGAAC-
129 ATAGGACTCAATCTTCAACGAACT
129627 TGTCCGCTCCCTATTCA-TCAGAGAGTATA-GACTCAATCTTCAAC
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
129671 AAAATGTTTG
Statistics
Matches: 304, Mismatches: 30, Indels: 27
0.84 0.08 0.07
Matches are distributed among these distances:
147 57 0.19
148 43 0.14
150 1 0.00
151 43 0.14
152 13 0.04
153 18 0.06
154 92 0.30
155 3 0.01
156 9 0.03
157 12 0.04
158 3 0.01
159 10 0.03
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (152 bp):
TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTGTCCGCTCCCTATT
CCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTAT
AGGACTCAATCTTCAACGAACT
Found at i:130813 original size:19 final size:19
Alignment explanation
Indices: 130789--130843 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
130779 CCTCCTTTTA
130789 TTTCTCTTTTTTTTTCATT
1 TTTCTCTTTTTTTTTCATT
*
130808 TTTCTCTTTTTATTT--TT
1 TTTCTCTTTTTTTTTCATT
*
130825 CTT-TC-TTTTTTTTCATT
1 TTTCTCTTTTTTTTTCATT
130842 TT
1 TT
130844 CATTTTTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 7 0.23
16 2 0.07
17 7 0.23
19 14 0.47
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTCTCTTTTTTTTTCATT
Found at i:130829 original size:25 final size:23
Alignment explanation
Indices: 130796--130936 Score: 93
Period size: 24 Copynumber: 6.1 Consensus size: 23
130786 TTATTTCTCT
*
130796 TTTTTTTTCATTTTTCTCTTTTTA
1 TTTTTTTTCATTTTT-TCTTTTCA
*
130820 TTTTTCTTTCTTTTTTTTCATTTTCA
1 TTTTT-TTTC-ATTTTTTC-TTTTCA
*
130846 TTTTTTCTCATTTTTTCTTTTC-
1 TTTTTTTTCATTTTTTCTTTTCA
*
130868 TTCTTTTTCTCATTTTTAT-TATT-A
1 TT-TTTTT-TCATTTTT-TCTTTTCA
130892 TTATTTTTTC-TTTTTTC---TCA
1 TT-TTTTTTCATTTTTTCTTTTCA
*
130912 TTTTTTCTTC-TTTTCTCTTTT-A
1 TTTTTT-TTCATTTTTTCTTTTCA
130934 TTT
1 TTT
130937 CTTCTTCAAG
Statistics
Matches: 96, Mismatches: 8, Indels: 28
0.73 0.06 0.21
Matches are distributed among these distances:
19 5 0.05
20 12 0.12
21 1 0.01
22 11 0.11
23 12 0.12
24 30 0.31
25 10 0.10
26 15 0.16
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTTTTTCATTTTTTCTTTTCA
Found at i:130834 original size:33 final size:33
Alignment explanation
Indices: 130784--130887 Score: 94
Period size: 33 Copynumber: 3.2 Consensus size: 33
130774 TGAACCCTCC
*
130784 TTTTATTTCTC-TT-TTTTTTTCATTTTTCTCT
1 TTTTATTTTTCTTTCTTTTTTTCATTTTTCTCT
130815 TTTTATTTTTCTTTCTTTTTTTTCA-TTTTCAT-T
1 TTTTATTTTTCTTTC-TTTTTTTCATTTTTC-TCT
* * *
130848 TTTTCTCATTT-TTTCTTTTCTTC-TTTTTCTCAT
1 TTTTAT-TTTTCTTTCTTTTTTTCATTTTTCTC-T
130881 TTTTATT
1 TTTTATT
130888 ATTATTATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
31 11 0.19
32 14 0.24
33 21 0.36
34 13 0.22
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (33 bp):
TTTTATTTTTCTTTCTTTTTTTCATTTTTCTCT
Found at i:130850 original size:32 final size:32
Alignment explanation
Indices: 130796--130915 Score: 98
Period size: 34 Copynumber: 3.4 Consensus size: 32
130786 TTATTTCTCT
*
130796 TTTTTTTTCATTTTTCTCTTTTTATTTTTCTTTC
1 TTTTTTTTCA-TTTTC-ATTTTTATTTTTCTTTC
130830 TTTTTTTTCATTTTCATTTTTTCTCATTTTTTCTTTTC
1 TTTTTTTTCATTTTCA--TTTT-T-A-TTTTTC-TTTC
* *
130868 TTCTTTTTCTCATTTTTATTATTATTATTT-TTTC
1 TT-TTTTT-TCATTTTCATTTTTATT-TTTCTTTC
*
130902 TTTTTTCTCATTTT
1 TTTTTTTTCATTTT
130916 TTCTTCTTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
32 7 0.10
33 9 0.12
34 20 0.27
35 3 0.04
36 5 0.07
37 7 0.10
38 9 0.12
39 5 0.07
40 8 0.11
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (32 bp):
TTTTTTTTCATTTTCATTTTTATTTTTCTTTC
Found at i:130884 original size:49 final size:50
Alignment explanation
Indices: 130796--130916 Score: 121
Period size: 50 Copynumber: 2.5 Consensus size: 50
130786 TTATTTCTCT
* * *
130796 TTTTTTTTCATTTTTCTCTTTTTATTTTTCTTTC-TTTTTTTTCATT-TTCA
1 TTTTTTCTCATTTTTCTCTTTTTATTTTTCTCTCATTTTTATT-ATTATT-A
130846 TTTTTTCTCATTTTT-TCTTTTCT-TCTTTT-TCTCATTTTTATTATTATTA
1 TTTTTTCTCATTTTTCTCTTTT-TAT-TTTTCTCTCATTTTTATTATTATTA
130895 TTTTTTCT--TTTTTCTCATTTTT
1 TTTTTTCTCATTTTTCTC-TTTTT
130917 TCTTCTTTTC
Statistics
Matches: 62, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
47 5 0.08
48 3 0.05
49 26 0.42
50 28 0.45
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (50 bp):
TTTTTTCTCATTTTTCTCTTTTTATTTTTCTCTCATTTTTATTATTATTA
Found at i:130915 original size:15 final size:15
Alignment explanation
Indices: 130826--130868 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
130816 TTTATTTTTC
*
130826 TTTCTTTTTTTTCAT
1 TTTCTTTTTTCTCAT
130841 TTTCATTTTTTCTCAT
1 TTTC-TTTTTTCTCAT
130857 TTT-TTCTTTTCT
1 TTTCTT-TTTTCT
130869 TCTTTTTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 2 0.08
15 10 0.40
16 13 0.52
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTCTTTTTTCTCAT
Found at i:131470 original size:170 final size:168
Alignment explanation
Indices: 131191--131528 Score: 626
Period size: 170 Copynumber: 2.0 Consensus size: 168
131181 ATCTGACCAT
131191 GACAAATAGCTTTTCAATCTCTTTTCTTCAATCAATTCAACTGGTCATACTAGCTTGGACCCATT
1 GACAAATAGCTTTTCAATCTCTTTTCTTCAATCAATTCAACTGGTCATACTAGCTTGGACCCATT
131256 CTGCCTCATCAGCTTACCTCTGACAAAATCCGAAGTGAAGGAATTTCCACCTCAATAGGTAAGAC
66 CTGCCTCATCAGCTTACCTCTGACAAAATCCGAAGTGAAGGAATTTCCACCTCAATAGGTAAGAC
131321 AGCTTCCATCCCA-AAACCAAAGAAAATGGTGTTGCCC
131 AGCTTCCATCCCATAAACCAAAGAAAATGGTGTTGCCC
131358 GACAAATAGC-TTTCAATCTCTTTTCTTCAATCAAATTCAACTGGTCATACCTAGCTTGGACCCA
1 GACAAATAGCTTTTCAATCTCTTTTCTTCAATC-AATTCAACTGGTCATA-CTAGCTTGGACCCA
131422 TTCTGCCTCATCAAGCTTTACCTCTGACAAAATCCGAAGTGAAGGAATTTCCACCTCAATAGGTA
64 TTCTGCCTCATC-AGC-TTACCTCTGACAAAATCCGAAGTGAAGGAATTTCCACCTCAATAGGTA
131487 AGACAGCTTCCATCCCATAAACCAAAGAAAATGGTGTTGCCC
127 AGACAGCTTCCATCCCATAAACCAAAGAAAATGGTGTTGCCC
131529 CAGTTGAAGT
Statistics
Matches: 166, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
166 22 0.13
167 26 0.16
168 26 0.16
169 3 0.02
170 65 0.39
171 24 0.14
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (168 bp):
GACAAATAGCTTTTCAATCTCTTTTCTTCAATCAATTCAACTGGTCATACTAGCTTGGACCCATT
CTGCCTCATCAGCTTACCTCTGACAAAATCCGAAGTGAAGGAATTTCCACCTCAATAGGTAAGAC
AGCTTCCATCCCATAAACCAAAGAAAATGGTGTTGCCC
Found at i:153168 original size:46 final size:46
Alignment explanation
Indices: 153108--153201 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
153098 AACTTGTCAA
153108 TTAAATCAACCCAATTTTATATCAAACCTTGAAATATGTCAACGGG
1 TTAAATCAACCCAATTTTATATCAAACCTTGAAATATGTCAACGGG
* *
153154 TTAAATCAATCCAATTTTATATCAAACCTTGAAATATGTCGACGGG
1 TTAAATCAACCCAATTTTATATCAAACCTTGAAATATGTCAACGGG
153200 TT
1 TT
153202 TGATTTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (46 bp):
TTAAATCAACCCAATTTTATATCAAACCTTGAAATATGTCAACGGG
Found at i:153783 original size:15 final size:16
Alignment explanation
Indices: 153763--153800 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
153753 ATTTTGTTAG
153763 TAATTTATTTAA-ATT
1 TAATTTATTTAATATT
*
153778 TAATTTTTTTAATATT
1 TAATTTATTTAATATT
*
153794 TTATTTA
1 TAATTTA
153801 CAGATATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TAATTTATTTAATATT
Found at i:153796 original size:27 final size:28
Alignment explanation
Indices: 153734--153800 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
153724 TGTTTAAGGT
*
153734 ATATTTTA-TTATATTTAGTATTTTGTTA
1 ATATTTTATTTAAATTTAG-ATTTTGTTA
* * *
153762 GTAATTTATTTAAATTTA-ATTTTTTTA
1 ATATTTTATTTAAATTTAGATTTTGTTA
153789 ATATTTTATTTA
1 ATATTTTATTTA
153801 CAGATATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 18 0.56
28 6 0.19
29 8 0.25
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (28 bp):
ATATTTTATTTAAATTTAGATTTTGTTA
Found at i:156095 original size:32 final size:32
Alignment explanation
Indices: 156035--156095 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
156025 TAATACTTAT
*
156035 TTTATTTTGTTAATTTGGTTAGATTTTTTTAA
1 TTTATTTTGTTAATTTGGTTAGACTTTTTTAA
*
156067 TTTATTTTGTTAATATT-GTTGGACTTTTT
1 TTTATTTTGTTAAT-TTGGTTAGACTTTTT
156096 GTTAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 24 0.92
33 2 0.08
ACGTcount: A:0.20, C:0.02, G:0.13, T:0.66
Consensus pattern (32 bp):
TTTATTTTGTTAATTTGGTTAGACTTTTTTAA
Found at i:156105 original size:32 final size:31
Alignment explanation
Indices: 156036--156106 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 31
156026 AATACTTATT
156036 TTATTTTGTTAATTTGGTTAGATTTTTTTAA
1 TTATTTTGTTAATTTGGTTAGATTTTTTTAA
*
156067 TTTATTTTGTTAATATT-GTTGGACTTTTTGTTAA
1 -TTATTTTGTTAAT-TTGGTTAGA-TTTTT-TTAA
156101 -TATTTT
1 TTATTTT
156107 TAGGTTAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
32 24 0.69
33 7 0.20
34 4 0.11
ACGTcount: A:0.21, C:0.01, G:0.13, T:0.65
Consensus pattern (31 bp):
TTATTTTGTTAATTTGGTTAGATTTTTTTAA
Found at i:157826 original size:10 final size:10
Alignment explanation
Indices: 157811--157835 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
157801 CATCCTCCGC
157811 ACCAGCCTAA
1 ACCAGCCTAA
157821 ACCAGCCTAA
1 ACCAGCCTAA
157831 ACCAG
1 ACCAG
157836 TCTCAGCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.40, G:0.12, T:0.08
Consensus pattern (10 bp):
ACCAGCCTAA
Found at i:171782 original size:23 final size:24
Alignment explanation
Indices: 171739--171783 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
171729 ATAAAAGAGA
*
171739 AAAAATGAAAAAAAATGGAAAAAC
1 AAAAATGAAAAAAAATAGAAAAAC
171763 AAAAA-GAAAGAAAAA-AGAAAA
1 AAAAATGAAA-AAAAATAGAAAA
171784 TGGAAAAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.04
Consensus pattern (24 bp):
AAAAATGAAAAAAAATAGAAAAAC
Found at i:171796 original size:25 final size:27
Alignment explanation
Indices: 171768--171830 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 27
171758 AAAACAAAAA
*
171768 GAAAGAAAAAAG-AAAATGGAAAAG-G
1 GAAAGAAAAAAGAAAAATGAAAAAGAG
*
171793 GAAA-AAAAATGAAAAATGAAAAAGAG
1 GAAAGAAAAAAGAAAAATGAAAAAGAG
*
171819 AAAATGAAAAAA
1 GAAA-GAAAAAA
171831 AGAATAAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
24 6 0.20
25 15 0.50
26 4 0.13
28 5 0.17
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (27 bp):
GAAAGAAAAAAGAAAAATGAAAAAGAG
Found at i:171814 original size:14 final size:14
Alignment explanation
Indices: 171772--171834 Score: 62
Period size: 14 Copynumber: 4.8 Consensus size: 14
171762 CAAAAAGAAA
171772 GAAAAA-AGAAAAT
1 GAAAAAGAGAAAAT
* *
171785 GGAAAAGGGAAAA-
1 GAAAAAGAGAAAAT
*
171798 -AAAATGA-AAAAT
1 GAAAAAGAGAAAAT
171810 GAAAAAGAGAAAAT
1 GAAAAAGAGAAAAT
*
171824 GAAAAAAAGAA
1 GAAAAAGAGAA
171835 TAAAAGGAGG
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
11 4 0.10
12 4 0.10
13 11 0.28
14 20 0.51
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (14 bp):
GAAAAAGAGAAAAT
Found at i:171828 original size:31 final size:30
Alignment explanation
Indices: 171763--171840 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 30
171753 ATGGAAAAAC
*
171763 AAAAAGAAAGAAAAAAGAAAATGGAAAAGGG
1 AAAAA-AAAGAAAAAAGAAAAAGGAAAAGGG
* *
171794 AAAAAAAATGAAAAATGAAAAAGAGAAAA-TG
1 AAAAAAAA-GAAAAAAGAAAAAG-GAAAAGGG
171825 -AAAAAAAGAATAAAAG
1 AAAAAAAAGAA-AAAAG
171841 GAGGTTCAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 3 0.08
30 14 0.35
31 18 0.45
32 5 0.12
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (30 bp):
AAAAAAAAGAAAAAAGAAAAAGGAAAAGGG
Found at i:173107 original size:50 final size:43
Alignment explanation
Indices: 173008--173107 Score: 128
Period size: 43 Copynumber: 2.2 Consensus size: 43
172998 AAACTCGTTT
*
173008 GTTGAAGATTGAGTCATACTCTCAGGAATAGAGCGGACAATTC
1 GTTGAAGATTGAGTCATACTCTCAAGAATAGAGCGGACAATTC
173051 GTTGAAGATTGAGTCCTATACTCTCTGAAGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGT-C-ATACTCTC--AAGAATA--GAGCGGACAA-TTC
173101 GTTGAAG
1 GTTGAAG
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
43 14 0.29
44 1 0.02
45 8 0.16
47 6 0.12
49 10 0.20
50 10 0.20
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (43 bp):
GTTGAAGATTGAGTCATACTCTCAAGAATAGAGCGGACAATTC
Done.