Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008035.1 Hibiscus syriacus cultivar Beakdansim tig00110520_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: 262018
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:4779 original size:14 final size:14
Alignment explanation
Indices: 4760--4793 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
4750 ATTATTAGCT
4760 TTATAATATATTTA
1 TTATAATATATTTA
4774 TTATAATATATTTA
1 TTATAATATATTTA
*
4788 TGATAA
1 TTATAA
4794 GAATATTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
TTATAATATATTTA
Found at i:13327 original size:15 final size:14
Alignment explanation
Indices: 13307--13341 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
13297 ATTATTAGCT
13307 TTATAATATATGTTA
1 TTATAATATAT-TTA
13322 TTATAATATATTTA
1 TTATAATATATTTA
*
13336 TGATAA
1 TTATAA
13342 GAATATTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (14 bp):
TTATAATATATTTA
Found at i:19105 original size:13 final size:13
Alignment explanation
Indices: 19087--19115 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
19077 GTACCATACA
19087 TCAACATACCTTT
1 TCAACATACCTTT
19100 TCAACATACCTTT
1 TCAACATACCTTT
19113 TCA
1 TCA
19116 TCTTTGGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
TCAACATACCTTT
Found at i:23436 original size:15 final size:16
Alignment explanation
Indices: 23416--23448 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
23406 AATATGGAAG
*
23416 AAGAAAGGAAAT-GAT
1 AAGAAAGAAAATGGAT
23431 AAGAAAGAAAATGGAT
1 AAGAAAGAAAATGGAT
23447 AA
1 AA
23449 AAATGTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.12
Consensus pattern (16 bp):
AAGAAAGAAAATGGAT
Found at i:23445 original size:32 final size:32
Alignment explanation
Indices: 23384--23445 Score: 74
Period size: 32 Copynumber: 1.9 Consensus size: 32
23374 ACAAAATTAA
* *
23384 AAGAAAGAAATGATTAAAATGGAATATGGAAG
1 AAGAAAGAAATGATTAAAATAGAAAATGGAAG
23416 AAGAAAGGAAATGA-TAAGAA-AGAAAATGGA
1 AAGAAA-GAAATGATTAA-AATAGAAAATGGA
23446 TAAAAATGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.26, T:0.15
Consensus pattern (32 bp):
AAGAAAGAAATGATTAAAATAGAAAATGGAAG
Found at i:28719 original size:11 final size:13
Alignment explanation
Indices: 28687--28716 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28677 TGGCCAAAGA
28687 TGAAAAGGTATGT
1 TGAAAAGGTATGT
28700 TGAAAAGGTATG-
1 TGAAAAGGTATGT
28712 TGAAA
1 TGAAA
28717 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:33074 original size:6 final size:6
Alignment explanation
Indices: 33063--33096 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
33053 TGATGTAGGA
33063 TTCTTT TTCTTT TTCTTCT TTCTTT TTCTATT TT
1 TTCTTT TTCTTT TTCTT-T TTCTTT TTCT-TT TT
33097 TGTTGCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 16 0.62
7 10 0.38
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (6 bp):
TTCTTT
Found at i:33088 original size:12 final size:12
Alignment explanation
Indices: 33063--33096 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
33053 TGATGTAGGA
33063 TTCTTTTTCTTT
1 TTCTTTTTCTTT
33075 TTCTTCTTTCTTT
1 TTCTT-TTTCTTT
33088 TTCTATTTT
1 TTCT-TTTT
33097 TGTTGCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 14 0.70
14 1 0.05
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (12 bp):
TTCTTTTTCTTT
Found at i:33332 original size:32 final size:33
Alignment explanation
Indices: 33271--33337 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
33261 ACAAAATTAA
* *
33271 AAGAAAGAAATGATTAAAATGGAATATGGA-AG
1 AAGAAAGAAATGATTAAAATAGAAAATGGATAG
33303 AAGAAAGGAAATGA-TAAGAA-AGAAAATGGATAG
1 AAGAAA-GAAATGATTAA-AATAGAAAATGGATAG
33336 AA
1 AA
33338 ATGTTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.60, C:0.00, G:0.25, T:0.15
Consensus pattern (33 bp):
AAGAAAGAAATGATTAAAATAGAAAATGGATAG
Found at i:36479 original size:19 final size:20
Alignment explanation
Indices: 36437--36487 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
36427 GAAACTCCTT
*
36437 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTGAA
36457 TGAAAATACATGA-TTTGAA
1 TGAAAATACATGATTTTGAA
*
36476 TGAAGATACATG
1 TGAAAATACATG
36488 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTGAA
Found at i:39821 original size:19 final size:20
Alignment explanation
Indices: 39783--39833 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
39773 GAAACCCCTT
39783 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
*
39803 TGAAAATACATTA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
39822 TGAAGATACATG
1 TGAAAATACATG
39834 CTCTTAGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:40306 original size:30 final size:30
Alignment explanation
Indices: 40272--40347 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
40262 GTCCAAAGCT
* *
40272 CTCCTCCAGCTAAGTTCAGCTGCATGCTAG
1 CTCCTCCAGCTAAGTTCAACTACATGCTAG
40302 CTCCTCCAGCTAAGTTCAACTACATGCTAG
1 CTCCTCCAGCTAAGTTCAACTACATGCTAG
*
40332 CTCCTCCGGCTAAGTT
1 CTCCTCCAGCTAAGTT
40348 GAAGCTCCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.21, C:0.34, G:0.17, T:0.28
Consensus pattern (30 bp):
CTCCTCCAGCTAAGTTCAACTACATGCTAG
Found at i:42946 original size:26 final size:26
Alignment explanation
Indices: 42910--42977 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
42900 TCCTAGAACA
42910 CCCATGTGCCTTGCATATGACCAGCC
1 CCCATGTGCCTTGCATATGACCAGCC
42936 CCCATGTGCCTTGCATATGACCAGCC
1 CCCATGTGCCTTGCATATGACCAGCC
* *
42962 CCAATATGCCTTGCAT
1 CCCATGTGCCTTGCAT
42978 GAGGATCATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.25
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGACCAGCC
Found at i:44973 original size:27 final size:26
Alignment explanation
Indices: 44935--45003 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 26
44925 TCCTAGAACA
44935 CCCATGTGCCTTGCATATGACCAGCCC
1 CCCATGTGCCTTGCATATGACCAG-CC
44962 CCCATGTGCCTTGCATATGACCAGCC
1 CCCATGTGCCTTGCATATGACCAGCC
*
44988 CCAATGTGCCTTGCAT
1 CCCATGTGCCTTGCAT
45004 GAGGATCATT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 17 0.41
27 24 0.59
ACGTcount: A:0.19, C:0.38, G:0.19, T:0.25
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGACCAGCC
Found at i:46995 original size:27 final size:26
Alignment explanation
Indices: 46957--47025 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 26
46947 TCCTAGAAAA
46957 CCCATGTGCCTTGCATATGACCAGCCC
1 CCCATGTGCCTTGCATATGACCAG-CC
46984 CCCATGTGCCTTGCATATGACCAGCC
1 CCCATGTGCCTTGCATATGACCAGCC
*
47010 CCAATGTGCCTTGCAT
1 CCCATGTGCCTTGCAT
47026 GAGGATCATT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 17 0.41
27 24 0.59
ACGTcount: A:0.19, C:0.38, G:0.19, T:0.25
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGACCAGCC
Found at i:49020 original size:27 final size:26
Alignment explanation
Indices: 48982--49050 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 26
48972 TCCTAGAACA
48982 CCCATGTGCCTTGCATATGACCAGCCC
1 CCCATGTGCCTTGCATATGACCAG-CC
49009 CCCATGTGCCTTGCATATGACCAGCC
1 CCCATGTGCCTTGCATATGACCAGCC
*
49035 CCAATGTGCCTTGCAT
1 CCCATGTGCCTTGCAT
49051 GAGGATCATT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 17 0.41
27 24 0.59
ACGTcount: A:0.19, C:0.38, G:0.19, T:0.25
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGACCAGCC
Found at i:52766 original size:11 final size:13
Alignment explanation
Indices: 52734--52763 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
52724 TGGCAAAAGA
52734 TGAAAAGGTATGT
1 TGAAAAGGTATGT
52747 TGAAAAGGTATG-
1 TGAAAAGGTATGT
52759 TGAAA
1 TGAAA
52764 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:54772 original size:90 final size:90
Alignment explanation
Indices: 54614--54794 Score: 281
Period size: 90 Copynumber: 2.0 Consensus size: 90
54604 CCTAGAACAC
*
54614 CCATGTGCCTTGCATATGACCAGCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATAA
1 CCATGTGCCTTGCATATGAACAGCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATAA
*
54679 AGAGTTCTCTCCCTATTCGGCCAAG
66 AGAGCTCTCTCCCTATTCGGCCAAG
** * * * * *
54704 CCATGTGTTTTGCATGTGAACAGCCCCATGTGCCTTGCATGTGGTTTATTTAGGCGCCAAGATGA
1 CCATGTGCCTTGCATATGAACAGCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATAA
54769 AGAGCTCTCTCCCTATTCGGCCAAG
66 AGAGCTCTCTCCCTATTCGGCCAAG
54794 C
1 C
54795 ATCATTTCCT
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.28
Consensus pattern (90 bp):
CCATGTGCCTTGCATATGAACAGCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATAA
AGAGCTCTCTCCCTATTCGGCCAAG
Found at i:55957 original size:23 final size:22
Alignment explanation
Indices: 55931--55986 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
55921 ATAACCATAG
55931 ATATTATATATATGAAA-ATAAC
1 ATATTATATATATGAAATA-AAC
*
55953 TATATTATAATATTTGAAATAAAC
1 -ATATTAT-ATATATGAAATAAAC
55977 ATA-TATATAT
1 ATATTATATAT
55987 GTGTAAAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.13
22 3 0.10
23 10 0.33
24 12 0.40
25 1 0.03
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (22 bp):
ATATTATATATATGAAATAAAC
Found at i:57916 original size:36 final size:36
Alignment explanation
Indices: 57864--57976 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
57854 GATACTATTT
*
57864 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
57900 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
57936 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
57971 ACATCA
1 TCATCA
57977 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:57919 original size:13 final size:11
Alignment explanation
Indices: 57864--57962 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
57854 GATACTATTT
57864 TCATCACCATAA
1 TCATCACCAT-A
*
57876 TCCATCTCCATTA
1 T-CATCACCA-TA
*
57889 TCA-CGCCTATA
1 TCATCACC-ATA
57900 TCATCACCATA
1 TCATCACCATA
57911 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
57925 TCA-CGCCTATA
1 TCATCACC-ATA
57936 TCATCACCATA
1 TCATCACCATA
57947 TTCCATCACCATA
1 -T-CATCACCATA
57960 TCA
1 TCA
57963 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:57991 original size:33 final size:33
Alignment explanation
Indices: 57876--58015 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
57866 ATCACCATAA
* * *
57876 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
57910 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
57948 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
57981 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
58014 TC
1 TC
58016 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:60605 original size:13 final size:13
Alignment explanation
Indices: 60589--60618 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
60579 AACAAAAAAC
60589 AAAAAAAGGCAAA
1 AAAAAAAGGCAAA
60602 AAAAAAAGGCAAA
1 AAAAAAAGGCAAA
60615 AAAA
1 AAAA
60619 CAAAAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAAAAGGCAAA
Found at i:60607 original size:22 final size:21
Alignment explanation
Indices: 60576--60645 Score: 70
Period size: 23 Copynumber: 3.2 Consensus size: 21
60566 TTTTTTTCAA
*
60576 AAAAACAAAAAACAAAAAAAGGC
1 AAAAA-AAAAAGCAAAAAAA-GC
60599 AAAAAAAAAAGGCAAAAAAA-C
1 AAAAAAAAAA-GCAAAAAAAGC
* *
60620 AAAAAAAAGAGCCAAAAAAGAC
1 AAAAAAAAAAGCAAAAAAAG-C
60642 AAAA
1 AAAA
60646 TTTCAAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 8 0.20
21 10 0.24
22 10 0.24
23 13 0.32
ACGTcount: A:0.79, C:0.11, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAGCAAAAAAAGC
Found at i:60608 original size:21 final size:20
Alignment explanation
Indices: 60577--60627 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 20
60567 TTTTTTCAAA
60577 AAAACAAAAAACAAAAAAAGGC
1 AAAA-AAAAAACAAAAAAA-GC
60599 AAAAAAAAAAGGCAAAAAAA-C
1 AAAAAAAAAA--CAAAAAAAGC
60620 AAAAAAAA
1 AAAAAAAA
60628 GAGCCAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 15 0.56
22 4 0.15
23 8 0.30
ACGTcount: A:0.82, C:0.10, G:0.08, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAACAAAAAAAGC
Found at i:60623 original size:20 final size:22
Alignment explanation
Indices: 60590--60645 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
60580 ACAAAAAACA
* * *
60590 AAAAAAGGCAAAAAAAAAAGGC
1 AAAAAAGACAAAAAAAAGAGCC
60612 AAAAAA-ACAAAAAAAAGAGCC
1 AAAAAAGACAAAAAAAAGAGCC
60633 AAAAAAGACAAAA
1 AAAAAAGACAAAA
60646 TTTCAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.77, C:0.11, G:0.12, T:0.00
Consensus pattern (22 bp):
AAAAAAGACAAAAAAAAGAGCC
Found at i:67815 original size:36 final size:36
Alignment explanation
Indices: 67763--67875 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
67753 GATACTATTT
*
67763 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
67799 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* * *
67835 TCATCACCATATTCCATCACCA-TATCATGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
67870 ACATCA
1 TCATCA
67876 TCCTTCCATT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 55 0.77
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:67818 original size:13 final size:11
Alignment explanation
Indices: 67763--67862 Score: 69
Period size: 13 Copynumber: 8.4 Consensus size: 11
67753 GATACTATTT
67763 TCATCACCATAA
1 TCATCACCAT-A
*
67775 TCCATCTCCATTA
1 T-CATCACCA-TA
*
67788 TCA-CGCCTATA
1 TCATCACC-ATA
67799 TCATCACCATA
1 TCATCACCATA
67810 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
67824 TCA-CGCCTATA
1 TCATCACC-ATA
67835 TCATCACCATA
1 TCATCACCATA
67846 TTCCATCACCATA
1 -T-CATCACCATA
67859 TCAT
1 TCAT
67863 GCCAATAACA
Statistics
Matches: 72, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 25 0.35
12 16 0.22
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (11 bp):
TCATCACCATA
Found at i:67890 original size:33 final size:33
Alignment explanation
Indices: 67846--67914 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
67836 CATCACCATA
*
67846 TTCCATCACCATATCAT-GCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
67879 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
67912 TTC
1 TTC
67915 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.30, C:0.35, G:0.01, T:0.33
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:70598 original size:18 final size:19
Alignment explanation
Indices: 70560--70598 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
70550 ATCAGAAAAG
* *
70560 AAGCCCTCAAAAAGATTGA
1 AAGCACTCAAAAAGATAGA
70579 AAGCACTCAAAAAGA-AGA
1 AAGCACTCAAAAAGATAGA
70597 AA
1 AA
70599 AAGAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.56, C:0.18, G:0.15, T:0.10
Consensus pattern (19 bp):
AAGCACTCAAAAAGATAGA
Found at i:70697 original size:63 final size:62
Alignment explanation
Indices: 70578--70697 Score: 163
Period size: 64 Copynumber: 1.9 Consensus size: 62
70568 AAAAAGATTG
*
70578 AAAGCACTCAAAAAGAAGAAAAAGAAAAAAAATCAGCAAAGAAAATTGAAGGACTCAAAAGTC
1 AAAGCACTCAAAAAGAAGAAAAAGAAAAAAAA-CAGCAAAGAAAATTGAAGCACTCAAAAGTC
* *
70641 AAAGCACTCAAAAAAGAAGAAAAAGCAAAGAAA-AG-AAAGAAAAGTTGGAAGCACTCA
1 AAAGCACTC-AAAAAGAAGAAAAAGAAAAAAAACAGCAAAGAAAA-TT-GAAGCACTCA
70698 TCAACAATTC
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
61 8 0.16
62 4 0.08
63 18 0.35
64 21 0.41
ACGTcount: A:0.62, C:0.12, G:0.17, T:0.08
Consensus pattern (62 bp):
AAAGCACTCAAAAAGAAGAAAAAGAAAAAAAACAGCAAAGAAAATTGAAGCACTCAAAAGTC
Found at i:77508 original size:24 final size:21
Alignment explanation
Indices: 77473--77515 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
77463 GGCTCATTCT
*
77473 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
77496 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
77516 ATCTTGTGGA
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:80985 original size:24 final size:22
Alignment explanation
Indices: 80941--80987 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 22
80931 ATTTAGAAGT
80941 TGGTGATAATATAGGTGTGATA
1 TGGTGATAATATAGGTGTGATA
80963 TGGTGATGGAATAT-GGTGATGATA
1 TGGTGAT--AATATAGGTG-TGATA
80987 T
1 T
80988 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 4 0.18
24 11 0.50
ACGTcount: A:0.30, C:0.00, G:0.34, T:0.36
Consensus pattern (22 bp):
TGGTGATAATATAGGTGTGATA
Found at i:80988 original size:35 final size:36
Alignment explanation
Indices: 80941--81008 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
80931 ATTTAGAAGT
*
80941 TGGTGATAATATAGGTGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
80976 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
81009 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.29, C:0.01, G:0.37, T:0.32
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:82587 original size:36 final size:36
Alignment explanation
Indices: 82535--82647 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
82525 GATACTATTT
* **
82535 TCATCACCATAATCCATCTCCATTATCACGTTTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
82571 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
82607 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
82642 ACATCA
1 TCATCA
82648 TCCTTCAATT
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 17 0.24
36 53 0.76
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.29
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:82590 original size:13 final size:11
Alignment explanation
Indices: 82568--82633 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
82558 TATCACGTTT
82568 ATATCATCACC
1 ATATCATCACC
82579 ATAGTCCATCACC
1 ATA-T-CATCACC
*
82592 ATTATCA-CGCC
1 A-TATCATCACC
82603 TATATCATCACC
1 -ATATCATCACC
82615 ATATTCCATCACC
1 ATA-T-CATCACC
82628 ATATCA
1 ATATCA
82634 CGCCAATAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:83059 original size:12 final size:12
Alignment explanation
Indices: 83037--83095 Score: 57
Period size: 12 Copynumber: 4.6 Consensus size: 12
83027 CAAAAGCAAC
83037 AAAAAGA-AAAA
1 AAAAAGAGAAAA
83048 AAAAAGAGAAAA
1 AAAAAGAGAAAA
83060 AAAAAGAAAGAAGAAA
1 AAAAAG--AG-A-AAA
83076 ACAAAAGAGAAAA
1 A-AAAAGAGAAAA
*
83089 TAAAAGA
1 AAAAAGA
83096 CTCCTACAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
11 7 0.17
12 16 0.39
13 3 0.07
14 3 0.07
15 3 0.07
16 4 0.10
17 5 0.12
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (12 bp):
AAAAAGAGAAAA
Found at i:83059 original size:13 final size:13
Alignment explanation
Indices: 83037--83093 Score: 62
Period size: 13 Copynumber: 4.2 Consensus size: 13
83027 CAAAAGCAAC
83037 AAAA-AGAAAAAA
1 AAAAGAGAAAAAA
83049 AAAAGAGAAAAAA
1 AAAAGAGAAAAAA
*
83062 AAAGAAAGAAGAAAA
1 AAA-AGAGAA-AAAA
83077 CAAAAGAGAAAATAA
1 -AAAAGAGAAAA-AA
83092 AA
1 AA
83094 GACTCCTACA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
12 4 0.11
13 11 0.29
14 9 0.24
15 11 0.29
16 3 0.08
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (13 bp):
AAAAGAGAAAAAA
Found at i:83062 original size:16 final size:17
Alignment explanation
Indices: 83043--83081 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
83033 CAACAAAAAG
83043 AAAAAAAAAAG-AGAAA
1 AAAAAAAAAAGAAGAAA
*
83059 AAAAAAGAAAGAAGAAA
1 AAAAAAAAAAGAAGAAA
83076 ACAAAA
1 A-AAAA
83082 GAGAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 10 0.50
17 6 0.30
18 4 0.20
ACGTcount: A:0.85, C:0.03, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGAAGAAA
Found at i:83073 original size:19 final size:18
Alignment explanation
Indices: 83037--83088 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
83027 CAAAAGCAAC
*
83037 AAAAAGAAAA-AAAAAAG
1 AAAAAAAAAAGAAAAAAG
*
83054 AGAAAAAAAAAGAAAGAAG
1 A-AAAAAAAAAGAAAAAAG
*
83073 AAAACAAAAGAGAAAA
1 AAAA-AAAAAAGAAAA
83089 TAAAAGACTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.04
18 11 0.39
19 16 0.57
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAGAAAAAAG
Found at i:83074 original size:17 final size:16
Alignment explanation
Indices: 83043--83083 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
83033 CAACAAAAAG
83043 AAAAAAA-AAAGAGAA
1 AAAAAAAGAAAGAGAA
83058 AAAAAAAGAAAGAAGAA
1 AAAAAAAGAAAG-AGAA
*
83075 AACAAAAGA
1 AAAAAAAGA
83084 GAAAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.30
16 4 0.17
17 12 0.52
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAGAGAA
Found at i:83081 original size:29 final size:27
Alignment explanation
Indices: 83039--83095 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 27
83029 AAAGCAACAA
83039 AAAGAAAAAAAAAAGAGAAAAAAAAAG
1 AAAGAAAAAAAAAAGAGAAAAAAAAAG
*
83066 AAAGAAGAAAACAAAAGAGAAAATAAAAG
1 AAAGAA-AAAA-AAAAGAGAAAAAAAAAG
83095 A
1 A
83096 CTCCTACAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 6 0.22
28 4 0.15
29 17 0.63
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.02
Consensus pattern (27 bp):
AAAGAAAAAAAAAAGAGAAAAAAAAAG
Found at i:86742 original size:36 final size:36
Alignment explanation
Indices: 86690--86802 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
86680 GATATTATTT
*
86690 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
86726 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
86762 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
86797 ACATCA
1 TCATCA
86803 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:86745 original size:13 final size:11
Alignment explanation
Indices: 86690--86788 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
86680 GATATTATTT
86690 TCATCACCATAA
1 TCATCACCAT-A
*
86702 TCCATCTCCATTA
1 T-CATCACCA-TA
*
86715 TCA-CGCCTATA
1 TCATCACC-ATA
86726 TCATCACCATA
1 TCATCACCATA
86737 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
86751 TCA-CGCCTATA
1 TCATCACC-ATA
86762 TCATCACCATA
1 TCATCACCATA
86773 TTCCATCACCATA
1 -T-CATCACCATA
86786 TCA
1 TCA
86789 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:86817 original size:33 final size:33
Alignment explanation
Indices: 86702--86841 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
86692 ATCACCATAA
* * *
86702 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
86736 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
86774 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
86807 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
86840 TC
1 TC
86842 ATTCATCAAG
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:90470 original size:19 final size:20
Alignment explanation
Indices: 90423--90473 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
90413 GAAACCCCTT
**
90423 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
90443 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
90462 TGAAGATACATG
1 TGAAAATACATG
90474 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:93100 original size:23 final size:21
Alignment explanation
Indices: 93074--93121 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
93064 AAAGAAAACA
93074 AAAGCACTT-AAAAGAAGAAATTG
1 AAAGCACTTGAAAA-AA-AAA-TG
93097 AAAGCACTTGAAAAAAAAATG
1 AAAGCACTTGAAAAAAAAATG
93118 AAAG
1 AAAG
93122 AAAGAAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.25
22 3 0.12
23 11 0.46
24 4 0.17
ACGTcount: A:0.60, C:0.08, G:0.17, T:0.15
Consensus pattern (21 bp):
AAAGCACTTGAAAAAAAAATG
Found at i:94374 original size:24 final size:21
Alignment explanation
Indices: 94340--94382 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
94330 TGCACAAGAT
*
94340 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
94362 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
94383 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:100154 original size:202 final size:202
Alignment explanation
Indices: 99808--100210 Score: 761
Period size: 202 Copynumber: 2.0 Consensus size: 202
99798 AAAGACACCA
*
99808 AATGCTACACCTTGAATTGGAAAACAATCTGCGCAAAAGAAGAATTATTGGTTAAATAAATGAAT
1 AATGCTACACCTTGAATTGGAAAACAATCTGCACAAAAGAAGAATTATTGGTTAAATAAATGAAT
99873 AATAAAGAAAGGAAATAGAAATGGAAAGAATTGAAATGGATAGAATAGTTATCAAAGAAGGGCTG
66 AATAAAGAAAGGAAATAGAAATGGAAAGAATTGAAATGGATAGAATAGTTATCAAAGAAGGGCTG
*
99938 CGGAAGTGTTGTAGAATGATCCTTTAAGTGATGATGGATTCGGCCTCTAATGGTGATGATGGATG
131 CGGAAGTGTTGTAGAATGATCCTTCAAGTGATGATGGATTCGGCCTCTAATGGTGATGATGGATG
100003 AATGCCC
196 AATGCCC
100010 AATGCTACACCTTGAATTGGAAAACAATCTGCACAAAAGAAGAATTATTGGTTAAATAAATGAAT
1 AATGCTACACCTTGAATTGGAAAACAATCTGCACAAAAGAAGAATTATTGGTTAAATAAATGAAT
100075 AATAAAGAAAGGAAATAGAAATGGAAAGAATTGAAATGGATAGAATAGTTATCAAAGAAGGGCTG
66 AATAAAGAAAGGAAATAGAAATGGAAAGAATTGAAATGGATAGAATAGTTATCAAAGAAGGGCTG
* * *
100140 TGTAAGTGTTGTAGAATGATCCTTCAAGTGATGATGGATTCGGTCTCTAATGGTGATGATGGATG
131 CGGAAGTGTTGTAGAATGATCCTTCAAGTGATGATGGATTCGGCCTCTAATGGTGATGATGGATG
100205 AATGCC
196 AATGCC
100211 TTGTTGATGA
Statistics
Matches: 196, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
202 196 1.00
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.26
Consensus pattern (202 bp):
AATGCTACACCTTGAATTGGAAAACAATCTGCACAAAAGAAGAATTATTGGTTAAATAAATGAAT
AATAAAGAAAGGAAATAGAAATGGAAAGAATTGAAATGGATAGAATAGTTATCAAAGAAGGGCTG
CGGAAGTGTTGTAGAATGATCCTTCAAGTGATGATGGATTCGGCCTCTAATGGTGATGATGGATG
AATGCCC
Found at i:100309 original size:35 final size:37
Alignment explanation
Indices: 100263--100343 Score: 130
Period size: 35 Copynumber: 2.2 Consensus size: 37
100253 TTTGAGAATT
*
100263 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
100298 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
100335 TGGTGATGA
1 TGGTGATGA
100344 AAATAGTATC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.50
36 4 0.10
37 17 0.40
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:105973 original size:35 final size:37
Alignment explanation
Indices: 105927--106006 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
105917 TTTGAGAATT
*
105927 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
105962 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
105999 TGGTGATG
1 TGGTGATG
106007 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:107734 original size:35 final size:36
Alignment explanation
Indices: 107684--107753 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 36
107674 CAATATGTCT
*
107684 ATCACCATTATCACGCCTATATCATCACCATATTCC
1 ATCACCATTATCACGCCTATATCATCACCAAATTCC
*
107720 ATCACCA-TATCACGCCTATATTATCACCAAATTC
1 ATCACCATTATCACGCCTATATCATCACCAAATTC
107754 TAAATTTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 25 0.78
36 7 0.22
ACGTcount: A:0.33, C:0.34, G:0.03, T:0.30
Consensus pattern (36 bp):
ATCACCATTATCACGCCTATATCATCACCAAATTCC
Found at i:108255 original size:24 final size:24
Alignment explanation
Indices: 108200--108248 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
108190 ACTGCAAAAG
* *
108200 AAAGAAAAGAAAAAGAAGAATCAA
1 AAAGCAAAGAAAAAGAAGAAGCAA
*
108224 AAAGCAAAGAAAAAG-TGAAGCAA
1 AAAGCAAAGAAAAAGAAGAAGCAA
108247 AA
1 AA
108249 TTGCAAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.71, C:0.06, G:0.18, T:0.04
Consensus pattern (24 bp):
AAAGCAAAGAAAAAGAAGAAGCAA
Found at i:113573 original size:15 final size:14
Alignment explanation
Indices: 113553--113590 Score: 67
Period size: 14 Copynumber: 2.6 Consensus size: 14
113543 TCTTTTTTTG
113553 TTTTTTTTTGCCGT
1 TTTTTTTTTGCCGT
113567 TTTTTTTTTGCCGT
1 TTTTTTTTTGCCGT
113581 TTTTTGTTTT
1 TTTTT-TTTT
113591 TTTTTTGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.00, C:0.11, G:0.13, T:0.76
Consensus pattern (14 bp):
TTTTTTTTTGCCGT
Found at i:113605 original size:21 final size:21
Alignment explanation
Indices: 113526--113605 Score: 61
Period size: 21 Copynumber: 3.6 Consensus size: 21
113516 TTTTTTGAAA
* * *
113526 TTTTGGCTTTTTTTGGCTCTTT
1 TTTTGG-TTTTTTTTGTTTTTT
*
113548 TTTTGTTTTTTTTTGCCGTTTTTT
1 TTTTGGTTTTTTTT---GTTTTTT
***
113572 TTTTGCCGTTTTTTGTTTTTT
1 TTTTGGTTTTTTTTGTTTTTT
113593 TTTTGGTTTTTTT
1 TTTTGGTTTTTTT
113606 GAAAAAAAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
21 24 0.53
22 5 0.11
24 16 0.36
ACGTcount: A:0.00, C:0.09, G:0.15, T:0.76
Consensus pattern (21 bp):
TTTTGGTTTTTTTTGTTTTTT
Found at i:113606 original size:20 final size:20
Alignment explanation
Indices: 113565--113604 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
113555 TTTTTTTGCC
113565 GTTTTTTTTTTGCCGTTTTTT
1 GTTTTTTTTTTG-CGTTTTTT
113586 GTTTTTTTTTTG-GTTTTTT
1 GTTTTTTTTTTGCGTTTTTT
113605 TGAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.00, C:0.05, G:0.15, T:0.80
Consensus pattern (20 bp):
GTTTTTTTTTTGCGTTTTTT
Found at i:117858 original size:22 final size:23
Alignment explanation
Indices: 117822--117873 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
117812 CAATCTGTCC
117822 ATCACCATTATCACGCCTATATG
1 ATCACCATTATCACGCCTATATG
*
117845 ATCACCA-TATCACGCCTATATT
1 ATCACCATTATCACGCCTATATG
117867 ATCACCA
1 ATCACCA
117874 ACTTCTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 21 0.75
23 7 0.25
ACGTcount: A:0.33, C:0.33, G:0.06, T:0.29
Consensus pattern (23 bp):
ATCACCATTATCACGCCTATATG
Found at i:126338 original size:19 final size:20
Alignment explanation
Indices: 126300--126350 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
126290 GAAACCCCTT
*
126300 TGAAAATATATGATTTTTAA
1 TGAAAATACATGATTTTTAA
126320 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
126339 TGAAGATACATG
1 TGAAAATACATG
126351 CTCTTGGACG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.45, C:0.04, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:127877 original size:36 final size:36
Alignment explanation
Indices: 127825--127937 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
127815 GATACTATTT
*
127825 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
127861 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* * *
127897 TCATCACCATATTCCATCAACA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
127932 ACATCA
1 TCATCA
127938 TCCTTCCATT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 17 0.24
36 54 0.76
ACGTcount: A:0.34, C:0.35, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:128340 original size:10 final size:10
Alignment explanation
Indices: 128327--128380 Score: 63
Period size: 10 Copynumber: 5.0 Consensus size: 10
128317 CAAAAGCAAC
128327 AAAAAGAAAA
1 AAAAAGAAAA
128337 AAAAAGAAAA
1 AAAAAGAAAA
128347 AAAAAGAAAGA
1 AAAAAGAAA-A
*
128358 AGAAAACAAAA
1 A-AAAAGAAAA
128369 GAGAAAAGAAAA
1 -A-AAAAGAAAA
128381 GACTCCTACA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
10 19 0.49
11 3 0.08
12 17 0.44
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:128347 original size:17 final size:17
Alignment explanation
Indices: 128327--128380 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
128317 CAAAAGCAAC
*
128327 AAAAAGAAA-AAAAAAG
1 AAAAAAAAAGAAAAAAG
*
128343 AAAAAAAAAGAAAGAAG
1 AAAAAAAAAGAAAAAAG
* *
128360 AAAACAAAAGAGAAAAG
1 AAAAAAAAAGAAAAAAG
128377 AAAA
1 AAAA
128381 GACTCCTACA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 8 0.25
17 24 0.75
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGAAAAAAG
Found at i:131131 original size:22 final size:22
Alignment explanation
Indices: 131105--131146 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
131095 TAATTATAGT
* *
131105 TATGATGTTGATATTATGAATG
1 TATGAAGTTAATATTATGAATG
*
131127 TATGAAGTTAATGTTATGAA
1 TATGAAGTTAATATTATGAA
131147 CCACATATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (22 bp):
TATGAAGTTAATATTATGAATG
Found at i:132228 original size:36 final size:36
Alignment explanation
Indices: 132176--132288 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
132166 GATACTATTT
*
132176 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
132212 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* * *
132248 TCATCACCATATTCCATCACCA-TATCATGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
132283 ACATCA
1 TCATCA
132289 TCCTTCCATT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 55 0.77
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:132231 original size:13 final size:11
Alignment explanation
Indices: 132176--132275 Score: 69
Period size: 13 Copynumber: 8.4 Consensus size: 11
132166 GATACTATTT
132176 TCATCACCATAA
1 TCATCACCAT-A
*
132188 TCCATCTCCATTA
1 T-CATCACCA-TA
*
132201 TCA-CGCCTATA
1 TCATCACC-ATA
132212 TCATCACCATA
1 TCATCACCATA
132223 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
132237 TCA-CGCCTATA
1 TCATCACC-ATA
132248 TCATCACCATA
1 TCATCACCATA
132259 TTCCATCACCATA
1 -T-CATCACCATA
132272 TCAT
1 TCAT
132276 GCCAATAACA
Statistics
Matches: 72, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 25 0.35
12 16 0.22
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (11 bp):
TCATCACCATA
Found at i:132303 original size:33 final size:33
Alignment explanation
Indices: 132259--132327 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
132249 CATCACCATA
*
132259 TTCCATCACCATATCAT-GCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
132292 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
132325 TTC
1 TTC
132328 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.30, C:0.35, G:0.01, T:0.33
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:136709 original size:19 final size:20
Alignment explanation
Indices: 136668--136718 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
136658 GAAACCCCTT
*
136668 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
136688 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
136707 TGAAGATACATG
1 TGAAAATACATG
136719 CTCTTGGACG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:139662 original size:25 final size:25
Alignment explanation
Indices: 139612--139667 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
139602 TTTCTTTGTT
* *
139612 TTTTC-TTCTTTTTGAGTACTGGAA
1 TTTTCTTTCTTTTGGAGTACTGCAA
* *
139636 TTTTCTTTCTTTTGGAGTGCTTCAA
1 TTTTCTTTCTTTTGGAGTACTGCAA
139661 -TTTCTTT
1 TTTTCTTT
139668 TCTCATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.12, C:0.14, G:0.14, T:0.59
Consensus pattern (25 bp):
TTTTCTTTCTTTTGGAGTACTGCAA
Found at i:142756 original size:33 final size:32
Alignment explanation
Indices: 142692--142756 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
142682 CTTGTTGATG
*
142692 AATGAAGGATGATTTAATGGTGATGAAATGGT
1 AATGAAGGATGATTTAATGGCGATGAAATGGT
* *
142724 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
1 AATG-AAGGATGAT-TTAATGGCGATGAAATGGT
142757 GAAGGAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 4 0.14
33 17 0.61
34 7 0.25
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.32
Consensus pattern (32 bp):
AATGAAGGATGATTTAATGGCGATGAAATGGT
Found at i:142804 original size:36 final size:36
Alignment explanation
Indices: 142734--142846 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
142724 AATGAAAGGA
* * *
142734 TGATGTTATTGGCGTGAT-ATGGTGAAGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
142769 TGATGATATAGGTGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
142805 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
142841 TGATGA
1 TGATGA
142847 AAATAGTATC
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 15 0.22
36 54 0.78
ACGTcount: A:0.28, C:0.03, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:142806 original size:13 final size:12
Alignment explanation
Indices: 142749--142845 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
142739 TTATTGGCGT
*
142749 GATATGGTGAAG
1 GATATGGTGATG
142761 GAATATGGTGAT-
1 G-ATATGGTGATG
142773 GATATAGGTG-T-
1 GATAT-GGTGATG
142784 GATAATGGTGATG
1 GAT-ATGGTGATG
142797 GACTATGGTGAT-
1 GA-TATGGTGATG
*
142809 GATATAGGCG-T-
1 GATAT-GGTGATG
*
142820 GATAATGGAGATG
1 GAT-ATGGTGATG
142833 GATTATGGTGATG
1 GA-TATGGTGATG
142846 AAAATAGTAT
Statistics
Matches: 70, Mismatches: 4, Indels: 21
0.74 0.04 0.22
Matches are distributed among these distances:
11 22 0.31
12 17 0.24
13 29 0.41
14 2 0.03
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:148530 original size:36 final size:35
Alignment explanation
Indices: 148460--148572 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 35
148450 AATGAAAGGA
* * *
148460 TGATGTTATTGGCGTGAT-ATGGTGAAGGAATATGG
1 TGATGATATAGGCGTGATAATGGTG-ATGAATATGG
148495 TGATGATATAGGCGTGATAATGGTGATGAACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGAA-TATGG
*
148531 TGATGATATAGGCGTGATAATGGAGATGAATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGAA-TATGG
148567 TGATGA
1 TGATGA
148573 AAATATCTTA
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 20 0.28
36 51 0.72
ACGTcount: A:0.30, C:0.04, G:0.35, T:0.32
Consensus pattern (35 bp):
TGATGATATAGGCGTGATAATGGTGATGAATATGG
Found at i:150155 original size:36 final size:36
Alignment explanation
Indices: 150108--150211 Score: 174
Period size: 36 Copynumber: 2.9 Consensus size: 36
150098 ATACTATTTC
*
150108 ATCATCACCATAATCCATCTCCATTATCACGCCTAT
1 ATCATCACCATAATCCATCACCATTATCACGCCTAT
*
150144 ATCATCACCATAGTCCATCACCATTATCACGCCTAT
1 ATCATCACCATAATCCATCACCATTATCACGCCTAT
*
150180 ATCATCACCATATTCCATCACCA-TATCACGCC
1 ATCATCACCATAATCCATCACCATTATCACGCC
150212 AATAACATTA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 9 0.14
36 56 0.86
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (36 bp):
ATCATCACCATAATCCATCACCATTATCACGCCTAT
Found at i:150164 original size:13 final size:11
Alignment explanation
Indices: 150108--150207 Score: 69
Period size: 13 Copynumber: 8.4 Consensus size: 11
150098 ATACTATTTC
150108 ATCATCACCAT
1 ATCATCACCAT
*
150119 AATCCATCTCCATT
1 -AT-CATCACCA-T
*
150133 ATCA-CGCCTAT
1 ATCATCACC-AT
150144 ATCATCACCAT
1 ATCATCACCAT
150155 AGTCCATCACCATT
1 A-T-CATCACCA-T
*
150169 ATCA-CGCCTAT
1 ATCATCACC-AT
150180 ATCATCACCAT
1 ATCATCACCAT
150191 ATTCCATCACCAT
1 A-T-CATCACCAT
150204 ATCA
1 ATCA
150208 CGCCAATAAC
Statistics
Matches: 72, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.33
12 17 0.24
13 28 0.39
14 3 0.04
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
ATCATCACCAT
Found at i:150629 original size:22 final size:22
Alignment explanation
Indices: 150603--150646 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
150593 GTGCTACAAC
*
150603 AAAAAGCAACAAG-AAAGAAAAA
1 AAAAAG-AAAAAGAAAAGAAAAA
150625 AAAAAGAAAAAGAAAAGAAAAA
1 AAAAAGAAAAAGAAAAGAAAAA
150647 GACTCCTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.82, C:0.05, G:0.14, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAGAAAAGAAAAA
Found at i:150634 original size:6 final size:6
Alignment explanation
Indices: 150616--150648 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
150606 AAGCAACAAG
150616 AAAGAA AAA-AA AAAGAA AAAG-A AAAGAA AAAGA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGA
150649 CTCCTACATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:150636 original size:17 final size:17
Alignment explanation
Indices: 150616--150648 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
150606 AAGCAACAAG
150616 AAAGAAAAAAAAAAGAA
1 AAAGAAAAAAAAAAGAA
*
150633 AAAGAAAAGAAAAAGA
1 AAAGAAAAAAAAAAGA
150649 CTCCTACATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAAAAAGAA
Found at i:150647 original size:11 final size:11
Alignment explanation
Indices: 150616--150648 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
150606 AAGCAACAAG
*
150616 AAAGAAAAAAA
1 AAAGAAAAAGA
150627 AAAGAAAAAGA
1 AAAGAAAAAGA
150638 AAAGAAAAAGA
1 AAAGAAAAAGA
150649 CTCCTACATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:154080 original size:13 final size:12
Alignment explanation
Indices: 154063--154158 Score: 56
Period size: 13 Copynumber: 7.9 Consensus size: 12
154053 AAGACTATTT
154063 TCATCACCATAA
1 TCATCACCATAA
* *
154075 TCCATCTCCATTA
1 T-CATCACCATAA
*
154088 TCA-CGCC-TATA
1 TCATCACCATA-A
*
154099 TCATCACCATAG
1 TCATCACCATAA
*
154111 TCCATCACCATTA
1 T-CATCACCATAA
*
154124 TCA-CTCC-TATA
1 TCATCACCATA-A
*
154135 TCATCACCATAT
1 TCATCACCATAA
154147 TCCATCACCATA
1 T-CATCACCATA
154159 TCACGCCAAT
Statistics
Matches: 63, Mismatches: 12, Indels: 17
0.68 0.13 0.18
Matches are distributed among these distances:
10 2 0.03
11 14 0.22
12 13 0.21
13 34 0.54
ACGTcount: A:0.31, C:0.36, G:0.02, T:0.30
Consensus pattern (12 bp):
TCATCACCATAA
Found at i:154115 original size:36 final size:36
Alignment explanation
Indices: 154063--154175 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
154053 AAGACTATTT
*
154063 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
154099 TCATCACCATAGTCCATCACCATTATCACTCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
154135 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
154170 ACATCA
1 TCATCA
154176 TCCTTCCATT
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 16 0.23
36 54 0.77
ACGTcount: A:0.33, C:0.36, G:0.03, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:154190 original size:33 final size:33
Alignment explanation
Indices: 154146--154214 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
154136 CATCACCATA
*
154146 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
154179 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
154212 TTC
1 TTC
154215 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:156640 original size:15 final size:15
Alignment explanation
Indices: 156612--156652 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
156602 TGAATATAAA
156612 GAAAGGAATAGAAATG
1 GAAA-GAATAGAAATG
*
156628 GAAAGAATTGAAATG
1 GAAAGAATAGAAATG
*
156643 GATAGAATAG
1 GAAAGAATAG
156653 TTATCAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.17
Consensus pattern (15 bp):
GAAAGAATAGAAATG
Found at i:159782 original size:36 final size:36
Alignment explanation
Indices: 159734--159842 Score: 157
Period size: 36 Copynumber: 3.1 Consensus size: 36
159724 ACTATTTTCA
*
159734 CACCATAATCCATCTCCATTATCACGCCTATATCAT
1 CACCATAATCCATCACCATTATCACGCCTATATCAT
*
159770 CACCATAGTCCATCACCATTATCACGCCTATATCAT
1 CACCATAATCCATCACCATTATCACGCCTATATCAT
* * * *
159806 CACCATATTCCTTCACCA-TATCACGCCAATAACAT
1 CACCATAATCCATCACCATTATCACGCCTATATCAT
159841 CA
1 CA
159843 TCCTTTCATT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 17 0.25
36 50 0.75
ACGTcount: A:0.32, C:0.37, G:0.04, T:0.28
Consensus pattern (36 bp):
CACCATAATCCATCACCATTATCACGCCTATATCAT
Found at i:159864 original size:35 final size:36
Alignment explanation
Indices: 159749--159864 Score: 116
Period size: 36 Copynumber: 3.3 Consensus size: 36
159739 TAATCCATCT
* * *
159749 CCATTATCACGCCTATATCATCACCATAGTCCA-TCA
1 CCATTATCACGCCAATAACATCACCATA-TTCATTCA
* * *
159785 CCATTATCACGCCTATATCATCACCATATTCCTTCA
1 CCATTATCACGCCAATAACATCACCATATTCATTCA
159821 CCA-TATCACGCCAATAACATCATCC-T-TTCATT-A
1 CCATTATCACGCCAATAACATCA-CCATATTCATTCA
159854 CCATTCATCAC
1 CCATT-ATCAC
159865 CATTAAATCT
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
33 4 0.06
34 6 0.08
35 25 0.35
36 36 0.51
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.30
Consensus pattern (36 bp):
CCATTATCACGCCAATAACATCACCATATTCATTCA
Found at i:164716 original size:19 final size:20
Alignment explanation
Indices: 164666--164708 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
164656 GAAACCCCTT
164666 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
164686 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
164705 TGAA
1 TGAA
164709 GTCACATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:169627 original size:6 final size:6
Alignment explanation
Indices: 169616--169659 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
169606 GATGTAGGAG
169616 TCTTTT TC-TTT TCTTTT TCTTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
169660 TGTTGCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.14
6 20 0.57
7 10 0.29
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:169639 original size:12 final size:12
Alignment explanation
Indices: 169616--169659 Score: 63
Period size: 13 Copynumber: 3.6 Consensus size: 12
169606 GATGTAGGAG
169616 TCTTTTTC-TTT
1 TCTTTTTCTTTT
169627 TCTTTTTCTTTT
1 TCTTTTTCTTTT
169639 TCTTCTTTCTTTT
1 TCTT-TTTCTTTT
169652 TCTCTTTT
1 TCT-TTTT
169660 TGTTGCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.27
12 7 0.23
13 14 0.47
14 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TCTTTTTCTTTT
Found at i:169649 original size:19 final size:17
Alignment explanation
Indices: 169616--169659 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 17
169606 GATGTAGGAG
169616 TCTTTTTCTTTTCTTTT
1 TCTTTTTCTTTTCTTTT
169633 TCTTTTTCTTCTTTCTTTT
1 TCTTTTTC-T-TTTCTTTT
169652 TCTCTTTT
1 TCT-TTTT
169660 TGTTGCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.33
18 1 0.04
19 11 0.46
20 4 0.17
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
TCTTTTTCTTTTCTTTT
Found at i:169884 original size:15 final size:15
Alignment explanation
Indices: 169834--169893 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
169824 ACAAAATTAA
169834 AAGAAA-GAAATGATT
1 AAGAAAGGAAATGA-T
*
169849 AA-AATGGAATATGGAAT
1 AAGAAAGGAA-AT-G-AT
169866 AAGAAAGGAAATGAT
1 AAGAAAGGAAATGAT
*
169881 AAGAAAGAAAATG
1 AAGAAAGGAAATG
169894 GATAGAAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 2 0.05
15 19 0.51
16 3 0.08
17 6 0.16
18 7 0.19
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (15 bp):
AAGAAAGGAAATGAT
Found at i:169895 original size:32 final size:32
Alignment explanation
Indices: 169834--169895 Score: 74
Period size: 32 Copynumber: 1.9 Consensus size: 32
169824 ACAAAATTAA
* *
169834 AAGAAAGAAATGATTAAAATGGAATATGGAAT
1 AAGAAAGAAATGATTAAAATAGAAAATGGAAT
169866 AAGAAAGGAAATGA-TAAGAA-AGAAAATGGA
1 AAGAAA-GAAATGATTAA-AATAGAAAATGGA
169896 TAGAAATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (32 bp):
AAGAAAGAAATGATTAAAATAGAAAATGGAAT
Found at i:175110 original size:66 final size:65
Alignment explanation
Indices: 174988--175111 Score: 153
Period size: 66 Copynumber: 1.9 Consensus size: 65
174978 CTTTTCTTTC
* *
174988 TTTTCTTTGCTTTTTCTTCTTTTTTGAGTGCTTTGACTTTTGAGTCCTTCAATTTTCTTTGCTGA
1 TTTTCTTTGCTTTTTCTTCTTTTTTGAGTGCTTTAACTTTTGAGGCCTTC-ATTTTCTTTGCTGA
175053 T
65 T
* * *
175054 TTTTTTTTTCTTTTTCTTC-TTTTTGAGTGCTTTCAATCTTTTTGAGGGCTTC-TTTTCT
1 TTTTCTTTGCTTTTTCTTCTTTTTTGAGTGCTTT-AA-C-TTTTGAGGCCTTCATTTTCT
175112 GATTTTTCTT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
65 14 0.28
66 24 0.48
67 1 0.02
68 11 0.22
ACGTcount: A:0.08, C:0.16, G:0.13, T:0.63
Consensus pattern (65 bp):
TTTTCTTTGCTTTTTCTTCTTTTTTGAGTGCTTTAACTTTTGAGGCCTTCATTTTCTTTGCTGAT
Found at i:175161 original size:12 final size:13
Alignment explanation
Indices: 175135--175163 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
175125 TTTCTTTGAC
175135 TTTGCACTTCACT
1 TTTGCACTTCACT
175148 TTTGCACTTC-CT
1 TTTGCACTTCACT
175160 TTTG
1 TTTG
175164 TATTTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.10, C:0.28, G:0.10, T:0.52
Consensus pattern (13 bp):
TTTGCACTTCACT
Found at i:177306 original size:19 final size:20
Alignment explanation
Indices: 177264--177314 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
177254 GAAACTCCTT
*
177264 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTGAA
177284 TGAAAATACATGA-TTTGAA
1 TGAAAATACATGATTTTGAA
*
177303 TGAAGATACATG
1 TGAAAATACATG
177315 CTCTTGGCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTGAA
Found at i:180645 original size:19 final size:20
Alignment explanation
Indices: 180607--180657 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
180597 GAAACCCCTT
180607 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
*
180627 TGAAAATACATTA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
180646 TGAAGATACATG
1 TGAAAATACATG
180658 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:181129 original size:30 final size:30
Alignment explanation
Indices: 181095--181170 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
181085 GTCCAAAGCT
* *
181095 CTCCTCCAGCTAAGTTCAGCTATATGCTAG
1 CTCCTCCAGCTAAGTTCAACTACATGCTAG
181125 CTCCTCCAGCTAAGTTCAACTACATGCTAG
1 CTCCTCCAGCTAAGTTCAACTACATGCTAG
*
181155 CTCCTCCGGCTAAGTT
1 CTCCTCCAGCTAAGTT
181171 GAAGCTCCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.29
Consensus pattern (30 bp):
CTCCTCCAGCTAAGTTCAACTACATGCTAG
Found at i:182990 original size:22 final size:23
Alignment explanation
Indices: 182965--183014 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
182955 AATGGAAGGA
* *
182965 TGATGTTATTGGCGTGAT-ATGG
1 TGATGATATAGGCGTGATAATGG
182987 TGATGATATAGGCGTGATAATGG
1 TGATGATATAGGCGTGATAATGG
183010 TGATG
1 TGATG
183015 GACTATGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.24, C:0.04, G:0.36, T:0.36
Consensus pattern (23 bp):
TGATGATATAGGCGTGATAATGG
Found at i:183029 original size:36 final size:36
Alignment explanation
Indices: 182982--183064 Score: 148
Period size: 36 Copynumber: 2.3 Consensus size: 36
182972 ATTGGCGTGA
*
182982 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGAGATGGAC
*
183018 TATGGTGATGATATAGGCGTGATAATGGAGATGGAT
1 TATGGTGATGATATAGGCGTGATAATGGAGATGGAC
183054 TATGGTGATGA
1 TATGGTGATGA
183065 AAATAGTATC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGAGATGGAC
Found at i:183451 original size:19 final size:20
Alignment explanation
Indices: 183404--183454 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
183394 GAAACCCCTT
**
183404 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
183424 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
183443 TGAAGATACATG
1 TGAAAATACATG
183455 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:185945 original size:16 final size:16
Alignment explanation
Indices: 185924--185955 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
185914 TCTTCCACCA
185924 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
185940 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
185956 GAGCTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:189411 original size:16 final size:16
Alignment explanation
Indices: 189390--189421 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
189380 TCTTCCACCA
189390 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
189406 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
189422 GAGCTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:197502 original size:24 final size:21
Alignment explanation
Indices: 197468--197510 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
197458 TGCACAAGAT
*
197468 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
197490 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
197511 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:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:199067 original size:12 final size:12
Alignment explanation
Indices: 199037--199075 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
199027 AAAAGTGGAT
199037 AGAG-GTAGCTG
1 AGAGAGTAGCTG
199048 -GA-AGTAGCTG
1 AGAGAGTAGCTG
199058 AGAGAGTAGCTG
1 AGAGAGTAGCTG
199070 AG-GAGT
1 AGAGAGT
199076 TGAGAAGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.36
11 6 0.24
12 10 0.40
ACGTcount: A:0.31, C:0.08, G:0.44, T:0.18
Consensus pattern (12 bp):
AGAGAGTAGCTG
Found at i:201489 original size:24 final size:21
Alignment explanation
Indices: 201455--201497 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
201445 TGCACAAGAT
*
201455 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
201477 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
201498 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:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:203030 original size:12 final size:12
Alignment explanation
Indices: 203000--203038 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
202990 AAAGTGGACT
203000 AGAG-GTAGCTG
1 AGAGAGTAGCTG
203011 -GA-AGTAGCTG
1 AGAGAGTAGCTG
203021 AGAGAGTAGCTG
1 AGAGAGTAGCTG
203033 AG-GAGT
1 AGAGAGT
203039 TGAGAAGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.36
11 6 0.24
12 10 0.40
ACGTcount: A:0.31, C:0.08, G:0.44, T:0.18
Consensus pattern (12 bp):
AGAGAGTAGCTG
Found at i:205460 original size:24 final size:21
Alignment explanation
Indices: 205426--205468 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
205416 TGCACAAGAT
*
205426 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
205448 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
205469 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:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:207005 original size:12 final size:12
Alignment explanation
Indices: 206975--207013 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
206965 AAAGTGGACT
206975 AGAG-GTAGCTG
1 AGAGAGTAGCTG
206986 -GA-AGTAGCTG
1 AGAGAGTAGCTG
206996 AGAGAGTAGCTG
1 AGAGAGTAGCTG
207008 AG-GAGT
1 AGAGAGT
207014 TGAGAAGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.36
11 6 0.24
12 10 0.40
ACGTcount: A:0.31, C:0.08, G:0.44, T:0.18
Consensus pattern (12 bp):
AGAGAGTAGCTG
Found at i:209437 original size:24 final size:21
Alignment explanation
Indices: 209403--209445 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
209393 TGCACAAGAT
*
209403 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
209425 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
209446 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:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:221524 original size:11 final size:13
Alignment explanation
Indices: 221493--221521 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
221483 GGCCAAAGAT
221493 GAAAAGGTATGTA
1 GAAAAGGTATGTA
221506 GAAAAGGTATGT-
1 GAAAAGGTATGTA
221518 GAAA
1 GAAA
221522 GGTGTTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (13 bp):
GAAAAGGTATGTA
Found at i:237570 original size:24 final size:21
Alignment explanation
Indices: 237535--237577 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
237525 GGCTCATTCT
*
237535 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
237558 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
237578 ATCTTGTGGA
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:241169 original size:19 final size:19
Alignment explanation
Indices: 241147--241211 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
241137 TTTTTTGAAT
241147 TTCTTTTTCT-TTTCTTTTC
1 TTCTTTTTCTATTT-TTTTC
241166 TTC-TTTTCTGATTTTTTTC
1 TTCTTTTTCT-ATTTTTTTC
* *
241185 TTCTTTTT-TGTCTTTTTC
1 TTCTTTTTCTATTTTTTTC
241203 TTTCTTTTT
1 -TTCTTTTT
241212 GCACTCCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 13 0.32
19 20 0.50
20 7 0.17
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (19 bp):
TTCTTTTTCTATTTTTTTC
Found at i:241211 original size:10 final size:10
Alignment explanation
Indices: 241146--241211 Score: 54
Period size: 10 Copynumber: 6.9 Consensus size: 10
241136 TTTTTTTGAA
241146 TTTCTTTTTC
1 TTTCTTTTTC
241156 TTT-TCTTTTC
1 TTTCT-TTTTC
241166 -TTC-TTTTC
1 TTTCTTTTTC
241174 TGATT-TTTTTC
1 T--TTCTTTTTC
241185 -TTCTTTTT-
1 TTTCTTTTTC
*
241193 TGTCTTTTTC
1 TTTCTTTTTC
241203 TTTCTTTTT
1 TTTCTTTTT
241212 GCACTCCAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 18
0.69 0.03 0.28
Matches are distributed among these distances:
8 7 0.16
9 15 0.33
10 16 0.36
11 7 0.16
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.79
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:241211 original size:18 final size:18
Alignment explanation
Indices: 241161--241212 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
241151 TTTTCTTTTC
*
241161 TTTTCTTCTTTTCTGATTT
1 TTTTCTTCTTTT-TGATCT
241180 TTTTCTTCTTTTTTG-TCT
1 TTTTCTTC-TTTTTGATCT
241198 TTTTCTTTCTTTTTG
1 TTTTC-TTCTTTTTG
241213 CACTCCAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 13 0.43
19 13 0.43
20 4 0.13
ACGTcount: A:0.02, C:0.15, G:0.06, T:0.77
Consensus pattern (18 bp):
TTTTCTTCTTTTTGATCT
Found at i:241886 original size:19 final size:20
Alignment explanation
Indices: 241839--241889 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
241829 GAAACCCCTT
**
241839 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
241859 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
241878 TGAAGATACATG
1 TGAAAATACATG
241890 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:245786 original size:24 final size:21
Alignment explanation
Indices: 245752--245794 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
245742 TGCACAAGAT
*
245752 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
245774 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
245795 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:252384 original size:35 final size:37
Alignment explanation
Indices: 252315--252394 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
252305 ATACTATTTC
*
252315 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
252352 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
252387 CATCACCA
1 CATCACCA
252395 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:256332 original size:35 final size:37
Alignment explanation
Indices: 256260--256334 Score: 109
Period size: 35 Copynumber: 2.1 Consensus size: 37
256250 ATACTATTTC
* *
256260 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTAACACGCCTATAT
*
256297 CATCACCATAGTCCATC-ACCA-TAACACGCCTATAT
1 CATCACCATAATCCATCTACCATTAACACGCCTATAT
256332 CAT
1 CAT
256335 AACAAAATTC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 16 0.46
36 3 0.09
37 16 0.46
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTAACACGCCTATAT
Found at i:257347 original size:35 final size:36
Alignment explanation
Indices: 257290--257357 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
257280 ATACAATCTG
257290 TCCATCACCATTATCACGCCTATAACATCACCATAT
1 TCCATCACCATTATCACGCCTATAACATCACCATAT
**
257326 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATAACATCACCA
257358 ACTTCTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 20 0.67
36 10 0.33
ACGTcount: A:0.32, C:0.37, G:0.03, T:0.28
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATAACATCACCATAT
Found at i:257517 original size:16 final size:16
Alignment explanation
Indices: 257496--257531 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
257486 TCTTCGAAAA
257496 CTTTTC-TATCCATTTC
1 CTTTTCTTAT-CATTTC
257512 CTTTTCTTATCATTTC
1 CTTTTCTTATCATTTC
257528 CTTT
1 CTTT
257532 CTTCTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.84
17 3 0.16
ACGTcount: A:0.11, C:0.28, G:0.00, T:0.61
Consensus pattern (16 bp):
CTTTTCTTATCATTTC
Found at i:257770 original size:18 final size:20
Alignment explanation
Indices: 257737--257778 Score: 70
Period size: 18 Copynumber: 2.2 Consensus size: 20
257727 ACAAAAAAGC
257737 AACAATAAAGAAGAAAAAAA
1 AACAATAAAGAAGAAAAAAA
257757 AACAA-AAA-AAGAAAAAAA
1 AACAATAAAGAAGAAAAAAA
257775 AACA
1 AACA
257779 CTCCTACATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 14 0.64
19 3 0.14
20 5 0.23
ACGTcount: A:0.83, C:0.07, G:0.07, T:0.02
Consensus pattern (20 bp):
AACAATAAAGAAGAAAAAAA
Found at i:257862 original size:24 final size:24
Alignment explanation
Indices: 257807--257855 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
257797 AGTGCAAAAG
* *
257807 AAAGAAAAGAAAAAGAAGAATCAA
1 AAAGCAAAGAAAAAGAAGAAGCAA
*
257831 AAAGCAAAGAAAAAG-TGAAGCAA
1 AAAGCAAAGAAAAAGAAGAAGCAA
257854 AA
1 AA
257856 TTGCAAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.71, C:0.06, G:0.18, T:0.04
Consensus pattern (24 bp):
AAAGCAAAGAAAAAGAAGAAGCAA
Done.