Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 92 of 226
Found at i:32090696 original size:9 final size:9
Alignment explanation
Indices: 32090667--32090751 Score: 52
Period size: 9 Copynumber: 9.4 Consensus size: 9
32090657 ACATGTGGTA
32090667 AAAAATTAT
1 AAAAATTAT
*
32090676 AATAA--AT
1 AAAAATTAT
*
32090683 AAAAATTGT
1 AAAAATTAT
32090692 AAAAATTAT
1 AAAAATTAT
*
32090701 -AAAATTTT
1 AAAAATTAT
*
32090709 AATAGTAAATAT
1 AA-A--AATTAT
32090721 -AAAATTAT
1 AAAAATTAT
*
32090729 AAAAAATCAT
1 -AAAAATTAT
*
32090739 AAAAATCAT
1 AAAAATTAT
32090748 AAAA
1 AAAA
32090752 TATATAGAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
7 6 0.10
8 12 0.20
9 27 0.46
10 9 0.15
11 1 0.02
12 4 0.07
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:32091035 original size:19 final size:19
Alignment explanation
Indices: 32091011--32091049 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
32091001 GTTAGACGGT
32091011 ATTTTTGATGCA-TTTTATA
1 ATTTTTGATG-ATTTTTATA
*
32091030 ATTTTTTATGATTTTTATA
1 ATTTTTGATGATTTTTATA
32091049 A
1 A
32091050 AATTTTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 17 0.94
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (19 bp):
ATTTTTGATGATTTTTATA
Found at i:32091036 original size:10 final size:10
Alignment explanation
Indices: 32091023--32091168 Score: 55
Period size: 10 Copynumber: 15.4 Consensus size: 10
32091013 TTTTGATGCA
32091023 TTTTATAATT
1 TTTTATAATT
*
32091033 TTTTATGA-T
1 TTTTATAATT
**
32091042 TTTTATAAAA
1 TTTTATAATT
*
32091052 TTTTACAATT
1 TTTTATAATT
*
32091062 TTTTA-CA--
1 TTTTATAATT
*
32091069 TTTTA-AAGAT
1 TTTTATAA-TT
32091079 TTTTATAATAT
1 TTTTATAAT-T
*
32091090 TTTTCTAATT
1 TTTTATAATT
*
32091100 TTTAAT-ATT
1 TTTTATAATT
**
32091109 TTTTATTAAAA
1 TTTTA-TAATT
*
32091120 TTTAATAATT
1 TTTTATAATT
*
32091130 TTTT-TAA-A
1 TTTTATAATT
32091138 TTTTAT--TT
1 TTTTATAATT
32091146 ATTTT-T-ATT
1 -TTTTATAATT
*
32091155 TCTTATAATT
1 TTTTATAATT
32091165 TTTT
1 TTTT
32091169 TGCTACATGT
Statistics
Matches: 99, Mismatches: 23, Indels: 28
0.66 0.15 0.19
Matches are distributed among these distances:
7 6 0.06
8 8 0.08
9 27 0.27
10 42 0.42
11 16 0.16
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:32091149 original size:19 final size:20
Alignment explanation
Indices: 32091100--32091154 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
32091090 TTTTCTAATT
*
32091100 TTTAATATTTTTTATTAAAA
1 TTTAATAATTTTTATTAAAA
*
32091120 TTTAATAATTTTT-TTAAAT
1 TTTAATAATTTTTATTAAAA
* *
32091139 TTTATTTATTTTTATT
1 TTTAATAATTTTTATT
32091155 TCTTATAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTAATAATTTTTATTAAAA
Found at i:32094050 original size:18 final size:19
Alignment explanation
Indices: 32094015--32094050 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
32094005 GAACTGATAT
*
32094015 ATAAAATTTTATAATATAG
1 ATAAAATTTGATAATATAG
32094034 ATAAAATTTGA-AATATA
1 ATAAAATTTGATAATATA
32094051 CAATTCACGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (19 bp):
ATAAAATTTGATAATATAG
Found at i:32102989 original size:58 final size:58
Alignment explanation
Indices: 32102894--32103008 Score: 194
Period size: 58 Copynumber: 2.0 Consensus size: 58
32102884 CTTGGCTCCA
* * * *
32102894 ATAGATCCCTTGTTCCTTTCTGAAAGGTTAGCCTTGACAAGTGAAATGGTAAGGCAGG
1 ATAGATCCCTTGTTCCTTTCCGAAAGGTTAGCATTGACAAATGAAATGGCAAGGCAGG
32102952 ATAGATCCCTTGTTCCTTTCCGAAAGGTTAGCATTGACAAATGAAATGGCAAGGCAG
1 ATAGATCCCTTGTTCCTTTCCGAAAGGTTAGCATTGACAAATGAAATGGCAAGGCAG
32103009 AAATTGTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (58 bp):
ATAGATCCCTTGTTCCTTTCCGAAAGGTTAGCATTGACAAATGAAATGGCAAGGCAGG
Found at i:32108017 original size:29 final size:29
Alignment explanation
Indices: 32107983--32108043 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
32107973 TTTTTAAAGA
32107983 AATAATGACTAATTTTCAATCAATTTTTC
1 AATAATGACTAATTTTCAATCAATTTTTC
32108012 AATAATGACTAATTTTCAATCAATTTTTC
1 AATAATGACTAATTTTCAATCAATTTTTC
32108041 AAT
1 AAT
32108044 TTTTCAAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.44
Consensus pattern (29 bp):
AATAATGACTAATTTTCAATCAATTTTTC
Found at i:32108029 original size:17 final size:17
Alignment explanation
Indices: 32107983--32108031 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
32107973 TTTTTAAAGA
32107983 AATAATGACTAATTTTC
1 AATAATGACTAATTTTC
*
32108000 AATCA--A-T--TTTTC
1 AATAATGACTAATTTTC
32108012 AATAATGACTAATTTTC
1 AATAATGACTAATTTTC
32108029 AAT
1 AAT
32108032 CAATTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
12 9 0.36
14 2 0.08
15 2 0.08
17 12 0.48
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (17 bp):
AATAATGACTAATTTTC
Found at i:32112053 original size:31 final size:32
Alignment explanation
Indices: 32111975--32112053 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 32
32111965 ATAATGACGT
*
32111975 CGAAGACTTAATTGATTTTTTTAATTATTTTA
1 CGAAAACTTAATTGATTTTTTTAATTATTTTA
*** * *
32112007 CGAGGGCTTATTTGATTTTTTT-ATTATTTTG
1 CGAAAACTTAATTGATTTTTTTAATTATTTTA
*
32112038 TGAAAACTTAATTGAT
1 CGAAAACTTAATTGAT
32112054 CATTTGATCA
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
31 19 0.50
32 19 0.50
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.52
Consensus pattern (32 bp):
CGAAAACTTAATTGATTTTTTTAATTATTTTA
Found at i:32113695 original size:2 final size:2
Alignment explanation
Indices: 32113688--32113723 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
32113678 TCTAAAATTA
32113688 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32113724 TGGCATATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32115091 original size:10 final size:10
Alignment explanation
Indices: 32115076--32115104 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
32115066 ATTGTGTGTT
32115076 TGAATAGAAA
1 TGAATAGAAA
32115086 TGAATAG-AA
1 TGAATAGAAA
32115095 TGAATAGAAA
1 TGAATAGAAA
32115105 AAGAGAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (10 bp):
TGAATAGAAA
Found at i:32116560 original size:21 final size:21
Alignment explanation
Indices: 32116521--32116560 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
32116511 TTTATTTAAA
*
32116521 AATATAAATGATATAGAATAT
1 AATATAAATGAAATAGAATAT
*
32116542 AATATAAATGAAATGGAAT
1 AATATAAATGAAATAGAAT
32116561 TACTGATAAA
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:0.57, C:0.00, G:0.12, T:0.30
Consensus pattern (21 bp):
AATATAAATGAAATAGAATAT
Found at i:32116601 original size:21 final size:21
Alignment explanation
Indices: 32116568--32116608 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
32116558 AATTACTGAT
* *
32116568 AAAAGTTCTATATCTCTATAG
1 AAAAGTTCGATATATCTATAG
*
32116589 AAAAGTTGGATATATCTATA
1 AAAAGTTCGATATATCTATA
32116609 TAATCAATCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (21 bp):
AAAAGTTCGATATATCTATAG
Found at i:32118929 original size:8 final size:8
Alignment explanation
Indices: 32118911--32118976 Score: 82
Period size: 8 Copynumber: 8.4 Consensus size: 8
32118901 CTATACACAG
32118911 ATACAGA-
1 ATACAGAT
32118918 ATACAGAT
1 ATACAGAT
32118926 ATACCA-AT
1 ATA-CAGAT
*
32118934 ATGCAGAT
1 ATACAGAT
*
32118942 GTACAGAT
1 ATACAGAT
32118950 ATACAGAT
1 ATACAGAT
*
32118958 ATACAAAT
1 ATACAGAT
32118966 ATACAGAT
1 ATACAGAT
32118974 ATA
1 ATA
32118977 ATACATGCTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
7 9 0.18
8 39 0.78
9 2 0.04
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (8 bp):
ATACAGAT
Found at i:32123001 original size:15 final size:15
Alignment explanation
Indices: 32122981--32123034 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
32122971 ATACTACAAA
32122981 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
32122996 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
32123013 AGATATTTATTATTAAA
1 --ATATTTATTATTAAT
32123030 ATATT
1 ATATT
32123035 AAATTTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:32124166 original size:16 final size:16
Alignment explanation
Indices: 32124138--32124181 Score: 63
Period size: 16 Copynumber: 2.7 Consensus size: 16
32124128 TTCCTCTTCA
32124138 TCCTCTATTTC-TTTTC
1 TCCTCT-TTTCTTTTTC
32124154 TTCCTCTTTTCTTTTTC
1 -TCCTCTTTTCTTTTTC
32124171 TCCTCTTTTCT
1 TCCTCTTTTCT
32124182 CTCATAATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.58
17 11 0.42
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (16 bp):
TCCTCTTTTCTTTTTC
Found at i:32125046 original size:38 final size:38
Alignment explanation
Indices: 32125004--32125079 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
32124994 CACCCTACCA
* * *
32125004 AGTACATGTTAAGTATGTCTATTGCTAATAATGAATTG
1 AGTACATATTAAGCATGTCTACTGCTAATAATGAATTG
* *
32125042 AGTACATATTAAGCATGTCTACTGCTAGTATTGAATTG
1 AGTACATATTAAGCATGTCTACTGCTAATAATGAATTG
32125080 TTCTATTACA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (38 bp):
AGTACATATTAAGCATGTCTACTGCTAATAATGAATTG
Found at i:32125204 original size:43 final size:43
Alignment explanation
Indices: 32125140--32125414 Score: 267
Period size: 43 Copynumber: 6.5 Consensus size: 43
32125130 ATGGAGGAAG
* *
32125140 AGTGGCAG--TTTATCTGTAAATATGTTGTGCATCCACAGCCC
1 AGTGGCAGTTTTTATCTGCAAATATGTTGTGCATCCACAACCC
* * *
32125181 AGTGGCAGTTTTTATCTACAAATATGTTGTGCACCCACAGCCC
1 AGTGGCAGTTTTTATCTGCAAATATGTTGTGCATCCACAACCC
* *** * * * *
32125224 AATGATTGTTTTTATCTTCAAATATGTTATGTATCCACAAACC
1 AGTGGCAGTTTTTATCTGCAAATATGTTGTGCATCCACAACCC
* * * * *
32125267 AGCGGCAATTTTTATCTACAAATATGTTATGCATCCACAACCT
1 AGTGGCAGTTTTTATCTGCAAATATGTTGTGCATCCACAACCC
* *
32125310 AATGGCAG--TTTATCTGCAAATATGTTGTGCATCCACAACCT
1 AGTGGCAGTTTTTATCTGCAAATATGTTGTGCATCCACAACCC
* * *
32125351 AGTGGTCA---TTTATCTGTAAATATGTTGTGCATCCATAGCCC
1 AGTGG-CAGTTTTTATCTGCAAATATGTTGTGCATCCACAACCC
* *
32125392 AGTAGTAGTTTTTATCTGCAAAT
1 AGTGGCAGTTTTTATCTGCAAAT
32125415 TAGTGGTGGT
Statistics
Matches: 192, Mismatches: 36, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
40 1 0.01
41 76 0.40
42 2 0.01
43 113 0.59
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.35
Consensus pattern (43 bp):
AGTGGCAGTTTTTATCTGCAAATATGTTGTGCATCCACAACCC
Found at i:32131596 original size:19 final size:20
Alignment explanation
Indices: 32131558--32131597 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
32131548 CATCTATTTC
* *
32131558 TTTTCTTCTTCTTCTTCTTT
1 TTTTCTTCTTCCTCTCCTTT
32131578 TTTTCTT-TTCCTCTCCTTT
1 TTTTCTTCTTCCTCTCCTTT
32131597 T
1 T
32131598 CTCTCATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTCTTCTTCCTCTCCTTT
Found at i:32132881 original size:18 final size:19
Alignment explanation
Indices: 32132855--32132891 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
32132845 TTATTAAATT
32132855 AATTGATTT-TAAATCATTA
1 AATTGATTTATAAAT-ATTA
32132874 AATT-ATTTATAAATATTA
1 AATTGATTTATAAATATTA
32132892 TAAATAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (19 bp):
AATTGATTTATAAATATTA
Found at i:32133448 original size:11 final size:11
Alignment explanation
Indices: 32133427--32133485 Score: 66
Period size: 11 Copynumber: 5.3 Consensus size: 11
32133417 ACTAATCCTA
32133427 TCTCAAATTTCC
1 TCTC-AATTTCC
*
32133439 TCTCAATTTCT
1 TCTCAATTTCC
32133450 TC-CAAATTTCC
1 TCTC-AATTTCC
*
32133461 TCTCAATTTGC
1 TCTCAATTTCC
*
32133472 TCTCAAATTCC
1 TCTCAATTTCC
32133483 TCT
1 TCT
32133486 TAAATTTCTC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
10 1 0.03
11 34 0.85
12 5 0.12
ACGTcount: A:0.22, C:0.32, G:0.02, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:32133490 original size:11 final size:11
Alignment explanation
Indices: 32133427--32133501 Score: 62
Period size: 11 Copynumber: 6.7 Consensus size: 11
32133417 ACTAATCCTA
32133427 TCTCAAATTTCC
1 TCTCAAA-TTCC
* *
32133439 TCTCAATTTCT
1 TCTCAAATTCC
32133450 TC-CAAATTTCC
1 TCTCAAA-TTCC
* *
32133461 TCTCAATTTGC
1 TCTCAAATTCC
32133472 TCTCAAATTCC
1 TCTCAAATTCC
* *
32133483 TCTTAAATTTC
1 TCTCAAATTCC
*
32133494 TCTTAAAT
1 TCTCAAAT
32133502 CCCTATTTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
10 3 0.06
11 39 0.76
12 9 0.18
ACGTcount: A:0.25, C:0.28, G:0.01, T:0.45
Consensus pattern (11 bp):
TCTCAAATTCC
Found at i:32133491 original size:34 final size:34
Alignment explanation
Indices: 32133427--32133501 Score: 82
Period size: 33 Copynumber: 2.2 Consensus size: 34
32133417 ACTAATCCTA
* *
32133427 TCTCAAATTTCCTCTCAATTTCTTCCAAATTTCC
1 TCTCAAATTTCCTCTCAAATTCCTCCAAATTTCC
* *
32133461 TCTC-AATTTGCTCTCAAATTCCTCTTAAATTT-C
1 TCTCAAATTTCCTCTCAAATTCCTC-CAAATTTCC
*
32133494 TCTTAAAT
1 TCTCAAAT
32133502 CCCTATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
33 21 0.62
34 13 0.38
ACGTcount: A:0.25, C:0.28, G:0.01, T:0.45
Consensus pattern (34 bp):
TCTCAAATTTCCTCTCAAATTCCTCCAAATTTCC
Found at i:32133496 original size:22 final size:22
Alignment explanation
Indices: 32133427--32133501 Score: 91
Period size: 22 Copynumber: 3.4 Consensus size: 22
32133417 ACTAATCCTA
32133427 TCTCAAATTTCCTCTCAATTTC
1 TCTCAAATTTCCTCTCAATTTC
32133449 T-TCCAAATTTCCTCTCAATTTGC
1 TCT-CAAATTTCCTCTCAATTT-C
*
32133472 TCTCAAA-TTCCTCTTAAATTTC
1 TCTCAAATTTCCTC-TCAATTTC
*
32133494 TCTTAAAT
1 TCTCAAAT
32133502 CCCTATTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
21 1 0.02
22 32 0.70
23 12 0.26
24 1 0.02
ACGTcount: A:0.25, C:0.28, G:0.01, T:0.45
Consensus pattern (22 bp):
TCTCAAATTTCCTCTCAATTTC
Found at i:32134662 original size:7 final size:7
Alignment explanation
Indices: 32134650--32134675 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
32134640 TAGTCGATTG
32134650 GTATTTA
1 GTATTTA
32134657 GTATTTA
1 GTATTTA
32134664 GTATTTA
1 GTATTTA
32134671 GTATT
1 GTATT
32134676 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:32135689 original size:16 final size:16
Alignment explanation
Indices: 32135668--32135700 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
32135658 CAGCGCGTGT
32135668 GGCACTGAATCCCGCG
1 GGCACTGAATCCCGCG
32135684 GGCACTGAATCCCGCG
1 GGCACTGAATCCCGCG
32135700 G
1 G
32135701 ACACAGACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.36, G:0.33, T:0.12
Consensus pattern (16 bp):
GGCACTGAATCCCGCG
Found at i:32135921 original size:27 final size:27
Alignment explanation
Indices: 32135886--32135983 Score: 100
Period size: 27 Copynumber: 3.8 Consensus size: 27
32135876 ACAAACCTTA
*
32135886 AACCTTTAACCTAAAAACCCTAACCCT
1 AACCCTTAACCTAAAAACCCTAACCCT
* * *
32135913 AACCCTTAA-ATTAAAA--CT---CAT
1 AACCCTTAACCTAAAAACCCTAACCCT
32135934 AAACCCTTAACCTAAAAACCCTAACCCT
1 -AACCCTTAACCTAAAAACCCTAACCCT
*
32135962 AACCCTTAACTTAAAAACCCTA
1 AACCCTTAACCTAAAAACCCTA
32135984 GCCCCTTAAC
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
21 2 0.04
22 9 0.16
23 5 0.09
24 2 0.04
25 2 0.04
26 5 0.09
27 29 0.52
28 2 0.04
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (27 bp):
AACCCTTAACCTAAAAACCCTAACCCT
Found at i:32135922 original size:22 final size:22
Alignment explanation
Indices: 32135897--32135970 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 22
32135887 ACCTTTAACC
32135897 TAAAAACCCTAACCCTAACCCT
1 TAAAAACCCTAACCCTAACCCT
*
32135919 TAAATTAAAACTCATAAACCCTTAA-CC-
1 T--A--AAAAC-CCT-AACCC-TAACCCT
32135946 TAAAAACCCTAACCCTAACCCT
1 TAAAAACCCTAACCCTAACCCT
32135968 TAA
1 TAA
32135971 CTTAAAAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 18
0.67 0.03 0.30
Matches are distributed among these distances:
20 3 0.07
21 7 0.17
22 6 0.15
23 5 0.12
24 1 0.02
25 1 0.02
26 5 0.12
27 3 0.07
28 7 0.17
29 3 0.07
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.22
Consensus pattern (22 bp):
TAAAAACCCTAACCCTAACCCT
Found at i:32135954 original size:15 final size:15
Alignment explanation
Indices: 32135934--32135982 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
32135924 TAAAACTCAT
32135934 AAACCCTTAACCTAA
1 AAACCCTTAACCTAA
32135949 AAACCC-TAACCCT--
1 AAACCCTTAA-CCTAA
*
32135962 -AACCCTTAACTTAA
1 AAACCCTTAACCTAA
32135976 AAACCCT
1 AAACCCT
32135983 AGCCCCTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
12 7 0.25
13 3 0.11
14 3 0.11
15 15 0.54
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (15 bp):
AAACCCTTAACCTAA
Found at i:32135959 original size:43 final size:42
Alignment explanation
Indices: 32135907--32136842 Score: 894
Period size: 43 Copynumber: 21.9 Consensus size: 42
32135897 TAAAAACCCT
* * *
32135907 AACCCTAACCCTTAAATTAAAACTCATAAACCCTTAACCTAAAAA
1 AACCCTAACCCTTAACTTAAAAC-CCTAAACCCTTAA-CT-TAAA
** *
32135952 CCCTAACCCTAACCCTTAACTTAAAAACCCTAGCCCCTTAACCT-AA
1 ----AACCCTAACCCTTAACTT-AAAACCCTAAACCCTTAACTTAAA
* * *
32135998 AA-TCTAACCCTTAACTTTAAAA---T----GCTTAACTTTAA
1 AACCCTAACCCTTAAC-TTAAAACCCTAAACCCTTAACTTAAA
* * *
32136033 AACCCTAAACCCTTAACTTAAAAACCATAAACCCTTAGCCTAAA
1 AACCCT-AACCCTTAACTT-AAAACCCTAAACCCTTAACTTAAA
* *
32136077 AACCTTAA-CC----C-T--AACCCT-AACCCTTAACTTTAA
1 AACCCTAACCCTTAACTTAAAACCCTAAACCCTTAACTTAAA
*
32136110 AACCGTAAACCCTTAACTTAAAACCCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAAA-CCCTAAACCCTTAACTTAAA
*
32136154 AACACTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTT-AAAACCCTAAACCCTTAACTTAAA
* *
32136198 AACCCTAGCCCTTAACCTAAAACCCTAAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAAACCCTAAACCCTTAACTTAAA
* * * * *
32136240 AACCATAAGCACTTAACCTAAAAAGCCT-AACCCTTAACTTTAA
1 AACCCTAA-CCCTTAA-CTTAAAACCCTAAACCCTTAACTTAAA
* *
32136283 AACCATAAACCCTTAACTTTAAAACCATAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAAC-TTAAAACCCTAAACCCTTAACTTAAA
*
32136327 ACCCCATAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
1 AACCC-T-AACCCTTAACTT-AAAACCCTAAACCCTTAACTTAAA
* * * *
32136372 AACCCTAGCCCCTTAACCTAAAAACCCT-AACCCTTACCTTTAA
1 AACCCTA-ACCCTTAA-CTTAAAACCCTAAACCCTTAACTTAAA
* *
32136415 AACCCTAAACCCTTAACTTAAAAACCCT-AACTCTTAACTTTAA
1 AACCCT-AACCCTTAACTT-AAAACCCTAAACCCTTAACTTAAA
* * *
32136458 AACCCTAAACCTTTAAATTAAAAACCCAAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTT-AAAACCCTAAACCCTTAACTTAAA
32136502 AACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTT-AAAACCCTAAACCCTTAACTTAAA
*
32136546 AATCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTT-AAAACCCTAAACCCTTAACTTAAA
** *
32136589 AACCCTAACCCTTAACTTTAAAACCC-AGCCCCTTAACCTAAA
1 AACCCTAACCCTTAAC-TTAAAACCCTAAACCCTTAACTTAAA
*
32136631 AACCCTAATCCTTAACTTTAAAACCCTAAACCCTTAACTT-AA
1 AACCCTAACCCTTAAC-TTAAAACCCTAAACCCTTAACTTAAA
* *
32136673 AACCCATAAACCCTTAACTTAAAAACCCT-AACCATTAACTTTAA
1 AACCC-T-AACCCTTAACTT-AAAACCCTAAACCCTTAACTTAAA
*
32136717 AACCCTAAACTCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTT-AAAACCCTAAACCCTTAACTTAAA
**
32136761 AACATTAACCCCTTAACTTTAAAACCCTAAACCCTTAACTTAAA
1 AACCCTAA-CCCTTAAC-TTAAAACCCTAAACCCTTAACTTAAA
* * **
32136805 AACCCTCACACTTAACTTAAAAACCCTAGCCCCTTAAC
1 AACCCTAACCCTTAACTT-AAAACCCTAAACCCTTAAC
32136843 CGGTGTGGTA
Statistics
Matches: 759, Mismatches: 81, Indels: 100
0.81 0.09 0.11
Matches are distributed among these distances:
33 17 0.02
34 14 0.02
35 6 0.01
36 4 0.01
37 15 0.02
38 2 0.00
39 1 0.00
40 2 0.00
41 16 0.02
42 88 0.12
43 259 0.34
44 253 0.33
45 47 0.06
46 2 0.00
48 1 0.00
49 27 0.04
50 5 0.01
ACGTcount: A:0.43, C:0.32, G:0.01, T:0.24
Consensus pattern (42 bp):
AACCCTAACCCTTAACTTAAAACCCTAAACCCTTAACTTAAA
Found at i:32135992 original size:22 final size:21
Alignment explanation
Indices: 32135956--32136092 Score: 76
Period size: 22 Copynumber: 6.8 Consensus size: 21
32135946 TAAAAACCCT
*
32135956 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACCTAAA
*
32135977 AACCCTAGCCCCTTAACCT-AA
1 AACCCTA-ACCCTTAACCTAAA
* * *
32135998 AA-TCTAACCCTTAACTTTAA
1 AACCCTAACCCTTAACCTAAA
* * *
32136018 AA---T---GCTTAACTTTAA
1 AACCCTAACCCTTAACCTAAA
*
32136033 AACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACCTAAA
* *
32136055 AACCATAAACCCTTAGCCTAAA
1 AACCCT-AACCCTTAACCTAAA
*
32136077 AACCTTAACCC-TAACC
1 AACCCTAACCCTTAACC
32136093 CTAACCCTTA
Statistics
Matches: 94, Mismatches: 13, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
15 13 0.14
18 2 0.02
19 9 0.10
20 11 0.12
21 16 0.17
22 43 0.46
ACGTcount: A:0.41, C:0.32, G:0.02, T:0.25
Consensus pattern (21 bp):
AACCCTAACCCTTAACCTAAA
Found at i:32136123 original size:22 final size:22
Alignment explanation
Indices: 32136089--32136842 Score: 1003
Period size: 22 Copynumber: 34.8 Consensus size: 22
32136079 CCTTAACCCT
*
32136089 AACCCT-AACCCTTAACTTTAA
1 AACCCTAAACCCTTAACTTAAA
*
32136110 AACCGTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
32136132 ACCCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
32136154 AACACTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
32136176 AACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
32136198 AACCCT-AGCCCTTAACCT-AA
1 AACCCTAAACCCTTAACTTAAA
32136218 AACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* * * *
32136240 AACCATAAGCACTTAACCTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
32136262 AAGCCT-AACCCTTAACTTTAA
1 AACCCTAAACCCTTAACTTAAA
* *
32136283 AACCATAAACCCTTAACTTTAA
1 AACCCTAAACCCTTAACTTAAA
*
32136305 AACCATAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
32136327 ACCCCATAAACCCTTAACTTAAA
1 AACCC-TAAACCCTTAACTTAAA
32136350 AACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
** *
32136372 AACCCTAGCCCCTTAACCTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
32136394 AACCCT-AACCCTTACCTTTAA
1 AACCCTAAACCCTTAACTTAAA
32136415 AACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
32136437 AACCCT-AACTCTTAACTTTAA
1 AACCCTAAACCCTTAACTTAAA
* *
32136458 AACCCTAAACCTTTAAATTAAA
1 AACCCTAAACCCTTAACTTAAA
*
32136480 AACCCAAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
32136502 AACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
32136524 AACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
32136546 AATCCT-AACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
32136567 AACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
32136589 AACCCT-AACCCTTAACTTTAA
1 AACCCTAAACCCTTAACTTAAA
** *
32136610 AACCC-AGCCCCTTAACCTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
32136631 AACCCT-AATCCTTAACTTTAA
1 AACCCTAAACCCTTAACTTAAA
32136652 AACCCTAAACCCTTAACTT-AA
1 AACCCTAAACCCTTAACTTAAA
32136673 AACCCATAAACCCTTAACTTAAA
1 AACCC-TAAACCCTTAACTTAAA
* *
32136696 AACCCT-AACCATTAACTTTAA
1 AACCCTAAACCCTTAACTTAAA
*
32136717 AACCCTAAACTCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
32136739 AACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
** * *
32136761 AACATTAACCCCTTAACTTTAA
1 AACCCTAAACCCTTAACTTAAA
32136783 AACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
32136805 AACCCT-CACACTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
**
32136826 AACCCTAGCCCCTTAAC
1 AACCCTAAACCCTTAAC
32136843 CGGTGTGGTA
Statistics
Matches: 639, Mismatches: 79, Indels: 29
0.86 0.11 0.04
Matches are distributed among these distances:
20 8 0.01
21 191 0.30
22 412 0.64
23 28 0.04
ACGTcount: A:0.43, C:0.32, G:0.01, T:0.24
Consensus pattern (22 bp):
AACCCTAAACCCTTAACTTAAA
Found at i:32136307 original size:65 final size:66
Alignment explanation
Indices: 32136095--32136842 Score: 905
Period size: 65 Copynumber: 11.5 Consensus size: 66
32136085 CCCTAACCCT
* * * *
32136095 AACCCTTAACTTTAAAACCGTAAACCCTTAACTTAAAACCCCTAAACCCTTAAC-TTAAAAACAC
1 AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTTAAAACCA-
32136159 TA
65 TA
* * *
32136161 AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCT-AGCCCTTAAC-CTAAAACCCT
1 AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTTAAAACCAT
32136224 A
66 A
* * * * *
32136225 AACCCTTAACTTAAAAACCATAAGCACTTAACCTAAAAAGCCT-AACCCTTAACTTTAAAACCAT
1 AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTTAAAACCAT
32136289 A
66 A
* * * * *
32136290 AACCCTTAACTTTAAAACCATAAACCCTTAACTTAAAACCCCATAAACCCTTAACTTAAAAACCC
1 AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCC-TAAACCCTTAACTTTAAAACCA
32136355 TA
65 TA
** * * *
32136357 AACCCTTAACTTAAAAACCCTAGCCCCTTAACCTAAAAACCCT-AACCCTTACCTTTAAAACCCT
1 AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTTAAAACCAT
32136421 A
66 A
* * * * *
32136422 AACCCTTAACTTAAAAACCCT-AACTCTTAACTTTAAAACCCTAAACCTTTAAATTAAAAACCCA
1 AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTTAAAA-CCA
32136486 -A
65 TA
*
32136487 AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAATCC-
1 AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTTAAAA-CCA
32136551 T-
65 TA
*
32136552 AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTTAAAACC-C
1 AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTTAAAACCAT
32136615 A
66 A
** * * *
32136616 GCCCCTTAACCTAAAAACCCT-AATCCTTAACTTTAAAACCCTAAACCCTTAAC-TTAAAACCCA
1 AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTTAAAA-CCA
32136679 TA
65 TA
* * * * *
32136681 AACCCTTAACTTAAAAACCCT-AACCATTAACTTTAAAACCCTAAACTCTTAACTTAAAAACCCT
1 AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTTAAAACCAT
32136745 A
66 A
** * * * *
32136746 AACCCTTAACTTAAAAACATTAACCCCTTAACTTTAAAACCCTAAACCCTTAACTTAAAAACCCT
1 AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTTAAAACCAT
32136811 -
66 A
* * **
32136811 CACACTTAACTTAAAAACCCTAGCCCCTTAAC
1 AACCCTTAACTTAAAAACCCTAAACCCTTAAC
32136843 CGGTGTGGTA
Statistics
Matches: 597, Mismatches: 72, Indels: 27
0.86 0.10 0.04
Matches are distributed among these distances:
63 27 0.05
64 111 0.19
65 277 0.46
66 126 0.21
67 56 0.09
ACGTcount: A:0.43, C:0.32, G:0.01, T:0.24
Consensus pattern (66 bp):
AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTTAAAACCAT
A
Found at i:32138876 original size:3 final size:3
Alignment explanation
Indices: 32138868--32138919 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
32138858 TTTTTAATCC
32138868 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
32138916 TAT T
1 TAT T
32138920 TCTCCTTTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:32141894 original size:17 final size:17
Alignment explanation
Indices: 32141872--32141904 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
32141862 ATTCAATTTG
32141872 AAATTAAATAATTAACT
1 AAATTAAATAATTAACT
*
32141889 AAATTAATTAATTAAC
1 AAATTAAATAATTAAC
32141905 CGAAATAAAT
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:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTAAATAATTAACT
Found at i:32143114 original size:63 final size:61
Alignment explanation
Indices: 32143002--32143125 Score: 214
Period size: 63 Copynumber: 2.0 Consensus size: 61
32142992 AAAAGGTGGA
32143002 GAGGCGGAAAGGAGCAAGAGGACAAGTTGATTAAGAGATATAGAAAGAGAGAGCACAAGTTTG
1 GAGGCGGAAAGGAGCAAGAGGACAAGTTGATT-AGAGATATAG-AAGAGAGAGCACAAGTTTG
32143065 GAGGCGGAAAGGAGCAAGAGGACAAGTTGATT-GAGATATAGCAAGAGAGAGCACAAGTTTG
1 GAGGCGGAAAGGAGCAAGAGGACAAGTTGATTAGAGATATAG-AAGAGAGAGCACAAGTTTG
32143126 CTTAGAGTAA
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
61 28 0.47
63 32 0.53
ACGTcount: A:0.41, C:0.09, G:0.35, T:0.15
Consensus pattern (61 bp):
GAGGCGGAAAGGAGCAAGAGGACAAGTTGATTAGAGATATAGAAGAGAGAGCACAAGTTTG
Found at i:32143392 original size:29 final size:29
Alignment explanation
Indices: 32143350--32143408 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
32143340 TTGTATTGAG
32143350 AATGTGTTCACACTTAAAAACAGGTGTTC
1 AATGTGTTCACACTTAAAAACAGGTGTTC
32143379 AATGTGTTCACACTTAAAAACAGGTGTTC
1 AATGTGTTCACACTTAAAAACAGGTGTTC
32143408 A
1 A
32143409 TCTCATTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (29 bp):
AATGTGTTCACACTTAAAAACAGGTGTTC
Found at i:32145998 original size:19 final size:17
Alignment explanation
Indices: 32145974--32146017 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
32145964 TCTTATACAT
*
32145974 TATAAAAAAAATCATATAA
1 TATAAAAAAAAT-ACA-AA
*
32145993 TATAAAAACAATACAAA
1 TATAAAAAAAATACAAA
32146010 TATAAAAA
1 TATAAAAA
32146018 TGATATAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 10 0.43
18 2 0.09
19 11 0.48
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (17 bp):
TATAAAAAAAATACAAA
Found at i:32146469 original size:24 final size:24
Alignment explanation
Indices: 32146419--32146471 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
32146409 AACAAGTATT
* *
32146419 TTTAAAAGGAACTGTATGTCAATA
1 TTTAAAAGAAACTGTATGTCAACA
* *
32146443 TTTAAGAGAAACTGTATGTCAGCA
1 TTTAAAAGAAACTGTATGTCAACA
32146467 TTTAA
1 TTTAA
32146472 CAGATTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (24 bp):
TTTAAAAGAAACTGTATGTCAACA
Found at i:32147571 original size:31 final size:32
Alignment explanation
Indices: 32147517--32147581 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
32147507 TCACACATGA
32147517 AATATTTTAAAATTGTAACTATAATAATAAAT
1 AATATTTTAAAATTGTAACTATAATAATAAAT
* * *
32147549 AATA-TTTAAATATTTTAA-TATAATGATAGAT
1 AATATTTTAAA-ATTGTAACTATAATAATAAAT
32147580 AA
1 AA
32147582 AATATAGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 19 0.66
32 10 0.34
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (32 bp):
AATATTTTAAAATTGTAACTATAATAATAAAT
Found at i:32149736 original size:30 final size:30
Alignment explanation
Indices: 32149683--32149741 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
32149673 CAAAATAGAT
* *
32149683 AAATATAAATAAATATTTATATATATAATG
1 AAATATAAATAAACAATTATATATATAATG
*
32149713 AAATATAAATAGAACAATT-TATATTTAAT
1 AAATATAAATA-AACAATTATATATATAAT
32149742 TTTCAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (30 bp):
AAATATAAATAAACAATTATATATATAATG
Found at i:32151647 original size:30 final size:30
Alignment explanation
Indices: 32151613--32151678 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
32151603 CTTACAATGA
*
32151613 CGTTCAGGAATTTGAGAAGACCCAATATCT
1 CGTTCAGGAACTTGAGAAGACCCAATATCT
* * *
32151643 CGTTCAGGAGCTTGAGAAGACTCGATATCT
1 CGTTCAGGAACTTGAGAAGACCCAATATCT
*
32151673 CATTCA
1 CGTTCA
32151679 AGGTCTTGGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (30 bp):
CGTTCAGGAACTTGAGAAGACCCAATATCT
Found at i:32153606 original size:22 final size:25
Alignment explanation
Indices: 32153555--32153607 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
32153545 TATTTAATAC
32153555 ATATA-TATGCATGTTTTTTTATCTA
1 ATATACTATGCATGTTTTTTTA-CTA
*
32153580 GTATACTA-GCATG-TTTTTTA-TA
1 ATATACTATGCATGTTTTTTTACTA
32153602 ATATAC
1 ATATAC
32153608 ATATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 7 0.28
24 7 0.28
25 9 0.36
26 2 0.08
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.51
Consensus pattern (25 bp):
ATATACTATGCATGTTTTTTTACTA
Found at i:32154566 original size:89 final size:89
Alignment explanation
Indices: 32154387--32154565 Score: 324
Period size: 88 Copynumber: 2.0 Consensus size: 89
32154377 TTATTTTTTT
32154387 AAGGTGGGCCGATAACACCTTAATAAAAGAATCGGTGGCGACTCCAGTTTTGTTTTTTAAAGTCG
1 AAGGTGGGCCGATAACACCTTAATAAAAGAATCGGTGGCGACTCCAGTTTTGTTTTTTAAAGTCG
*
32154452 ATAACTAAATTTTTGGTTTCAAAA
66 ACAACTAAATTTTTGGTTTCAAAA
* *
32154476 AAGGTGGGCCGATAACACCTTAAT-AAAGGATCGGTGGCGACTCCAGTTTTGTTTTTTAAAGTTG
1 AAGGTGGGCCGATAACACCTTAATAAAAGAATCGGTGGCGACTCCAGTTTTGTTTTTTAAAGTCG
32154540 ACAACTAAATTTTTGGTTTCAAAA
66 ACAACTAAATTTTTGGTTTCAAAA
32154564 AA
1 AA
32154566 ACGGTTCCGA
Statistics
Matches: 87, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
88 63 0.72
89 24 0.28
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (89 bp):
AAGGTGGGCCGATAACACCTTAATAAAAGAATCGGTGGCGACTCCAGTTTTGTTTTTTAAAGTCG
ACAACTAAATTTTTGGTTTCAAAA
Found at i:32155568 original size:13 final size:13
Alignment explanation
Indices: 32155550--32155575 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32155540 AAAGAGATTT
32155550 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
32155563 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
32155576 AAAATTGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GTTTTCTAGTAAA
Found at i:32155646 original size:19 final size:19
Alignment explanation
Indices: 32155606--32155647 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
32155596 GTCTCTTTTC
* *
32155606 GCATTCATTTCATGCATTT
1 GCATTCATTACATGCATAT
32155625 GCATTACATTACAT-CATAT
1 GCATT-CATTACATGCATAT
32155644 GCAT
1 GCAT
32155648 CAAAGATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (19 bp):
GCATTCATTACATGCATAT
Found at i:32157526 original size:14 final size:14
Alignment explanation
Indices: 32157507--32157535 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
32157497 TGAGCAAATA
32157507 TTCTTTCATTCTTT
1 TTCTTTCATTCTTT
32157521 TTCTTTCATTCTTT
1 TTCTTTCATTCTTT
32157535 T
1 T
32157536 GGATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (14 bp):
TTCTTTCATTCTTT
Found at i:32160039 original size:132 final size:130
Alignment explanation
Indices: 32159867--32160437 Score: 803
Period size: 132 Copynumber: 4.4 Consensus size: 130
32159857 CAGCGAAGCT
*
32159867 GATCAAAGATGGCAGATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCTAGTAATTCTA
1 GATCAAAGATGG-AGATTTTACCTCC-TGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA
*
32159932 CTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAG
64 CTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAG
32159997 CA
129 CA
* *
32159999 GATCAAAGATGGCAGATTTTACCTCTCTGAGGTTACAGTGGAGTATATTGAAGCCAGTAATTCTA
1 GATCAAAGATGG-AGATTTTACCTC-CTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA
* *
32160064 CTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT----
64 CTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAG
32160125 --
129 CA
* *
32160125 G------G-T-GA-ATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAATAATTCTAC
1 GATCAAAGATGGAGATTTTACCT-CCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTAC
* * * *
32160181 TTCCCTGGGCAGCAGTGAAATAAATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGGGC
65 TTCCCTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGC
32160246 A
130 A
* *
32160247 GATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTAAAGCCAGTAATTCTA
1 GATCAAAGATGGAG-ATTTTACCT-CCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA
*
32160312 CTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAG
64 CTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAG
32160377 CA
129 CA
* *
32160379 GATCAAAGATGGTGGATTTTACCTCCATGAGGTTACAGTGGAGTACATTGAAGCCAGTA
1 GATCAAAGATGG-AGATTTTACCTCC-TGTGGTTACAGTGGAGTACATTGAAGCCAGTA
32160438 TTCCTATCTC
Statistics
Matches: 396, Mismatches: 23, Indels: 40
0.86 0.05 0.09
Matches are distributed among these distances:
116 102 0.26
117 2 0.01
118 1 0.00
119 1 0.00
120 1 0.00
122 1 0.00
126 1 0.00
128 1 0.00
129 1 0.00
130 1 0.00
131 2 0.01
132 280 0.71
133 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (130 bp):
GATCAAAGATGGAGATTTTACCTCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT
TCCCTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCA
Found at i:32160218 original size:116 final size:116
Alignment explanation
Indices: 32160014--32160242 Score: 386
Period size: 116 Copynumber: 2.0 Consensus size: 116
32160004 AAGATGGCAG
* * *
32160014 ATTTTACCTCTCTGAGGTTACAGTGGAGTATATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCA
1 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCA
* * *
32160079 GTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGTGA
66 GTGAAATAAATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGTGA
* *
32160130 ATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCA
1 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCA
32160195 GTGAAATAAATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGG
66 GTGAAATAAATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGG
32160243 GGCAGATCAA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
116 105 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (116 bp):
ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCA
GTGAAATAAATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGTGA
Found at i:32160320 original size:248 final size:248
Alignment explanation
Indices: 32159882--32160374 Score: 817
Period size: 248 Copynumber: 2.0 Consensus size: 248
32159872 AAGATGGCAG
* * *
32159882 ATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCTAGTAATTCTACTTCCCTGGGCAGCA
1 ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCA
* * *
32159947 GTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
66 GTGAAATAAATTAAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
* * *
32160012 AGATTTTACCTCTCTGAGGTTACAGTGGAGTATATTGAAGCCAGTAATTCTACTTCCCTGGGCAG
131 AGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCTGGGCAG
* * *
32160077 CAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGTGA
196 CAGTGGAATAGATTAAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGTGA
*
32160130 ATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCA
1 ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCA
* *
32160195 GTGAAATAAATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGGGCAGATCAAAGATGG-
66 GTGAAATAAATTAAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
* *
32160259 TGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCTGGGCA
131 AG-ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCTGGGCA
32160324 GCAGTGGAATAGATTAAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
195 GCAGTGGAATAGATTAAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
32160375 AGCAGATCAA
Statistics
Matches: 227, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
247 1 0.00
248 226 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (248 bp):
ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCA
GTGAAATAAATTAAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
AGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCTGGGCAG
CAGTGGAATAGATTAAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGTGA
Found at i:32162002 original size:26 final size:26
Alignment explanation
Indices: 32161938--32162015 Score: 83
Period size: 26 Copynumber: 3.1 Consensus size: 26
32161928 TATTTAATAC
*
32161938 ATATATATATGCATGTTTTTT-TTAT
1 ATATATATATGCATGTTTTTTATAAT
*
32161963 CTAGTATACT-TGCATGTTTTTTATAAT
1 ATA-TATA-TATGCATGTTTTTTATAAT
*
32161990 ATATATATATGCAT-TTTTATA-AAT
1 ATATATATATGCATGTTTTTTATAAT
32162014 AT
1 AT
32162016 TTTTTACTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
24 5 0.11
25 9 0.20
26 25 0.56
27 6 0.13
ACGTcount: A:0.32, C:0.06, G:0.08, T:0.54
Consensus pattern (26 bp):
ATATATATATGCATGTTTTTTATAAT
Found at i:32162940 original size:89 final size:89
Alignment explanation
Indices: 32162761--32162939 Score: 324
Period size: 88 Copynumber: 2.0 Consensus size: 89
32162751 ATTATTTTTT
*
32162761 AAGGTGGGCCGATAACACCTTAATAAAAGAATCGGTGGCGACTCTAGTTTTGTTTTTTAAAGTCG
1 AAGGTGGGCCGATAACACCTTAATAAAAGAATCGGTGGCGACTCCAGTTTTGTTTTTTAAAGTCG
*
32162826 ACAACTAAATTTTTGGTTTCAAAA
66 ACAACTAAATTTTTGATTTCAAAA
*
32162850 AAGGTGGGCCGATAACACCTTAAT-AAAGGATCGGTGGCGACTCCAGTTTTGTTTTTTAAAGTCG
1 AAGGTGGGCCGATAACACCTTAATAAAAGAATCGGTGGCGACTCCAGTTTTGTTTTTTAAAGTCG
32162914 ACAACTAAATTTTTGATTTCAAAA
66 ACAACTAAATTTTTGATTTCAAAA
32162938 AA
1 AA
32162940 ACGGTTCTGA
Statistics
Matches: 87, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
88 63 0.72
89 24 0.28
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (89 bp):
AAGGTGGGCCGATAACACCTTAATAAAAGAATCGGTGGCGACTCCAGTTTTGTTTTTTAAAGTCG
ACAACTAAATTTTTGATTTCAAAA
Found at i:32163817 original size:3 final size:3
Alignment explanation
Indices: 32163809--32163871 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
32163799 AAGTTTTCTT
32163809 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
32163857 TTA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA T
32163872 CTGTGAACTG
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 57 0.97
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:32171451 original size:16 final size:16
Alignment explanation
Indices: 32171430--32171461 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
32171420 TATTTAGTGC
32171430 TATTGTTAAATGATGT
1 TATTGTTAAATGATGT
32171446 TATTGTTAAATGATGT
1 TATTGTTAAATGATGT
32171462 ATCTAAAGAG
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:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (16 bp):
TATTGTTAAATGATGT
Found at i:32171931 original size:14 final size:14
Alignment explanation
Indices: 32171912--32171951 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
32171902 TTGATTGCCA
32171912 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
32171926 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
32171940 GGAAAATGTTTT
1 GTAAAATGTTTT
32171952 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:32171960 original size:20 final size:20
Alignment explanation
Indices: 32171935--32171974 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
32171925 CGTAAAATGA
*
32171935 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
32171955 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
32171975 GGAAAATATT
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:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:32171964 original size:34 final size:35
Alignment explanation
Indices: 32171920--32171986 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
32171910 CAGTAAAATG
*
32171920 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
32171954 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
32171987 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:32171990 original size:14 final size:15
Alignment explanation
Indices: 32171914--32171990 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
32171904 GATTGCCAGT
* *
32171914 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
32171928 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
32171942 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
32171962 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
32171977 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
32171991 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:32172143 original size:22 final size:24
Alignment explanation
Indices: 32172118--32172168 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
32172108 TTATTTATAA
32172118 ATAAATAA-A-TCAA-ATT-AAAT
1 ATAAATAATACTCAATATTAAAAT
32172138 ATATAATAATACTCAATTATTAAAAT
1 ATA-AATAATACTCAA-TATTAAAAT
32172164 ATAAA
1 ATAAA
32172169 AGCATTGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
20 3 0.12
21 5 0.20
22 1 0.04
23 4 0.16
25 5 0.20
26 7 0.28
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAAATAATACTCAATATTAAAAT
Found at i:32175171 original size:6 final size:6
Alignment explanation
Indices: 32175125--32175172 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
32175115 ATCAGGTGTC
* * *
32175125 AAGGG- AAGGGG AAGGGG AAGGGG AAGGGA AAGGGA AAGGGA AAGGGA
1 AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA
32175172 A
1 A
32175173 GATCGGTGTC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
5 5 0.12
6 36 0.88
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (6 bp):
AAGGGA
Found at i:32175428 original size:12 final size:12
Alignment explanation
Indices: 32175411--32175436 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
32175401 CCCTACACTT
32175411 AGCACTAATTCA
1 AGCACTAATTCA
32175423 AGCACTAATTCA
1 AGCACTAATTCA
32175435 AG
1 AG
32175437 ATTCTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (12 bp):
AGCACTAATTCA
Found at i:32175983 original size:20 final size:21
Alignment explanation
Indices: 32175958--32175996 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
32175948 AAACATAAAC
32175958 AACTTTAC-ATTTTTTAAAGT
1 AACTTTACAATTTTTTAAAGT
32175978 AACTTTACAATTTTTTAAA
1 AACTTTACAATTTTTTAAA
32175997 ATTTATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (21 bp):
AACTTTACAATTTTTTAAAGT
Found at i:32178848 original size:22 final size:24
Alignment explanation
Indices: 32178820--32178865 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
32178810 CCGAAAAATA
32178820 TTAAATAT-ATA-TTTTTTATTTT
1 TTAAATATAATAGTTTTTTATTTT
32178842 TTAAATATAATAGTTTTTTATTTT
1 TTAAATATAATAGTTTTTTATTTT
32178866 AAGTTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 8 0.36
23 3 0.14
24 11 0.50
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
TTAAATATAATAGTTTTTTATTTT
Found at i:32178867 original size:22 final size:21
Alignment explanation
Indices: 32178820--32178865 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 21
32178810 CCGAAAAATA
32178820 TTAAATATATATTTTTTATTTT
1 TTAAATATATATTTTTTA-TTT
32178842 TTAAATATAATAGTTTTTTATTT
1 TTAAATAT-ATA-TTTTTTATTT
32178865 T
1 T
32178866 AAGTTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.36
23 7 0.32
24 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TTAAATATATATTTTTTATTT
Found at i:32178976 original size:9 final size:9
Alignment explanation
Indices: 32178962--32178989 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
32178952 TTTTGTTACA
32178962 ACAATTAAT
1 ACAATTAAT
32178971 ACAATTAAT
1 ACAATTAAT
32178980 ACAATTAAT
1 ACAATTAAT
32178989 A
1 A
32178990 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:32179011 original size:68 final size:66
Alignment explanation
Indices: 32178932--32179073 Score: 239
Period size: 68 Copynumber: 2.1 Consensus size: 66
32178922 TCAAGTTTGT
* *
32178932 TTTAATAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
32178997 AAA
64 AAA
32179000 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
*
32179065 T
66 A
32179066 TTTACTAA
1 TTTACTAA
32179074 CAATTAATTT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
66 27 0.38
67 1 0.01
68 43 0.61
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
A
Found at i:32179083 original size:16 final size:16
Alignment explanation
Indices: 32179062--32179103 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
32179052 AATAATTTGA
*
32179062 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
32179078 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
32179094 TAGTTTTAAT
1 TAATTTTAAT
32179104 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:32179087 original size:22 final size:22
Alignment explanation
Indices: 32179077--32179137 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
32179067 TTACTAACAA
* * *
32179077 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
32179099 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
*
32179121 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
32179138 CGGGCCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:32179092 original size:59 final size:66
Alignment explanation
Indices: 32178932--32179095 Score: 207
Period size: 68 Copynumber: 2.5 Consensus size: 66
32178922 TCAAGTTTGT
* *
32178932 TTTAATAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTT-ATACAACAATTAATACAATTAATACAATTAATAATTTGAT
32178997 AAA
64 AAA
32179000 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTTA-TACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
32179063 AAT
64 AAA
*
32179066 TTTACTAA-C-AA-TTA-ATTTTA-ATAACAATTA
1 TTTACTAATCAAAGTTAGATTTTATACAACAATTA
32179096 GTTTTAATTT
Statistics
Matches: 91, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
59 9 0.10
61 6 0.07
62 3 0.03
64 2 0.02
65 1 0.01
66 27 0.30
67 1 0.01
68 42 0.46
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAAGTTAGATTTTATACAACAATTAATACAATTAATACAATTAATAATTTGATAA
A
Found at i:32184689 original size:23 final size:21
Alignment explanation
Indices: 32184633--32184691 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
32184623 ATGCCAAAAG
* *
32184633 AAGCCACAAAAGAACAACAGA
1 AAGCCATAAAAGAACAACAAA
*
32184654 AATCCATAAAAGAACAACAAA
1 AAGCCATAAAAGAACAACAAA
32184675 AAGCCATATAAAAGAAC
1 AAGCC--ATAAAAGAAC
32184692 GTACGAGAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 22 0.69
23 10 0.31
ACGTcount: A:0.63, C:0.20, G:0.10, T:0.07
Consensus pattern (21 bp):
AAGCCATAAAAGAACAACAAA
Found at i:32186548 original size:29 final size:30
Alignment explanation
Indices: 32186500--32186628 Score: 140
Period size: 30 Copynumber: 4.3 Consensus size: 30
32186490 GCAAAAAATA
* **
32186500 AAAATTACGTTTTAACCCCTGTACTTTT-T
1 AAAATTACATTTTAACCCCTAAACTTTTCT
*
32186529 AAAATTTACATTTTGA-CCCTAAACTTTTCT
1 AAAA-TTACATTTTAACCCCTAAACTTTTCT
*
32186559 AAAATTACATTTCAACCCCTAAAC-TTTCT
1 AAAATTACATTTTAACCCCTAAACTTTTCT
* *
32186588 CAAAATTACACTTTAACCACTAAAC-TTTCT
1 -AAAATTACATTTTAACCCCTAAACTTTTCT
32186618 AAAAATTACAT
1 -AAAATTACAT
32186629 CTTGGCCCTA
Statistics
Matches: 85, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
29 28 0.33
30 57 0.67
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.38
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCTAAACTTTTCT
Found at i:32186564 original size:30 final size:29
Alignment explanation
Indices: 32186500--32186669 Score: 132
Period size: 30 Copynumber: 5.8 Consensus size: 29
32186490 GCAAAAAATA
* **
32186500 AAAATTACGTTTTAACCCCTGTACTTTT-T
1 AAAATTACATTTTAA-CCCTAAACTTTTCT
*
32186529 AAAATTTACATTTTGACCCTAAACTTTTCT
1 AAAA-TTACATTTTAACCCTAAACTTTTCT
*
32186559 AAAATTACATTTCAACCCCTAAAC-TTTCT
1 AAAATTACATTTTAA-CCCTAAACTTTTCT
*
32186588 CAAAATTACACTTTAACCACTAAAC-TTTCT
1 -AAAATTACATTTTAACC-CTAAACTTTTCT
* ** * *
32186618 AAAAATTACATCTTGGCCCTATA-TTTTCCC
1 -AAAATTACATTTTAACCCTAAACTTTT-CT
* *
32186648 AAAATTACATTTTTACCTTAAA
1 AAAATTACATTTTAACCCTAAA
32186670 TATTTTGTGT
Statistics
Matches: 114, Mismatches: 20, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
29 54 0.47
30 60 0.53
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAATTACATTTTAACCCTAAACTTTTCT
Found at i:32186566 original size:59 final size:60
Alignment explanation
Indices: 32186498--32186628 Score: 160
Period size: 59 Copynumber: 2.2 Consensus size: 60
32186488 ATGCAAAAAA
* * ** * * *
32186498 TAAAAATTACGTTTTAACCCCTGTACTTT-TTAAAATTTACATTTTGACC-CTAAACTTTTC
1 TAAAAATTACATTTCAACCCCTAAACTTTCTCAAAA-TTACACTTTAACCACTAAAC-TTTC
32186558 T-AAAATTACATTTCAACCCCTAAACTTTCTCAAAATTACACTTTAACCACTAAACTTTC
1 TAAAAATTACATTTCAACCCCTAAACTTTCTCAAAATTACACTTTAACCACTAAACTTTC
32186617 TAAAAATTACAT
1 TAAAAATTACAT
32186629 CTTGGCCCTA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
59 39 0.64
60 22 0.36
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.38
Consensus pattern (60 bp):
TAAAAATTACATTTCAACCCCTAAACTTTCTCAAAATTACACTTTAACCACTAAACTTTC
Found at i:32187264 original size:20 final size:21
Alignment explanation
Indices: 32187231--32187286 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
32187221 GCAAAGGAAA
*
32187231 AAGA-GAAGAGAAAGAAG-AG
1 AAGAGGAAGAAAAAGAAGAAG
*
32187250 AAGGGGAAGAAAAAGAAGAAAG
1 AAGAGGAAGAAAAAGAAG-AAG
32187272 AAGAGGAA-AAAAAGA
1 AAGAGGAAGAAAAAGA
32187287 GGAGTGCCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 3 0.10
20 12 0.39
21 7 0.23
22 9 0.29
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (21 bp):
AAGAGGAAGAAAAAGAAGAAG
Found at i:32187284 original size:22 final size:23
Alignment explanation
Indices: 32187242--32187284 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
32187232 AGAGAAGAGA
* *
32187242 AAGAAGAGAAGGGGAAGAAAAAG
1 AAGAAGAGAAGAGGAAAAAAAAG
32187265 AAGAA-AGAAGAGGAAAAAAA
1 AAGAAGAGAAGAGGAAAAAAA
32187285 GAGGAGTGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
AAGAAGAGAAGAGGAAAAAAAAG
Found at i:32187413 original size:18 final size:18
Alignment explanation
Indices: 32187370--32187414 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
32187360 AGAGGGTTTT
32187370 GAAAGAAAAAAACAAAGCA
1 GAAA-AAAAAAACAAAGCA
**
32187389 GCCAAAAAAAACAAAGCA
1 GAAAAAAAAAACAAAGCA
32187407 GAAAAAAA
1 GAAAAAAA
32187415 TAAAAATAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.73, C:0.13, G:0.13, T:0.00
Consensus pattern (18 bp):
GAAAAAAAAAACAAAGCA
Found at i:32187566 original size:26 final size:26
Alignment explanation
Indices: 32187535--32187590 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
32187525 AAGCATACCA
*
32187535 AGCAGG-CCTCTAGGCCCGAATTCGGC
1 AGCAGGCCCTC-AGGCCCGAATCCGGC
*
32187561 AGCAGGCCCTCAGGCCCGAATCCTGC
1 AGCAGGCCCTCAGGCCCGAATCCGGC
32187587 AGCA
1 AGCA
32187591 AAAAAAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.21, C:0.38, G:0.29, T:0.12
Consensus pattern (26 bp):
AGCAGGCCCTCAGGCCCGAATCCGGC
Found at i:32188117 original size:17 final size:17
Alignment explanation
Indices: 32188074--32188121 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
32188064 AAATAAATAA
32188074 TCGTGTTTCAAAAGTTT
1 TCGTGTTTCAAAAGTTT
*
32188091 TCATGTTTTCAAAA-TTT
1 TCGTG-TTTCAAAAGTTT
32188108 CTCGTGTTTCAAAA
1 -TCGTGTTTCAAAA
32188122 AATAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (17 bp):
TCGTGTTTCAAAAGTTT
Found at i:32188199 original size:16 final size:16
Alignment explanation
Indices: 32188180--32188228 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 16
32188170 AAAAAAACAG
32188180 TTTCCGTGTTTCAAAT
1 TTTCCGTGTTTCAAAT
32188196 TTT-CGTGTTTTCAAAAT
1 TTTCCGTG-TTTC-AAAT
32188213 TTTCTCGTGTTTCAAA
1 TTTC-CGTGTTTCAAA
32188229 AATTTTCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.14
16 7 0.24
17 10 0.34
18 4 0.14
19 4 0.14
ACGTcount: A:0.20, C:0.16, G:0.12, T:0.51
Consensus pattern (16 bp):
TTTCCGTGTTTCAAAT
Found at i:32188214 original size:17 final size:17
Alignment explanation
Indices: 32188184--32188235 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
32188174 AAACAGTTTC
32188184 CGTG-TTTC-AAATTTT
1 CGTGTTTTCAAAATTTT
32188199 CGTGTTTTCAAAATTTT
1 CGTGTTTTCAAAATTTT
32188216 C-TCGTGTTTCAAAAATTTT
1 CGT-GT-TTTC-AAAATTTT
32188235 C
1 C
32188236 AAATTCTCGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 4 0.12
16 5 0.16
17 10 0.31
18 4 0.12
19 9 0.28
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (17 bp):
CGTGTTTTCAAAATTTT
Found at i:32188222 original size:19 final size:18
Alignment explanation
Indices: 32188180--32188235 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
32188170 AAAAAAACAG
32188180 TTTC-CGTGTTTC-AAA-
1 TTTCTCGTGTTTCAAAAT
32188195 TTT-TCGTGTTTTCAAAAT
1 TTTCTCGTG-TTTCAAAAT
32188213 TTTCTCGTGTTTCAAAAAT
1 TTTCTCGTGTTTC-AAAAT
32188232 TTTC
1 TTTC
32188236 AAATTCTCGT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 7 0.20
16 4 0.11
17 3 0.09
18 7 0.20
19 14 0.40
ACGTcount: A:0.21, C:0.16, G:0.11, T:0.52
Consensus pattern (18 bp):
TTTCTCGTGTTTCAAAAT
Found at i:32188258 original size:26 final size:25
Alignment explanation
Indices: 32188214--32188262 Score: 89
Period size: 26 Copynumber: 1.9 Consensus size: 25
32188204 TTTCAAAATT
32188214 TTCTCGTGTTTCAAAAATTTTCAAA
1 TTCTCGTGTTTCAAAAATTTTCAAA
32188239 TTCTCGTGTTTTCAAAAATTTTCA
1 TTCTCGTG-TTTCAAAAATTTTCA
32188263 TTTTTTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (25 bp):
TTCTCGTGTTTCAAAAATTTTCAAA
Found at i:32188270 original size:44 final size:43
Alignment explanation
Indices: 32188188--32188274 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 43
32188178 AGTTTCCGTG
*
32188188 TTTCAAATTTTCGTGTTTTCAAAATTTTCTCGTGTTTCAAAAAT
1 TTTCAAATTCTCGTGTTTTCAAAATTTTCTC-TGTTTCAAAAAT
*
32188232 TTTCAAATTCTCGTGTTTTCAAAAATTTTCAT-TTTTTCAAAAA
1 TTTCAAATTCTCGTGTTTTC-AAAATTTTC-TCTGTTTCAAAAA
32188275 AAAATTTCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 29 0.74
45 9 0.23
46 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.49
Consensus pattern (43 bp):
TTTCAAATTCTCGTGTTTTCAAAATTTTCTCTGTTTCAAAAAT
Found at i:32188344 original size:18 final size:18
Alignment explanation
Indices: 32188236--32188362 Score: 85
Period size: 18 Copynumber: 6.6 Consensus size: 18
32188226 AAAAATTTTC
* *
32188236 AAATTCTCGTGTTTTCAA
1 AAATTTTCGTGTTTTAAA
* *
32188254 AAATTTTCATTTTTTCAAAAAA
1 AAATTTTCGTGTTTT----AAA
32188276 AAATTTCTCGTG-TTTAAA
1 AAATTT-TCGTGTTTTAAA
** **
32188294 ATTTTTTCGCATTTTAAA
1 AAATTTTCGTGTTTTAAA
*
32188312 AAATTTTTCGCGTTTTAAA
1 AAA-TTTTCGTGTTTTAAA
32188331 AAATTTTCGTGTTTTCTAAA
1 AAATTTTCGTG-TTT-TAAA
32188351 AAATTTTTCGTG
1 AAA-TTTTCGTG
32188363 CTTCAATGAG
Statistics
Matches: 85, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
17 3 0.04
18 33 0.39
19 20 0.24
20 7 0.08
21 8 0.09
22 11 0.13
23 3 0.04
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (18 bp):
AAATTTTCGTGTTTTAAA
Found at i:32188350 original size:20 final size:19
Alignment explanation
Indices: 32188273--32188362 Score: 96
Period size: 19 Copynumber: 4.8 Consensus size: 19
32188263 TTTTTTCAAA
*
32188273 AAAAAATTTCTCGTG-TTT
1 AAAAAATTTTTCGTGTTTT
* **
32188291 -AAAATTTTTTCGCATTTT
1 AAAAAATTTTTCGTGTTTT
*
32188309 AAAAAATTTTTCGCGTTTT
1 AAAAAATTTTTCGTGTTTT
32188328 AAAAAA-TTTTCGTGTTTTCT
1 AAAAAATTTTTCGTG-TTT-T
32188348 AAAAAATTTTTCGTG
1 AAAAAATTTTTCGTG
32188363 CTTCAATGAG
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
17 10 0.17
18 10 0.17
19 25 0.42
20 7 0.12
21 8 0.13
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (19 bp):
AAAAAATTTTTCGTGTTTT
Found at i:32192231 original size:9 final size:9
Alignment explanation
Indices: 32192185--32192231 Score: 51
Period size: 9 Copynumber: 4.9 Consensus size: 9
32192175 ATTATGCCTA
32192185 AAAAAAAAC
1 AAAAAAAAC
32192194 AATAACAACAAC
1 AA-AA-AA-AAC
32192206 AAAAAAAAGC
1 AAAAAAAA-C
32192216 -AAAAAAAC
1 AAAAAAAAC
32192224 AAAAAAAA
1 AAAAAAAA
32192232 GAAGAAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
8 1 0.03
9 18 0.55
10 5 0.15
11 4 0.12
12 5 0.15
ACGTcount: A:0.83, C:0.13, G:0.02, T:0.02
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:32192249 original size:21 final size:20
Alignment explanation
Indices: 32192184--32192240 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
32192174 TATTATGCCT
*
32192184 AAAAAAAAA-CAATAACAACA
1 AAAAAAAAAGCAA-AAAAACA
32192204 ACAAAAAAAAGCAAAAAAACA
1 A-AAAAAAAAGCAAAAAAACA
32192225 AAAAAAAGAAG-AAAAA
1 AAAAAAA-AAGCAAAAA
32192241 GAAGAAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 12 0.36
21 18 0.55
22 3 0.09
ACGTcount: A:0.82, C:0.11, G:0.05, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAGCAAAAAAACA
Found at i:32193200 original size:76 final size:75
Alignment explanation
Indices: 32193105--32193568 Score: 581
Period size: 77 Copynumber: 6.1 Consensus size: 75
32193095 TGTTTCTTTT
* * *
32193105 ATTTCTGTTTTTTCAAAAAATCAAATCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCTGAG
1 ATTTTTGTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAG
32193170 GTATTTTTAA
66 GTATTTTTAA
* *
32193180 ATTTTTGTTTTTTTTCAAAAAATCAACTCATAATATAGAGGTGAGTTGAGCCTCGGATCACGCTG
1 ATTTTTG--TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTG
*
32193245 AGGTATTTTTTTA
64 AGGTA-TTTTTAA
* *
32193258 ATTTTTGTTTTTTCAAAAAATCAACTCATAATACAAAGGTGAGTTAAGCCTCGGGTCACGCTGAG
1 ATTTTTGTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAG
32193323 GTATTTTTAA
66 GTATTTTTAA
*
32193333 ATTTCTGTTTTTTTCAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTG
1 ATTTTTG-TTTTTTC-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTG
*
32193398 AGGTATTTTTTTA
64 AGGTA-TTTTTAA
* * ** * ** *
32193411 ATTTCTATTTTTTCAAAAAATCAACTCATAATTTAGAGGTGAGTTGAGCCTCGGGCCATACGGAG
1 ATTTTTGTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGA-
*
32193476 GTGTTTCTTTTAA
65 G-GTAT-TTTTAA
* * * * *
32193489 ATTTCTG-TTTTTC-ACAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGTC
1 ATTTTTGTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGC-T-
*
32193552 GAGGTATTTTTCA
63 GAGGTATTTTTAA
32193565 ATTT
1 ATTT
32193569 CTATTTTTCA
Statistics
Matches: 343, Mismatches: 34, Indels: 23
0.86 0.09 0.06
Matches are distributed among these distances:
75 18 0.05
76 132 0.38
77 152 0.44
78 39 0.11
79 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.37
Consensus pattern (75 bp):
ATTTTTGTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAG
GTATTTTTAA
Found at i:32193278 original size:153 final size:152
Alignment explanation
Indices: 32193101--32193576 Score: 656
Period size: 153 Copynumber: 3.1 Consensus size: 152
32193091 ACCCTGTTTC
*
32193101 TTTT-ATTTCTGTTTTTTCAAAAAATCAAATCATAATACAGAGGTGAGTTGAGCCTCGGGTCATG
1 TTTTAATTTCTGTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATG
* *
32193165 CTGAGGTATTTTTAAATTTTTGTTTTTTTTCAAAAAATCAACTCATAATATAGAGGTGAGTTGAG
66 CTGAGGTATTTTTAAATTTCTG-TTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAG
*
32193230 CCTCGGATCACGCTGAGGTATTT
130 CCTCGGGTCACGCTGAGGTATTT
* * * *
32193253 TTTTAATTTTTGTTTTTTCAAAAAATCAACTCATAATACAAAGGTGAGTTAAGCCTCGGGTCACG
1 TTTTAATTTCTGTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATG
32193318 CTGAGGTATTTTTAAATTTCTGTTTTTTTCAAAAAAATCAACTCATAATACAGAGGTGAGTTGAG
66 CTGAGGTATTTTTAAATTTCTGTTTTTTTC-AAAAAATCAACTCATAATACAGAGGTGAGTTGAG
32193383 CCTCGGGTCACGCTGAGGTATTT
130 CCTCGGGTCACGCTGAGGTATTT
* ** * *
32193406 TTTTAATTTCTATTTTTTCAAAAAATCAACTCATAATTTAGAGGTGAGTTGAGCCTCGGGCCATA
1 TTTTAATTTCTGTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATG
* * * * *
32193471 CGGAGGTGTTTCTTTTAAATTTCTG--TTTTTC-ACAAATCAACTCATATTGCGAGAGGTGAGTT
66 CTGA-G-GTAT-TTTTAAATTTCTGTTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTT
*
32193533 GAGCCTCGGGTCACACGTCGAGGTA-TT
127 GAGCCTCGGGTCACGC-T-GAGGTATTT
* *
32193560 TTTCAATTTCTATTTTT
1 TTTTAATTTCTGTTTTT
32193577 CAAGGCTCAA
Statistics
Matches: 292, Mismatches: 24, Indels: 14
0.88 0.07 0.04
Matches are distributed among these distances:
152 28 0.10
153 216 0.74
154 26 0.09
155 9 0.03
156 13 0.04
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (152 bp):
TTTTAATTTCTGTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATG
CTGAGGTATTTTTAAATTTCTGTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGC
CTCGGGTCACGCTGAGGTATTT
Found at i:32194094 original size:29 final size:29
Alignment explanation
Indices: 32193957--32194097 Score: 140
Period size: 30 Copynumber: 4.8 Consensus size: 29
32193947 TGTACTTTTT
*
32193957 AAAATTTACATTTTGACCCCAAACTTT-TC
1 AAAA-TTACATTTTGACCCTAAACTTTCTC
**
32193986 TAAAATTACATTTCAACCCCTAAACTTTCTC
1 -AAAATTACATTTTGA-CCCTAAACTTTCTC
* *
32194017 AAAATTACACTTTGACCACTAAACTTTCTA
1 AAAATTACATTTTGACC-CTAAACTTTCTC
* * * * *
32194047 AAAATTACATCTTGGCCCTATATTTTCCC
1 AAAATTACATTTTGACCCTAAACTTTCTC
*
32194076 AAAATTACATTTTTACCCTAAA
1 AAAATTACATTTTGACCCTAAA
32194098 TATTTTTTAT
Statistics
Matches: 90, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
29 37 0.41
30 51 0.57
31 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATTACATTTTGACCCTAAACTTTCTC
Found at i:32194847 original size:24 final size:25
Alignment explanation
Indices: 32194806--32194853 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
32194796 TTGAAAGAAA
* **
32194806 AAAACAAAGTAGCCAAAAA-AAAAT
1 AAAACAAAGCAGAAAAAAATAAAAT
32194830 AAAACAAAGCAGAAAAAAATAAAA
1 AAAACAAAGCAGAAAAAAATAAAA
32194854 ATAGAAGCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.75, C:0.10, G:0.08, T:0.06
Consensus pattern (25 bp):
AAAACAAAGCAGAAAAAAATAAAAT
Found at i:32195558 original size:17 final size:17
Alignment explanation
Indices: 32195515--32195562 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
32195505 AAATAAATAA
32195515 TCGTGTTTCAAAAGTTT
1 TCGTGTTTCAAAAGTTT
*
32195532 TCATGTTTTCAAAA-TTT
1 TCGTG-TTTCAAAAGTTT
32195549 CTCGTGTTTCAAAA
1 -TCGTGTTTCAAAA
32195563 AATAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (17 bp):
TCGTGTTTCAAAAGTTT
Found at i:32195656 original size:17 final size:18
Alignment explanation
Indices: 32195628--32195677 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
32195618 ACAGTTTCCC
32195628 TGTTTC-AAA-TTT-TCG
1 TGTTTCAAAATTTTCTCG
32195643 TGTTTTCAAAATTTTCTCG
1 TG-TTTCAAAATTTTCTCG
32195662 TGTTTCAAAAATTTTC
1 TGTTTC-AAAATTTTC
32195678 AAATTTTCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.07
16 4 0.13
17 3 0.10
18 7 0.23
19 14 0.47
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.52
Consensus pattern (18 bp):
TGTTTCAAAATTTTCTCG
Found at i:32195664 original size:19 final size:19
Alignment explanation
Indices: 32195640--32196025 Score: 108
Period size: 17 Copynumber: 20.7 Consensus size: 19
32195630 TTTCAAATTT
32195640 TCGTGTTTTC-AAAATTTTC
1 TCGTG-TTTCAAAAATTTTC
32195659 TCGTGTTTCAAAAATTTTC
1 TCGTGTTTCAAAAATTTTC
32195678 AAATTTTCGTGTTTTCAAAAATTTTC
1 ------TCGTG-TTTCAAAAATTTTC
* * **
32195704 T-TTTTTTCAAAAAAAAAATTC
1 TCGTGTTTC---AAAAATTTTC
*
32195725 TCGTATTT-AAAAATTTT-
1 TCGTGTTTCAAAAATTTTC
*
32195742 TCGCGTTTTCAAAAA-TTT-
1 TCGTG-TTTCAAAAATTTTC
*
32195760 TCGTGTTTTCTAAAAA-CTT-
1 TCGTG-TTTC-AAAAATTTTC
** * *
32195779 TCGCATTTCACAAATCTTC
1 TCGTGTTTCAAAAATTTTC
**
32195798 AT-GT-TTTCAAAAAAAATTC
1 -TCGTGTTTC-AAAAATTTTC
* * *
32195817 TCGCGTTTCACAAATCTTC
1 TCGTGTTTCAAAAATTTTC
**
32195836 AT-GT-TTTCAAAAAAAAATTC
1 -TCGTGTTTC--AAAAATTTTC
* *
32195856 TCGTGTTTCAAAAA--ATG
1 TCGTGTTTCAAAAATTTTC
*
32195873 TCGTGTTTTAAAAATTTT-
1 TCGTGTTTCAAAAATTTTC
*
32195891 T-GTGTTTCTAAAA-TTT-
1 TCGTGTTTCAAAAATTTTC
*
32195907 TCGTGTTTTAAAAA--TTC
1 TCGTGTTTCAAAAATTTTC
*** *
32195924 TCGTGTTTCAAAAAAAATG
1 TCGTGTTTCAAAAATTTTC
* *
32195943 TTGTGTTTTAAAAA-TTT-
1 TCGTGTTTCAAAAATTTTC
*
32195960 TCGTGTTTCTAAAA-TTT-
1 TCGTGTTTCAAAAATTTTC
**
32195977 TCGTGTTT-AAAAAAATTC
1 TCGTGTTTCAAAAATTTTC
32195995 TCGTGTTTTCAAAAA--TTC
1 TCGTG-TTTCAAAAATTTTC
32196013 TCGTGTTT-AAAAA
1 TCGTGTTTCAAAAA
32196026 AACTTTCGTT
Statistics
Matches: 284, Mismatches: 47, Indels: 75
0.70 0.12 0.18
Matches are distributed among these distances:
16 15 0.05
17 81 0.29
18 61 0.21
19 70 0.25
20 21 0.07
21 13 0.05
22 4 0.01
25 5 0.02
26 14 0.05
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (19 bp):
TCGTGTTTCAAAAATTTTC
Found at i:32195697 original size:26 final size:28
Alignment explanation
Indices: 32195645--32195703 Score: 88
Period size: 26 Copynumber: 2.2 Consensus size: 28
32195635 AATTTTCGTG
32195645 TTTTCAAAATTTTCTCGTGTTTCAAAAA
1 TTTTCAAAATTTTCTCGTGTTTCAAAAA
32195673 TTTTC-AAA-TTT-TCGTGTTTTCAAAAA
1 TTTTCAAAATTTTCTCGTG-TTTCAAAAA
32195699 TTTTC
1 TTTTC
32195704 TTTTTTTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 5 0.17
26 17 0.57
27 3 0.10
28 5 0.17
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.51
Consensus pattern (28 bp):
TTTTCAAAATTTTCTCGTGTTTCAAAAA
Found at i:32195699 original size:18 final size:18
Alignment explanation
Indices: 32195678--32196045 Score: 202
Period size: 18 Copynumber: 20.2 Consensus size: 18
32195668 AAAAATTTTC
32195678 AAATTTTCGTGTTTTCAA
1 AAATTTTCGTGTTTTCAA
* *
32195696 AAATTTTCTTTTTTTCAAAAAAA
1 AAATTTTCGTGTTTTC-----AA
* *
32195719 AAATTCTCGT-ATTT-AA
1 AAATTTTCGTGTTTTCAA
*
32195735 AAATTTTTCGCGTTTTCAA
1 AAA-TTTTCGTGTTTTCAA
32195754 AAATTTTCGTGTTTTCTAA
1 AAATTTTCGTGTTTTC-AA
* ** *
32195773 AAACTTTCG-CATTTCAC
1 AAATTTTCGTGTTTTCAA
* *
32195790 AAATCTTCATGTTTTCAAAAA
1 AAATTTTCGTGTTTTC---AA
* * *
32195811 AAATTCTCGCG-TTTCAC
1 AAATTTTCGTGTTTTCAA
* *
32195828 AAATCTTCATGTTTTCAAAAAA
1 AAATTTTCGTGTTTTC----AA
*
32195850 AAATTCTCGTG-TTTCAA
1 AAATTTTCGTGTTTTCAA
* *
32195867 AAAATGTCGTGTTTT-AA
1 AAATTTTCGTGTTTTCAA
* *
32195884 AAATTTTTGTG-TTTCTA
1 AAATTTTCGTGTTTTCAA
32195901 AAATTTTCGTGTTTT-AA
1 AAATTTTCGTGTTTTCAA
*
32195918 AAATTCTCGTG-TTTCAAAAA
1 AAATTTTCGTGTTTTC---AA
*
32195938 AAATGTT-GTGTTTT-AA
1 AAATTTTCGTGTTTTCAA
*
32195954 AAATTTTCGTG-TTTCTA
1 AAATTTTCGTGTTTTCAA
**
32195971 AAATTTTCGTGTTTAAAA
1 AAATTTTCGTGTTTTCAA
*
32195989 AAATTCTCGTGTTTTCAA
1 AAATTTTCGTGTTTTCAA
* **
32196007 AAATTCTCGTGTTTAAAA
1 AAATTTTCGTGTTTTCAA
* * *
32196025 AAACTTTCGTTTTTTTAA
1 AAATTTTCGTGTTTTCAA
32196043 AAA
1 AAA
32196046 ATTCATGCTT
Statistics
Matches: 263, Mismatches: 58, Indels: 58
0.69 0.15 0.15
Matches are distributed among these distances:
16 22 0.08
17 78 0.30
18 97 0.37
19 18 0.07
20 14 0.05
21 12 0.05
22 12 0.05
23 10 0.04
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (18 bp):
AAATTTTCGTGTTTTCAA
Found at i:32195710 original size:26 final size:25
Alignment explanation
Indices: 32195653--32195711 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
32195643 TGTTTTCAAA
*
32195653 ATTTTCTCGTGTTTCAAAAATTTTC
1 ATTTTTTCGTGTTTCAAAAATTTTC
**
32195678 AAATTTTCGTGTTTTCAAAAATTTTC
1 ATTTTTTCGTG-TTTCAAAAATTTTC
*
32195704 TTTTTTTC
1 ATTTTTTC
32195712 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.56
Consensus pattern (25 bp):
ATTTTTTCGTGTTTCAAAAATTTTC
Found at i:32195864 original size:39 final size:38
Alignment explanation
Indices: 32195733--32195865 Score: 153
Period size: 38 Copynumber: 3.5 Consensus size: 38
32195723 TCTCGTATTT
* * * * * *
32195733 AAAAATTTTTCGCGTTTTCAAAAATTTTCGTGTTTTC-T
1 AAAAAATTCTCGCG-TTTCACAAATCTTCATGTTTTCAA
* *
32195771 AAAAACTT-TCGCATTTCACAAATCTTCATGTTTTCAA
1 AAAAAATTCTCGCGTTTCACAAATCTTCATGTTTTCAA
32195808 AAAAAATTCTCGCGTTTCACAAATCTTCATGTTTTCAAA
1 AAAAAATTCTCGCGTTTCACAAATCTTCATGTTTTC-AA
*
32195847 AAAAAATTCTCGTGTTTCA
1 AAAAAATTCTCGCGTTTCA
32195866 AAAAATGTCG
Statistics
Matches: 83, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
36 19 0.23
37 11 0.13
38 33 0.40
39 20 0.24
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (38 bp):
AAAAAATTCTCGCGTTTCACAAATCTTCATGTTTTCAA
Found at i:32195876 original size:17 final size:17
Alignment explanation
Indices: 32195848--32196025 Score: 171
Period size: 17 Copynumber: 10.3 Consensus size: 17
32195838 GTTTTCAAAA
*
32195848 AAAAATTCTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* * *
32195865 AAAAAATGTCGTGTTTT
1 AAAAATTTTCGTGTTTC
*
32195882 AAAAATTTTTGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
32195899 TAAAATTTTCGTGTTTT
1 AAAAATTTTCGTGTTTC
*
32195916 AAAAATTCTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
32195933 AAAAAAAATGTT-GTGTTTT
1 ---AAAAATTTTCGTGTTTC
32195952 AAAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
32195969 TAAAATTTTCGTGTTTAA
1 AAAAATTTTCGTGTTT-C
*
32195987 AAAAATTCTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
*
32196005 AAAAATTCTCGTGTTT-
1 AAAAATTTTCGTGTTTC
32196021 AAAAA
1 AAAAA
32196026 AACTTTCGTT
Statistics
Matches: 132, Mismatches: 23, Indels: 13
0.79 0.14 0.08
Matches are distributed among these distances:
16 13 0.10
17 79 0.60
18 24 0.18
19 9 0.07
20 7 0.05
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTC
Found at i:32195953 original size:70 final size:71
Alignment explanation
Indices: 32195846--32196009 Score: 271
Period size: 70 Copynumber: 2.3 Consensus size: 71
32195836 ATGTTTTCAA
*
32195846 AAAAAAATTCTCGTGTTTC--AAAAAATGTCGTGTTTTAAAAATTTTTGTGTTTCTAAAATTTTC
1 AAAAAAATTCTCGTGTTTCAAAAAAAATGTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTTC
32195909 GTGTTT
66 GTGTTT
* *
32195915 -TAAAAATTCTCGTGTTTCAAAAAAAATGTTGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTTC
1 AAAAAAATTCTCGTGTTTCAAAAAAAATGTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTTC
32195979 GTGTTT
66 GTGTTT
32195985 AAAAAAATTCTCGTGTTTTCAAAAA
1 AAAAAAATTCTCGTG-TTTCAAAAA
32196010 TTCTCGTGTT
Statistics
Matches: 87, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
68 17 0.20
70 48 0.55
71 13 0.15
72 9 0.10
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (71 bp):
AAAAAAATTCTCGTGTTTCAAAAAAAATGTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTTC
GTGTTT
Found at i:32195962 original size:53 final size:52
Alignment explanation
Indices: 32195848--32196077 Score: 195
Period size: 53 Copynumber: 4.4 Consensus size: 52
32195838 GTTTTCAAAA
* * * * *
32195848 AAAAATTCTCGTGTTTCAAAAAATGTCGTGTTT-TAAAAATTTTTGTGTTTCT
1 AAAAATTCTCGTGTTTTAAAAATTCTCGTGTTTAAAAAAATTCTTGTGTTT-T
* * *
32195900 -AAAATTTTCGTGTTTTAAAAATTCTCGTGTTTCAAAAAAAATGTTGTGTTTT
1 AAAAATTCTCGTGTTTTAAAAATTCTCGTGTTT-AAAAAAATTCTTGTGTTTT
* * *
32195952 AAAAATTTTCGTGTTTCT-AAAATTTTCGTGTTTAAAAAAATTCTCGTGTTTT
1 AAAAATTCTCGTGTTT-TAAAAATTCTCGTGTTTAAAAAAATTCTTGTGTTTT
* * * * *
32196004 CAAAAATTCTCGTGTTTAAAAAAACTT-TCGTTTTTTTAAAAAATTC--ATG-CTT
1 -AAAAATTCTCGTGTTT-TAAAAA-TTCTCG-TGTTTAAAAAAATTCTTGTGTTTT
*
32196056 CAAAATTCTCGTGTTTTAAAAA
1 AAAAATTCTCGTGTTTTAAAAA
32196078 AAATTTTCTC
Statistics
Matches: 150, Mismatches: 20, Indels: 18
0.80 0.11 0.10
Matches are distributed among these distances:
50 5 0.03
51 43 0.29
52 19 0.13
53 60 0.40
54 8 0.05
55 15 0.10
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.45
Consensus pattern (52 bp):
AAAAATTCTCGTGTTTTAAAAATTCTCGTGTTTAAAAAAATTCTTGTGTTTT
Found at i:32197800 original size:25 final size:24
Alignment explanation
Indices: 32197772--32197863 Score: 69
Period size: 25 Copynumber: 3.7 Consensus size: 24
32197762 ACAGACCACA
* *
32197772 GCTCTTATGAGCGTCCTGATACTTG
1 GCTCTTATAAGCTTCCTGATA-TTG
* * *
32197797 GCTCTCATAAGCTTTCC-GTTATTTA
1 GCTCTTATAAGC-TTCCTGATA-TTG
* *
32197822 GCTCTTATAAGCATCCCGATATATG
1 GCTCTTATAAGCTTCCTGATAT-TG
*
32197847 GCTCTTATGAGCTTCCT
1 GCTCTTATAAGCTTCCT
32197864 AATTAATGGC
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
24 4 0.08
25 44 0.86
26 3 0.06
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (24 bp):
GCTCTTATAAGCTTCCTGATATTG
Found at i:32197909 original size:23 final size:23
Alignment explanation
Indices: 32197869--32197916 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
32197859 TTCCTAATTA
* * *
32197869 ATGGCTCTCTAGAGCTTCTCGAT
1 ATGGCTCGCTAGAACTTCCCGAT
*
32197892 ATGGCTCGCTTGAACTTCCCGAT
1 ATGGCTCGCTAGAACTTCCCGAT
32197915 AT
1 AT
32197917 ATAGCTATCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (23 bp):
ATGGCTCGCTAGAACTTCCCGAT
Found at i:32198161 original size:26 final size:25
Alignment explanation
Indices: 32198130--32198205 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 25
32198120 ACAGCTCTTA
32198130 TGAGCTCTCC-ATTATATGGCTCTTCG
1 TGAGCT-TCCAATTA-ATGGCTCTTCG
* * *
32198156 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCTT-CCAATTAATGGCTCTTCG
32198182 TGAGCTTCCTAATTAATGGCTCTT
1 TGAGCTTCC-AATTAATGGCTCTT
32198206 TAGAGCTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
25 3 0.07
26 36 0.84
27 4 0.09
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (25 bp):
TGAGCTTCCAATTAATGGCTCTTCG
Found at i:32198206 original size:26 final size:26
Alignment explanation
Indices: 32198140--32198206 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
32198130 TGAGCTCTCC
* *
32198140 ATTATATGGCTCTTCGTGAGCTTCCCG
1 ATTA-ATGGCTCTTTGTGAGCTTCCCA
* *
32198167 ATTAAAGGCTCTTTGTGAGCTTCCTA
1 ATTAATGGCTCTTTGTGAGCTTCCCA
32198193 ATTAATGGCTCTTT
1 ATTAATGGCTCTTT
32198207 AGAGCTTTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
26 31 0.89
27 4 0.11
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (26 bp):
ATTAATGGCTCTTTGTGAGCTTCCCA
Found at i:32202199 original size:26 final size:25
Alignment explanation
Indices: 32202147--32202208 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 25
32202137 CCTATAAGTG
32202147 TTCTGAAACTATACATGCTATGATA
1 TTCTGAAACTATACATGCTATGATA
* * *
32202172 TTCTAAAACTGATATATGTTATGATA
1 TTCTGAAACT-ATACATGCTATGATA
32202198 TTCTGAAACTA
1 TTCTGAAACTA
32202209 CTGTAGGTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 10 0.31
26 22 0.69
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (25 bp):
TTCTGAAACTATACATGCTATGATA
Found at i:32209177 original size:19 final size:19
Alignment explanation
Indices: 32209150--32209188 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
32209140 TTATTCCAGC
*
32209150 AACTTAATTAACGAAGATG
1 AACTCAATTAACGAAGATG
*
32209169 AACTCAATTAACTAAGATG
1 AACTCAATTAACGAAGATG
32209188 A
1 A
32209189 GTAATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.26
Consensus pattern (19 bp):
AACTCAATTAACGAAGATG
Found at i:32211789 original size:37 final size:37
Alignment explanation
Indices: 32211748--32211933 Score: 309
Period size: 37 Copynumber: 5.0 Consensus size: 37
32211738 GCTGAAGCTA
* *
32211748 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
32211785 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
* *
32211822 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
32211859 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
32211896 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
32211933 C
1 C
32211934 TAAAACTACC
Statistics
Matches: 142, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 142 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (37 bp):
CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
Found at i:32219531 original size:37 final size:37
Alignment explanation
Indices: 32219490--32219638 Score: 253
Period size: 37 Copynumber: 4.0 Consensus size: 37
32219480 GCTGAAGCTA
*
32219490 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
* *
32219527 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
**
32219564 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
32219601 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
32219638 C
1 C
32219639 TAAAACTACC
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 105 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (37 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
Found at i:32241161 original size:31 final size:31
Alignment explanation
Indices: 32241120--32241178 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
32241110 ATTTAATGGA
* *
32241120 GAGTGGCCAAAATAGAAATGATCTAAAATGT
1 GAGTGACCAAAATAAAAATGATCTAAAATGT
*
32241151 GAGTGACCAAAATAAAAATGATTTAAAA
1 GAGTGACCAAAATAAAAATGATCTAAAA
32241179 CATTAATGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.51, C:0.08, G:0.19, T:0.22
Consensus pattern (31 bp):
GAGTGACCAAAATAAAAATGATCTAAAATGT
Found at i:32246171 original size:20 final size:20
Alignment explanation
Indices: 32246104--32246205 Score: 65
Period size: 20 Copynumber: 5.4 Consensus size: 20
32246094 TTTATTTTAC
32246104 AATTTTTA-AA-TTTTTAAT
1 AATTTTTACAACTTTTTAAT
* * *
32246122 GATTTTCACAA-TCTTT--T
1 AATTTTTACAACTTTTTAAT
* *
32246139 AATTTGT-CAAACTTTTTGAT
1 AATTTTTAC-AACTTTTTAAT
*
32246159 AATTTTTACAACTTATTAAT
1 AATTTTTACAACTTTTTAAT
* **
32246179 -ATTTTTATAGTTTTTTAAT
1 AATTTTTACAACTTTTTAAT
32246198 AATTTTTA
1 AATTTTTA
32246206 ATTTTTCTAT
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
16 1 0.02
17 7 0.11
18 10 0.16
19 21 0.33
20 23 0.37
21 1 0.02
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (20 bp):
AATTTTTACAACTTTTTAAT
Found at i:32246906 original size:17 final size:17
Alignment explanation
Indices: 32246884--32246945 Score: 58
Period size: 16 Copynumber: 3.7 Consensus size: 17
32246874 TGTTGGGTCG
32246884 AATTTATAATAAATTAA
1 AATTTATAATAAATTAA
*
32246901 AATTTAAAAT-AATTAA
1 AATTTATAATAAATTAA
* *
32246917 AA-TCATAA-ATAATTTA
1 AATTTATAATA-AATTAA
32246933 AATTTATTAATAA
1 AATTTA-TAATAA
32246946 CACAGTTCTC
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
15 4 0.11
16 15 0.43
17 11 0.31
18 4 0.11
19 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTTATAATAAATTAA
Found at i:32250383 original size:19 final size:18
Alignment explanation
Indices: 32250352--32250396 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 18
32250342 ACAAATGGAA
32250352 ATGAAATTAAAATGAAAT
1 ATGAAATTAAAATGAAAT
*
32250370 GTGAAATGTAAAATGAAAT
1 ATGAAAT-TAAAATGAAAT
32250389 ATGAAATT
1 ATGAAATT
32250397 GTGGAATGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.29
Consensus pattern (18 bp):
ATGAAATTAAAATGAAAT
Found at i:32258769 original size:30 final size:28
Alignment explanation
Indices: 32258715--32258774 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 28
32258705 CCGCATGGTC
*
32258715 TGAGACACATGCATGTGACTCAGCCGTG
1 TGAGACACATGCATGTGACACAGCCGTG
*
32258743 TGAGACACATGGCTTGGTGACACAGCCGTG
1 TGAGACACAT-GCAT-GTGACACAGCCGTG
32258773 TG
1 TG
32258775 TCATCAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 10 0.36
29 3 0.11
30 15 0.54
ACGTcount: A:0.23, C:0.23, G:0.32, T:0.22
Consensus pattern (28 bp):
TGAGACACATGCATGTGACACAGCCGTG
Found at i:32259843 original size:7 final size:7
Alignment explanation
Indices: 32259831--32259936 Score: 59
Period size: 7 Copynumber: 15.0 Consensus size: 7
32259821 AAAAGAATAT
32259831 AATTGAG
1 AATTGAG
32259838 AATTGAG
1 AATTGAG
* * *
32259845 AAATAAT
1 AATTGAG
*
32259852 AATTAAG
1 AATTGAG
*
32259859 GATTGAGG
1 AATTGA-G
*
32259867 ATTTGAG
1 AATTGAG
*
32259874 GATTGAG
1 AATTGAG
*
32259881 GATTGAG
1 AATTGAG
*
32259888 AATTAAG
1 AATTGAG
* *
32259895 AAATGAA
1 AATTGAG
*
32259902 AATTGGG
1 AATTGAG
*
32259909 GATTGAG
1 AATTGAG
*
32259916 TATTGAG
1 AATTGAG
*
32259923 TATTGAG
1 AATTGAG
*
32259930 TATTGAG
1 AATTGAG
32259937 TTGAAAAGAA
Statistics
Matches: 76, Mismatches: 22, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
7 71 0.93
8 5 0.07
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (7 bp):
AATTGAG
Found at i:32259874 original size:8 final size:7
Alignment explanation
Indices: 32259857--32259936 Score: 61
Period size: 7 Copynumber: 11.3 Consensus size: 7
32259847 ATAATAATTA
32259857 AGGATTG
1 AGGATTG
32259864 AGGATTTG
1 AGGA-TTG
32259872 AGGATTG
1 AGGATTG
32259879 AGGATTG
1 AGGATTG
* *
32259886 AGAATTA
1 AGGATTG
* *
32259893 AGAAATG
1 AGGATTG
**
32259900 AAAATTG
1 AGGATTG
*
32259907 GGGATTG
1 AGGATTG
*
32259914 AGTATTG
1 AGGATTG
*
32259921 AGTATTG
1 AGGATTG
*
32259928 AGTATTG
1 AGGATTG
32259935 AG
1 AG
32259937 TTGAAAAGAA
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
7 54 0.89
8 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.34, T:0.31
Consensus pattern (7 bp):
AGGATTG
Found at i:32261707 original size:22 final size:22
Alignment explanation
Indices: 32261679--32261722 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
32261669 ATTAAGCTAC
32261679 AACGTCCACAAAAACATAAAAT
1 AACGTCCACAAAAACATAAAAT
32261701 AACGTCCACAAAAACATAAAAT
1 AACGTCCACAAAAACATAAAAT
32261723 TTATGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.59, C:0.23, G:0.05, T:0.14
Consensus pattern (22 bp):
AACGTCCACAAAAACATAAAAT
Found at i:32266196 original size:12 final size:13
Alignment explanation
Indices: 32266163--32266205 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
32266153 AATATGAGTG
*
32266163 AAAATAATTATAT
1 AAAAAAATTATAT
*
32266176 AACAAAATTATA-
1 AAAAAAATTATAT
*
32266188 AAAAAAATTACAT
1 AAAAAAATTATAT
32266201 AAAAA
1 AAAAA
32266206 TCAAATATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAAAATTATAT
Found at i:32266976 original size:20 final size:19
Alignment explanation
Indices: 32266952--32267000 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
32266942 TTTTTTAATT
*
32266952 ATTTTAGAA-ATTGTTTATA
1 ATTTTAGAATATT-TTTAGA
*
32266971 ATTTTTATAATATTTTTAGA
1 A-TTTTAGAATATTTTTAGA
32266991 ATTTTAGAAT
1 ATTTTAGAAT
32267001 TTTAATTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 9 0.36
20 13 0.52
21 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (19 bp):
ATTTTAGAATATTTTTAGA
Found at i:32267030 original size:28 final size:27
Alignment explanation
Indices: 32266944--32267038 Score: 77
Period size: 28 Copynumber: 3.4 Consensus size: 27
32266934 CTTTTTAATT
32266944 TTTTAATTA--TTTTAGAAATTGTTTATAA
1 TTTTAATTATTTTTTAGAAA---TTTATAA
* * * *
32266972 TTTTTATAATATTTTTAGAATTTTAGAA
1 TTTTAATTAT-TTTTTAGAAATTTATAA
*
32267000 TTTTAATTATTTTTTATAAATTTATATA
1 TTTTAATTATTTTTTAGAAATTTATA-A
*
32267028 TTTTAAATATT
1 TTTTAATTATT
32267039 ATTTGTTTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
27 13 0.25
28 32 0.60
31 8 0.15
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (27 bp):
TTTTAATTATTTTTTAGAAATTTATAA
Done.