Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008374.1 Hibiscus syriacus cultivar Beakdansim tig00111131_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: 1731758
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 10
Found at i:912750 original size:13 final size:13
Alignment explanation
Indices: 912732--912760 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
912722 TTAATTGCGA
912732 AAATTTAAAATTT
1 AAATTTAAAATTT
912745 AAATTTAAAATTT
1 AAATTTAAAATTT
912758 AAA
1 AAA
912761 AAACCTGATT
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATTTAAAATTT
Found at i:917775 original size:155 final size:155
Alignment explanation
Indices: 917493--917802 Score: 620
Period size: 155 Copynumber: 2.0 Consensus size: 155
917483 CACCTATTAT
917493 GAAAGAAGCAGATTTCCAGCCGCCGTAGCTGGTTCTGTCGACAGGGCGGCCTTTGTAGTCAAGGC
1 GAAAGAAGCAGATTTCCAGCCGCCGTAGCTGGTTCTGTCGACAGGGCGGCCTTTGTAGTCAAGGC
917558 AACCATCGACGATGTCTTCCACTAAAAGTGGGGTTTCAATGCCGGAGGAGTCATCGGAGATTGCC
66 AACCATCGACGATGTCTTCCACTAAAAGTGGGGTTTCAATGCCGGAGGAGTCATCGGAGATTGCC
917623 ATGTCGAGTATTAACCCGATGATCG
131 ATGTCGAGTATTAACCCGATGATCG
917648 GAAAGAAGCAGATTTCCAGCCGCCGTAGCTGGTTCTGTCGACAGGGCGGCCTTTGTAGTCAAGGC
1 GAAAGAAGCAGATTTCCAGCCGCCGTAGCTGGTTCTGTCGACAGGGCGGCCTTTGTAGTCAAGGC
917713 AACCATCGACGATGTCTTCCACTAAAAGTGGGGTTTCAATGCCGGAGGAGTCATCGGAGATTGCC
66 AACCATCGACGATGTCTTCCACTAAAAGTGGGGTTTCAATGCCGGAGGAGTCATCGGAGATTGCC
917778 ATGTCGAGTATTAACCCGATGATCG
131 ATGTCGAGTATTAACCCGATGATCG
917803 TCGTGTATTA
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
155 155 1.00
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (155 bp):
GAAAGAAGCAGATTTCCAGCCGCCGTAGCTGGTTCTGTCGACAGGGCGGCCTTTGTAGTCAAGGC
AACCATCGACGATGTCTTCCACTAAAAGTGGGGTTTCAATGCCGGAGGAGTCATCGGAGATTGCC
ATGTCGAGTATTAACCCGATGATCG
Found at i:917915 original size:26 final size:26
Alignment explanation
Indices: 917882--917934 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
917872 AATTGTCTTA
917882 TATTTTAGGATTTTAACCAATTTTTT
1 TATTTTAGGATTTTAACCAATTTTTT
917908 TATTTTAGGATTTTAACCAATTTTTT
1 TATTTTAGGATTTTAACCAATTTTTT
917934 T
1 T
917935 TAAATTGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.58
Consensus pattern (26 bp):
TATTTTAGGATTTTAACCAATTTTTT
Found at i:918032 original size:20 final size:20
Alignment explanation
Indices: 918007--918045 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
917997 AAATTTACAA
918007 CGCGAATCTGTAAATCGCAT
1 CGCGAATCTGTAAATCGCAT
* *
918027 CGCGAATTTGTAATTCGCA
1 CGCGAATCTGTAAATCGCA
918046 ACACAGAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (20 bp):
CGCGAATCTGTAAATCGCAT
Found at i:918103 original size:21 final size:20
Alignment explanation
Indices: 918078--918156 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 20
918068 GCGATTTCCT
918078 AATTCACAACACTGAATTTCA
1 AATTCACAACAC-GAATTTCA
*
918099 AATTCACAACTCG-ATTTCTA
1 AATTCACAACACGAATTTC-A
* * * *
918119 AATTCGCAACTCGATTTTCG
1 AATTCACAACACGAATTTCA
*
918139 AATTCTCAACACGAATTT
1 AATTCACAACACGAATTT
918157 TAATTTCGCA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
19 5 0.10
20 29 0.59
21 15 0.31
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (20 bp):
AATTCACAACACGAATTTCA
Found at i:918123 original size:20 final size:20
Alignment explanation
Indices: 918069--918135 Score: 75
Period size: 20 Copynumber: 3.3 Consensus size: 20
918059 ATTCGTAATG
*
918069 CGATTTCCT-AATTCACAACA
1 CGATTT-CTAAATTCACAACT
918089 CTGAATTTC-AAATTCACAACT
1 C-G-ATTTCTAAATTCACAACT
*
918110 CGATTTCTAAATTCGCAACT
1 CGATTTCTAAATTCACAACT
918130 CGATTT
1 CGATTT
918136 TCGAATTCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
19 5 0.12
20 19 0.46
21 13 0.32
22 4 0.10
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.34
Consensus pattern (20 bp):
CGATTTCTAAATTCACAACT
Found at i:918176 original size:18 final size:18
Alignment explanation
Indices: 918153--918187 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
918143 CTCAACACGA
918153 ATTTTAATTTCGCAACAG
1 ATTTTAATTTCGCAACAG
*
918171 ATTTTATTTTCGCAACA
1 ATTTTAATTTCGCAACA
918188 CAAATGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (18 bp):
ATTTTAATTTCGCAACAG
Found at i:918976 original size:12 final size:12
Alignment explanation
Indices: 918955--918988 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
918945 ACCACATTTC
*
918955 CAATACCAAACA
1 CAATATCAAACA
918967 CAATATCAAACA
1 CAATATCAAACA
*
918979 CAATTTCAAA
1 CAATATCAAA
918989 ACCCACAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.18
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:919165 original size:24 final size:24
Alignment explanation
Indices: 919114--919167 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
919104 GTATTCAAAA
*
919114 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
919138 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
919162 TTTGAT
1 TTTGAT
919168 GATGTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:923162 original size:21 final size:21
Alignment explanation
Indices: 923138--923210 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
923128 GCGGGAGGGG
* *
923138 CCTCTTGAATGATGAGAGAGA
1 CCTCTTGAACGATAAGAGAGA
* *
923159 CCTCTTGAACGATAAGAGGGG
1 CCTCTTGAACGATAAGAGAGA
* *
923180 CCTCTTGAAAGATATG-G-G-
1 CCTCTTGAACGATAAGAGAGA
923198 CCTCTTGAACGAT
1 CCTCTTGAACGAT
923211 GACAGGTGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
18 12 0.27
19 1 0.02
20 1 0.02
21 31 0.69
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (21 bp):
CCTCTTGAACGATAAGAGAGA
Found at i:923584 original size:21 final size:21
Alignment explanation
Indices: 923560--923603 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
923550 ATTTTCATCG
923560 CGTAAA-ACCTCTACCTCACCA
1 CGTAAAGACC-CTACCTCACCA
* *
923581 CGTAAAGACCGTACCTCATCA
1 CGTAAAGACCCTACCTCACCA
923602 CG
1 CG
923604 CCATGCACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.32, C:0.39, G:0.11, T:0.18
Consensus pattern (21 bp):
CGTAAAGACCCTACCTCACCA
Found at i:923650 original size:21 final size:21
Alignment explanation
Indices: 923617--923666 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
923607 TGCACCATTG
** *
923617 TCATCACGTAAAGTACCGACC
1 TCATCACACAAAGCACCGACC
* *
923638 TCCTCACACAAAGCACTGACC
1 TCATCACACAAAGCACCGACC
923659 TCATCACA
1 TCATCACA
923667 TAACTCCCAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.38, G:0.10, T:0.18
Consensus pattern (21 bp):
TCATCACACAAAGCACCGACC
Found at i:925288 original size:20 final size:20
Alignment explanation
Indices: 925263--925306 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
925253 AGTAGTTTCT
925263 GAAAATGAAAATCACAATGC
1 GAAAATGAAAATCACAATGC
**
925283 GAAAATGAAAATTGCAATGC
1 GAAAATGAAAATCACAATGC
925303 GAAA
1 GAAA
925307 CTAAAATCGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.11, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCACAATGC
Found at i:925338 original size:20 final size:21
Alignment explanation
Indices: 925313--925364 Score: 88
Period size: 20 Copynumber: 2.5 Consensus size: 21
925303 GAAACTAAAA
925313 TCGCGTTGCGATTTTCA-TTT
1 TCGCGTTGCGATTTTCATTTT
925333 TCGCGTTGCGATTTTCATTTT
1 TCGCGTTGCGATTTTCATTTT
*
925354 TCGTGTTGCGA
1 TCGCGTTGCGA
925365 ATTTAAGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.48
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCATTTT
Found at i:925755 original size:22 final size:21
Alignment explanation
Indices: 925700--925761 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
925690 TCTGAGAGAT
925700 GGAGATA--GACGGATTTCGC
1 GGAGATAGGGACGGATTTCGC
** *
925719 GGAGACGGGGTCGGATTTCGTC
1 GGAGATAGGGACGGATTTCG-C
*
925741 GGAGATAGGGACGGATGTCGC
1 GGAGATAGGGACGGATTTCGC
925762 CGTAGAGAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
19 5 0.15
21 11 0.33
22 17 0.52
ACGTcount: A:0.21, C:0.16, G:0.44, T:0.19
Consensus pattern (21 bp):
GGAGATAGGGACGGATTTCGC
Found at i:927741 original size:7 final size:7
Alignment explanation
Indices: 927729--927765 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
927719 GTCAAATAAA
927729 GTCAACG
1 GTCAACG
927736 GTCAACG
1 GTCAACG
927743 GTC-ACG
1 GTCAACG
927749 GTCAACG
1 GTCAACG
927756 GTCAACG
1 GTCAACG
927763 GTC
1 GTC
927766 GGGTCAACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:927751 original size:13 final size:14
Alignment explanation
Indices: 927729--927765 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
927719 GTCAAATAAA
927729 GTCAACGGTCAACG
1 GTCAACGGTCAACG
927743 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
927756 GTCAACGGTC
1 GTCAACGGTC
927766 GGGTCAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:927808 original size:19 final size:19
Alignment explanation
Indices: 927784--927851 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
927774 AGTCGGGTCA
*
927784 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
*
927803 GGTCAAACCGATTCAGACC
1 GGTCAAACCGGTTCAGACC
* *
927822 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
927842 GGTCAAACCG
1 GGTCAAACCG
927852 ATTTTCCAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 30 0.70
20 13 0.30
ACGTcount: A:0.29, C:0.31, G:0.24, T:0.16
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:927837 original size:10 final size:9
Alignment explanation
Indices: 927784--927851 Score: 55
Period size: 9 Copynumber: 7.1 Consensus size: 9
927774 AGTCGGGTCA
*
927784 GGTCAACCC
1 GGTCAAACC
*
927793 GGTTCAGACC
1 GG-TCAAACC
927803 GGTCAAACC
1 GGTCAAACC
* *
927812 GATTCAGACC
1 G-GTCAAACC
927822 GGTCAAACC
1 GGTCAAACC
*
927831 GGTTCAAAACT
1 GG-TC-AAACC
927842 GGTCAAACC
1 GGTCAAACC
927851 G
1 G
927852 ATTTTCCAAC
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 22 0.48
10 18 0.39
11 6 0.13
ACGTcount: A:0.29, C:0.31, G:0.24, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:935017 original size:13 final size:14
Alignment explanation
Indices: 934996--935031 Score: 65
Period size: 13 Copynumber: 2.6 Consensus size: 14
934986 CAAAGAAAAA
934996 TCAACGGTCAACGG
1 TCAACGGTCAACGG
935010 TC-ACGGTCAACGG
1 TCAACGGTCAACGG
935023 TCAACGGTC
1 TCAACGGTC
935032 GGGTCGGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.25, C:0.31, G:0.28, T:0.17
Consensus pattern (14 bp):
TCAACGGTCAACGG
Found at i:935043 original size:17 final size:17
Alignment explanation
Indices: 935021--935078 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
935011 CACGGTCAAC
935021 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
935038 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
935055 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
935072 GGTCAAC
1 GGTCAAC
935079 CCGGTTCAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:935048 original size:7 final size:7
Alignment explanation
Indices: 934996--935031 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
934986 CAAAGAAAAA
934996 TCAACGG
1 TCAACGG
935003 TCAACGG
1 TCAACGG
935010 TC-ACGG
1 TCAACGG
935016 TCAACGG
1 TCAACGG
935023 TCAACGG
1 TCAACGG
935030 TC
1 TC
935032 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.25, C:0.31, G:0.28, T:0.17
Consensus pattern (7 bp):
TCAACGG
Found at i:935096 original size:19 final size:19
Alignment explanation
Indices: 935072--935139 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
935062 AGTCGGGTCG
*
935072 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
* *
935091 GGTCAAACTGTTTCAGACC
1 GGTCAAACCGGTTCAGACC
* *
935110 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
935130 GGTCAAACCG
1 GGTCAAACCG
935140 ATTTTCCAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 28 0.68
20 13 0.32
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:935139 original size:29 final size:28
Alignment explanation
Indices: 935072--935139 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 28
935062 AGTCGGGTCG
* *
935072 GGTCAACCCGGTTCAGACCGGTCAAACT
1 GGTCAAACCGGTTCAAACCGGTCAAACT
* *
935100 GTTTCAGACCGG-TCAAACCGGTTCAAAACT
1 G-GTCAAACCGGTTCAAACCGG-TC-AAACT
935130 GGTCAAACCG
1 GGTCAAACCG
935140 ATTTTCCAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
28 9 0.29
29 16 0.52
30 6 0.19
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (28 bp):
GGTCAAACCGGTTCAAACCGGTCAAACT
Found at i:938185 original size:51 final size:51
Alignment explanation
Indices: 938012--938192 Score: 222
Period size: 51 Copynumber: 3.6 Consensus size: 51
938002 TTCATACTGC
* * *
938012 AAAAAA-TGTAACACTTAACACGTACTTACATCGGTGTAAGTAAATAAAAT
1 AAAAAAGTGTAACACTTAACACATACTTACAACAGTGTAAGTAAATAAAAT
* * * * * *
938062 AAACAAGTGTAACACTTAATAAAAACTTAC-ACTAGTGTAAGTGAATAAAAC
1 AAAAAAGTGTAACACTTAACACATACTTACAAC-AGTGTAAGTAAATAAAAT
* * * *
938113 AAAAAAGTGTACCATTTAACACATATTTACAACAGTATAAGTAAATAAAAT
1 AAAAAAGTGTAACACTTAACACATACTTACAACAGTGTAAGTAAATAAAAT
938164 AAAAAAGTGTAACACTTAACACATACTTA
1 AAAAAAGTGTAACACTTAACACATACTTA
938193 TACCGATATA
Statistics
Matches: 106, Mismatches: 22, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
50 6 0.06
51 98 0.92
52 2 0.02
ACGTcount: A:0.51, C:0.14, G:0.10, T:0.25
Consensus pattern (51 bp):
AAAAAAGTGTAACACTTAACACATACTTACAACAGTGTAAGTAAATAAAAT
Found at i:938403 original size:13 final size:13
Alignment explanation
Indices: 938385--938411 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
938375 AAAGTGTTAA
938385 TGAATTTTAAGAT
1 TGAATTTTAAGAT
938398 TGAATTTTAAGAT
1 TGAATTTTAAGAT
938411 T
1 T
938412 TTATATTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TGAATTTTAAGAT
Found at i:938688 original size:18 final size:18
Alignment explanation
Indices: 938665--938708 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
938655 AAGAGGTACG
938665 GATACCCCACAGGATATC
1 GATACCCCACAGGATATC
*
938683 GATACCCCACAGGGTATC
1 GATACCCCACAGGATATC
938701 GATACCCC
1 GATACCCC
938709 TCTATATAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.36, G:0.18, T:0.16
Consensus pattern (18 bp):
GATACCCCACAGGATATC
Found at i:938873 original size:21 final size:21
Alignment explanation
Indices: 938843--938889 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
938833 TAGTAGTATC
*
938843 GATA-CCCCTTGATAGGTACT
1 GATACCCCCTTGACAGGTACT
938863 GATACCCCCTTGACAGGTACT
1 GATACCCCCTTGACAGGTACT
938884 GATACC
1 GATACC
938890 ATTGATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (21 bp):
GATACCCCCTTGACAGGTACT
Found at i:944508 original size:14 final size:13
Alignment explanation
Indices: 944482--944506 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
944472 TAAGGGGGAA
944482 TAATTTTTCAAAG
1 TAATTTTTCAAAG
944495 TAATTTTTCAAA
1 TAATTTTTCAAA
944507 AGAAAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
TAATTTTTCAAAG
Found at i:948014 original size:21 final size:21
Alignment explanation
Indices: 947988--948044 Score: 98
Period size: 20 Copynumber: 2.8 Consensus size: 21
947978 CCTCCATAGG
947988 ATGAGGTCGGTACTTTGCGTT
1 ATGAGGTCGGTACTTTGCGTT
*
948009 ATGAGGTC-GTGCTTTGCGTT
1 ATGAGGTCGGTACTTTGCGTT
948029 ATGAGGTCGGTACTTT
1 ATGAGGTCGGTACTTT
948045 ACGTGAAGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.14, C:0.14, G:0.33, T:0.39
Consensus pattern (21 bp):
ATGAGGTCGGTACTTTGCGTT
Found at i:948500 original size:21 final size:21
Alignment explanation
Indices: 948476--948567 Score: 103
Period size: 21 Copynumber: 4.4 Consensus size: 21
948466 CCCCTTATCA
*
948476 TTCAAGATGCCCCTCTCATTG
1 TTCAAGAGGCCCCTCTCATTG
* *
948497 TTCAAGAGGCCCCTCCCACTG
1 TTCAAGAGGCCCCTCTCATTG
* *
948518 TTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGGCCCCTCTCATTG
* * **
948539 TTCAAGAGGTCCCTCCCACCG
1 TTCAAGAGGCCCCTCTCATTG
948560 TTCAAGAG
1 TTCAAGAG
948568 CCCGATTCAC
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.21, C:0.36, G:0.20, T:0.24
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCTCATTG
Found at i:948522 original size:42 final size:41
Alignment explanation
Indices: 948476--948570 Score: 136
Period size: 42 Copynumber: 2.3 Consensus size: 41
948466 CCCCTTATCA
* *
948476 TTCAAGATGCCCCTCTCATTGTTCAAGAGGCCCCTCCCACTG
1 TTCAAGA-GCCCCTCTCATCGTTCAAGAGGCCCCTCCCACCG
* *
948518 TTCAAGAGGCCCCTGTCATCGTTCAAGAGGTCCCTCCCACCG
1 TTCAAGA-GCCCCTCTCATCGTTCAAGAGGCCCCTCCCACCG
948560 TTCAAGAGCCC
1 TTCAAGAGCCC
948571 GATTCACATG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 4 0.08
42 44 0.92
ACGTcount: A:0.20, C:0.38, G:0.19, T:0.23
Consensus pattern (41 bp):
TTCAAGAGCCCCTCTCATCGTTCAAGAGGCCCCTCCCACCG
Found at i:950084 original size:20 final size:20
Alignment explanation
Indices: 950067--950164 Score: 160
Period size: 20 Copynumber: 4.9 Consensus size: 20
950057 TACAAATTTT
950067 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
** *
950087 CATTGCGATAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
950107 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
*
950127 CAACGTGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
950147 CAACGCGAAAGTCAAATT
1 CAACGCGAAAGTCAAATT
950165 GGCGATGCAA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.19
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:951410 original size:24 final size:24
Alignment explanation
Indices: 951355--951410 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
951345 ATTTATATAT
951355 ATTGAAATTCAAACTCAAATTGAC
1 ATTGAAATTCAAACTCAAATTGAC
* *
951379 ATTTAAATTCAAACTCCAATT-AC
1 ATTGAAATTCAAACTCAAATTGAC
951402 ATATGAAAT
1 AT-TGAAAT
951411 GAATTTGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.32
Consensus pattern (24 bp):
ATTGAAATTCAAACTCAAATTGAC
Found at i:951805 original size:25 final size:25
Alignment explanation
Indices: 951777--951826 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
951767 CATTATTTTC
*
951777 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
951802 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
951827 TATGTTGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:951947 original size:20 final size:20
Alignment explanation
Indices: 951924--951968 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
951914 TGCGATAATC
*
951924 AAATTCGCAACGCGAAAGTA
1 AAATTCACAACGCGAAAGTA
*
951944 AAATTCACGACGCGAAAGTA
1 AAATTCACAACGCGAAAGTA
951964 AAATT
1 AAATT
951969 TGCGTTGCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATTCACAACGCGAAAGTA
Found at i:954599 original size:24 final size:24
Alignment explanation
Indices: 954572--954637 Score: 123
Period size: 24 Copynumber: 2.8 Consensus size: 24
954562 CAAAATCCGA
954572 GTATTGACCAAGATCAAAGTCTGG
1 GTATTGACCAAGATCAAAGTCTGG
*
954596 GTATTGACCAAGATCAGAGTCTGG
1 GTATTGACCAAGATCAAAGTCTGG
954620 GTATTGACCAAGATCAAA
1 GTATTGACCAAGATCAAA
954638 TTTCGAATAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTCTGG
Found at i:955638 original size:21 final size:21
Alignment explanation
Indices: 955569--955643 Score: 88
Period size: 19 Copynumber: 3.8 Consensus size: 21
955559 AACTAAAACC
955569 TGTTGCGAAA-TT-AAATTC-G
1 TGTTGC-AAATTTGAAATTCAG
*
955588 TGTTGCGAATTTGAAATTCA-
1 TGTTGCAAATTTGAAATTCAG
*
955608 -GTTGCGAATTTGAAATTCAG
1 TGTTGCAAATTTGAAATTCAG
955628 TGTTGCAAATTTGAAA
1 TGTTGCAAATTTGAAA
955644 ATCACATTAC
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
18 2 0.04
19 27 0.55
20 6 0.12
21 14 0.29
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.37
Consensus pattern (21 bp):
TGTTGCAAATTTGAAATTCAG
Found at i:955639 original size:40 final size:40
Alignment explanation
Indices: 955570--955661 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 40
955560 ACTAAAACCT
* * *
955570 GTTGCGAAATT-AAATTCGTGTTGCGAATTTGAAATTCA-
1 GTTGCGAATTTGAAATTCGTGTTGCAAATTTGAAAATCAC
955608 GTTGCGAATTTGAAATTCAGTGTTGCAAATTTGAAAATCAC
1 GTTGCGAATTTGAAATTC-GTGTTGCAAATTTGAAAATCAC
* *
955649 ATTACGAATTTGA
1 GTTGCGAATTTGA
955662 CTTATGTGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 10 0.22
39 6 0.13
40 19 0.41
41 11 0.24
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.36
Consensus pattern (40 bp):
GTTGCGAATTTGAAATTCGTGTTGCAAATTTGAAAATCAC
Found at i:959082 original size:84 final size:84
Alignment explanation
Indices: 958941--959109 Score: 338
Period size: 84 Copynumber: 2.0 Consensus size: 84
958931 AGTAACTTGT
958941 TTGCGCTACTTCTAGCCTTCCTTTCTGTTTTCTCCATTGCCTCTGTGCCATTGTTCACTACATGA
1 TTGCGCTACTTCTAGCCTTCCTTTCTGTTTTCTCCATTGCCTCTGTGCCATTGTTCACTACATGA
959006 CTCCGTAAAGCCTCAGCCG
66 CTCCGTAAAGCCTCAGCCG
959025 TTGCGCTACTTCTAGCCTTCCTTTCTGTTTTCTCCATTGCCTCTGTGCCATTGTTCACTACATGA
1 TTGCGCTACTTCTAGCCTTCCTTTCTGTTTTCTCCATTGCCTCTGTGCCATTGTTCACTACATGA
959090 CTCCGTAAAGCCTCAGCCG
66 CTCCGTAAAGCCTCAGCCG
959109 T
1 T
959110 GTCTTTCGCC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.14, C:0.33, G:0.15, T:0.37
Consensus pattern (84 bp):
TTGCGCTACTTCTAGCCTTCCTTTCTGTTTTCTCCATTGCCTCTGTGCCATTGTTCACTACATGA
CTCCGTAAAGCCTCAGCCG
Found at i:959966 original size:27 final size:26
Alignment explanation
Indices: 959906--959983 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 26
959896 TATTTTGTAT
* * *
959906 TAAT-AATTTATTTTATTTTTTAAATG
1 TAATAAATTTA-TTTATTATTAAAATA
*
959932 TAATAAATTTATTTATTCTTAAAATA
1 TAATAAATTTATTTATTATTAAAATA
* *
959958 TTATAAAATCATATTTATTATTAAAA
1 TAAT-AAAT-TTATTTATTATTAAAA
959984 ATTCATTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
26 19 0.44
27 10 0.23
28 14 0.33
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.53
Consensus pattern (26 bp):
TAATAAATTTATTTATTATTAAAATA
Found at i:960040 original size:15 final size:15
Alignment explanation
Indices: 960020--960067 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
960010 TTGTCGTGAT
*
960020 TAATTTTCTATAAAA
1 TAATTTTATATAAAA
*
960035 TAA-TTTATTTAAAAA
1 TAATTTTATAT-AAAA
*
960050 TTATTTTATATAAAA
1 TAATTTTATATAAAA
960065 TAA
1 TAA
960068 GTAAAATAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
14 5 0.19
15 15 0.58
16 6 0.23
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATTTTATATAAAA
Found at i:960087 original size:39 final size:39
Alignment explanation
Indices: 960030--960106 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
960020 TAATTTTCTA
* *
960030 TAAAATAATTTATTTAAAAA-TTATTTTATATAAAATAAG
1 TAAAATAAATTATATAAAAACTT-TTTTATATAAAATAAG
*
960069 TAAAATAAATTATATAAAAACTTTTTTATGTAAAATAA
1 TAAAATAAATTATATAAAAACTTTTTTATATAAAATAA
960107 ATTATCTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.42
Consensus pattern (39 bp):
TAAAATAAATTATATAAAAACTTTTTTATATAAAATAAG
Found at i:960133 original size:30 final size:30
Alignment explanation
Indices: 960069--960134 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
960059 ATAAAATAAG
* **
960069 TAAAATAAATTATATAAAAACTTTTTTATG
1 TAAAATAAATTATATAAAAACTTATTTACA
*
960099 TAAAATAAATTATCTAAAAA-TTAATTTACA
1 TAAAATAAATTATATAAAAACTT-ATTTACA
960129 TAAAAT
1 TAAAAT
960135 GGATTATGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (30 bp):
TAAAATAAATTATATAAAAACTTATTTACA
Found at i:966048 original size:21 final size:21
Alignment explanation
Indices: 966022--966074 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
966012 GTTTTCAGAT
*
966022 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCAACTA
* *
966043 TCGCAACGCGAACTTCAATTA
1 TCGCAACGCGAACATCAACTA
*
966064 TCGCAATGCGA
1 TCGCAACGCGA
966075 TTTTCCAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACATCAACTA
Found at i:966106 original size:19 final size:19
Alignment explanation
Indices: 966084--966182 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 19
966074 ATTTTCCAAA
*
966084 TTCGTTGCGGTAGTCGAAG
1 TTCGTTGCGATAGTCGAAG
* *
966103 TTCGCGTTGCGATTTATTCCAAG
1 TT--CGTTGCGA--TAGTCGAAG
966126 TTCGTTGCGATAGTCGAAG
1 TTCGTTGCGATAGTCGAAG
* * *
966145 TTCGTGTTGCGATTTATTCCAAA
1 TTC--GTTGCGA--TAGTCGAAG
966168 TTCGTTGCGATAGTC
1 TTCGTTGCGATAGTC
966183 CAAAATCGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
19 16 0.25
21 29 0.46
23 18 0.29
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (19 bp):
TTCGTTGCGATAGTCGAAG
Found at i:966112 original size:21 final size:21
Alignment explanation
Indices: 966086--966157 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
966076 TTTCCAAATT
*
966086 CGTTGCGGTAGTCGAAGTTCG
1 CGTTGCGATAGTCGAAGTTCG
* *
966107 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCGAAGTTCG
966128 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCGAAGTTCG
*
966149 TGTTGCGAT
1 CGTTGCGAT
966158 TTATTCCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
19 9 0.22
21 23 0.56
23 9 0.22
ACGTcount: A:0.17, C:0.18, G:0.31, T:0.35
Consensus pattern (21 bp):
CGTTGCGATAGTCGAAGTTCG
Found at i:966130 original size:42 final size:42
Alignment explanation
Indices: 966070--966182 Score: 185
Period size: 42 Copynumber: 2.7 Consensus size: 42
966060 ATTATCGCAA
*
966070 TGCGA-TT-TTCCAAATTCGTTGCGGTAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
* *
966110 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGTGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
966152 TGCGATTTATTCCAAATTCGTTGCGATAGTC
1 TGCGATTTATTCCAAATTCGTTGCGATAGTC
966183 CAAAATCGCA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 5 0.07
41 2 0.03
42 60 0.90
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (42 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
Found at i:966174 original size:21 final size:21
Alignment explanation
Indices: 966107--966178 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
966097 TCGAAGTTCG
966107 CGTTGCGATTTATTCCAAGTT
1 CGTTGCGATTTATTCCAAGTT
* *
966128 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAGTT
*
966147 CGTGTTGCGATTTATTCCAAATT
1 C--GTTGCGATTTATTCCAAGTT
966170 CGTTGCGAT
1 CGTTGCGAT
966179 AGTCCAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 10 0.24
21 23 0.55
23 9 0.21
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAGTT
Found at i:966292 original size:6 final size:6
Alignment explanation
Indices: 966274--966313 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
966264 AGACACGTAT
966274 GACCAC GACCCAC GACCAC GACCAC GACCAC GACC-C GACC
1 GACCAC GA-CCAC GACCAC GACCAC GACCAC GACCAC GACC
966314 TGAGACGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.15
6 22 0.67
7 6 0.18
ACGTcount: A:0.30, C:0.53, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:972234 original size:41 final size:40
Alignment explanation
Indices: 972163--972243 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 40
972153 TTTTTTTTTA
* **
972163 TATTATAATATATTATTTAATTGTTAAAAATATAA-AAAT
1 TATTATAAAATATTATTTAATCATTAAAAATATAATAAAT
*
972202 TATTATAAAAATATTAATTTAATCATTTAAAATATAATAAAT
1 TATTAT-AAAATATT-ATTTAATCATTAAAAATATAATAAAT
972244 AAATAAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
39 6 0.17
40 7 0.20
41 18 0.51
42 4 0.11
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (40 bp):
TATTATAAAATATTATTTAATCATTAAAAATATAATAAAT
Found at i:974327 original size:28 final size:28
Alignment explanation
Indices: 974287--974362 Score: 143
Period size: 28 Copynumber: 2.7 Consensus size: 28
974277 ATATTTTTTT
974287 TAATTAATTTGAATAATAGCAGAATAAA
1 TAATTAATTTGAATAATAGCAGAATAAA
974315 TAATTAATTTGAATAATAGCAGAATAAA
1 TAATTAATTTGAATAATAGCAGAATAAA
*
974343 TAATTAATTTGAATTATAGC
1 TAATTAATTTGAATAATAGC
974363 TCATATATTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.36
Consensus pattern (28 bp):
TAATTAATTTGAATAATAGCAGAATAAA
Found at i:974526 original size:26 final size:26
Alignment explanation
Indices: 974497--974546 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
974487 GTCAATAATT
974497 TTTTTTAAAATATATAAA-ATTTATAA
1 TTTTTTAAAATATA-AAATATTTATAA
*
974523 TTTTTTAAATTATAAAATATTTAT
1 TTTTTTAAAATATAAAATATTTAT
974547 TATTATCATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTTTTAAAATATAAAATATTTATAA
Found at i:977792 original size:29 final size:30
Alignment explanation
Indices: 977731--977793 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 30
977721 TGACATGATA
*
977731 TACATGCTTATATGAATATGCAATATGTAT
1 TACATGCTTATATGAATATGCAAGATGTAT
977761 TACATG-TTATATGAA-ATGACATAGATGT-T
1 TACATGCTTATATGAATATG-CA-AGATGTAT
977790 TACA
1 TACA
977794 CATACATATG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 3 0.10
29 16 0.53
30 11 0.37
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (30 bp):
TACATGCTTATATGAATATGCAAGATGTAT
Found at i:978767 original size:13 final size:13
Alignment explanation
Indices: 978751--978780 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
978741 GTTCATAGTG
978751 CTGTTTCACGGTA
1 CTGTTTCACGGTA
978764 CTG-TTCACGGTA
1 CTGTTTCACGGTA
978776 CTGTT
1 CTGTT
978781 CATACCATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.13, C:0.23, G:0.23, T:0.40
Consensus pattern (13 bp):
CTGTTTCACGGTA
Found at i:978770 original size:12 final size:12
Alignment explanation
Indices: 978755--978782 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
978745 ATAGTGCTGT
978755 TTCACGGTACTG
1 TTCACGGTACTG
978767 TTCACGGTACTG
1 TTCACGGTACTG
978779 TTCA
1 TTCA
978783 TACCATATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (12 bp):
TTCACGGTACTG
Found at i:990944 original size:15 final size:15
Alignment explanation
Indices: 990909--990947 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
990899 GCCGAGCCGA
*
990909 GCCGAGCCGTGTCAT
1 GCCGTGCCGTGTCAT
990924 GCCGTGCCGTGTCAT
1 GCCGTGCCGTGTCAT
*
990939 GTCGTGCCG
1 GCCGTGCCG
990948 AGCCGAGACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.08, C:0.33, G:0.36, T:0.23
Consensus pattern (15 bp):
GCCGTGCCGTGTCAT
Found at i:993550 original size:17 final size:17
Alignment explanation
Indices: 993528--993579 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 17
993518 GGCCGGGTAT
993528 ATATATATTTAAATTAA
1 ATATATATTTAAATTAA
*
993545 ATATATA---AATATTAT
1 ATATATATTTAA-ATTAA
993560 ATATATATTTAAATTTAA
1 ATATATATTTAAA-TTAA
993578 AT
1 AT
993580 TAAATTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
14 2 0.07
15 11 0.39
17 8 0.29
18 7 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATATTTAAATTAA
Found at i:993576 original size:38 final size:38
Alignment explanation
Indices: 993525--993608 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 38
993515 TCGGGCCGGG
*
993525 TATATATATATTTAAATTAAATATATAAATATTATATA
1 TATATATAAATTTAAATTAAATATATAAATATTATATA
* * *
993563 TATATTTAAATTTAAATTAAATTTATTAATATTATATA
1 TATATATAAATTTAAATTAAATATATAAATATTATATA
993601 TATATATA
1 TATATATA
993609 TAATAATTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (38 bp):
TATATATAAATTTAAATTAAATATATAAATATTATATA
Found at i:993609 original size:15 final size:15
Alignment explanation
Indices: 993527--993606 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 15
993517 GGGCCGGGTA
*
993527 TATATATATTTAAAT
1 TATATATATATAAAT
993542 TA-A-ATATATAAA-
1 TATATATATATAAAT
*
993554 TAT-TATATATATAT
1 TATATATATATAAAT
*
993568 T-TA-A-ATTTAAAT
1 TATATATATATAAAT
* *
993580 TAAATTTAT-TAATAT
1 TATATATATATAA-AT
993595 TATATATATATA
1 TATATATATATA
993607 TATAATAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 17
0.66 0.11 0.23
Matches are distributed among these distances:
12 9 0.19
13 19 0.40
14 5 0.10
15 13 0.27
16 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATATATATATAAAT
Found at i:996461 original size:24 final size:26
Alignment explanation
Indices: 996421--996471 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
996411 TTATTAATCT
996421 TTAGAATTTATAAATTTAT-TTTAAA
1 TTAGAATTTATAAATTTATCTTTAAA
*
996446 TTAGAA-TTATACATTTATCTTTAAA
1 TTAGAATTTATAAATTTATCTTTAAA
996471 T
1 T
996472 ATAATCATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (26 bp):
TTAGAATTTATAAATTTATCTTTAAA
Found at i:1000556 original size:21 final size:20
Alignment explanation
Indices: 1000496--1000556 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
1000486 ATGCTTATAG
*
1000496 GAGTATCGATACTAGGGGTA-
1 GAGTATCGATACTA-AGGTAT
* *
1000516 GAGTATCAATACTCCA-GTAT
1 GAGTATCGATACT-AAGGTAT
1000536 GAGGTATCGATACTAAGGTAT
1 GA-GTATCGATACTAAGGTAT
1000557 TTTTCAAAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
19 3 0.09
20 15 0.47
21 14 0.44
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
GAGTATCGATACTAAGGTAT
Found at i:1003249 original size:27 final size:28
Alignment explanation
Indices: 1003189--1003279 Score: 105
Period size: 27 Copynumber: 3.3 Consensus size: 28
1003179 TTTTGTCTGG
* * *
1003189 GATTTATTC-CCGATCTGTTATGTATGA
1 GATTTATTCACCAATCTATTCTGTATGA
* *
1003216 GATTTATTCTCTAATCTATTCTGTATGA
1 GATTTATTCACCAATCTATTCTGTATGA
* *
1003244 GA-TTATTCACCGATCTATTCTGTATGG
1 GATTTATTCACCAATCTATTCTGTATGA
1003271 GATTTATTC
1 GATTTATTC
1003280 CCTGATTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
27 32 0.59
28 22 0.41
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (28 bp):
GATTTATTCACCAATCTATTCTGTATGA
Found at i:1003305 original size:55 final size:54
Alignment explanation
Indices: 1003178--1003306 Score: 134
Period size: 55 Copynumber: 2.4 Consensus size: 54
1003168 GCCGGTATTA
* * *
1003178 TTTTTGTCTGGGATTTATTCCCGATCTGTTATGTATGAGATTTATTCTCTAATCT
1 TTTTTGTATGGGA-TTATTCCCGATCTATTATGTATGAGATTTATTCCCTAATCT
* * * * * *
1003233 ATTCTGTATGAGATTATTCACCGATCTATTCTGTATGGGATTTATTCCCTGAT-T
1 TTTTTGTATGGGATTATTC-CCGATCTATTATGTATGAGATTTATTCCCTAATCT
*
1003287 TTTTTGTGTGGGAGTTATTC
1 TTTTTGTATGGGA-TTATTC
1003307 TCTGCTCTGT
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
54 16 0.27
55 43 0.73
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (54 bp):
TTTTTGTATGGGATTATTCCCGATCTATTATGTATGAGATTTATTCCCTAATCT
Found at i:1011857 original size:37 final size:36
Alignment explanation
Indices: 1011758--1011876 Score: 170
Period size: 35 Copynumber: 3.3 Consensus size: 36
1011748 TGGTAACCAA
*
1011758 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATAGTTTTCAAAGTTTGGTAAATGTTT
1011795 CTTT-AAAAATAGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
* *
1011830 CTTTGAAAAATAATTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-AGTTTTCAAAGTTTGGTAAATGTTT
*
1011867 -GTTGAAAAAT
1 CTTTGAAAAAT
1011877 GATAATGGGA
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 34 0.45
36 15 0.20
37 27 0.36
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1012299 original size:16 final size:16
Alignment explanation
Indices: 1012273--1012311 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1012263 TCGGGTTACT
*
1012273 ATTTACGTGAATAGTGA
1 ATTT-CGTGAATACTGA
1012290 ATTTCGTGAATACTGA
1 ATTTCGTGAATACTGA
*
1012306 AATTCG
1 ATTTCG
1012312 GTCGGCGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (16 bp):
ATTTCGTGAATACTGA
Found at i:1012309 original size:17 final size:17
Alignment explanation
Indices: 1012273--1012306 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1012263 TCGGGTTACT
*
1012273 ATTTACGTGAATAGTGA
1 ATTTACGTGAATACTGA
1012290 ATTT-CGTGAATACTGA
1 ATTTACGTGAATACTGA
1012306 A
1 A
1012307 ATTCGGTCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (17 bp):
ATTTACGTGAATACTGA
Found at i:1012665 original size:3 final size:3
Alignment explanation
Indices: 1012653--1012748 Score: 90
Period size: 3 Copynumber: 32.0 Consensus size: 3
1012643 ACGGCGGGTC
** ***
1012653 TTA TTA -TA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TGC CCC TT-
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1012697 TTA TTA TTA TTA TTA TTA TTA TTA TTA GTTA TTA TT- TTT TTA GTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA -TTA
1012743 TTA TTA
1 TTA TTA
1012749 ATTTTTATTT
Statistics
Matches: 80, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
2 6 0.08
3 65 0.81
4 9 0.11
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1012902 original size:57 final size:57
Alignment explanation
Indices: 1012814--1012926 Score: 226
Period size: 57 Copynumber: 2.0 Consensus size: 57
1012804 CGGGTTTGGG
1012814 CCTGACCCAACCCTAACTCGATTAGGGTTTCATGTCTAGCTAGCAGGAGGGCATCGC
1 CCTGACCCAACCCTAACTCGATTAGGGTTTCATGTCTAGCTAGCAGGAGGGCATCGC
1012871 CCTGACCCAACCCTAACTCGATTAGGGTTTCATGTCTAGCTAGCAGGAGGGCATCG
1 CCTGACCCAACCCTAACTCGATTAGGGTTTCATGTCTAGCTAGCAGGAGGGCATCG
1012927 TTTTAGTTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23
Consensus pattern (57 bp):
CCTGACCCAACCCTAACTCGATTAGGGTTTCATGTCTAGCTAGCAGGAGGGCATCGC
Found at i:1013994 original size:16 final size:14
Alignment explanation
Indices: 1013959--1014014 Score: 62
Period size: 16 Copynumber: 4.0 Consensus size: 14
1013949 TTTTTTTCTT
*
1013959 TTTTAGTATTTTTA
1 TTTTATTATTTTTA
1013973 --TTATTATTTTTA
1 TTTTATTATTTTTA
1013985 CTTCTTATTATTTTTA
1 -TT-TTATTATTTTTA
*
1014001 TTTTATTACTTTTA
1 TTTTATTATTTTTA
1014015 AAATTTAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
12 11 0.31
14 11 0.31
15 2 0.06
16 12 0.33
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTATTATTTTTA
Found at i:1019284 original size:24 final size:24
Alignment explanation
Indices: 1019216--1019301 Score: 91
Period size: 24 Copynumber: 3.6 Consensus size: 24
1019206 CCAGAAGCTG
*
1019216 AGTTAACTCGGACCAAGTTGACCT
1 AGTTAACTCAGACCAAGTTGACCT
* * *
1019240 AGTAAACTCAGATCAAATTGACCT
1 AGTTAACTCAGACCAAGTTGACCT
** * *
1019264 AGTTAACTCAGACCGGGTTGATCG
1 AGTTAACTCAGACCAAGTTGACCT
*
1019288 AGTTAACTTAGACC
1 AGTTAACTCAGACC
1019302 GAGTCAACCC
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (24 bp):
AGTTAACTCAGACCAAGTTGACCT
Found at i:1019398 original size:21 final size:21
Alignment explanation
Indices: 1019335--1019398 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 21
1019325 GTTGACACGA
1019335 CTGTTGACCATTGACTTTGA-
1 CTGTTGACCATTGACTTTGAC
1019355 CTCGTTGA-CAGTTGACTTTGAC
1 CT-GTTGACCA-TTGACTTTGAC
* *
1019377 CTGTTGACCATTAATTTTGAC
1 CTGTTGACCATTGACTTTGAC
1019398 C
1 C
1019399 AAAAGTCGAC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 4 0.11
21 30 0.79
22 4 0.11
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (21 bp):
CTGTTGACCATTGACTTTGAC
Found at i:1023304 original size:20 final size:22
Alignment explanation
Indices: 1023267--1023315 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
1023257 TTTCTACCAT
*
1023267 ACAACAACCATTATA-TTT-CC
1 ACAACATCCATTATATTTTGCC
1023287 ACAACATCCATT-TCATTTTGCC
1 ACAACATCCATTAT-ATTTTGCC
1023309 ACAACAT
1 ACAACAT
1023316 TATCATTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 1 0.04
20 12 0.48
21 3 0.12
22 9 0.36
ACGTcount: A:0.37, C:0.31, G:0.02, T:0.31
Consensus pattern (22 bp):
ACAACATCCATTATATTTTGCC
Found at i:1035165 original size:21 final size:21
Alignment explanation
Indices: 1035139--1035299 Score: 213
Period size: 21 Copynumber: 7.7 Consensus size: 21
1035129 GTTTCCAGAT
*
1035139 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
1035160 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
1035181 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
1035202 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
1035222 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
1035243 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
1035264 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
1035285 TCGCAATGCGAACTT
1 TCGCAATGCGAACTT
1035300 GCGAACTTGG
Statistics
Matches: 125, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
20 17 0.14
21 108 0.86
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:1035225 original size:62 final size:62
Alignment explanation
Indices: 1035159--1035275 Score: 182
Period size: 62 Copynumber: 1.9 Consensus size: 62
1035149 AACTTCGACT
* *
1035159 ATCGCAACGCGA-ACTTCGACTATCGCAATGCGAACTTCGACTATCGCAATGCGAATATGTAA
1 ATCGCAACGCGATA-GTCGACTATCGCAATGCGAACTTCGACTATCGCAACGCGAATATGTAA
* *
1035221 ATCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAACGCGAA
1 ATCGCAACGCGATAGTCGACTATCGCAATGCGAACTTCGACTATCGCAACGCGAA
1035276 CTTCGACTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
62 49 0.98
63 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (62 bp):
ATCGCAACGCGATAGTCGACTATCGCAATGCGAACTTCGACTATCGCAACGCGAATATGTAA
Found at i:1035254 original size:104 final size:106
Alignment explanation
Indices: 1035139--1035351 Score: 340
Period size: 104 Copynumber: 2.0 Consensus size: 106
1035129 GTTTCCAGAT
1035139 TCGCAACGCGAACTTCGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAACTT-C-GACTA
1 TCGCAACGCGAACTTCGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTACTGACTA
1035202 TCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTA
66 TCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTA
* *
1035243 TCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGCGAACTT
1 TCGCAACGCGAACTTCGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAACTT----AC-T
1035308 GGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGA
61 -GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGA
1035352 AGTTCGCGTT
Statistics
Matches: 99, Mismatches: 2, Indels: 8
0.91 0.02 0.07
Matches are distributed among these distances:
104 55 0.56
109 1 0.01
112 43 0.43
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.23
Consensus pattern (106 bp):
TCGCAACGCGAACTTCGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTACTGACTA
TCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTA
Found at i:1035505 original size:6 final size:6
Alignment explanation
Indices: 1035496--1035545 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
1035486 CATTACCATT
1035496 ACCACG ACCACG ACCACG ACC-CG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1035543 ACC
1 ACC
1035546 CGAGACGGAC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.12
6 38 0.88
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1036063 original size:16 final size:16
Alignment explanation
Indices: 1036044--1036076 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1036034 CGGGTGTGTC
1036044 GTCGTGGTCGT-GTCGT
1 GTCGT-GTCGTGGTCGT
1036060 GTCGTGTCGTGGTCGT
1 GTCGTGTCGTGGTCGT
1036076 G
1 G
1036077 GTAATACGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.00, C:0.18, G:0.45, T:0.36
Consensus pattern (16 bp):
GTCGTGTCGTGGTCGT
Found at i:1036546 original size:18 final size:17
Alignment explanation
Indices: 1036525--1036564 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
1036515 TAATAGTGTG
1036525 TTATTATAAAATATATTT
1 TTATTAT-AAATATATTT
*
1036543 TTATTATAATTATATTT
1 TTATTATAAATATATTT
1036560 TTATT
1 TTATT
1036565 TGTATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATTATAAATATATTT
Found at i:1036593 original size:18 final size:18
Alignment explanation
Indices: 1036525--1036593 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
1036515 TAATAGTGTG
**
1036525 TTATTATAAAATATATTT
1 TTATTATAATTTATATTT
1036543 TTATTATAA-TTATATTT
1 TTATTATAATTTATATTT
*
1036560 TTATTTGTATATTTTATATTT
1 TTA--T-TATAATTTATATTT
1036581 TTATTATAATTTA
1 TTATTATAATTTA
1036594 AATTGATATA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
17 10 0.23
18 17 0.39
19 2 0.05
20 4 0.09
21 11 0.25
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (18 bp):
TTATTATAATTTATATTT
Found at i:1036605 original size:33 final size:33
Alignment explanation
Indices: 1036535--1036621 Score: 90
Period size: 32 Copynumber: 2.7 Consensus size: 33
1036525 TTATTATAAA
* * *
1036535 ATATATTTT-TATTATAATTATATTTTTATTTG
1 ATATATTTTATATTATAATTATAATTTAAATTG
* *
1036567 -TATATTTTATATTTTTATTATAATTTAAATTG
1 ATATATTTTATATTATAATTATAATTTAAATTG
* *
1036599 ATATATTTCATA-TATAATAATAA
1 ATATATTTTATATTATAATTATAA
1036622 CTTATTTTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
31 8 0.18
32 26 0.59
33 10 0.23
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (33 bp):
ATATATTTTATATTATAATTATAATTTAAATTG
Found at i:1042682 original size:29 final size:26
Alignment explanation
Indices: 1042645--1042710 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 26
1042635 TTATTTTTTA
*
1042645 TTAATAATTCATTATCATCTGTTAAAATT
1 TTAATAATTCATT-T-AT-TATTAAAATT
*
1042674 TTAATAATTTATTTATTATTAAAATT
1 TTAATAATTCATTTATTATTAAAATT
*
1042700 TTAAAAATTCA
1 TTAATAATTCA
1042711 CCTAATAACG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 18 0.55
27 2 0.06
28 1 0.03
29 12 0.36
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (26 bp):
TTAATAATTCATTTATTATTAAAATT
Found at i:1044033 original size:27 final size:26
Alignment explanation
Indices: 1043997--1044047 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
1043987 CATTTAAATG
1043997 ATAAACGAACACAAACGAACGAACATA
1 ATAAACGAACACAAACGAAC-AACATA
* *
1044024 ATAAAGGAACATAAACGAACAACA
1 ATAAACGAACACAAACGAACAACA
1044048 CAAACACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.61, C:0.20, G:0.12, T:0.08
Consensus pattern (26 bp):
ATAAACGAACACAAACGAACAACATA
Found at i:1045229 original size:20 final size:21
Alignment explanation
Indices: 1045198--1045240 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
1045188 TAAAACATTA
1045198 TATATAACCTTTGTCTTTACT
1 TATATAACCTTTGTCTTTACT
1045219 TATAT-ACCTTTGTCTTTACT
1 TATATAACCTTTGTCTTTACT
1045239 TA
1 TA
1045241 AATTCAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.23, C:0.19, G:0.05, T:0.53
Consensus pattern (21 bp):
TATATAACCTTTGTCTTTACT
Found at i:1046271 original size:27 final size:27
Alignment explanation
Indices: 1046234--1046288 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
1046224 GATTACAATA
*
1046234 ATAGTAGTAAATAATATACAAATGAAT
1 ATAGTAATAAATAATATACAAATGAAT
*
1046261 ATAGTAATAAATAATATACATATGAAT
1 ATAGTAATAAATAATATACAAATGAAT
1046288 A
1 A
1046289 ACAATTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.56, C:0.04, G:0.09, T:0.31
Consensus pattern (27 bp):
ATAGTAATAAATAATATACAAATGAAT
Found at i:1052393 original size:16 final size:16
Alignment explanation
Indices: 1052374--1052410 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1052364 TATATTTTCA
1052374 TTTTAT-TTATGGTTAG
1 TTTTATATTATGGTT-G
1052390 TTTTATATTATGGTTG
1 TTTTATATTATGGTTG
1052406 TTTTA
1 TTTTA
1052411 AAGTCAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.19, C:0.00, G:0.16, T:0.65
Consensus pattern (16 bp):
TTTTATATTATGGTTG
Found at i:1053699 original size:15 final size:15
Alignment explanation
Indices: 1053679--1053747 Score: 120
Period size: 15 Copynumber: 4.6 Consensus size: 15
1053669 TGTGAAGAAG
1053679 TTCTAGAAGGAAGAC
1 TTCTAGAAGGAAGAC
*
1053694 TTCTAGAAGGAAGAG
1 TTCTAGAAGGAAGAC
1053709 TTCTAGAAGGAAGAC
1 TTCTAGAAGGAAGAC
*
1053724 TTCTAGAAGGAAGAG
1 TTCTAGAAGGAAGAC
1053739 TTCTAGAAG
1 TTCTAGAAG
1053748 ACTAGGCTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 51 1.00
ACGTcount: A:0.39, C:0.10, G:0.29, T:0.22
Consensus pattern (15 bp):
TTCTAGAAGGAAGAC
Found at i:1053711 original size:30 final size:30
Alignment explanation
Indices: 1053672--1053747 Score: 143
Period size: 30 Copynumber: 2.5 Consensus size: 30
1053662 AGCTGGGTGT
1053672 GAAGAAGTTCTAGAAGGAAGACTTCTAGAAG
1 GAAG-AGTTCTAGAAGGAAGACTTCTAGAAG
1053703 GAAGAGTTCTAGAAGGAAGACTTCTAGAAG
1 GAAGAGTTCTAGAAGGAAGACTTCTAGAAG
1053733 GAAGAGTTCTAGAAG
1 GAAGAGTTCTAGAAG
1053748 ACTAGGCTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 41 0.91
31 4 0.09
ACGTcount: A:0.41, C:0.09, G:0.30, T:0.20
Consensus pattern (30 bp):
GAAGAGTTCTAGAAGGAAGACTTCTAGAAG
Found at i:1056311 original size:32 final size:32
Alignment explanation
Indices: 1056270--1056335 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
1056260 CCTTGTCATA
*
1056270 CGAGGGTACAAGCAACAACTGGTCTCTCTACG
1 CGAGGGTACAAGCAACAACTGGTCTCTCCACG
1056302 CGAGGGTACAAGCAACAACTGGTCTCTCCACG
1 CGAGGGTACAAGCAACAACTGGTCTCTCCACG
1056334 CG
1 CG
1056336 CTCTAATGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.27, C:0.30, G:0.26, T:0.17
Consensus pattern (32 bp):
CGAGGGTACAAGCAACAACTGGTCTCTCCACG
Found at i:1060370 original size:178 final size:178
Alignment explanation
Indices: 1060071--1060427 Score: 682
Period size: 178 Copynumber: 2.0 Consensus size: 178
1060061 CTTCTCTAGA
1060071 TCAATTTTAATGGTCATCCACCCAACTTTCCTAATCTTTCGCTTCATCGAATGGATTACCTCTTG
1 TCAATTTTAATGGTCATCCACCCAACTTTCCTAATCTTTCGCTTCATCGAATGGATTACCTCTTG
1060136 GGAAAAAATGATATTATTAGAGATATTCCATCTTGGAACAAACTTTTATGATCTTCAG-AATCCA
66 GGAAAAAATGATATTATTAGAGATATTCCATCTTGGAACAAACTTTTATGATCTTCAGAAATCCA
1060200 CTTCGGTTAAAAAAGGCTTGAGGTGATTAACCATCACTTTCGCGATTGT
131 CTTCGG-TAAAAAAGGCTTGAGGTGATTAACCATCACTTTCGCGATTGT
1060249 TCAATTTTAATGGTCATCCACCCAACTTTCCTAATCTTTCGCTTCATCGAATGGATTACCTCTT-
1 TCAATTTTAATGGTCATCCACCCAACTTTCCTAATCTTTCGCTTCATCGAATGGATTACCTCTTG
1060313 GGAAAAAATGATATTATTAGAGATATTCCATCTTGGAACAAAACTTTTATGATCTTCAGAAATCC
66 GGAAAAAATGATATTATTAGAGATATTCCATCTTGGAAC-AAACTTTTATGATCTTCAGAAATCC
1060378 ACTTCGGTAAAAAAGGCTTGAGGTGATTAACCATCACTTTCGCGATTGT
130 ACTTCGGTAAAAAAGGCTTGAGGTGATTAACCATCACTTTCGCGATTGT
1060427 T
1 T
1060428 TTGAATAATA
Statistics
Matches: 177, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
177 39 0.22
178 126 0.71
179 12 0.07
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (178 bp):
TCAATTTTAATGGTCATCCACCCAACTTTCCTAATCTTTCGCTTCATCGAATGGATTACCTCTTG
GGAAAAAATGATATTATTAGAGATATTCCATCTTGGAACAAACTTTTATGATCTTCAGAAATCCA
CTTCGGTAAAAAAGGCTTGAGGTGATTAACCATCACTTTCGCGATTGT
Found at i:1080444 original size:17 final size:16
Alignment explanation
Indices: 1080421--1080464 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
1080411 TGTTTACGCA
*
1080421 TAATATTATTTAAAAT
1 TAATATTATTTAAAAG
* *
1080437 TAAATATTACTTAAGAG
1 T-AATATTATTTAAAAG
1080454 TAATATTATTT
1 TAATATTATTT
1080465 CAATAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (16 bp):
TAATATTATTTAAAAG
Found at i:1081629 original size:112 final size:113
Alignment explanation
Indices: 1081431--1081650 Score: 433
Period size: 112 Copynumber: 2.0 Consensus size: 113
1081421 TTTCATGGCT
1081431 TCTATTCATGCGATTTCTTTAGTTGCTGATTTAGGTTTCCAGGAGATAGTGGTAGAAGGCGACTC
1 TCTATTCATGCGATTTCTTTAGTTGCTGATTTAGGTTTCCAGGAGATAGTGGTAGAAGGCGACTC
1081496 TAGGGCGATAATTGAAAAATTAATCTCATCGGAATTCGATCTCGGAAA
66 TAGGGCGATAATTGAAAAATTAATCTCATCGGAATTCGATCTCGGAAA
1081544 TCTATTCATGCGA-TTCTTTAGTTGCTGATTTAGGTTTCCAGGAGATAGTGGTAGAAGGCGACTC
1 TCTATTCATGCGATTTCTTTAGTTGCTGATTTAGGTTTCCAGGAGATAGTGGTAGAAGGCGACTC
1081608 TAGGGCGATAATTGAAAAATTAATCTCATCGGAATTCGATCTC
66 TAGGGCGATAATTGAAAAATTAATCTCATCGGAATTCGATCTC
1081651 TCGGAAATAA
Statistics
Matches: 107, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
112 94 0.88
113 13 0.12
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (113 bp):
TCTATTCATGCGATTTCTTTAGTTGCTGATTTAGGTTTCCAGGAGATAGTGGTAGAAGGCGACTC
TAGGGCGATAATTGAAAAATTAATCTCATCGGAATTCGATCTCGGAAA
Found at i:1085190 original size:31 final size:31
Alignment explanation
Indices: 1085147--1085227 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
1085137 TAGACTCTGA
* *
1085147 GGCCTCGAGATCTTTCTTGGGTAGGCCCTGT
1 GGCCCCGAGATCTTTCTTGGGTAGGCCCCGT
1085178 GGCCCCGAGATCTTTCTTGGGTAGGCCCCGT
1 GGCCCCGAGATCTTTCTTGGGTAGGCCCCGT
* *
1085209 GGCCCTGAGTAACTTTCTT
1 GGCCCCGAG-ATCTTTCTT
1085228 AGGAAGGCTC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 37 0.82
32 8 0.18
ACGTcount: A:0.11, C:0.28, G:0.30, T:0.31
Consensus pattern (31 bp):
GGCCCCGAGATCTTTCTTGGGTAGGCCCCGT
Found at i:1086509 original size:3 final size:3
Alignment explanation
Indices: 1086501--1086571 Score: 97
Period size: 3 Copynumber: 23.0 Consensus size: 3
1086491 TTTACTCATT
* * *
1086501 TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TAA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1086549 TATA TATA TTA TTA TTA TTA TTA
1 T-TA T-TA TTA TTA TTA TTA TTA
1086572 AAAAATAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
3 54 0.89
4 7 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1090155 original size:17 final size:17
Alignment explanation
Indices: 1090115--1090149 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1090105 GCAAGAATCG
1090115 GATTATGGGGAGGAATT
1 GATTATGGGGAGGAATT
1090132 GATTATGGGGAGGAATT
1 GATTATGGGGAGGAATT
1090149 G
1 G
1090150 GATATGCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.43, T:0.29
Consensus pattern (17 bp):
GATTATGGGGAGGAATT
Found at i:1091719 original size:15 final size:15
Alignment explanation
Indices: 1091699--1091730 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1091689 ATCAATACCT
1091699 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
1091714 TTTTGCATACATTCA
1 TTTTGCATACATGCA
1091729 TT
1 TT
1091731 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:1099022 original size:12 final size:12
Alignment explanation
Indices: 1098996--1099111 Score: 99
Period size: 13 Copynumber: 8.9 Consensus size: 12
1098986 TATTATGCTT
1098996 AAAGAAAAAAGAA
1 AAAGAAAAAA-AA
1099009 AAA-AAAAGAAAA
1 AAAGAAAA-AAAA
*
1099021 AAGGAAAAAAAGA
1 AAAGAAAAAAA-A
1099034 AGGAAGAAAAAAAA
1 A--AAGAAAAAAAA
*
1099048 GAAGGAAGAAAAAA
1 -AAAGAA-AAAAAA
*
1099062 AAAGAGAAAAAAG
1 AAAGA-AAAAAAA
1099075 AAAGAAAAGAAAA
1 AAAGAAAA-AAAA
*
1099088 AAAGAAAAGAAA
1 AAAGAAAAAAAA
1099100 AAAGAAAGAAAA
1 AAAGAAA-AAAA
1099112 GAGAAAAAGG
Statistics
Matches: 85, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
12 24 0.28
13 43 0.51
14 8 0.09
15 10 0.12
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:1099028 original size:16 final size:16
Alignment explanation
Indices: 1098996--1099121 Score: 89
Period size: 16 Copynumber: 7.8 Consensus size: 16
1098986 TATTATGCTT
*
1098996 AAAGAAAAAAGAAAAAA
1 AAAGAAAAAAG-GAAAA
1099013 AAAGAAAAAAGGAAAA
1 AAAGAAAAAAGGAAAA
** *
1099029 AAAGAAGGAAGAAAAA
1 AAAGAAAAAAGGAAAA
** *
1099045 AAAGAAGGAAGAAAAAA
1 AAAGAAAAAAG-GAAAA
*
1099062 AAAGAGAAAAAAGAAAGA
1 AAAGA-AAAAAGGAAA-A
*
1099080 AAAG-AAAAA--AAGA
1 AAAGAAAAAAGGAAAA
1099093 AAAGAAAAAA-GAAAGA
1 AAAGAAAAAAGGAAA-A
1099109 AAAGAGAAAAAGG
1 AAAGA-AAAAAGG
1099122 GGGTCAAGGT
Statistics
Matches: 91, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
13 5 0.05
14 7 0.08
15 2 0.02
16 39 0.43
17 29 0.32
18 9 0.10
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAGGAAAA
Found at i:1099106 original size:29 final size:29
Alignment explanation
Indices: 1098996--1099120 Score: 138
Period size: 29 Copynumber: 4.4 Consensus size: 29
1098986 TATTATGCTT
1098996 AAAG-AAAAAAG-AAA-AAAAAAGAAA-A
1 AAAGAAAAAAAGAAAAGAAAAAAGAAAGA
*
1099021 AAGGAAAAAAAGAAGGAAG-AAAAA-AAAGA
1 AAAGAAAAAAAGAA--AAGAAAAAAGAAAGA
*
1099050 AGGAAGAAAAAAA-AAGAGAAAAAAGAAAGA
1 A--AAGAAAAAAAGAAAAGAAAAAAGAAAGA
1099080 AAAGAAAAAAAGAAAAGAAAAAAGAAAGA
1 AAAGAAAAAAAGAAAAGAAAAAAGAAAGA
*
1099109 AAAGAGAAAAAG
1 AAAGAAAAAAAG
1099121 GGGGTCAAGG
Statistics
Matches: 84, Mismatches: 5, Indels: 18
0.79 0.05 0.17
Matches are distributed among these distances:
25 3 0.04
26 7 0.08
27 1 0.01
28 15 0.18
29 41 0.49
30 8 0.10
31 9 0.11
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (29 bp):
AAAGAAAAAAAGAAAAGAAAAAAGAAAGA
Found at i:1099117 original size:59 final size:58
Alignment explanation
Indices: 1099000--1099119 Score: 147
Period size: 59 Copynumber: 2.0 Consensus size: 58
1098990 ATGCTTAAAG
* *
1099000 AAAAAAGAAAAAAAAAGAAAAAAGGAAAAAAAGAAGGAAGAAAAAAAAGAAGGAAGAAA
1 AAAAAAGAAAAAAAAAGAAAAAAAGAAAAAAAGAA-GAAGAAAAAAAAGAAAGAAGAAA
*
1099059 AAAAAAG-AGAAAAAAGAAAGAAAAGAAAAAAAGAA-AAGAAAAAAGAAAGAAA-AGAGAAA
1 AAAAAAGAAAAAAAAAGAAA-AAAAGAAAAAAAGAAGAAG-AAAAA-AAAGAAAGA-AGAAA
1099118 AA
1 AA
1099120 GGGGGTCAAG
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
57 3 0.06
58 17 0.31
59 34 0.63
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (58 bp):
AAAAAAGAAAAAAAAAGAAAAAAAGAAAAAAAGAAGAAGAAAAAAAAGAAAGAAGAAA
Found at i:1100162 original size:93 final size:93
Alignment explanation
Indices: 1099963--1100225 Score: 431
Period size: 93 Copynumber: 2.8 Consensus size: 93
1099953 CGTAGACCCA
* * *
1099963 ATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACCCTAAAAAAACC
1 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCT--AAAAACC
1100028 AATCATTGAATTTGGAAGATGAATGTGCTC
64 AATCATTGAATTTGGAAGATGAATGTGCTC
1100058 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCTAAAAACCAA
1 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCTAAAAACCAA
1100123 TCATTGAATTTGGAAGATGAATGTGCTC
66 TCATTGAATTTGGAAGATGAATGTGCTC
* *
1100151 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAA-CC-ACAGAACCA
1 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCTA-AAAACCA
1100214 ATCATTGGAATT
65 ATCATT-GAATT
1100226 AAAAGATGAA
Statistics
Matches: 161, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
91 1 0.01
92 14 0.09
93 93 0.58
95 53 0.33
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (93 bp):
ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCTAAAAACCAA
TCATTGAATTTGGAAGATGAATGTGCTC
Found at i:1101123 original size:112 final size:111
Alignment explanation
Indices: 1100957--1101561 Score: 827
Period size: 112 Copynumber: 5.5 Consensus size: 111
1100947 TGTCAGTTAG
*
1100957 AGTTCATAATGAGAAGAACTCATCTGAAGAGAGAAGAAGAAGTTCATAATAAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGA-AGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1101022 AACTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAA
65 AACTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAA
* *
1101069 AGTTCATAATCAGAAGAACTCATCTGAAGAGAGAAGAAGAAATTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGA-AGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1101134 AACTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAA
65 AACTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAA
* * *
1101181 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
** * ** * * ****
1101246 AACCTTTTGCTAAAATCCATCATTCAATGGATCAGTTTTTCCAGTTCG
65 AA-CTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAA
1101294 AGTTCATAATGAGAAGAACTCATCT---GAAG-A-AA-AAGTTCATAATAAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCA
1101353 ACTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAA
66 ACTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAA
* * *
1101399 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGCTCATAATGAGAAGAACTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
* * * * * *
1101464 AACCCTTTG-TTCAAATTCATCACTTAATGGATCAACCTTT-ACAGAGAA
65 AA-CTTTTGCTT-GAATTCATCATTTGATGGATC-AGCTTTGCCAGAGAA
1101512 AGTTCATAATGAGAAGAACTCATCTGAAGAAG-AG-A-AAGTTCATAATAAGA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAAGA
1101562 GCTTATTCAA
Statistics
Matches: 438, Mismatches: 43, Indels: 27
0.86 0.08 0.05
Matches are distributed among these distances:
105 59 0.13
106 26 0.06
107 2 0.00
108 4 0.01
109 15 0.03
110 5 0.01
111 5 0.01
112 197 0.45
113 120 0.27
114 5 0.01
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (111 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCA
ACTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAA
Found at i:1101375 original size:330 final size:332
Alignment explanation
Indices: 1100921--1101557 Score: 961
Period size: 330 Copynumber: 1.9 Consensus size: 332
1100911 GCAAAGATTT
1100921 AAATCCATCATTCAATGGATCAACAGTGTCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTCAATGGATCAACAGTGTCAGTTAGAGTTCATAATGAGAAGAACTCATCT--AG
*
1100986 AGAGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACTTTTGCTTGAATTCATCATTTGATGG
64 AGAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTGCTTGAATTCATCATTTGATGG
*
1101051 ATCAGCTTTGCCAGAGAAAGTTCATAATCAGAAGAACTCATCTGAAG-AGAGAAGAAGAAATTCA
129 ATCAGCTTTGCCAGAGAAAGTTCATAATCAGAAGAACTCATCTGAAGAAG-GAAGAAGAAACTCA
* * * * * *
1101115 TAATAAGAAGAACTTGTTCAA-CTTTTGCTT-GAATTCATCATTTGATGGATC-AGCTTTGCCAG
193 TAATAAGAAGAACTTGTTCAACCCTTTG-TTCAAATTCATCACTTAATGGATCAACCTTT-ACAG
1101177 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTT
256 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-AG--AAAGTTCATAATGAGAAGAATTT
1101242 GTTCAACCTTTTGCTA
317 GTTCAACCTTTTGCTA
*** * *
1101258 AAATCCATCATTCAATGGATC-AGTTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCT-GA
1 AAATCCATCATTCAATGGATCAACAGTGT-CAGTTAGAGTTCATAATGAGAAGAACTCATCTAGA
1101321 -AG-A-AA-AAGTTCATAATAAGAAGAACTTGTTCAACTTTTGCTTGAATTCATCATTTGATGGA
65 GAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTGCTTGAATTCATCATTTGATGGA
* *
1101382 TCAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGCTCATA
130 TCAGCTTTGCCAGAGAAAGTTCATAATCAGAAGAACTCATCTGAAGAAGGAAGAAGAAACTCATA
* *
1101447 ATGAGAAGAACTTGTTTAACCCTTTGTTCAAATTCATCACTTAATGGATCAACCTTTACAGAGAA
195 ATAAGAAGAACTTGTTCAACCCTTTGTTCAAATTCATCACTTAATGGATCAACCTTTACAGAGAA
1101512 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAGAAAGTTCATAAT
260 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAGAAAGTTCATAAT
1101558 AAGAGCTTAT
Statistics
Matches: 278, Mismatches: 17, Indels: 20
0.88 0.05 0.06
Matches are distributed among these distances:
327 12 0.04
329 2 0.01
330 134 0.48
331 65 0.23
332 6 0.02
333 2 0.01
334 2 0.01
336 3 0.01
337 52 0.19
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (332 bp):
AAATCCATCATTCAATGGATCAACAGTGTCAGTTAGAGTTCATAATGAGAAGAACTCATCTAGAG
AGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTGCTTGAATTCATCATTTGATGGAT
CAGCTTTGCCAGAGAAAGTTCATAATCAGAAGAACTCATCTGAAGAAGGAAGAAGAAACTCATAA
TAAGAAGAACTTGTTCAACCCTTTGTTCAAATTCATCACTTAATGGATCAACCTTTACAGAGAAA
GTTCATAATGAGAAGAACTCATCTGAAGAAGAGAAAGTTCATAATGAGAAGAATTTGTTCAACCT
TTTGCTA
Found at i:1101390 original size:218 final size:218
Alignment explanation
Indices: 1100957--1101561 Score: 883
Period size: 218 Copynumber: 2.7 Consensus size: 218
1100947 TGTCAGTTAG
*
1100957 AGTTCATAATGAGAAGAACTCATCTGAAG-AGAGAAGAAGAAGTTCATAATAAGAAGAATTTGTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAG-GAAGAAGAAGTTCATAATGAGAAGAATTTGTT
** * * *
1101021 CAA-CTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAAAGTTCATAATCAGAAG
65 CAACCTTTTGCTAAAATTCATCA-TTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAG
1101085 AACTCATCTGAAGAGAGAAGAAGAAATTCATAATAAGAAGAACTTGTTCAACTTTTGCTTGAATT
129 AACTCATCTG-A-AGAGAA-AAG---TTCATAATAAGAAGAACTTGTTCAACTTTTGCTTGAATT
1101150 CATCATTTGATGGATCAGCTTTGCCAGAGAA
188 CATCATTTGATGGATCAGCTTTGCCAGAGAA
*
1101181 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * ****
1101246 AACCTTTTGCTAAAATCCATCATTCAATGGATCAGTTTTTCCAGTTCGAGTTCATAATGAGAAGA
66 AACCTTTTGCTAAAATTCATCATT-AATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGA
1101311 ACTCATCTGAAGA-AAAAGTTCATAATAAGAAGAACTTGTTCAACTTTTGCTTGAATTCATCATT
130 ACTCATCTGAAGAGAAAAGTTCATAATAAGAAGAACTTGTTCAACTTTTGCTTGAATTCATCATT
1101375 TGATGGATCAGCTTTGCCAGAGAA
195 TGATGGATCAGCTTTGCCAGAGAA
* * *
1101399 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGCTCATAATGAGAAGAACTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * * * *
1101464 AACCCTTTGTTCAAATTCATCACTTAATGGATCAACCTTTACAGAGAAAGTTCATAATGAGAAGA
66 AACCTTTTGCTAAAATTCATCA-TTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGA
1101529 ACTCATCTGAAGAAGAGAAAGTTCATAATAAGA
130 ACTCATCTGAAG-AGA-AAAGTTCATAATAAGA
1101562 GCTTATTCAA
Statistics
Matches: 345, Mismatches: 29, Indels: 17
0.88 0.07 0.04
Matches are distributed among these distances:
218 193 0.56
219 3 0.01
220 1 0.00
221 19 0.06
222 2 0.01
223 3 0.01
224 65 0.19
225 59 0.17
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (218 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTGCTAAAATTCATCATTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
CTCATCTGAAGAGAAAAGTTCATAATAAGAAGAACTTGTTCAACTTTTGCTTGAATTCATCATTT
GATGGATCAGCTTTGCCAGAGAA
Found at i:1101453 original size:24 final size:23
Alignment explanation
Indices: 1101410--1101454 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
1101400 GTTCATAATG
*
1101410 AGAAGAACTCATCTGAAGAAGGA
1 AGAAGAACTCATATGAAGAAGGA
1101433 AGAAGAAGCTCATAATG-AGAAG
1 AGAAGAA-CTCAT-ATGAAGAAG
1101455 AACTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.11, G:0.27, T:0.13
Consensus pattern (23 bp):
AGAAGAACTCATATGAAGAAGGA
Found at i:1101813 original size:3 final size:3
Alignment explanation
Indices: 1101807--1101869 Score: 92
Period size: 3 Copynumber: 21.0 Consensus size: 3
1101797 TTTACTCGTT
* *
1101807 TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TAA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1101854 TATA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA
1101870 AAAAAATAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.04
3 49 0.91
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1107083 original size:41 final size:41
Alignment explanation
Indices: 1107038--1107164 Score: 115
Period size: 41 Copynumber: 3.1 Consensus size: 41
1107028 TTTAGCAGTG
*
1107038 TTTTTATAAAAACGCCGCAATATGGTCATGTATAGTGGCGT
1 TTTTTATAAAAACGCCGCAATATGGTCATGTATAGCGGCGT
* *
1107079 TTTTT-GACAAACGCCGCTAA-A-GAGT-A-GTACTGTAGCGGCG-
1 TTTTTATAAAAACGCCGC-AATATG-GTCATGTA---TAGCGGCGT
*
1107119 TTTTTATAAAAACGCCGTAAT-TGGGTCATGTATAGCGGCGT
1 TTTTTATAAAAACGCCGCAATAT-GGTCATGTATAGCGGCGT
1107160 TTTTT
1 TTTTT
1107165 TGACAAACGA
Statistics
Matches: 68, Mismatches: 6, Indels: 24
0.69 0.06 0.24
Matches are distributed among these distances:
38 3 0.04
39 2 0.03
40 28 0.41
41 30 0.44
42 2 0.03
43 3 0.04
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.34
Consensus pattern (41 bp):
TTTTTATAAAAACGCCGCAATATGGTCATGTATAGCGGCGT
Found at i:1107146 original size:81 final size:82
Alignment explanation
Indices: 1107037--1107204 Score: 259
Period size: 82 Copynumber: 2.1 Consensus size: 82
1107027 CTTTAGCAGT
* * * *
1107037 GTTTTTATAAAAACGCCGCAATATGGTCATGTATAGTGGCG-TTTTTTGACAAACGCCGCTAAAG
1 GTTTTTATAAAAACGCCGCAATATGGTCATGTATAGCGGCGTTTTTTTGACAAACGACACTAAAA
1107101 AGTAGTACTGTAGCGGC
66 AGTAGTACTGTAGCGGC
*
1107118 GTTTTTATAAAAACGCCGTAAT-TGGGTCATGTATAGCGGCGTTTTTTTGACAAACGACACTAAA
1 GTTTTTATAAAAACGCCGCAATAT-GGTCATGTATAGCGGCGTTTTTTTGACAAACGACACTAAA
*
1107182 AAGTAGTACTTTAGCGGC
65 AAGTAGTACTGTAGCGGC
1107200 GTTTT
1 GTTTT
1107205 CATTTACAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
80 1 0.01
81 37 0.47
82 41 0.52
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (82 bp):
GTTTTTATAAAAACGCCGCAATATGGTCATGTATAGCGGCGTTTTTTTGACAAACGACACTAAAA
AGTAGTACTGTAGCGGC
Found at i:1107173 original size:41 final size:41
Alignment explanation
Indices: 1107047--1107173 Score: 113
Period size: 40 Copynumber: 3.1 Consensus size: 41
1107037 GTTTTTATAA
* *
1107047 AAACGCCGCAATAT-GGTCATGTATAGTGGCG-TTTTTTGAC
1 AAACGCCGTAAT-TGGGTCATGTATAGCGGCGTTTTTTTGAC
* * * *
1107087 AAACGCCGCTAA-AGAGT-A-GTACTGTAGCGGCGTTTTTAT-AA
1 AAACGCCG-TAATTGGGTCATGTA---TAGCGGCGTTTTTTTGAC
1107128 AAACGCCGTAATTGGGTCATGTATAGCGGCGTTTTTTTGAC
1 AAACGCCGTAATTGGGTCATGTATAGCGGCGTTTTTTTGAC
1107169 AAACG
1 AAACG
1107174 ACACTAAAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
38 3 0.04
39 1 0.01
40 27 0.40
41 27 0.40
42 6 0.09
43 3 0.04
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (41 bp):
AAACGCCGTAATTGGGTCATGTATAGCGGCGTTTTTTTGAC
Found at i:1107204 original size:82 final size:81
Alignment explanation
Indices: 1107025--1107204 Score: 263
Period size: 81 Copynumber: 2.2 Consensus size: 81
1107015 AACCGAGTTA
* * *
1107025 TACTTTAGCAGTGTTTTTATAAAAACGCCGCAATATGGTCATGTATAGTGGCGTTTTTTGACAAA
1 TACTTTAGCGGCGTTTTTATAAAAACGCCGCAATATGGTCATGTATAGCGGCGTTTTTTGACAAA
* * *
1107090 CGCCGCTAAAGAGTAG
66 CGACACTAAAAAGTAG
* *
1107106 TACTGTAGCGGCGTTTTTATAAAAACGCCGTAAT-TGGGTCATGTATAGCGGCGTTTTTTTGACA
1 TACTTTAGCGGCGTTTTTATAAAAACGCCGCAATAT-GGTCATGTATAGCGGCG-TTTTTTGACA
1107170 AACGACACTAAAAAGTAG
64 AACGACACTAAAAAGTAG
1107188 TACTTTAGCGGCGTTTT
1 TACTTTAGCGGCGTTTT
1107205 CATTTACAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
80 1 0.01
81 46 0.52
82 41 0.47
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (81 bp):
TACTTTAGCGGCGTTTTTATAAAAACGCCGCAATATGGTCATGTATAGCGGCGTTTTTTGACAAA
CGACACTAAAAAGTAG
Found at i:1112400 original size:15 final size:16
Alignment explanation
Indices: 1112368--1112400 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1112358 AAAATCTTTC
1112368 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
1112384 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
1112399 TT
1 TT
1112401 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:1113177 original size:16 final size:17
Alignment explanation
Indices: 1113150--1113184 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1113140 TATCGCCGAC
1113150 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
1113167 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
1113183 CG
1 CG
1113185 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:1115667 original size:42 final size:42
Alignment explanation
Indices: 1115549--1115934 Score: 362
Period size: 42 Copynumber: 9.1 Consensus size: 42
1115539 ATTAGCAGCT
* * * * * *
1115549 TTTGTTCCAAAAACACCACTATAGACCTAGATCTTTTGCGGCG
1 TTTGTTCCAAAAACGCCGCTATATA-TTTGACCTTTTGCGGCG
* * *
1115592 TTTGTACCAAAAAACGCCGTTATATATTTGACCTTTAGCGGCG
1 TTTGTTCC-AAAAACGCCGCTATATATTTGACCTTTTGCGGCG
* * * *
1115635 TTTGTTCCAAAAATGCCGCTATAGATATGACCTTTAGCGGCG
1 TTTGTTCCAAAAACGCCGCTATATATTTGACCTTTTGCGGCG
* * *
1115677 TTTGTTCCAAAAACGCCGCTATAGATCTAACCTTTTGCGGCG
1 TTTGTTCCAAAAACGCCGCTATATATTTGACCTTTTGCGGCG
* * * * * *
1115719 TTTGTTCAAAAAATGCAGCTATATATCTTGACATATTGCGGCT
1 TTTGTTCCAAAAACGCCGCTATATAT-TTGACCTTTTGCGGCG
* * * * * * * *
1115762 TTTCTT-GAACAAACACCGCTAAATGTCTAACCTTTTGCGGCA
1 TTTGTTCCAA-AAACGCCGCTATATATTTGACCTTTTGCGGCG
* *
1115804 TTTGTTCCAAAAACGCCGCTATATATCTTGACCTATTGCAGCG
1 TTTGTTCCAAAAACGCCGCTATATAT-TTGACCTTTTGCGGCG
** *
1115847 TTT-TTTGAACAAACGCCGCTATATATCTGACCTTTTGCGGCG
1 TTTGTTCCAA-AAACGCCGCTATATATTTGACCTTTTGCGGCG
* *
1115889 TTTGTTCCAAAAACGCCGTTATATATCTTGACCTATTGCGGCG
1 TTTGTTCCAAAAACGCCGCTATATAT-TTGACCTTTTGCGGCG
1115932 TTT
1 TTT
1115935 TTTGTTCTCA
Statistics
Matches: 276, Mismatches: 59, Indels: 16
0.79 0.17 0.05
Matches are distributed among these distances:
42 156 0.57
43 107 0.39
44 13 0.05
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (42 bp):
TTTGTTCCAAAAACGCCGCTATATATTTGACCTTTTGCGGCG
Found at i:1115781 original size:127 final size:126
Alignment explanation
Indices: 1115540--1115902 Score: 365
Period size: 127 Copynumber: 2.8 Consensus size: 126
1115530 AGAAAGGTAA
* * * * * * *
1115540 TTAGCAGCTTTTGTTCCAAAAACACCACTATAGACCTAGATCTTTTGCGGCGTTTGTACCAAAAA
1 TTAGCGGCATTTGTTCCAAAAACGCCGCTATAGATCTA-ACCTTTTGCGGCGTTTGT-TCAAAAA
* * ** * *
1115605 ACGCCGTTATATAT-TTGACCTTTAGCGGCGTTTGTTCCAAAAATGCCGCTATA-GATATGACCT
64 ACGCCGCTATATATCTTGACCTTT-GCGGCGTTTCTTCCAAAAACACCGCTAAATG-TATAACCT
* *
1115668 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCAAAAAAT
1 TTAGCGGCATTTGTTCCAAAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCAAAAAAC
* * * * *
1115733 GCAGCTATATATCTTGACATATTGCGGCTTTTCTT-GAACAAACACCGCTAAATGTCTAACCT
66 GCCGCTATATATCTTGACCT-TTGCGGCGTTTCTTCCAA-AAACACCGCTAAATGTATAACCT
* * * * * * * *
1115795 TTTGCGGCATTTGTTCCAAAAACGCCGCTATATATCTTGACCTATTGCAGCGTTTTTTGAACAAA
1 TTAGCGGCATTTGTTCCAAAAACGCCGCTATAGATC-TAACCTTTTGCGGCGTTTGTTCAAAAAA
*
1115860 CGCCGCTATATATC-TGACCTTTTGCGGCGTTTGTTCCAAAAAC
65 CGCCGCTATATATCTTGACC-TTTGCGGCGTTTCTTCCAAAAAC
1115903 GCCGTTATAT
Statistics
Matches: 194, Mismatches: 34, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
126 19 0.10
127 102 0.53
128 73 0.38
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (126 bp):
TTAGCGGCATTTGTTCCAAAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCAAAAAAC
GCCGCTATATATCTTGACCTTTGCGGCGTTTCTTCCAAAAACACCGCTAAATGTATAACCT
Found at i:1115802 original size:85 final size:85
Alignment explanation
Indices: 1115549--1115938 Score: 412
Period size: 85 Copynumber: 4.6 Consensus size: 85
1115539 ATTAGCAGCT
* * * * * * * *** * *
1115549 TTTGTTCCAAAAACACCACTATAGACCTAGATCTTTTGCGGCGTTTGTACCAAAAAACGCCGTTA
1 TTTGTTCCAAAAACGCCGCTATATATCTTGACCTATTGCGGCGTTT-TTTGAACAAACGCCGCTA
* * * *
1115614 TATATTTGACCTTTAGCGGCG
65 TATGTCTAACCTTTTGCGGCG
* * * **
1115635 TTTGTTCCAAAAATGCCGCTATAGAT-ATGACCT-TTAGCGGCGTTTGTTCCAA-AAACGCCGCT
1 TTTGTTCCAAAAACGCCGCTATATATCTTGACCTATT-GCGGCGTTT-TTTGAACAAACGCCGCT
1115697 ATA-GATCTAACCTTTTGCGGCG
64 ATATG-TCTAACCTTTTGCGGCG
* * * * *
1115719 TTTGTTCAAAAAATGCAGCTATATATCTTGACATATTGCGGC-TTTTCTTGAACAAACACCGCTA
1 TTTGTTCCAAAAACGCCGCTATATATCTTGACCTATTGCGGCGTTTT-TTGAACAAACGCCGCTA
* *
1115783 AATGTCTAACCTTTTGCGGCA
65 TATGTCTAACCTTTTGCGGCG
*
1115804 TTTGTTCCAAAAACGCCGCTATATATCTTGACCTATTGCAGCGTTTTTTGAACAAACGCCGCTAT
1 TTTGTTCCAAAAACGCCGCTATATATCTTGACCTATTGCGGCGTTTTTTGAACAAACGCCGCTAT
* *
1115869 ATATCTGACCTTTTGCGGCG
66 ATGTCTAACCTTTTGCGGCG
*
1115889 TTTGTTCCAAAAACGCCGTTATATATCTTGACCTATTGCGGCGTTTTTTG
1 TTTGTTCCAAAAACGCCGCTATATATCTTGACCTATTGCGGCGTTTTTTG
1115939 TTCTCAAACT
Statistics
Matches: 261, Mismatches: 35, Indels: 17
0.83 0.11 0.05
Matches are distributed among these distances:
83 1 0.00
84 57 0.22
85 174 0.67
86 29 0.11
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.34
Consensus pattern (85 bp):
TTTGTTCCAAAAACGCCGCTATATATCTTGACCTATTGCGGCGTTTTTTGAACAAACGCCGCTAT
ATGTCTAACCTTTTGCGGCG
Found at i:1125883 original size:26 final size:28
Alignment explanation
Indices: 1125788--1125963 Score: 162
Period size: 29 Copynumber: 6.2 Consensus size: 28
1125778 CCGTTGACCG
*
1125788 GGTGATATTTTAGTAATTATTTTGAAAA
1 GGTGATATTTTCGTAATTATTTTGAAAA
*
1125816 TGGTGATATTTTGGTAATTATTTTGAAAA
1 -GGTGATATTTTCGTAATTATTTTGAAAA
* *
1125845 TGGTGTTATTTTCGTAATT-TTTTTAAAA
1 -GGTGATATTTTCGTAATTATTTTGAAAA
* *
1125873 -GTGATAATTTCGTAA--ATTTTAAAAA
1 GGTGATATTTTCGTAATTATTTTGAAAA
*** *
1125898 AAAGATATTTTAGTAATTATTTTGAAAA
1 GGTGATATTTTCGTAATTATTTTGAAAA
* * *
1125926 GAGTGATATTTTTGTAAATATTTTTAAAAA
1 G-GTGATATTTTCGTAATTA-TTTTGAAAA
1125956 GGGTGATA
1 -GGTGATA
1125964 AATGTGTAAA
Statistics
Matches: 122, Mismatches: 18, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
25 8 0.07
26 24 0.20
28 17 0.14
29 58 0.48
30 14 0.11
31 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.16, T:0.46
Consensus pattern (28 bp):
GGTGATATTTTCGTAATTATTTTGAAAA
Found at i:1133150 original size:29 final size:29
Alignment explanation
Indices: 1133117--1133291 Score: 150
Period size: 29 Copynumber: 6.2 Consensus size: 29
1133107 CGTTGATCGA
1133117 GTGATATTTTAGTAATTATTTTGAAAATG
1 GTGATATTTTAGTAATTATTTTGAAAATG
* *
1133146 GTGATATTTTGGTAATTATTTTGAAAATT
1 GTGATATTTTAGTAATTATTTTGAAAATG
* * *
1133175 GTGCTATTTTCGTAATT-TTTTTAAAATG
1 GTGATATTTTAGTAATTATTTTGAAAATG
* * * *
1133203 AT-A-ATTTCA-T-ATATATTTTTATAAA-A
1 GTGATATTTTAGTAAT-TATTTTGA-AAATG
* *
1133229 ATGATATTTTAGTAATTATTTTGAAAAGG
1 GTGATATTTTAGTAATTATTTTGAAAATG
* *
1133258 GTGATATTTTTGTAAATT-TTTT-AAAAGG
1 GTGATATTTTAGT-AATTATTTTGAAAATG
1133286 GTGATA
1 GTGATA
1133292 AATGTGTAAA
Statistics
Matches: 121, Mismatches: 16, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
24 2 0.02
25 2 0.02
26 12 0.10
27 4 0.03
28 30 0.25
29 65 0.54
30 6 0.05
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (29 bp):
GTGATATTTTAGTAATTATTTTGAAAATG
Found at i:1133299 original size:28 final size:30
Alignment explanation
Indices: 1133242--1133301 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
1133232 ATATTTTAGT
** *
1133242 AATTATTTTGAAAAGGGTGATATTTTTGTA
1 AATTATTTTGAAAAGGGTGATAAATGTGTA
1133272 AATT-TTTT-AAAAGGGTGATAAATGTGTA
1 AATTATTTTGAAAAGGGTGATAAATGTGTA
1133300 AA
1 AA
1133302 ATGGTTGATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 19 0.70
29 4 0.15
30 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.20, T:0.42
Consensus pattern (30 bp):
AATTATTTTGAAAAGGGTGATAAATGTGTA
Found at i:1135280 original size:20 final size:20
Alignment explanation
Indices: 1135251--1135293 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1135241 ATTCCACCAC
*
1135251 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCGCCTAA
* *
1135271 ATGCATCTATATGGGCCTAA
1 ATGCAACTATATGCGCCTAA
1135291 ATG
1 ATG
1135294 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (20 bp):
ATGCAACTATATGCGCCTAA
Found at i:1139775 original size:16 final size:18
Alignment explanation
Indices: 1139754--1139790 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
1139744 TATTTTTAAC
1139754 TAAATTATTT-A-AAATT
1 TAAATTATTTGATAAATT
1139770 TAAATTATTTGATAAATT
1 TAAATTATTTGATAAATT
1139788 TAA
1 TAA
1139791 CAACAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
17 1 0.05
18 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
TAAATTATTTGATAAATT
Done.