Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold287
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: 1864789
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 140151 characters in sequence are not A, C, G, or T
File 5 of 7
Found at i:1026771 original size:13 final size:13
Alignment explanation
Indices: 1026753--1026777 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1026743 TTACAACATT
1026753 AATCTCGATATCG
1 AATCTCGATATCG
1026766 AATCTCGATATC
1 AATCTCGATATC
1026778 AACGGGGTTT
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:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (13 bp):
AATCTCGATATCG
Found at i:1027566 original size:6 final size:6
Alignment explanation
Indices: 1027548--1027610 Score: 65
Period size: 6 Copynumber: 10.5 Consensus size: 6
1027538 AAATTCGGAA
* * *
1027548 AAAAAT AACAAT AAAAAT AAAACT AAAACT AAAAAT AAAAAT AAATAA-
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA-AAT
* *
1027596 AAACAT AAAACT AAA
1 AAAAAT AAAAAT AAA
1027611 TAAAGTCACT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
5 1 0.02
6 45 0.94
7 2 0.04
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:1029173 original size:3 final size:3
Alignment explanation
Indices: 1029165--1029246 Score: 130
Period size: 3 Copynumber: 27.0 Consensus size: 3
1029155 ATGAAATTAC
*
1029165 TAA TAA TAA TCA TAA CCT-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA --TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1029211 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1029247 ACAGTAATAA
Statistics
Matches: 74, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
2 1 0.01
3 71 0.96
4 1 0.01
5 1 0.01
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1029260 original size:15 final size:16
Alignment explanation
Indices: 1029190--1029264 Score: 74
Period size: 15 Copynumber: 4.9 Consensus size: 16
1029180 CCTATAATAA
1029190 TAATAATAATAATA-A-
1 TAATAATAATAA-ACAG
1029205 TAATAATAATAATA-A-
1 TAATAATAATAA-ACAG
1029220 TAATAATAATAATA-A-
1 TAATAATAATAA-ACAG
1029235 TAATAATAATAAACAG
1 TAATAATAATAAACAG
1029251 TAATAA-AATAAACA
1 TAATAATAATAAACA
1029265 AGAAGACATG
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
14 1 0.02
15 51 0.88
16 6 0.10
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (16 bp):
TAATAATAATAAACAG
Found at i:1029689 original size:17 final size:19
Alignment explanation
Indices: 1029667--1029729 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
1029657 TATGAAAACA
1029667 TAATCTT-CA-AGGATATG
1 TAATCTTACATAGGATATG
* *
1029684 TAATCTTAGATATGATATG
1 TAATCTTACATAGGATATG
* *
1029703 TAATCTTAGATATGATATG
1 TAATCTTACATAGGATATG
*
1029722 CAATCTTA
1 TAATCTTA
1029730 GAATATATGA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
17 7 0.17
18 1 0.02
19 33 0.80
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.40
Consensus pattern (19 bp):
TAATCTTACATAGGATATG
Found at i:1029702 original size:19 final size:19
Alignment explanation
Indices: 1029678--1029754 Score: 100
Period size: 19 Copynumber: 3.8 Consensus size: 19
1029668 AATCTTCAAG
1029678 GATATGTAATCTTAGATAT
1 GATATGTAATCTTAGATAT
1029697 GATATGTAATCTTAGATAT
1 GATATGTAATCTTAGATAT
*
1029716 GATATGCAATCTTAGAATATAT
1 GATATGTAATCTTAG---ATAT
*
1029738 GATTTTGTAATCTTAGA
1 GA-TATGTAATCTTAGA
1029755 GATTTAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
19 33 0.65
20 1 0.02
22 6 0.12
23 11 0.22
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (19 bp):
GATATGTAATCTTAGATAT
Found at i:1030083 original size:3 final size:3
Alignment explanation
Indices: 1030075--1030122 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
1030065 TATTAAGTTG
* * *
1030075 TTA TTA TTA TTA TTG TTA TTA TTA TCA TTA TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1030123 CTATATATAC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1032426 original size:43 final size:43
Alignment explanation
Indices: 1032374--1032475 Score: 161
Period size: 43 Copynumber: 2.4 Consensus size: 43
1032364 CACATAGTCG
* *
1032374 TGTCGCTAGGCTGTGTGTCACACACGGCTAATTCACACACCCA
1 TGTCGCTAGGCCGTGTGTCACACACGGCTAAGTCACACACCCA
*
1032417 TGTCGCTAGGCCGTGTGTCACACACGGCTAAGTCACACACCCG
1 TGTCGCTAGGCCGTGTGTCACACACGGCTAAGTCACACACCCA
*
1032460 TGTCTC-AGGCCGTGTG
1 TGTCGCTAGGCCGTGTG
1032476 GACATGAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
42 10 0.18
43 45 0.82
ACGTcount: A:0.20, C:0.32, G:0.25, T:0.23
Consensus pattern (43 bp):
TGTCGCTAGGCCGTGTGTCACACACGGCTAAGTCACACACCCA
Found at i:1033936 original size:19 final size:19
Alignment explanation
Indices: 1033912--1033955 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1033902 TAAAATCAAC
1033912 ACAACATCAACCCAAATAA
1 ACAACATCAACCCAAATAA
* **
1033931 ACAACATGATTCCAAATAA
1 ACAACATCAACCCAAATAA
1033950 ACAACA
1 ACAACA
1033956 AAAATAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.57, C:0.27, G:0.02, T:0.14
Consensus pattern (19 bp):
ACAACATCAACCCAAATAA
Found at i:1047394 original size:2 final size:2
Alignment explanation
Indices: 1047389--1047430 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1047379 TATATATATA
1047389 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1047431 AACTTGACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1048672 original size:20 final size:18
Alignment explanation
Indices: 1048625--1048673 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
1048615 CAAGATAAAC
1048625 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
1048642 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
1048662 ATTAAATTAATA
1 ATTAAATTAATA
1048674 AAATATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:1050711 original size:7 final size:7
Alignment explanation
Indices: 1050699--1050739 Score: 61
Period size: 6 Copynumber: 6.3 Consensus size: 7
1050689 TTCAGGTAAA
1050699 TTTCATT
1 TTTCATT
1050706 TTTCATT
1 TTTCATT
1050713 TTTC-TT
1 TTTCATT
1050719 TTTC-TT
1 TTTCATT
1050725 TTTCA-T
1 TTTCATT
1050731 TTTCATT
1 TTTCATT
1050738 TT
1 TT
1050740 GGAGAAAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 18 0.56
7 14 0.44
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTCATT
Found at i:1052544 original size:10 final size:10
Alignment explanation
Indices: 1052529--1052562 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1052519 GAAAAAGTTG
1052529 AAAGAAAACT
1 AAAGAAAACT
1052539 AAAGAAAACCT
1 AAAGAAAA-CT
*
1052550 AGAGAAAACT
1 AAAGAAAACT
1052560 AAA
1 AAA
1052563 CCTAAACTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.68, C:0.12, G:0.12, T:0.09
Consensus pattern (10 bp):
AAAGAAAACT
Found at i:1052835 original size:20 final size:20
Alignment explanation
Indices: 1052810--1052864 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
1052800 CTTGGGAGGT
*
1052810 GGATATTGTGATACCCAAAA
1 GGATATCGTGATACCCAAAA
1052830 GGATATCGTGATACCCAAAA
1 GGATATCGTGATACCCAAAA
1052850 GGATATCGTGATACC
1 GGATATCGTGATACC
1052865 ACTGAAAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (20 bp):
GGATATCGTGATACCCAAAA
Found at i:1061486 original size:78 final size:78
Alignment explanation
Indices: 1061401--1061561 Score: 234
Period size: 78 Copynumber: 2.1 Consensus size: 78
1061391 TTTCTGTTTA
* * *
1061401 AAACAAAAATTAAAAAAAT-CTTGTTAAACGGCAAGAATAAAATCCTAAAACTGGATTATTCAAT
1 AAACAAAAATCAAAAAAATCCTT-TTAAACGACAAGAATAAAATCCTAAAACAGGATTATTCAAT
*
1061465 TGATTTTCAATTTG
65 TGAATTTCAATTTG
* * *
1061479 AAACAAAAATCAAACAAATCCTTTTAAACGACAAGAATAAATTCCTAAAACAGGATTGTTCAATT
1 AAACAAAAATCAAAAAAATCCTTTTAAACGACAAGAATAAAATCCTAAAACAGGATTATTCAATT
*
1061544 GAATTTCTATTTG
66 GAATTTCAATTTG
1061557 AAACA
1 AAACA
1061562 GAATACAATT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
78 71 0.96
79 3 0.04
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.29
Consensus pattern (78 bp):
AAACAAAAATCAAAAAAATCCTTTTAAACGACAAGAATAAAATCCTAAAACAGGATTATTCAATT
GAATTTCAATTTG
Found at i:1072009 original size:17 final size:18
Alignment explanation
Indices: 1071987--1072020 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1071977 TTTCGGCTGA
1071987 GTGGG-CCACACGGGCAT
1 GTGGGCCCACACGGGCAT
1072004 GTGGGCCCACACGGGCA
1 GTGGGCCCACACGGGCA
1072021 GGCCACATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.18, C:0.32, G:0.41, T:0.09
Consensus pattern (18 bp):
GTGGGCCCACACGGGCAT
Found at i:1076743 original size:27 final size:26
Alignment explanation
Indices: 1076689--1076752 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
1076679 TTTATTGAGG
*
1076689 TTATTAGTTTATCAATAAATGAAAATT
1 TTATTAATTTATCAATAAATGAAAA-T
* * * *
1076716 TTATTAATTTATCGATACATTAATAT
1 TTATTAATTTATCAATAAATGAAAAT
1076742 TTATTAATTTA
1 TTATTAATTTA
1076753 AAGAATATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 12 0.38
27 20 0.62
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (26 bp):
TTATTAATTTATCAATAAATGAAAAT
Found at i:1076868 original size:35 final size:37
Alignment explanation
Indices: 1076826--1076898 Score: 114
Period size: 35 Copynumber: 2.0 Consensus size: 37
1076816 TGAATTAAAG
* *
1076826 TTAATTGGTTCATGTAA-CAAAAA-AAAAAGAGTTAA
1 TTAATTGGCTCATGTAACCAAAAAGAAAAAAAGTTAA
1076861 TTAATTGGCTCATGTAACCAAAAAGAAAAAAAGTTAA
1 TTAATTGGCTCATGTAACCAAAAAGAAAAAAAGTTAA
1076898 T
1 T
1076899 GGTTTCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 16 0.47
36 6 0.18
37 12 0.35
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.27
Consensus pattern (37 bp):
TTAATTGGCTCATGTAACCAAAAAGAAAAAAAGTTAA
Found at i:1091160 original size:21 final size:21
Alignment explanation
Indices: 1091134--1091188 Score: 87
Period size: 19 Copynumber: 2.7 Consensus size: 21
1091124 AATCATATCT
1091134 TCTAAGATTGTATATATCATA
1 TCTAAGATTGTATATATCATA
*
1091155 TCTAAGATTG--CATATCATA
1 TCTAAGATTGTATATATCATA
1091174 TCTAAGATTGTATAT
1 TCTAAGATTGTATAT
1091189 CCTCGAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 18 0.60
21 12 0.40
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (21 bp):
TCTAAGATTGTATATATCATA
Found at i:1091174 original size:24 final size:22
Alignment explanation
Indices: 1091111--1091176 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
1091101 AAATTAAATC
* *
1091111 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTGC-ATATCATATCT
1091134 TCTAAGATTG--TAT-ATATCAT
1 TCTAAGATTGCATATCATATC-T
1091154 ATCTAAGATTGCATATCATATCT
1 -TCTAAGATTGCATATCATATCT
1091177 AAGATTGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
19 5 0.14
20 3 0.08
21 10 0.28
23 13 0.36
24 5 0.14
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (22 bp):
TCTAAGATTGCATATCATATCT
Found at i:1103089 original size:84 final size:84
Alignment explanation
Indices: 1102942--1103101 Score: 198
Period size: 84 Copynumber: 1.9 Consensus size: 84
1102932 TCGTGTTTAC
* * * * *
1102942 TTTCCGTTTAGCTCTCACGAGCTTCTGTTTAACTCATATGAGTTTTCGTTCAGCTCTATTGAGCT
1 TTTCCGTTCAGCTCTCACGAGCTTCCGTTCAACCCATATGAGTTTTCATTCAGCTCTATTGAGCT
*
1103007 TCTGTTTAACCTTTATGGG
66 TCTGTTCAACCTTTATGGG
* * * *
1103026 TTTCCGTTCAGCTCTTACGAGCTTCCGTTCAACCCTTATG-GGTTTCTATTTAGCTCTCA-TGAG
1 TTTCCGTTCAGCTCTCACGAGCTTCCGTTCAACCCATATGAGTTTTC-ATTCAGCTCT-ATTGAG
1103089 CTTCTGTTCAACC
64 CTTCTGTTCAACC
1103102 CTCAGGCTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
83 5 0.08
84 58 0.91
85 1 0.02
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.42
Consensus pattern (84 bp):
TTTCCGTTCAGCTCTCACGAGCTTCCGTTCAACCCATATGAGTTTTCATTCAGCTCTATTGAGCT
TCTGTTCAACCTTTATGGG
Found at i:1103102 original size:42 final size:42
Alignment explanation
Indices: 1102942--1103103 Score: 157
Period size: 42 Copynumber: 3.9 Consensus size: 42
1102932 TCGTGTTTAC
* * * * * *
1102942 TTTCCGTTTAGCTCTCACGAGCTTCTGTTTAACTCATATGAG
1 TTTCTGTTCAGCTCTCACGAGCTTCTGTTCAACCCTTATGGG
* * *
1102984 TTT-TCGTTCAGCTCT-ATTGAGCTTCTGTTTAACCTTTATGGG
1 TTTCT-GTTCAGCTCTCA-CGAGCTTCTGTTCAACCCTTATGGG
* * *
1103026 TTTCCGTTCAGCTCTTACGAGCTTCCGTTCAACCCTTATGGG
1 TTTCTGTTCAGCTCTCACGAGCTTCTGTTCAACCCTTATGGG
* * *
1103068 TTTCTATTTAGCTCTCATGAGCTTCTGTTCAACCCT
1 TTTCTGTTCAGCTCTCACGAGCTTCTGTTCAACCCT
1103104 CAGGCTTTTG
Statistics
Matches: 98, Mismatches: 18, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
41 1 0.01
42 96 0.98
43 1 0.01
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.42
Consensus pattern (42 bp):
TTTCTGTTCAGCTCTCACGAGCTTCTGTTCAACCCTTATGGG
Found at i:1103105 original size:21 final size:21
Alignment explanation
Indices: 1103044--1103105 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 21
1103034 CAGCTCTTAC
* *
1103044 GAGCTTCCGTTCAACCCTTAT
1 GAGCTTCTGTTCAACCCTCAT
* * * * * *
1103065 GGGTTTCTATTTAGCTCTCAT
1 GAGCTTCTGTTCAACCCTCAT
1103086 GAGCTTCTGTTCAACCCTCA
1 GAGCTTCTGTTCAACCCTCA
1103106 GGCTTTTGAA
Statistics
Matches: 27, Mismatches: 14, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.37
Consensus pattern (21 bp):
GAGCTTCTGTTCAACCCTCAT
Found at i:1108380 original size:20 final size:18
Alignment explanation
Indices: 1108352--1108393 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
1108342 ATATTTTTTT
1108352 AAAAATATTAGTTACT-ATA
1 AAAAATATTA-TTA-TGATA
1108371 AAAAATTATTATTATGATA
1 AAAAA-TATTATTATGATA
1108390 AAAA
1 AAAA
1108394 TAATTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 1 0.05
19 15 0.71
20 5 0.24
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (18 bp):
AAAAATATTATTATGATA
Found at i:1110427 original size:21 final size:22
Alignment explanation
Indices: 1110401--1110451 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
1110391 TTTTCTAGAA
1110401 TTTTTATACAA-AAATTTT-ATT
1 TTTTTATA-AACAAATTTTGATT
*
1110422 TTTTTA-AAACTAATTTTGATT
1 TTTTTATAAACAAATTTTGATT
1110443 TTTTTATAA
1 TTTTTATAA
1110452 TTTTTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 7 0.27
21 15 0.58
22 2 0.08
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTTATAAACAAATTTTGATT
Found at i:1110756 original size:22 final size:23
Alignment explanation
Indices: 1110728--1110772 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1110718 ATACAATCTT
1110728 AGATATGA-TATGCAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
* *
1110750 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
1110773 TATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:1111019 original size:23 final size:23
Alignment explanation
Indices: 1110975--1111019 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1110965 TCTTATTTTG
* *
1110975 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
1110998 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
1111020 TTNNNNNNNN
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:1111208 original size:3 final size:3
Alignment explanation
Indices: 1111200--1111442 Score: 486
Period size: 3 Copynumber: 81.0 Consensus size: 3
1111190 NNNNNNNNNN
1111200 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1111248 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1111296 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1111344 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1111392 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1111440 ATT
1 ATT
1111443 CTTGATCGTG
Statistics
Matches: 240, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 240 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1113033 original size:29 final size:28
Alignment explanation
Indices: 1112963--1113033 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
1112953 AATAAACACC
1112963 AAAAATTTATTTTAAAAATAAAAAAATA
1 AAAAATTTATTTTAAAAATAAAAAAATA
** *
1112991 AAAAAAGTATTTTAAAATTAAAAAAATA
1 AAAAATTTATTTTAAAAATAAAAAAATA
1113019 AAAAATTTATATTTA
1 AAAAATTTAT-TTTA
1113034 TTATATATTC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 33 0.89
29 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (28 bp):
AAAAATTTATTTTAAAAATAAAAAAATA
Found at i:1115849 original size:12 final size:12
Alignment explanation
Indices: 1115832--1115856 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1115822 ATCTACAGGT
1115832 ATACACGACCTA
1 ATACACGACCTA
1115844 ATACACGACCTA
1 ATACACGACCTA
1115856 A
1 A
1115857 CACATAGTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.32, G:0.08, T:0.16
Consensus pattern (12 bp):
ATACACGACCTA
Found at i:1117045 original size:19 final size:18
Alignment explanation
Indices: 1116994--1117082 Score: 83
Period size: 19 Copynumber: 4.8 Consensus size: 18
1116984 TTTTTGATGC
*
1116994 ATTTTATAATTTTTAAATAT
1 ATTTTATAATTTTT--ATAA
1117014 ATTTTAT-ATTTTTATTAA
1 ATTTTATAATTTTTA-TAA
1117032 ATTTTAGTAATTTTTATAA
1 ATTTTA-TAATTTTTATAA
* *
1117051 CTTTTATTAATTTTTAT-T
1 ATTTTA-TAATTTTTATAA
*
1117069 TTTTTATAATTTTT
1 ATTTTATAATTTTT
1117083 TGCCACATGT
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
17 9 0.15
18 13 0.21
19 25 0.41
20 14 0.23
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (18 bp):
ATTTTATAATTTTTATAA
Found at i:1117083 original size:10 final size:9
Alignment explanation
Indices: 1116995--1117082 Score: 81
Period size: 10 Copynumber: 9.4 Consensus size: 9
1116985 TTTTGATGCA
1116995 TTTTATAAT
1 TTTTATAAT
*
1117004 TTTTAAATAT
1 TTTTATA-AT
1117014 ATTTTAT-AT
1 -TTTTATAAT
*
1117023 TTTTATTAAA
1 TTTTA-TAAT
1117033 TTTTAGTAAT
1 TTTTA-TAAT
*
1117043 TTTTATAAC
1 TTTTATAAT
1117052 TTTTATTAAT
1 TTTTA-TAAT
*
1117062 TTTTAT-TT
1 TTTTATAAT
1117070 TTTTATAAT
1 TTTTATAAT
1117079 TTTT
1 TTTT
1117083 TGCCACATGT
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
8 12 0.19
9 23 0.36
10 24 0.38
11 5 0.08
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (9 bp):
TTTTATAAT
Found at i:1121012 original size:23 final size:23
Alignment explanation
Indices: 1120944--1121021 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 23
1120934 CTACATTGTA
* *
1120944 AATTT-TTTACTAATA-ATTTTT
1 AATTTATTTATTAATATAATTTT
*
1120965 AATTTA-ATATT-ATATAATATATT
1 AATTTATTTATTAATATAAT-T-TT
1120988 AATTTATTTATTAATATAATTTT
1 AATTTATTTATTAATATAATTTT
*
1121011 AATATATTTAT
1 AATTTATTTAT
1121022 GATATATATA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
20 3 0.07
21 10 0.22
22 1 0.02
23 20 0.43
24 5 0.11
25 7 0.15
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (23 bp):
AATTTATTTATTAATATAATTTT
Found at i:1123109 original size:29 final size:29
Alignment explanation
Indices: 1123067--1123142 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
1123057 TAATGCTCAA
*
1123067 ATTTGCTCACACAAGTTGTGATATTTTGG
1 ATTTGCTCACACAAGTTGTGACATTTTGG
1123096 ATTTGCTCACACAAGTTGTGACATTTTGG
1 ATTTGCTCACACAAGTTGTGACATTTTGG
** *
1123125 -GCTCCTCACACAAGTTGT
1 ATTTGCTCACACAAGTTGT
1123143 AGGTCAGGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 15 0.35
29 28 0.65
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (29 bp):
ATTTGCTCACACAAGTTGTGACATTTTGG
Found at i:1131752 original size:20 final size:19
Alignment explanation
Indices: 1131729--1131770 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 19
1131719 GCATATTTTC
1131729 TTTCTATATTATTAATATTA
1 TTTCTATATTATTAATA-TA
1131749 TTTCTATATTATTAATATA
1 TTTCTATATTATTAATATA
1131768 TTT
1 TTT
1131771 TTATTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTCTATATTATTAATATA
Found at i:1131780 original size:20 final size:19
Alignment explanation
Indices: 1131733--1131799 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
1131723 ATTTTCTTTC
*
1131733 TATATTATTAATATTATTTC
1 TATATTATTAATA-TATTTT
1131753 TATATTATTAATATATTTT
1 TATATTATTAATATATTTT
* * *
1131772 TATTTTTATTTATATATATT
1 TA-TATTATTAATATATTTT
*
1131792 TAAATTAT
1 TATATTAT
1131800 ATATTTAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.28
20 29 0.73
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (19 bp):
TATATTATTAATATATTTT
Found at i:1131802 original size:13 final size:13
Alignment explanation
Indices: 1131784--1131809 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1131774 TTTTTATTTA
1131784 TATATATTTAAAT
1 TATATATTTAAAT
1131797 TATATATTTAAAT
1 TATATATTTAAAT
1131810 GATAAATAAT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATTTAAAT
Found at i:1131835 original size:15 final size:15
Alignment explanation
Indices: 1131811--1131848 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1131801 TATTTAAATG
*
1131811 ATAAATAATAATAAA
1 ATAAACAATAATAAA
1131826 ATAAACAATAATAAA
1 ATAAACAATAATAAA
1131841 ATAAACAA
1 ATAAACAA
1131849 ACCAAATCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (15 bp):
ATAAACAATAATAAA
Found at i:1132002 original size:21 final size:21
Alignment explanation
Indices: 1131962--1132000 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1131952 AAATCATGGA
1131962 TAAATCCAAGCGACTCTTTCT
1 TAAATCCAAGCGACTCTTTCT
1131983 TAAATCCAAGCGA-TCTTT
1 TAAATCCAAGCGACTCTTT
1132001 TCGTAGGCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (21 bp):
TAAATCCAAGCGACTCTTTCT
Found at i:1132812 original size:54 final size:53
Alignment explanation
Indices: 1132745--1132942 Score: 193
Period size: 54 Copynumber: 3.7 Consensus size: 53
1132735 TCATAATTCA
* * * * *
1132745 CATGTTTATTGTCCCGGTGGACTACCCTGTGTTTATTGTCTTAGCGGACTACCT
1 CATGTTTACTGTCCCGATAGACTACCCTGTGTTTACTGTCATAGCGGACTA-CT
*
1132799 CATGTTTACTGTCCCGATAGACTACCCTGTGTTTACTGTCATGGCGGACTAC-
1 CATGTTTACTGTCCCGATAGACTACCCTGTGTTTACTGTCATAGCGGACTACT
* * * * * ** * *
1132851 CGTGTTTACTATCCC-AGCAGACTACCCTTTTTTTTACTGTCCCAGTGGATTACT
1 CATGTTTACTGTCCCGA-TAGACTACCC-TGTGTTTACTGTCATAGCGGACTACT
* *
1132905 CTGTGTTTACTGTCCCGATGGACTACCCTGTGTTTACT
1 C-ATGTTTACTGTCCCGATAGACTACCCTGTGTTTACT
1132943 ATCCTGACGG
Statistics
Matches: 118, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
51 1 0.01
52 22 0.19
53 19 0.16
54 54 0.46
55 21 0.18
56 1 0.01
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.37
Consensus pattern (53 bp):
CATGTTTACTGTCCCGATAGACTACCCTGTGTTTACTGTCATAGCGGACTACT
Found at i:1132848 original size:27 final size:27
Alignment explanation
Indices: 1132747--1133001 Score: 165
Period size: 27 Copynumber: 9.5 Consensus size: 27
1132737 ATAATTCACA
* *
1132747 TGTTTATTGTCCCGGTGGACTACCCTG
1 TGTTTACTGTCCCGGCGGACTACCCTG
* *** *
1132774 TGTTTATTGTCTTAGCGGACTA-CCTCA
1 TGTTTACTGTCCCGGCGGACTACCCT-G
***
1132801 TGTTTACTGTCCCGATAGACTACCCTG
1 TGTTTACTGTCCCGGCGGACTACCCTG
**
1132828 TGTTTACTGTCATGGCGGACTA-CC-G
1 TGTTTACTGTCCCGGCGGACTACCCTG
* * * *
1132853 TGTTTACTATCCCAGCAGACTACCCTTT
1 TGTTTACTGTCCCGGCGGACTACCC-TG
* * * * *
1132881 TTTTTACTGTCCCAGTGGATTACTCTG
1 TGTTTACTGTCCCGGCGGACTACCCTG
**
1132908 TGTTTACTGTCCCGATGGACTACCCTG
1 TGTTTACTGTCCCGGCGGACTACCCTG
* * * *
1132935 TGTTTACTATCCTGACGGACTACCCCG
1 TGTTTACTGTCCCGGCGGACTACCCTG
* * * * *
1132962 TGTTTGCTATCTCGACGGACTACCCCG
1 TGTTTACTGTCCCGGCGGACTACCCTG
* *
1132989 TTTTTATTGTCCC
1 TGTTTACTGTCCC
1133002 AGTGGGCTAA
Statistics
Matches: 175, Mismatches: 48, Indels: 10
0.75 0.21 0.04
Matches are distributed among these distances:
25 18 0.10
26 7 0.04
27 128 0.73
28 22 0.13
ACGTcount: A:0.16, C:0.28, G:0.20, T:0.36
Consensus pattern (27 bp):
TGTTTACTGTCCCGGCGGACTACCCTG
Found at i:1132935 original size:107 final size:107
Alignment explanation
Indices: 1132801--1133006 Score: 281
Period size: 107 Copynumber: 1.9 Consensus size: 107
1132791 GACTACCTCA
* *
1132801 TGTTTACTGTCCCGATAGACTACCCTGTGTTTACTGTCATGGCGGACTA-CCGTGTTTACTATCC
1 TGTTTACTGTCCCGATAGACTACCCTGTGTTTACTATCATGACGGACTACCCGTGTTTACTATCC
**
1132865 C-AGCAGACTACCCTTTTTTTTACTGTCCCAGTGGATTACTCTG
66 CGA-CAGACTACCC-CGTTTTTACTGTCCCAGTGGATTACTCTG
* * *
1132908 TGTTTACTGTCCCGATGGACTACCCTGTGTTTACTATCCTGACGGACTACCCCGTGTTTGCTATC
1 TGTTTACTGTCCCGATAGACTACCCTGTGTTTACTATCATGACGGACTA-CCCGTGTTTACTATC
* * *
1132973 TCGACGGACTACCCCGTTTTTATTGTCCCAGTGG
65 CCGACAGACTACCCCGTTTTTACTGTCCCAGTGG
1133007 GCTAAAATGG
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
107 45 0.52
108 17 0.20
109 23 0.27
110 1 0.01
ACGTcount: A:0.17, C:0.28, G:0.20, T:0.35
Consensus pattern (107 bp):
TGTTTACTGTCCCGATAGACTACCCTGTGTTTACTATCATGACGGACTACCCGTGTTTACTATCC
CGACAGACTACCCCGTTTTTACTGTCCCAGTGGATTACTCTG
Found at i:1134383 original size:25 final size:23
Alignment explanation
Indices: 1134355--1134405 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
1134345 AATTTTTTTG
* *
1134355 AAATAAAAAATTATGAAAAAAATAA
1 AAATAAAAAA--ATAAAAAAAACAA
1134380 AAATAAAAAAATAAAAAAAACAA
1 AAATAAAAAAATAAAAAAAACAA
1134403 AAA
1 AAA
1134406 ACCTTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 14 0.58
25 10 0.42
ACGTcount: A:0.82, C:0.02, G:0.02, T:0.14
Consensus pattern (23 bp):
AAATAAAAAAATAAAAAAAACAA
Found at i:1134404 original size:14 final size:14
Alignment explanation
Indices: 1134370--1134396 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1134360 AAAAATTATG
1134370 AAAAAAATAAAAAT
1 AAAAAAATAAAAAT
1134384 AAAAAAATAAAAA
1 AAAAAAATAAAAA
1134397 AAACAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:1134406 original size:25 final size:25
Alignment explanation
Indices: 1134355--1134406 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1134345 AATTTTTTTG
* * *
1134355 AAATAAAAAATTATGAAAAAAATAA
1 AAATAAAAAAATATAAAAAAAAAAA
*
1134380 AAATAAAAAAATA-AAAAAAACAAA
1 AAATAAAAAAATATAAAAAAAAAAA
1134404 AAA
1 AAA
1134407 CCTTTTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (25 bp):
AAATAAAAAAATATAAAAAAAAAAA
Found at i:1134722 original size:26 final size:27
Alignment explanation
Indices: 1134670--1134722 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
1134660 TTGAACTGCT
* *
1134670 TTTTATAATTTTTTTTAAATATTTTTA
1 TTTTATAATTTTTTATAAATATATTTA
1134697 TTTT-TAATTTTTTAATAAAT-TATTTA
1 TTTTATAATTTTTT-ATAAATATATTTA
1134723 CTTTGAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTTATAATTTTTTATAAATATATTTA
Found at i:1142879 original size:21 final size:21
Alignment explanation
Indices: 1142851--1142902 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1142841 CCCTTTTCCT
1142851 CTTG-GGTTTCTTCTTCCCAA
1 CTTGTGGTTTCTTCTTCCCAA
1142871 CTTGTGGTTTCTTCTTCCCAA
1 CTTGTGGTTTCTTCTTCCCAA
1142892 CTTGTGGTTTC
1 CTTGTGGTTTC
1142903 CCATTACCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.13
21 27 0.87
ACGTcount: A:0.08, C:0.27, G:0.17, T:0.48
Consensus pattern (21 bp):
CTTGTGGTTTCTTCTTCCCAA
Found at i:1145921 original size:45 final size:45
Alignment explanation
Indices: 1145789--1145968 Score: 170
Period size: 45 Copynumber: 4.0 Consensus size: 45
1145779 TAGTAGCTTG
* *
1145789 TCTGCACCGTTTAGTGGTTTA-CTCACA-CATATTAGCAACTTTTA
1 TCTGCACCATTTAATGGTTTATC-CACACCATATTAGCAACTTTTA
* *
1145833 TCCGCACCATTTAATGGTTTATCCACACCGTATTAGCAACTTTTA
1 TCTGCACCATTTAATGGTTTATCCACACCATATTAGCAACTTTTA
* * * ***
1145878 TCTGCACCATTTAGA-GGTTTATCCATATCATTTTAGTGGCTTTTA
1 TCTGCACCATTTA-ATGGTTTATCCACACCATATTAGCAACTTTTA
* *
1145923 TCTGTACCGATTT-ATGGTTTACCCACACCTTATTATTAGCAACTTT
1 TCTGCACC-ATTTAATGGTTTATCCACACC--A-TATTAGCAACTTT
1145969 CATTTGCAAA
Statistics
Matches: 108, Mismatches: 20, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
44 23 0.21
45 70 0.65
46 5 0.05
47 1 0.01
48 9 0.08
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (45 bp):
TCTGCACCATTTAATGGTTTATCCACACCATATTAGCAACTTTTA
Found at i:1146180 original size:24 final size:24
Alignment explanation
Indices: 1146148--1146200 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1146138 TAAAGGTAGA
*
1146148 GGAGTTCT-GAGGAACTCCTATTGT
1 GGAGTTCTGGA-GAACTCCTACTGT
1146172 GGAGTTCTGGAGAACTCCTACTGT
1 GGAGTTCTGGAGAACTCCTACTGT
1146196 GGAGT
1 GGAGT
1146201 GTAGTGGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (24 bp):
GGAGTTCTGGAGAACTCCTACTGT
Found at i:1150647 original size:8 final size:8
Alignment explanation
Indices: 1150634--1150669 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
1150624 TGACAAATTT
1150634 AAATTAAA
1 AAATTAAA
1150642 AAATTAAA
1 AAATTAAA
1150650 AAATTAAA
1 AAATTAAA
1150658 AAATTAAA
1 AAATTAAA
1150666 AAAT
1 AAAT
1150670 CTTTAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
AAATTAAA
Found at i:1152575 original size:6 final size:6
Alignment explanation
Indices: 1152564--1152590 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1152554 TGACTGACAC
1152564 ATACAT ATACAT ATACAT ATACAT ATA
1 ATACAT ATACAT ATACAT ATACAT ATA
1152591 TCAGAGAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:1170747 original size:50 final size:50
Alignment explanation
Indices: 1170560--1170798 Score: 185
Period size: 50 Copynumber: 4.7 Consensus size: 50
1170550 GATAATAACA
* * ** * * *
1170560 TGCCAAAGCCATGTCCTAGACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * **
1170609 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *** * *
1170659 TGCCCATGCCATGTCCCAGACATGGTCTTATGGGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * * *
1170709 TGCCAACGCCATGTCCCAGACATGTTCTTACATAGGACCTCACATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
**
1170765 TGCCAACACCATGTCCCAGACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
1170799 TGATCTCTTT
Statistics
Matches: 149, Mismatches: 33, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
48 1 0.01
49 38 0.26
50 76 0.51
53 2 0.01
56 32 0.21
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:1176784 original size:29 final size:29
Alignment explanation
Indices: 1176751--1176807 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1176741 ATTTAATTTA
1176751 ATTTAACAGTACAAAGATTAAATTGATCC
1 ATTTAACAGTACAAAGATTAAATTGATCC
* * * *
1176780 ATTTAATAGTAGAAATATTAATTTGATC
1 ATTTAACAGTACAAAGATTAAATTGATC
1176808 AAGTCATAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.37
Consensus pattern (29 bp):
ATTTAACAGTACAAAGATTAAATTGATCC
Found at i:1180268 original size:21 final size:20
Alignment explanation
Indices: 1180227--1180268 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1180217 TCATCTTGGG
**
1180227 CCGTTAAAATATTGATGTGA
1 CCGTTAAAATATTGACATGA
1180247 CCGTTAACAATATTGACATGA
1 CCGTTAA-AATATTGACATGA
1180268 C
1 C
1180269 ACTCCATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (20 bp):
CCGTTAAAATATTGACATGA
Found at i:1180344 original size:15 final size:15
Alignment explanation
Indices: 1180323--1180371 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
1180313 TTACCATGTC
1180323 ATCAAAAATAAAAAA
1 ATCAAAAATAAAAAA
*
1180338 TTCAAAAATAAAAAA
1 ATCAAAAATAAAAAA
*
1180353 ATAAAAAATTAAAAGAA
1 ATCAAAAA-TAAAA-AA
1180370 AT
1 AT
1180372 ACTTTTACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 20 0.69
16 5 0.17
17 4 0.14
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (15 bp):
ATCAAAAATAAAAAA
Found at i:1180352 original size:8 final size:8
Alignment explanation
Indices: 1180326--1180372 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
1180316 CCATGTCATC
1180326 AAAAAT-A
1 AAAAATAA
**
1180333 AAAAATTC
1 AAAAATAA
1180341 AAAAATAA
1 AAAAATAA
1180349 AAAAATAA
1 AAAAATAA
*
1180357 AAAATTAA
1 AAAAATAA
1180365 AAGAAATA
1 AA-AAATA
1180373 CTTTTACTAG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
7 6 0.18
8 23 0.70
9 4 0.12
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (8 bp):
AAAAATAA
Found at i:1180461 original size:10 final size:10
Alignment explanation
Indices: 1180448--1180531 Score: 52
Period size: 10 Copynumber: 8.6 Consensus size: 10
1180438 TTTAAAATTA
1180448 AAAAATATTT
1 AAAAATATTT
*
1180458 AAAAAAATTT
1 AAAAATATTT
1180468 --AAAT-TTT
1 AAAAATATTT
* *
1180475 ATAAATTTTT
1 AAAAATATTT
*
1180485 AAAAACATTAT
1 AAAAATATT-T
*
1180496 TAAAAT-TTAT
1 AAAAATATT-T
*
1180506 AAAAATATTA
1 AAAAATATTT
1180516 AATAAAT-TTT
1 AA-AAATATTT
1180526 AAAAAT
1 AAAAAT
1180532 TTCAAAAAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
7 3 0.05
8 3 0.05
9 8 0.14
10 33 0.57
11 11 0.19
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (10 bp):
AAAAATATTT
Found at i:1180528 original size:20 final size:19
Alignment explanation
Indices: 1180475--1180531 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
1180465 TTTAAATTTT
*
1180475 ATAAATTTTTAAAAACATTA
1 ATAAA-TTTTAAAAATATTA
*
1180495 TTAAAATTTATAAAAATATTAA
1 AT-AAATTT-TAAAAATATT-A
1180517 ATAAATTTTAAAAAT
1 ATAAATTTTAAAAAT
1180532 TTCAAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 11 0.35
21 18 0.58
22 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAATTTTAAAAATATTA
Found at i:1187166 original size:10 final size:10
Alignment explanation
Indices: 1187153--1187205 Score: 72
Period size: 10 Copynumber: 5.4 Consensus size: 10
1187143 AGTCATTGTA
1187153 AAAAAAATTG
1 AAAAAAATTG
1187163 AAAAAAATTG
1 AAAAAAATTG
*
1187173 AAAAAAATAG
1 AAAAAAATTG
*
1187183 -AAAAAATAG
1 AAAAAAATTG
*
1187192 AAAAAAATTC
1 AAAAAAATTG
1187202 AAAA
1 AAAA
1187206 TTTTTTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
9 9 0.23
10 30 0.77
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:1187167 original size:12 final size:11
Alignment explanation
Indices: 1187147--1187188 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
1187137 GGAGTAAGTC
1187147 ATTGTAAAAAAA
1 ATTG-AAAAAAA
1187159 ATTG-AAAAAA
1 ATTGAAAAAAA
1187169 ATTG-AAAAAA
1 ATTGAAAAAAA
*
1187179 ATAGAAAAAA
1 ATTGAAAAAA
1187189 TAGAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 19 0.68
11 5 0.18
12 4 0.14
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (11 bp):
ATTGAAAAAAA
Found at i:1187178 original size:19 final size:19
Alignment explanation
Indices: 1187153--1187205 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1187143 AGTCATTGTA
*
1187153 AAAAAAATTGAAAAAAATTG
1 AAAAAAATTG-AAAAAATAG
*
1187173 AAAAAAATAGAAAAAATAG
1 AAAAAAATTGAAAAAATAG
*
1187192 AAAAAAATTCAAAA
1 AAAAAAATTGAAAA
1187206 TTTTTTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 20 0.69
20 9 0.31
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (19 bp):
AAAAAAATTGAAAAAATAG
Found at i:1188462 original size:33 final size:33
Alignment explanation
Indices: 1188394--1188465 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
1188384 AGAAAACGAA
*
1188394 AGTGGAAAAGAAAAAGAGCCTGAAAAGAAATCG
1 AGTGAAAAAGAAAAAGAGCCTGAAAAGAAATCG
* *
1188427 AGTGAAAAAGAAAGAGAGTCTGTAAAAGAAA-CG
1 AGTGAAAAAGAAAAAGAGCCTG-AAAAGAAATCG
1188460 AGTGAA
1 AGTGAA
1188466 GAGAGTAATC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 27 0.77
34 8 0.23
ACGTcount: A:0.54, C:0.07, G:0.28, T:0.11
Consensus pattern (33 bp):
AGTGAAAAAGAAAAAGAGCCTGAAAAGAAATCG
Found at i:1197598 original size:28 final size:27
Alignment explanation
Indices: 1197553--1197614 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 27
1197543 ACGAGCCCTA
*
1197553 GAAAAAAATTGTGTCAAAA-GACAAAC
1 GAAAAAAATTGTGCCAAAACGACAAAC
* *
1197579 GAAAAAAATTGCGTGCCAAAACGGCAGAC
1 GAAAAAAATT--GTGCCAAAACGACAAAC
1197608 GAAAAAA
1 GAAAAAA
1197615 CTACTATGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 10 0.33
28 8 0.27
29 12 0.40
ACGTcount: A:0.55, C:0.15, G:0.19, T:0.11
Consensus pattern (27 bp):
GAAAAAAATTGTGCCAAAACGACAAAC
Found at i:1199845 original size:13 final size:13
Alignment explanation
Indices: 1199827--1199889 Score: 99
Period size: 13 Copynumber: 4.8 Consensus size: 13
1199817 TCTTCATTGT
1199827 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
1199840 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
*
1199853 TTTTGAAAAGTGT
1 TTTTGAAAAGTGC
* *
1199866 TTTTCAGAAGTGC
1 TTTTGAAAAGTGC
1199879 TTTTGAAAAGT
1 TTTTGAAAAGT
1199890 TTGGTTTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.30, C:0.06, G:0.22, T:0.41
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:1209063 original size:17 final size:17
Alignment explanation
Indices: 1209022--1209064 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1209012 TAAAGAGTGA
1209022 GAAGTAAAAGTTTAGGG
1 GAAGTAAAAGTTTAGGG
* *
1209039 GAAATAAATAGTTTTGGG
1 GAAGTAAA-AGTTTAGGG
1209057 G-AGTAAAA
1 GAAGTAAAA
1209065 TTTTGAGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 1 0.05
17 12 0.55
18 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (17 bp):
GAAGTAAAAGTTTAGGG
Found at i:1209379 original size:30 final size:29
Alignment explanation
Indices: 1209345--1209436 Score: 114
Period size: 30 Copynumber: 3.1 Consensus size: 29
1209335 GGATGGGAGG
*
1209345 GGAGTAAAAGTTTTGGGGAAAAAGTGAGAA
1 GGAGTCAAAGTTTTGGGG-AAAAGTGAGAA
1209375 GGAGTCAAAGTTTTGATGGG-AAAGTGAGAA
1 GGAGTCAAAGTTTTG--GGGAAAAGTGAGAA
* *
1209405 GGAGTCAAAGTTCTGGGGGAAAAGTGAAAA
1 GGAGTCAAAGTT-TTGGGGAAAAGTGAGAA
1209435 GG
1 GG
1209437 TTTGAGGGTT
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
29 3 0.05
30 47 0.85
31 2 0.04
32 3 0.05
ACGTcount: A:0.39, C:0.03, G:0.38, T:0.20
Consensus pattern (29 bp):
GGAGTCAAAGTTTTGGGGAAAAGTGAGAA
Found at i:1210577 original size:17 final size:18
Alignment explanation
Indices: 1210555--1210590 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1210545 CACTAATGAA
*
1210555 TACAAATAATCAAT-CAG
1 TACAAATAAGCAATACAG
1210572 TACAAATAAGCAATACAG
1 TACAAATAAGCAATACAG
1210590 T
1 T
1210591 GTACATGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.53, C:0.17, G:0.08, T:0.22
Consensus pattern (18 bp):
TACAAATAAGCAATACAG
Found at i:1211091 original size:15 final size:15
Alignment explanation
Indices: 1211045--1211092 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
1211035 ATAACCAAAT
* *
1211045 ATAATAATATCAATA
1 ATAATAAGATTAATA
*
1211060 ATAATAAGAGTAATA
1 ATAATAAGATTAATA
1211075 ATAATAA-ATTAATTA
1 ATAATAAGATTAA-TA
1211090 ATA
1 ATA
1211093 GCAAAAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (15 bp):
ATAATAAGATTAATA
Found at i:1213319 original size:16 final size:16
Alignment explanation
Indices: 1213298--1213331 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1213288 ATATAAATTC
1213298 AATAACAATTAATTTT
1 AATAACAATTAATTTT
*
1213314 AATAACAATTAGTTTT
1 AATAACAATTAATTTT
1213330 AA
1 AA
1213332 CTTTTAAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (16 bp):
AATAACAATTAATTTT
Found at i:1216491 original size:18 final size:18
Alignment explanation
Indices: 1216440--1216492 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
1216430 TTGCAAAAAG
1216440 GACGATGAGGACGATGAC
1 GACGATGAGGACGATGAC
* *
1216458 GACAATGACGACGATGAC
1 GACGATGAGGACGATGAC
*
1216476 GACGATGAGGATGATGA
1 GACGATGAGGACGATGA
1216493 TGTTTCTTCG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.36, C:0.15, G:0.36, T:0.13
Consensus pattern (18 bp):
GACGATGAGGACGATGAC
Found at i:1216492 original size:9 final size:9
Alignment explanation
Indices: 1216440--1216483 Score: 70
Period size: 9 Copynumber: 4.9 Consensus size: 9
1216430 TTGCAAAAAG
*
1216440 GACGATGAG
1 GACGATGAC
1216449 GACGATGAC
1 GACGATGAC
*
1216458 GACAATGAC
1 GACGATGAC
1216467 GACGATGAC
1 GACGATGAC
1216476 GACGATGA
1 GACGATGA
1216484 GGATGATGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.36, C:0.18, G:0.34, T:0.11
Consensus pattern (9 bp):
GACGATGAC
Found at i:1218930 original size:45 final size:44
Alignment explanation
Indices: 1218797--1218930 Score: 112
Period size: 44 Copynumber: 3.0 Consensus size: 44
1218787 GTCTGATGCG
* * * * *
1218797 ATCTGCTCTATTGCAACTTCAGAGAGATAAGA-TCCATCATTTT-A
1 ATCTGCTCCACTGCAACTTAAGGGAGATAAGACT-TAT-ATTTTCA
* * **
1218841 ATCTGCTCCACTGCAACTTAAGGGAGATAGGATTTATAACTTCA
1 ATCTGCTCCACTGCAACTTAAGGGAGATAAGACTTATATTTTCA
* *
1218885 ATCTGCTCCACTGCAACTTTCAA-GGAGATAAGACTTGTTTTTTCA
1 ATCTGCTCCACTGCAAC-TT-AAGGGAGATAAGACTTATATTTTCA
1218930 A
1 A
1218931 CTTTGACGCC
Statistics
Matches: 72, Mismatches: 14, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
43 3 0.04
44 47 0.65
45 20 0.28
46 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTAAGGGAGATAAGACTTATATTTTCA
Found at i:1219341 original size:89 final size:89
Alignment explanation
Indices: 1219248--1219580 Score: 474
Period size: 89 Copynumber: 3.8 Consensus size: 89
1219238 TACTCTACTA
* * * * * * *
1219248 CAAACTCAGAGAGGCAAGGCTGGTGTTTTCGATCTGCTTCACTGCCAATATAGGAAGACAAAATA
1 CAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATC
*
1219313 TGTTATCTTCAGTCTGTTCCGCTG
66 TGTTATCTTCAGTCTGTTCTGCTG
* * *
1219337 CAAACTCAGGGAGGCAAGGTTGGT-TTTTCGATCTACTAT-GCTGCCAATACAAGAAGACAAGAT
1 CAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACT-TCGCTGCCAATACAGGAAGACAAGAT
1219400 CTGTTATCTTCAGTCTGCTT-TGCTG
65 CTGTTATCTTCAGTCTG-TTCTGCTG
* *
1219425 CAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTCGTTGCCAATACAGAAAGACAAGATC
1 CAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATC
*
1219490 TGTTATCTTCAGTCTGCTCTGCTG
66 TGTTATCTTCAGTCTGTTCTGCTG
* **
1219514 CAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTTGCTGCCAATACATAAAGACAAGATC
1 CAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATC
1219579 TG
66 TG
1219581 CTGCAAACTC
Statistics
Matches: 221, Mismatches: 18, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
88 77 0.35
89 144 0.65
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (89 bp):
CAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATC
TGTTATCTTCAGTCTGTTCTGCTG
Found at i:1219516 original size:177 final size:178
Alignment explanation
Indices: 1219248--1219580 Score: 517
Period size: 177 Copynumber: 1.9 Consensus size: 178
1219238 TACTCTACTA
* * * *
1219248 CAAACTCAGAGAGGCAAGGCTGGTGTTTTCGATCTGCTTCACTGCCAATATAGGAAGACAAAATA
1 CAAACTCAGAGAGGCAAGGCTGGTGTCTTCGATCTACTTCACTGCCAATACAGAAAGACAAAATA
* * *
1219313 TGTTATCTTCAGTCTGTTCCGCTGCAAACTCAGGGAGGCAAGGTTGGT-TTTTCGATCTACTATG
66 TGTTATCTTCAGTCTGCTCCGCTGCAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTATG
1219377 CTGCCAATACA-AGAAGACAAGATCTGTTATCTTCAGTCTGCTTTGCTG
131 CTGCCAATACATA-AAGACAAGATCTGTTATCTTCAGTCTGCTTTGCTG
* ** * *
1219425 CAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTCGTTGCCAATACAGAAAGACAAGATC
1 CAAACTCAGAGAGGCAAGGCTGGTGTCTTCGATCTACTTCACTGCCAATACAGAAAGACAAAATA
* *
1219490 TGTTATCTTCAGTCTGCTCTGCTGCAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTTG
66 TGTTATCTTCAGTCTGCTCCGCTGCAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTATG
1219555 CTGCCAATACATAAAGACAAGATCTG
131 CTGCCAATACATAAAGACAAGATCTG
1219581 CTGCAAACTC
Statistics
Matches: 140, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
177 101 0.72
178 38 0.27
179 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (178 bp):
CAAACTCAGAGAGGCAAGGCTGGTGTCTTCGATCTACTTCACTGCCAATACAGAAAGACAAAATA
TGTTATCTTCAGTCTGCTCCGCTGCAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTATG
CTGCCAATACATAAAGACAAGATCTGTTATCTTCAGTCTGCTTTGCTG
Found at i:1219648 original size:70 final size:70
Alignment explanation
Indices: 1219507--1219650 Score: 180
Period size: 70 Copynumber: 2.1 Consensus size: 70
1219497 TTCAGTCTGC
* * ** *
1219507 TCTGCTGCAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTTGCTGCCAATACATAAAGA
1 TCTGCTGCAAACTCAAGGAGGCAAGACTGGTGTCTTCGATCTACTTCACTGCCAATACAGAAAGA
1219572 CAAGA
66 CAAGA
* * * * *
1219577 TCTGCTGCAAACTCAAGGAGGCAAGACTGGTGTTTTTGATCTGCTTCACTGCCAGTACAGGAAGA
1 TCTGCTGCAAACTCAAGGAGGCAAGACTGGTGTCTTCGATCTACTTCACTGCCAATACAGAAAGA
**
1219642 TGAGA
66 CAAGA
1219647 TCTG
1 TCTG
1219651 TTATCTTCAG
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (70 bp):
TCTGCTGCAAACTCAAGGAGGCAAGACTGGTGTCTTCGATCTACTTCACTGCCAATACAGAAAGA
CAAGA
Found at i:1219709 original size:159 final size:159
Alignment explanation
Indices: 1219420--1219738 Score: 458
Period size: 159 Copynumber: 2.0 Consensus size: 159
1219410 CAGTCTGCTT
* * **
1219420 TGCTGCAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTCGTTGCCAATACAGAAAGACA
1 TGCTGCAAACTCAAGGAGGCAAGACTGGTGTCTTCGATCTACTTCACTGCCAATACAGAAAGACA
* * *
1219485 AGATCTGTTATCTTCAGTCTGCTCTGCTGCAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTA
66 AGATCTGTTATCTTCAGTCTCCTCTACTGCAAACTCAGGGAGGCAAGACTGGTGTCTTCGATCTA
* *
1219550 CTTTGCTGCCAATACATAAAGACAAGATC
131 CTTCGCTGCCAATACAGAAAGACAAGATC
* * * * * **
1219579 TGCTGCAAACTCAAGGAGGCAAGACTGGTGTTTTTGATCTGCTTCACTGCCAGTACAGGAAGATG
1 TGCTGCAAACTCAAGGAGGCAAGACTGGTGTCTTCGATCTACTTCACTGCCAATACAGAAAGACA
* * *
1219644 AGATCTGTTATCTTCAGTCTCCTCTACTGTAAACTGAGGGAGGCAAGATTGGTGTCTTCGATCTA
66 AGATCTGTTATCTTCAGTCTCCTCTACTGCAAACTCAGGGAGGCAAGACTGGTGTCTTCGATCTA
*
1219709 CTTCGCTGCCAATACAGGAAGACAAGATC
131 CTTCGCTGCCAATACAGAAAGACAAGATC
1219738 T
1 T
1219739 ATTATCTTTA
Statistics
Matches: 140, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
159 140 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.27
Consensus pattern (159 bp):
TGCTGCAAACTCAAGGAGGCAAGACTGGTGTCTTCGATCTACTTCACTGCCAATACAGAAAGACA
AGATCTGTTATCTTCAGTCTCCTCTACTGCAAACTCAGGGAGGCAAGACTGGTGTCTTCGATCTA
CTTCGCTGCCAATACAGAAAGACAAGATC
Found at i:1219737 original size:89 final size:89
Alignment explanation
Indices: 1219581--1219942 Score: 492
Period size: 89 Copynumber: 4.1 Consensus size: 89
1219571 ACAAGATCTG
* * * * * *
1219581 CTGCAAACTCAAGGAGGCAAGACTGGTGTTTTTGATCTGCTTCACTGCCAGTACAGGAAGATGAG
1 CTGCAAACTCAAGGAGGCAAGACTGGTGTCTTCGATCTACTTCGCTGCCAATACAGGAAGATAAG
*
1219646 ATCTGTTATCTTCAGTCTCCTCTA
66 ATCTGTTATCTTCAGTCTGCTCTA
* * * * *
1219670 CTGTAAACTGAGGGAGGCAAGATTGGTGTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAG
1 CTGCAAACTCAAGGAGGCAAGACTGGTGTCTTCGATCTACTTCGCTGCCAATACAGGAAGATAAG
* * *
1219735 ATCTATTATCTTTAGTCTGCTCTG
66 ATCTGTTATCTTCAGTCTGCTCTA
* *
1219759 CTGCAAACTCAAGGAGGCAAGGCTGGTGTCATT-GATCTACTTCGCTGCCAATATAGGAAGATAA
1 CTGCAAACTCAAGGAGGCAAGACTGGTGTC-TTCGATCTACTTCGCTGCCAATACAGGAAGATAA
* **
1219823 GATCTGTTATCTTCAGTCTACTCCG
65 GATCTGTTATCTTCAGTCTGCTCTA
* * * *
1219848 TTGCAAACTCATGGAGGCAAGGCTGGTGTCTTCGATCTACTTCGCTGCCAATATAGGAAGATAAG
1 CTGCAAACTCAAGGAGGCAAGACTGGTGTCTTCGATCTACTTCGCTGCCAATACAGGAAGATAAG
1219913 ATCTGTTATCTTCAGTCTGCTCTA
66 ATCTGTTATCTTCAGTCTGCTCTA
1219937 CTGCAA
1 CTGCAA
1219943 CTTCAGGGAG
Statistics
Matches: 239, Mismatches: 32, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
88 2 0.01
89 235 0.98
90 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (89 bp):
CTGCAAACTCAAGGAGGCAAGACTGGTGTCTTCGATCTACTTCGCTGCCAATACAGGAAGATAAG
ATCTGTTATCTTCAGTCTGCTCTA
Found at i:1219866 original size:337 final size:336
Alignment explanation
Indices: 1219248--1219900 Score: 979
Period size: 337 Copynumber: 1.9 Consensus size: 336
1219238 TACTCTACTA
* *
1219248 CAAACTCAGAGAGGCAAGGCTGGTGTTTTCGATCTGCTTCACTGCCAATATAGGAAGACAAAATA
1 CAAACTCAGAGAGGCAAGACTGGTGTTTTCGATCTGCTTCACTGCCAATACAGGAAGACAAAATA
** * * *
1219313 TGTTATCTTCAGTCTGTTCCGCTGCAAACTCAGGGAGGCAAGGTTGGTTTTTCGATCTACTATGC
66 TGTTATCTTCAGTCTCCTCCACTGCAAACTCAGGGAGGCAAGATTGGTTCTTCGATCTACTATGC
* * *
1219378 TGCCAATACAAGAAGACAAGATCTGTTATCTTCAGTCTGCTTTGCTGCAAACTCAGGGAGGCAAG
131 TGCCAATACAAGAAGACAAGATCTATTATCTTCAGTCTGCTCTGCTGCAAACTCAAGGAGGCAAG
* *
1219443 GCTGGTGTCTTCGATCTACTTCGTTGCCAATACAGAAAGACAAGATCTGTTATCTTCAGTCTGCT
196 GCTGGTGTCTTCGATCTACTTCGCTGCCAATACAGAAAGACAAGATCTGTTATCTTCAGTCTACT
* *
1219508 CTGCTGCAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTTGCTGCCAATACATAAAGAC
261 CCGCTGCAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTCGCTGCCAATACATAAAGAC
1219573 AAGATCTGCTG
326 AAGATCTGCTG
* * ** *
1219584 CAAACTCA-AGGAGGCAAGACTGGTGTTTTTGATCTGCTTCACTGCCAGTACAGGAAGATGAGAT
1 CAAACTCAGA-GAGGCAAGACTGGTGTTTTCGATCTGCTTCACTGCCAATACAGGAAGACAAAAT
* * * *
1219648 CTGTTATCTTCAGTCTCCTCTACTGTAAACTGAGGGAGGCAAGATTGGTGTCTTCGATCTACT-T
65 ATGTTATCTTCAGTCTCCTCCACTGCAAACTCAGGGAGGCAAGATTGGT-TCTTCGATCTACTAT
* *
1219712 CGCTGCCAATACAGGAAGACAAGATCTATTATCTTTAGTCTGCTCTGCTGCAAACTCAAGGAGGC
129 -GCTGCCAATACAAGAAGACAAGATCTATTATCTTCAGTCTGCTCTGCTGCAAACTCAAGGAGGC
* * *
1219777 AAGGCTGGTGTCATT-GATCTACTTCGCTGCCAATATAGGAAGATAAGATCTGTTATCTTCAGTC
193 AAGGCTGGTGTC-TTCGATCTACTTCGCTGCCAATACAGAAAGACAAGATCTGTTATCTTCAGTC
* *
1219841 TACTCCGTTGCAAACTCATGGAGGCAAGGCTGGTGTCTTCGATCTACTTCGCTGCCAATA
257 TACTCCGCTGCAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTCGCTGCCAATA
1219901 TAGGAAGATA
Statistics
Matches: 283, Mismatches: 30, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
335 1 0.00
336 97 0.34
337 183 0.65
338 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (336 bp):
CAAACTCAGAGAGGCAAGACTGGTGTTTTCGATCTGCTTCACTGCCAATACAGGAAGACAAAATA
TGTTATCTTCAGTCTCCTCCACTGCAAACTCAGGGAGGCAAGATTGGTTCTTCGATCTACTATGC
TGCCAATACAAGAAGACAAGATCTATTATCTTCAGTCTGCTCTGCTGCAAACTCAAGGAGGCAAG
GCTGGTGTCTTCGATCTACTTCGCTGCCAATACAGAAAGACAAGATCTGTTATCTTCAGTCTACT
CCGCTGCAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTCGCTGCCAATACATAAAGAC
AAGATCTGCTG
Found at i:1219887 original size:44 final size:44
Alignment explanation
Indices: 1219758--1219895 Score: 113
Period size: 44 Copynumber: 3.1 Consensus size: 44
1219748 AGTCTGCTCT
* *
1219758 GCTGCAAACTCAAGGAGGCAAGGCTGGTGTCATT-GATCTACTTC
1 GCTGCAAACTCATGGAGGCAAGGCTGGTGTC-TTCGATCTACTCC
* ** * * *
1219802 GCTGCCAA-T-ATAGGAAGATAAGATCTGTTATCTTC-AGTCTACTCC
1 GCTGCAAACTCAT-GG-AGGCAAG-GCTGGTGTCTTCGA-TCTACTCC
* *
1219847 GTTGCAAACTCATGGAGGCAAGGCTGGTGTCTTCGATCTACTTC
1 GCTGCAAACTCATGGAGGCAAGGCTGGTGTCTTCGATCTACTCC
1219891 GCTGC
1 GCTGC
1219896 CAATATAGGA
Statistics
Matches: 69, Mismatches: 17, Indels: 16
0.68 0.17 0.16
Matches are distributed among these distances:
42 1 0.01
43 3 0.04
44 35 0.51
45 25 0.36
46 3 0.04
47 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (44 bp):
GCTGCAAACTCATGGAGGCAAGGCTGGTGTCTTCGATCTACTCC
Found at i:1219996 original size:178 final size:177
Alignment explanation
Indices: 1219581--1219999 Score: 459
Period size: 178 Copynumber: 2.4 Consensus size: 177
1219571 ACAAGATCTG
* ** * * * * * *
1219581 CTGCAAACTCAAGGAGGCAAGACTGGTGTTTTTGATCTGCTTCACTGCCAGTACAGGAAGATGAG
1 CTGCAAACTCAAGGAGACAAGACT-GTGTCATTAATCTACTCCACTGCCAATATAGGAAGATAAG
* * * * *
1219646 ATCTGTTATCTTCAGTCTCCTCTACTGTAAACTGAGGGAGGCAAGATTGGTGTCTTCGATCTACT
65 ATCTGTTATCTTCAGTCTACTCCACTGCAAACTCAGGGAGGCAAGACTGGTGTCTTCGATCTACT
* *
1219711 TCGCTGCCAATACAGGAAGACAAGATCTATTATCTTTAGTCTGCTCTG
130 TCGCTGCCAATACAGGAAGACAAGATCTATTATCTTCAGTCTGCTCTA
* * * * *
1219759 CTGCAAACTCAAGGAGGCAAGGCTGGTGTCATTGATCTACTTCGCTGCCAATATAGGAAGATAAG
1 CTGCAAACTCAAGGAGACAAGACT-GTGTCATTAATCTACTCCACTGCCAATATAGGAAGATAAG
** * *
1219824 ATCTGTTATCTTCAGTCTACTCCGTTGCAAACTCATGGAGGCAAGGCTGGTGTCTTCGATCTACT
65 ATCTGTTATCTTCAGTCTACTCCACTGCAAACTCAGGGAGGCAAGACTGGTGTCTTCGATCTACT
* * *
1219889 TCGCTGCCAATATAGGAAGATAAGATCTGTTATCTTCAGTCTGCTCTA
130 TCGCTGCCAATACAGGAAGACAAGATCTATTATCTTCAGTCTGCTCTA
* * * *
1219937 CTGC-AACTTCAGGGAGATAAGACT-TG-CAACTTCAATCTGCTCCACTG-CAACTTTAGGAAGA
1 CTGCAAAC-TCAAGGAGACAAGACTGTGTC-A-TT-AATCTACTCCACTGCCAA-TATAGGAAGA
1219998 TA
61 TA
1220000 GGATTATTGG
Statistics
Matches: 205, Mismatches: 31, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
175 1 0.00
176 3 0.01
177 8 0.04
178 193 0.94
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (177 bp):
CTGCAAACTCAAGGAGACAAGACTGTGTCATTAATCTACTCCACTGCCAATATAGGAAGATAAGA
TCTGTTATCTTCAGTCTACTCCACTGCAAACTCAGGGAGGCAAGACTGGTGTCTTCGATCTACTT
CGCTGCCAATACAGGAAGACAAGATCTATTATCTTCAGTCTGCTCTA
Found at i:1221206 original size:42 final size:42
Alignment explanation
Indices: 1221143--1221264 Score: 147
Period size: 42 Copynumber: 2.9 Consensus size: 42
1221133 GTATAACAAG
* * * ** *
1221143 ATCATCACATGCCCCAATCTGATCAAAATTCGAGTTGCTCTG
1 ATCATCCCATGCCCCATTCTGATCAAGATTCGAGCCGCTCTA
* *
1221185 ATCA-CCTCATGCCCCATTCTGATTAAGATTCGAACCGCTCTA
1 ATCATCC-CATGCCCCATTCTGATCAAGATTCGAGCCGCTCTA
*
1221227 ATCATCCCATGCCCCATTCTAATCAAGATTCGAGCCGC
1 ATCATCCCATGCCCCATTCTGATCAAGATTCGAGCCGC
1221265 CCTTTTCAAG
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 1 0.01
42 64 0.96
43 2 0.03
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.27
Consensus pattern (42 bp):
ATCATCCCATGCCCCATTCTGATCAAGATTCGAGCCGCTCTA
Found at i:1232158 original size:17 final size:18
Alignment explanation
Indices: 1232136--1232171 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1232126 CACTAATGAA
*
1232136 TACAAATAATCAAT-CAG
1 TACAAATAAGCAATACAG
1232153 TACAAATAAGCAATACAG
1 TACAAATAAGCAATACAG
1232171 T
1 T
1232172 GTACATGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.53, C:0.17, G:0.08, T:0.22
Consensus pattern (18 bp):
TACAAATAAGCAATACAG
Found at i:1237568 original size:41 final size:40
Alignment explanation
Indices: 1237471--1237580 Score: 125
Period size: 40 Copynumber: 2.8 Consensus size: 40
1237461 AAGTTACCCG
* * *
1237471 GGATAACACATGAAAAGGTTGAAAAGGATATATTCGAAAA
1 GGATATCAAATGAAAAGGTTGAAAAGGATATATCCGAAAA
*
1237511 GGATATCAAATGAAAAGGTTGAAAAGG-TCGCTATCCGAAAA
1 GGATATCAAATGAAAAGGTTGAAAAGGAT--ATATCCGAAAA
* * *
1237552 GGATATC-AATGAAAAAGTCGAAAATGATA
1 GGATATCAAATGAAAAGGTTGAAAAGGATA
1237581 GCAATGGAAG
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
39 1 0.02
40 41 0.69
41 17 0.29
ACGTcount: A:0.48, C:0.09, G:0.23, T:0.20
Consensus pattern (40 bp):
GGATATCAAATGAAAAGGTTGAAAAGGATATATCCGAAAA
Found at i:1248026 original size:20 final size:19
Alignment explanation
Indices: 1248001--1248065 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
1247991 ACCAATAAAA
1248001 TATAAAAAAGATATAAATTT
1 TATAAAAAA-ATATAAATTT
*
1248021 TATAAAATAAATA-CAATTT
1 TATAAAA-AAATATAAATTT
* *
1248040 TTTAAAAAAAATTATAAAATT
1 TAT-AAAAAAA-TATAAATTT
1248061 TATAA
1 TATAA
1248066 GACTTAATCG
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
19 10 0.28
20 18 0.50
21 8 0.22
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
TATAAAAAAATATAAATTT
Found at i:1249490 original size:16 final size:18
Alignment explanation
Indices: 1249456--1249493 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1249446 ATCCTTATTT
*
1249456 AAATAAAATATAATGGTA
1 AAATAAAATATAATAGTA
1249474 AAATAAAATA-AA-AGTA
1 AAATAAAATATAATAGTA
1249490 AAAT
1 AAAT
1249494 CCGTATAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 2 0.11
18 10 0.53
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (18 bp):
AAATAAAATATAATAGTA
Found at i:1250153 original size:23 final size:24
Alignment explanation
Indices: 1250101--1250153 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 24
1250091 ATAAAATAAT
1250101 TATTTTTCAAAGATTTTGACAGGA
1 TATTTTTCAAAGATTTTGACAGGA
* * * *
1250125 -ACTTTTCAAA-TTTTTTATAGGA
1 TATTTTTCAAAGATTTTGACAGGA
1250147 TATTTTT
1 TATTTTT
1250154 TTTATCAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (24 bp):
TATTTTTCAAAGATTTTGACAGGA
Found at i:1252661 original size:21 final size:20
Alignment explanation
Indices: 1252637--1252705 Score: 77
Period size: 21 Copynumber: 3.4 Consensus size: 20
1252627 ATTTAAAATG
*
1252637 AATTATAAAAAAATTGTTTAA
1 AATTATAAAAAAATT-ATTAA
**
1252658 AATTAT-TTAAAATTATTAA
1 AATTATAAAAAAATTATTAA
*
1252677 AATTGAAAAAAAAATTATTAA
1 AATT-ATAAAAAAATTATTAA
1252698 AATTATAA
1 AATTATAA
1252706 TTTTAACATC
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 8 0.21
20 10 0.26
21 21 0.54
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
AATTATAAAAAAATTATTAA
Found at i:1272879 original size:15 final size:15
Alignment explanation
Indices: 1272855--1272893 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
1272845 TATATTAACT
1272855 TAATATATATAAGTTA
1 TAATA-ATATAAGTTA
*
1272871 TAATAATATATGTTA
1 TAATAATATAAGTTA
1272886 TAATAATA
1 TAATAATA
1272894 AAATTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (15 bp):
TAATAATATAAGTTA
Found at i:1281835 original size:45 final size:45
Alignment explanation
Indices: 1281767--1281939 Score: 170
Period size: 45 Copynumber: 3.8 Consensus size: 45
1281757 ATCATCAAAG
** * * *
1281767 GATGCCATAGTGTCTCCCAGCTATGGTCTTAGTCCTTTTTACCAT
1 GATGCCATAGTGTCTTTCAGCTATGGTCTTACTCATTTATACCAT
* * * **
1281812 GATTCCATAGTGTCTTTTAGCTATAGTCTTACTCATTTATGTCAT
1 GATGCCATAGTGTCTTTCAGCTATGGTCTTACTCATTTATACCAT
* *
1281857 GATGCCATAGCGTCTTTCAGCTATGGTCTTAATCATTCTAGT-CC-T
1 GATGCCATAGTGTCTTTCAGCTATGGTCTTACTCATT-TA-TACCAT
* ** *
1281902 GATGTCATAGCATCTTTTAGCTATGGTCTTACTCATTT
1 GATGCCATAGTGTCTTTCAGCTATGGTCTTACTCATTT
1281940 TAGGTGTATA
Statistics
Matches: 106, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
44 1 0.01
45 101 0.95
46 3 0.03
47 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (45 bp):
GATGCCATAGTGTCTTTCAGCTATGGTCTTACTCATTTATACCAT
Found at i:1283346 original size:16 final size:16
Alignment explanation
Indices: 1283325--1283377 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
1283315 TGTTTGGTTT
1283325 GCTGTAATGAAATAGA
1 GCTGTAATGAAATAGA
*
1283341 GCTGTAATGGAATAGA
1 GCTGTAATGAAATAGA
*
1283357 GTTGTAATGAAATAGA
1 GCTGTAATGAAATAGA
*
1283373 ACTGT
1 GCTGT
1283378 TTGGTTGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.40, C:0.06, G:0.26, T:0.28
Consensus pattern (16 bp):
GCTGTAATGAAATAGA
Found at i:1288698 original size:29 final size:29
Alignment explanation
Indices: 1288643--1288698 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1288633 TTTTTAAAAG
**
1288643 TAATTTTATACTATCTGAATTTTTTTTTA
1 TAATTTTATACTATCTGAATTACTTTTTA
1288672 TAATTTTATACTATCTG-ATATACTTTT
1 TAATTTTATACTATCTGAAT-TACTTTT
1288699 AAAAAAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.29, C:0.09, G:0.04, T:0.59
Consensus pattern (29 bp):
TAATTTTATACTATCTGAATTACTTTTTA
Found at i:1289828 original size:34 final size:34
Alignment explanation
Indices: 1289785--1289856 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
1289775 CCATTTTATA
1289785 ACTTTGGATGGTTGGGTAACCAAGAAAGAAATTT
1 ACTTTGGATGGTTGGGTAACCAAGAAAGAAATTT
1289819 ACTTTGGATGGTTGGGTAACCAAGAAAGAAATTT
1 ACTTTGGATGGTTGGGTAACCAAGAAAGAAATTT
1289853 ACTT
1 ACTT
1289857 ATAGGTGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.31
Consensus pattern (34 bp):
ACTTTGGATGGTTGGGTAACCAAGAAAGAAATTT
Found at i:1295078 original size:18 final size:20
Alignment explanation
Indices: 1295036--1295078 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
1295026 TTGAGATCGT
* *
1295036 AAATTGAGCACGAGAGCCTA
1 AAATTGAGCACAAGAGCCCA
1295056 AAATTGAG-ACAAGA-CCCA
1 AAATTGAGCACAAGAGCCCA
1295074 AAATT
1 AAATT
1295079 TGGTCAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 5 0.24
20 8 0.38
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.16
Consensus pattern (20 bp):
AAATTGAGCACAAGAGCCCA
Found at i:1295439 original size:25 final size:26
Alignment explanation
Indices: 1295401--1295467 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 26
1295391 TTAATTTAAT
*
1295401 TTAATACTT-ATATTAATAGT-ATTTTA
1 TTAATA-TTAATATTAA-AGTGATTATA
*
1295427 TTAAT-TTAATATTAAAGTGATTATC
1 TTAATATTAATATTAAAGTGATTATA
1295452 TTAATATTAA-ATTAAA
1 TTAATATTAATATTAAA
1295468 TTTAATGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
24 5 0.14
25 22 0.61
26 9 0.25
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.49
Consensus pattern (26 bp):
TTAATATTAATATTAAAGTGATTATA
Found at i:1295488 original size:30 final size:29
Alignment explanation
Indices: 1295447--1295512 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 29
1295437 ATTAAAGTGA
1295447 TTATCTTAATATTAAATTAAATTTAATGT
1 TTATCTTAATATTAAATTAAATTTAATGT
*
1295476 TTATCTATAATATTAAATTTAATTTAATGT
1 TTATCT-TAATATTAAATTAAATTTAATGT
1295506 TTATCTT
1 TTATCTT
1295513 GTAGATAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 7 0.20
30 28 0.80
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (29 bp):
TTATCTTAATATTAAATTAAATTTAATGT
Found at i:1299025 original size:13 final size:14
Alignment explanation
Indices: 1299006--1299043 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
1298996 TAATTGCATA
1299006 GAAATAATATAAAC
1 GAAATAATATAAAC
1299020 -AAATAA-ATAAAC
1 GAAATAATATAAAC
1299032 GAAATTAATATA
1 GAAA-TAATATA
1299044 TATAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 3 0.14
15 3 0.14
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (14 bp):
GAAATAATATAAAC
Found at i:1299590 original size:26 final size:25
Alignment explanation
Indices: 1299555--1299611 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
1299545 ATATTAGTTT
*
1299555 AAAA-AAATATAAATATGTACATAAA
1 AAAATAAATATAAATATATA-ATAAA
* *
1299580 AAAATAAATATACATATATATTAAA
1 AAAATAAATATAAATATATAATAAA
1299605 AAAATAA
1 AAAATAA
1299612 TTACATATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (25 bp):
AAAATAAATATAAATATATAATAAA
Found at i:1299604 original size:25 final size:25
Alignment explanation
Indices: 1299576--1299637 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
1299566 AATATGTACA
*
1299576 TAAAAAAATAAATATACATAT-ATAT
1 TAAAAAAATAAAT-TACATATAAAAT
1299601 TAAAAAAAT-AATTACATATGAAAAT
1 TAAAAAAATAAATTACATAT-AAAAT
*
1299626 TATAAAAATAAA
1 TAAAAAAATAAA
1299638 AATAATAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 7 0.22
24 3 0.09
25 20 0.62
26 2 0.06
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (25 bp):
TAAAAAAATAAATTACATATAAAAT
Found at i:1301593 original size:45 final size:45
Alignment explanation
Indices: 1301544--1301766 Score: 125
Period size: 44 Copynumber: 5.0 Consensus size: 45
1301534 TGTCTTTGAT
1301544 CTGCTTCACTGTCAGTACAGGAAGGCAAGATTTGCTATCTTTAAC
1 CTGCTTCACTGTCAGTACAGGAAGGCAAGATTTGCTATCTTTAAC
* * ** * * * * ** * * * *
1301589 CTGCTCCGCTACCA--CCGAGGGAGGTAGGGCTAG-TGTCTTCAAT
1 CTGCTTCACTGTCAGTAC-AGGAAGGCAAGATTTGCTATCTTTAAC
* * *
1301632 CTGCTTCACTGTCAGTACAGAAATGCAAGATCTGCTATCTTTAAC
1 CTGCTTCACTGTCAGTACAGGAAGGCAAGATTTGCTATCTTTAAC
* * ** * * * * *
1301677 CTGCTCCACTGCCA-T-CGAGGAAGGCAAGGCTAG-TGTCGTCAAT
1 CTGCTTCACTGTCAGTAC-AGGAAGGCAAGATTTGCTATCTTTAAC
* * *
1301720 CTGCTTCACTGTTAGTACAGGAAGGTAAGATCTGCTATCTTTAAC
1 CTGCTTCACTGTCAGTACAGGAAGGCAAGATTTGCTATCTTTAAC
1301765 CT
1 CT
1301767 ACTCCGCTGC
Statistics
Matches: 115, Mismatches: 55, Indels: 16
0.62 0.30 0.09
Matches are distributed among these distances:
43 36 0.31
44 40 0.35
45 39 0.34
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (45 bp):
CTGCTTCACTGTCAGTACAGGAAGGCAAGATTTGCTATCTTTAAC
Found at i:1301640 original size:88 final size:88
Alignment explanation
Indices: 1301533--1301845 Score: 455
Period size: 88 Copynumber: 3.6 Consensus size: 88
1301523 GATAAGACTG
** *
1301533 GTGTCTTTGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATTTGCTATCTTTAACCTGCTCCGC
1 GTGTCTTCAATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGC
* * *
1301598 TACCACCGAGGGAGGTAGGGCTA
66 TGCCACCGAGGGAGGCAAGGCTA
* * *
1301621 GTGTCTTCAATCTGCTTCACTGTCAGTACAGAAATGCAAGATCTGCTATCTTTAACCTGCTCCAC
1 GTGTCTTCAATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGC
* *
1301686 TGCCATCGAGGAAGGCAAGGCTA
66 TGCCACCGAGGGAGGCAAGGCTA
* * * *
1301709 GTGTCGTCAATCTGCTTCACTGTTAGTACAGGAAGGTAAGATCTGCTATCTTTAACCTACTCCGC
1 GTGTCTTCAATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGC
*
1301774 TGCCACTGAGGGAGGCAAGGCTA
66 TGCCACCGAGGGAGGCAAGGCTA
* * *
1301797 GTGTCTTCAATCTGCTTCACTATTAGTACAGGAAGGCAATATCTGCTAT
1 GTGTCTTCAATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTAT
1301846 TTCCGATCCA
Statistics
Matches: 200, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 200 1.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (88 bp):
GTGTCTTCAATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGC
TGCCACCGAGGGAGGCAAGGCTA
Found at i:1301742 original size:44 final size:44
Alignment explanation
Indices: 1301616--1301835 Score: 144
Period size: 44 Copynumber: 5.0 Consensus size: 44
1301606 AGGGAGGTAG
* *
1301616 GGCTAGTGTCTTCAATCTGCTTCACTGTCAGTACAGAAATGCAA
1 GGCTAGTGTCTTCAATCTGCTTCACTGTCAGTACAGGAAGGCAA
* * * * * *
1301660 GATCT-GCTATCTTTAACCTGCTCCACTGCCA-T-CGAGGAAGGCAA
1 G-GCTAG-TGTCTTCAATCTGCTTCACTGTCAGTAC-AGGAAGGCAA
* * *
1301704 GGCTAGTGTCGTCAATCTGCTTCACTGTTAGTACAGGAAGGTAA
1 GGCTAGTGTCTTCAATCTGCTTCACTGTCAGTACAGGAAGGCAA
* * * * * * * * * * *
1301748 GATCT-GCTATCTTTAACCTACTCCGCTGCCACT-GAGGGAGGCAA
1 G-GCTAG-TGTCTTCAATCTGCTTCACTGTCAGTACAGGAAGGCAA
* *
1301792 GGCTAGTGTCTTCAATCTGCTTCACTATTAGTACAGGAAGGCAA
1 GGCTAGTGTCTTCAATCTGCTTCACTGTCAGTACAGGAAGGCAA
1301836 TATCTGCTAT
Statistics
Matches: 122, Mismatches: 44, Indels: 20
0.66 0.24 0.11
Matches are distributed among these distances:
43 38 0.31
44 44 0.36
45 40 0.33
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (44 bp):
GGCTAGTGTCTTCAATCTGCTTCACTGTCAGTACAGGAAGGCAA
Found at i:1301887 original size:44 final size:43
Alignment explanation
Indices: 1301826--1302682 Score: 436
Period size: 44 Copynumber: 19.4 Consensus size: 43
1301816 CTATTAGTAC
* * * *
1301826 AGGAAGGCAATATCTGCTATTTCCGATCCACTTCATGCCAATAC
1 AGGAAGACAAGATCTGCTATTT-CGATCTACTTCATGCCAATAT
* * * *** *
1301870 ATGAAGATAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATGT
1 AGGAAGACAAGATCTGCTAT-TTCGATCTACTTC-ATGCCAATAT
* * * *
1301915 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTCCTACCAATAT
1 AGGAAGACAAGATCTGCTAT-TTCGATCTACTTCATGCCAATAT
* * * * *
1301958 AGGAAGACATGATCTGCTACCTTCGATTTACTTCACGCCAATAC
1 AGGAAGACAAGATCTGCTA-TTTCGATCTACTTCATGCCAATAT
* ** *
1302002 ATGAAGATGAGATCTGCTTTCTTCGATCTACTT--TGCCACCAATAT
1 AGGAAGACAAGATCTGCTAT-TTCGATCTACTTCATG---CCAATAT
* * * * *
1302047 GGGAATACAAGATCTGC-ATCTTCGATCCACTTCCTACCAATAT
1 AGGAAGACAAGATCTGCTAT-TTCGATCTACTTCATGCCAATAT
* * * * *
1302090 AGGAAGACATGATCTGCTACCTTCGATTTACTTCACGCCAATAC
1 AGGAAGACAAGATCTGCTA-TTTCGATCTACTTCATGCCAATAT
* ** *
1302134 ATGAAGATGAGATCTGCTTTCTTCGATCTACTTC--GCCACCAGTAT
1 AGGAAGACAAGATCTGCTAT-TTCGATCTACTTCATGCCA--A-TAT
* * * * *
1302179 GGGAAGATAAGATCTG-TATCTTCGATCCACTTCGCTACCAATAT
1 AGGAAGACAAGATCTGCTAT-TTCGATCTACTTC-ATGCCAATAT
* * *
1302223 AGGAAGAC-AGCATCTGTTATCTTCGATCTACTTCACGCCAATAC
1 AGGAAGACAAG-ATCTGCTAT-TTCGATCTACTTCATGCCAATAT
* * * * * *
1302267 ATGAAGGCAAGATCTTCTTTCTTTGATCTTCTTC--GCCACCAGTAT
1 AGGAAGACAAGATCTGCTAT-TTCGATCTACTTCATGCCA--A-TAT
* * * *
1302312 GGGAAGACAAGATCTG-TATCTTCGATCCACTTCGCTACCAATAT
1 AGGAAGACAAGATCTGCTAT-TTCGATCTACTTC-ATGCCAATAT
* * *
1302356 AGGAAGAC-AGCATCTGTTATCTTCGATCTACTTCACGCCAATAC
1 AGGAAGACAAG-ATCTGCTAT-TTCGATCTACTTCATGCCAATAT
* * * * * *
1302400 ATGAAGGCAAGATCTTCTTTCTTTGATCTTCTTC--GCCACCAGTAT
1 AGGAAGACAAGATCTGCTAT-TTCGATCTACTTCATGCCA--A-TAT
* * * *
1302445 GGGAAGACAAGATCTG-TATCTTCGATCCACTTCGCTACCAATAT
1 AGGAAGACAAGATCTGCTAT-TTCGATCTACTTC-ATGCCAATAT
* * * * * *
1302489 AGGAAGACATGATATGTTATCTTCGATCTACTTTACGCCAATAC
1 AGGAAGACAAGATCTGCTAT-TTCGATCTACTTCATGCCAATAT
* * * *
1302533 ATGAAGATAAGATCTGCTTTCTTTGATCTACTT--TGCCACCAATAT
1 AGGAAGACAAGATCTGCTAT-TTCGATCTACTTCATG---CCAATAT
* * * * *
1302578 GGGAAGACAAGATCTGC-ATCTTCGATCCAATTCCTACCAATAT
1 AGGAAGACAAGATCTGCTAT-TTCGATCTACTTCATGCCAATAT
* * *
1302621 AGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATAC
1 AGGAAGACAAGATCTGCTAT-TTCGATCTACTTCATGCCAATAT
*
1302665 ATGAAGACAAGATCTGCT
1 AGGAAGACAAGATCTGCT
1302683 TCTTTTTAGC
Statistics
Matches: 618, Mismatches: 151, Indels: 88
0.72 0.18 0.10
Matches are distributed among these distances:
42 14 0.02
43 70 0.11
44 367 0.59
45 156 0.25
46 2 0.00
47 9 0.01
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (43 bp):
AGGAAGACAAGATCTGCTATTTCGATCTACTTCATGCCAATAT
Found at i:1301991 original size:132 final size:133
Alignment explanation
Indices: 1301837--1302683 Score: 1283
Period size: 133 Copynumber: 6.4 Consensus size: 133
1301827 GGAAGGCAAT
* *
1301837 ATCTGCTAT-TTCCGATCCACTTCATGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTAC
1 ATCTGCTATCTT-CGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTAC
*
1301901 TTCGCCACCAATGTGGGAAGACAAGATCTGCATCTTCGATCCACTTC-CTACCAATATAGGAAGA
65 TTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGA
1301965 CATG
130 CATG
* * *
1301969 ATCTGCTACCTTCGATTTACTTCACGCCAATACATGAAGATGAGATCTGCTTTCTTCGATCTACT
1 ATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTACT
* *
1302034 TTGCCACCAATATGGGAATACAAGATCTGCATCTTCGATCCACTTC-CTACCAATATAGGAAGAC
66 TCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGAC
1302098 ATG
131 ATG
* * *
1302101 ATCTGCTACCTTCGATTTACTTCACGCCAATACATGAAGATGAGATCTGCTTTCTTCGATCTACT
1 ATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTACT
* * *
1302166 TCGCCACCAGTATGGGAAGATAAGATCTGTATCTTCGATCCACTTCGCTACCAATATAGGAAGAC
66 TCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGAC
1302231 A-G
131 ATG
* ** * * *
1302233 CATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGGCAAGATCTTCTTTCTTTGATCTTC
1 -ATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTAC
* *
1302298 TTCGCCACCAGTATGGGAAGACAAGATCTGTATCTTCGATCCACTTCGCTACCAATATAGGAAGA
65 TTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGA
1302363 CA-G
130 CATG
* ** * * *
1302366 CATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGGCAAGATCTTCTTTCTTTGATCTTC
1 -ATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTAC
* *
1302431 TTCGCCACCAGTATGGGAAGACAAGATCTGTATCTTCGATCCACTTCGCTACCAATATAGGAAGA
65 TTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGA
1302496 CATG
130 CATG
* * * *
1302500 ATATGTTATCTTCGATCTACTTTACGCCAATACATGAAGATAAGATCTGCTTTCTTTGATCTACT
1 ATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTACT
* *
1302565 TTGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCAATTC-CTACCAATATAGGAAGAC
66 TCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGAC
*
1302629 AGG
131 ATG
*
1302632 ATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
1 ATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTT
1302684 CTTTTTAGCC
Statistics
Matches: 673, Mismatches: 38, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
132 296 0.44
133 376 0.56
134 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.30
Consensus pattern (133 bp):
ATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTACT
TCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGAC
ATG
Found at i:1304035 original size:17 final size:16
Alignment explanation
Indices: 1304002--1304033 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1303992 CTTTTTCATC
1304002 ATTTTGATTTTTTTTT
1 ATTTTGATTTTTTTTT
1304018 ATTTTGATTTTTTTTT
1 ATTTTGATTTTTTTTT
1304034 TAGAATCTGA
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:0.12, C:0.00, G:0.06, T:0.81
Consensus pattern (16 bp):
ATTTTGATTTTTTTTT
Found at i:1304839 original size:25 final size:26
Alignment explanation
Indices: 1304788--1304848 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
1304778 AAGAAAATCC
* **
1304788 AAAAGAATGAAAGAATAATTATTTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
*
1304814 AAAAGAATGAAAAAAT-ATTGGCTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
1304839 AAAATGAATG
1 AAAA-GAATG
1304849 TAAAGATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.57, C:0.05, G:0.15, T:0.23
Consensus pattern (26 bp):
AAAAGAATGAAAAAATAATTAGCTCA
Found at i:1308549 original size:13 final size:14
Alignment explanation
Indices: 1308531--1308567 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
1308521 AATTGCATAA
1308531 AAATAATATAAAC-
1 AAATAATATAAACG
1308544 AAATAA-ATAAACG
1 AAATAATATAAACG
1308557 AAATTAATATA
1 AAA-TAATATA
1308568 TATANNNNNN
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 3 0.14
15 3 0.14
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (14 bp):
AAATAATATAAACG
Found at i:1314234 original size:24 final size:23
Alignment explanation
Indices: 1314186--1314243 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
1314176 TATGTACATA
*
1314186 AAAAAATAAATATACATATATATT
1 AAAAAAT-AATATACATATAAATT
1314210 AAAAAATAAT-TACATATGAAAATT
1 AAAAAATAATATACATAT--AAATT
1314234 ATAAAAATAA
1 A-AAAAATAA
1314244 GAATAATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 7 0.23
23 3 0.10
24 12 0.40
25 8 0.27
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAAAATAATATACATATAAATT
Found at i:1317557 original size:58 final size:59
Alignment explanation
Indices: 1317445--1317592 Score: 153
Period size: 59 Copynumber: 2.5 Consensus size: 59
1317435 TTTTAAAAAG
*
1317445 ATTATTATTAAATATAATTTAATAAAAATAAAAAAATAATTCGATCATATTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAAAAAAATAATTCAATCATATTTTAACATA
* * * *
1317504 ATTATTATTAAATA-AATTTTAAT-AAAAT-AACATATAATTTAATAACAT-TTTTAATATA
1 ATTATTATTAAATATAA-TTTAATAAAAATAAAAAAATAATTCAAT--CATATTTTAACATA
* *
1317562 ATTATTAATAAAATATGAA-TTAATAATAATA
1 ATTATT-ATTAAATAT-AATTTAATAAAAATA
1317593 TATATTATTA
Statistics
Matches: 74, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
57 11 0.15
58 22 0.30
59 35 0.47
60 4 0.05
61 2 0.03
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAAAAAAATAATTCAATCATATTTTAACATA
Found at i:1317588 original size:18 final size:17
Alignment explanation
Indices: 1317556--1317596 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
1317546 TAACATTTTT
*
1317556 AATATAATTATTAATAA
1 AATATAATTAATAATAA
1317573 AATATGAATTAATAATAA
1 AATAT-AATTAATAATAA
*
1317591 TATATA
1 AATATA
1317597 TTATTATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
AATATAATTAATAATAA
Found at i:1327985 original size:15 final size:15
Alignment explanation
Indices: 1327965--1327994 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1327955 GTGATTTTCG
1327965 AAGGCAACTCCCTTA
1 AAGGCAACTCCCTTA
1327980 AAGGCAACTCCCTTA
1 AAGGCAACTCCCTTA
1327995 TTGTGATTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.20
Consensus pattern (15 bp):
AAGGCAACTCCCTTA
Found at i:1340862 original size:236 final size:236
Alignment explanation
Indices: 1340449--1340930 Score: 813
Period size: 236 Copynumber: 2.0 Consensus size: 236
1340439 ATATTTCTTT
1340449 CTATTTAAAGCTAAATGTTCTAATTTGTACTGTAATACTTCGTAACCCTAATCCAAAGACGAAGA
1 CTATTTAAAGCTAAATGTTCTAATTTGTACTGTAATACTTCGTAACCCTAATCCAAAGACGAAGA
* * *
1340514 CGGGTTAGGGGTGTTGCAAAGGTTACCGCCAAAGGTATAGTATGCCTAGTTTGCTTGAACGCTGT
66 CAGGTTAGGGGTGTTACAAAGGTTACCGCCAAAGGTATAGTATGCCTAGTTTGCTTGAACACTGT
* *
1340579 GTCAAGTAGGTTTTGGTAATGAGATCTGGTTAGGAACCAACAGAATTGACTGGTCAAATAATATA
131 GTCAAGCAAGTTTTGGTAATGAGATCTGGTTAGGAACCAACAGAATTGACTGGTCAAATAATATA
*
1340644 TGTATAGGATTATCTTTTATGTTTCTCTCGATACTTGTAGG
196 TGTATAGGATTATCTTCTATGTTTCTCTCGATACTTGTAGG
* * * * *
1340685 CTATTTAAAGTTAAATGTTCTGATTTGTACTGTAATACTTTGTAACCCTAATCTAGAGACGAAGA
1 CTATTTAAAGCTAAATGTTCTAATTTGTACTGTAATACTTCGTAACCCTAATCCAAAGACGAAGA
*
1340750 CAGGTTAGGGGTGTTACAAAGGTTACCGCCAAAGGTATAGTATGCCTGGTTTGCTTGAACACTGT
66 CAGGTTAGGGGTGTTACAAAGGTTACCGCCAAAGGTATAGTATGCCTAGTTTGCTTGAACACTGT
* *
1340815 GTCAAGCAAGTTTTGGTAATGAGATCTGGTTAGGAACCAACAGAATTGACTGGTCAAATAGTATT
131 GTCAAGCAAGTTTTGGTAATGAGATCTGGTTAGGAACCAACAGAATTGACTGGTCAAATAATATA
*
1340880 TGTATAGGATTATCTTCTATGTTTCTCTCGGTACTTGTAGG
196 TGTATAGGATTATCTTCTATGTTTCTCTCGATACTTGTAGG
1340921 -TCATTTAAAG
1 CT-ATTTAAAG
1340931 GACAATCTTT
Statistics
Matches: 230, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
235 1 0.00
236 229 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (236 bp):
CTATTTAAAGCTAAATGTTCTAATTTGTACTGTAATACTTCGTAACCCTAATCCAAAGACGAAGA
CAGGTTAGGGGTGTTACAAAGGTTACCGCCAAAGGTATAGTATGCCTAGTTTGCTTGAACACTGT
GTCAAGCAAGTTTTGGTAATGAGATCTGGTTAGGAACCAACAGAATTGACTGGTCAAATAATATA
TGTATAGGATTATCTTCTATGTTTCTCTCGATACTTGTAGG
Found at i:1350642 original size:16 final size:17
Alignment explanation
Indices: 1350621--1350652 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1350611 AAATATGCAA
1350621 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
1350637 TCACATAACTTCATAT
1 TCACATAACTTCATAT
1350653 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:1350837 original size:43 final size:42
Alignment explanation
Indices: 1350771--1350941 Score: 157
Period size: 43 Copynumber: 4.0 Consensus size: 42
1350761 GACTCGTACA
* *
1350771 ATGCCAACGTCCCAGACATGGTCTTACATGTAATCACATATCG
1 ATGCCAATGCCCCAGACATGGTCTTACA-GTAATCACATATCG
* * ** *
1350814 ATGCCACTGCCCCAGACAGGGTCTTACACAAATCAAATA-CG
1 ATGCCAATGCCCCAGACATGGTCTTACAGTAATCACATATCG
* *
1350855 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTCG
1 ATGCCAATGCCCCAGACATGGTCTTACA-GTAATCACATA-TCG
* * * * * *
1350898 ATGCCAACGTCCCAGACGTGGTTTTACACGAAAACACATATCG
1 ATGCCAATGCCCCAGACATGGTCTTACA-GTAATCACATATCG
1350941 A
1 A
1350942 AATCCTATGT
Statistics
Matches: 106, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
41 28 0.26
42 13 0.12
43 64 0.60
44 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.21
Consensus pattern (42 bp):
ATGCCAATGCCCCAGACATGGTCTTACAGTAATCACATATCG
Found at i:1364863 original size:17 final size:17
Alignment explanation
Indices: 1364838--1364871 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1364828 TGGATTGGGC
1364838 CTTTATGACTCATATCA
1 CTTTATGACTCATATCA
* *
1364855 CTTTGTGACTCGTATCA
1 CTTTATGACTCATATCA
1364872 TGATCTAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (17 bp):
CTTTATGACTCATATCA
Found at i:1379063 original size:13 final size:13
Alignment explanation
Indices: 1379028--1379064 Score: 53
Period size: 11 Copynumber: 3.1 Consensus size: 13
1379018 TAAATATAAA
1379028 ATAAAAATAT-TT
1 ATAAAAATATATT
1379040 A-AAAAAT-TATT
1 ATAAAAATATATT
1379051 ATAAAAATATATT
1 ATAAAAATATATT
1379064 A
1 A
1379065 AACTGCGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.05
11 9 0.41
12 7 0.32
13 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAAAAATATATT
Found at i:1389585 original size:6 final size:6
Alignment explanation
Indices: 1389574--1389605 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1389564 CTACCTTCTT
1389574 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TC
1389606 GATATGTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.34, G:0.00, T:0.50
Consensus pattern (6 bp):
TCTTCA
Found at i:1390419 original size:36 final size:34
Alignment explanation
Indices: 1390374--1390444 Score: 88
Period size: 34 Copynumber: 2.0 Consensus size: 34
1390364 TATAAAAAAT
*
1390374 ATTACAATTTTTTAAAAATATATAAAAACATTGAAA
1 ATTACAA-TTTTTAAAAA-ATATAAAAACATAGAAA
* * *
1390410 ATTATAATTTTTAGAAAATATAAAAATATAGAAA
1 ATTACAATTTTTAAAAAATATAAAAACATAGAAA
1390444 A
1 A
1390445 ACTATTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 16 0.52
35 9 0.29
36 6 0.19
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (34 bp):
ATTACAATTTTTAAAAAATATAAAAACATAGAAA
Found at i:1391403 original size:19 final size:18
Alignment explanation
Indices: 1391357--1391410 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
1391347 TTTTTATATA
*
1391357 ATTTTTTCTAATATTTTTAT
1 ATTTTTT-T-ATATTTTTAC
*
1391377 ATTCTTTTATATTTTTAGC
1 ATTTTTTTATATTTTTA-C
1391396 ATTTTTTTATATTTT
1 ATTTTTTTATATTTT
1391411 CTGCCACATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.30
19 15 0.50
20 6 0.20
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.70
Consensus pattern (18 bp):
ATTTTTTTATATTTTTAC
Found at i:1393864 original size:27 final size:27
Alignment explanation
Indices: 1393826--1394267 Score: 547
Period size: 27 Copynumber: 16.4 Consensus size: 27
1393816 TATGATTCAT
1393826 GGGTAAAATGACTGAAATACCCTCGAA
1 GGGTAAAATGACTGAAATACCCTCGAA
* *
1393853 GGGTAAAATGACCGAAATACCCCCGAA
1 GGGTAAAATGACTGAAATACCCTCGAA
*
1393880 GGGTAAAATGACTGAAATACCCTCGAG
1 GGGTAAAATGACTGAAATACCCTCGAA
** *
1393907 GGGTAAAATGACCAAAATACCC-CTAAA
1 GGGTAAAATGACTGAAATACCCTC-GAA
*
1393934 GGGTAAAATGACTGAAATACCCCCGAA
1 GGGTAAAATGACTGAAATACCCTCGAA
* * *
1393961 GGATAAAAT-AATCGAAATACCCTTGAA
1 GGGTAAAATGACT-GAAATACCCTCGAA
*
1393988 GGGTGAAATGA-TCGAAATACCCTCGAA
1 GGGTAAAATGACT-GAAATACCCTCGAA
*
1394015 GGGTAAAATGACTGCAATACCCTCGAA
1 GGGTAAAATGACTGAAATACCCTCGAA
* *
1394042 AGGTAAAATGATTGAAATACCCTCGAA
1 GGGTAAAATGACTGAAATACCCTCGAA
*
1394069 GGGTAAAATGA-TCGAAATACCCTTGAA
1 GGGTAAAATGACT-GAAATACCCTCGAA
* *
1394096 GGGTAAAATAACTGAAATACCCCCGAA
1 GGGTAAAATGACTGAAATACCCTCGAA
* * *
1394123 GGGTAAAATAATTGAAATACCCCCGAA
1 GGGTAAAATGACTGAAATACCCTCGAA
*
1394150 GGGTAAAATGA-TCAAAATACCC-CGAA
1 GGGTAAAATGACT-GAAATACCCTCGAA
* *
1394176 AGGTAAAATGACCGAAATACCCTCGAA
1 GGGTAAAATGACTGAAATACCCTCGAA
* *
1394203 GGGTAAAATGATTGAAATACCCTTGAA
1 GGGTAAAATGACTGAAATACCCTCGAA
*
1394230 GGGTAAAATGACTGAAATACCC-CAATA
1 GGGTAAAATGACTGAAATACCCTCGA-A
1394257 GGGTAAAATGA
1 GGGTAAAATGA
1394268 TTGTTATACC
Statistics
Matches: 362, Mismatches: 42, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
26 28 0.08
27 330 0.91
28 4 0.01
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.18
Consensus pattern (27 bp):
GGGTAAAATGACTGAAATACCCTCGAA
Found at i:1412075 original size:15 final size:15
Alignment explanation
Indices: 1412057--1412088 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1412047 GGAAATTTAG
1412057 TTTAATTATTATTGA
1 TTTAATTATTATTGA
1412072 TTTAATTATTATTGA
1 TTTAATTATTATTGA
1412087 TT
1 TT
1412089 ATTTGGGTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (15 bp):
TTTAATTATTATTGA
Done.