Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 4 of 378
Found at i:1076862 original size:51 final size:50
Alignment explanation
Indices: 1076791--1076950 Score: 241
Period size: 51 Copynumber: 3.2 Consensus size: 50
1076781 CTGATCACAT
1076791 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCAC
*
1076842 TTATCACTTGTCACTGATCAGATAAGAGTAGCTAAGCTACCACTTATCTA-
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATC-AC
* * *
1076892 TTGTCACTTATCACTGATCAGATAAGTGTAGCTGAGGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCAC
*
1076943 TTGTCACT
1 TTATCACT
1076951 GATCAGAAGT
Statistics
Matches: 101, Mismatches: 5, Indels: 6
0.90 0.04 0.05
Matches are distributed among these distances:
50 46 0.46
51 55 0.54
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (50 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCAC
Found at i:1078566 original size:23 final size:23
Alignment explanation
Indices: 1078507--1078558 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
1078497 TTTAAGTGTA
1078507 TGTGTTGGGAGGGTATATTTTGT
1 TGTGTTGGGAGGGTATATTTTGT
1078530 TGTGTTGGGAGGGTATATTTTGT
1 TGTGTTGGGAGGGTATATTTTGT
1078553 TGTGTT
1 TGTGTT
1078559 TGGTGGGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.50
Consensus pattern (23 bp):
TGTGTTGGGAGGGTATATTTTGT
Found at i:1079599 original size:16 final size:16
Alignment explanation
Indices: 1079578--1079611 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1079568 GGTCTATGTG
1079578 AAAATAGAATGTCAAT
1 AAAATAGAATGTCAAT
1079594 AAAATAGAATGTCAAT
1 AAAATAGAATGTCAAT
1079610 AA
1 AA
1079612 TGGCAATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (16 bp):
AAAATAGAATGTCAAT
Found at i:1086574 original size:17 final size:15
Alignment explanation
Indices: 1086556--1086593 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1086546 TTAAAATTTA
1086556 AAATTATAATAAATAT
1 AAATT-TAATAAATAT
*
1086572 AAATTTAATAAA-AA
1 AAATTTAATAAATAT
1086586 AAATTTAA
1 AAATTTAA
1086594 CGATTTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
15 7 0.33
16 5 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATTTAATAAATAT
Found at i:1089894 original size:29 final size:29
Alignment explanation
Indices: 1089852--1089909 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1089842 GCTCAGCTTC
1089852 AAGAATCCTCCAAAAATACGAAAAACTTA
1 AAGAATCCTCCAAAAATACGAAAAACTTA
1089881 AAGAATCCTCCAAAAATACGAAAAACTTA
1 AAGAATCCTCCAAAAATACGAAAAACTTA
1089910 GGGAAAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.55, C:0.21, G:0.07, T:0.17
Consensus pattern (29 bp):
AAGAATCCTCCAAAAATACGAAAAACTTA
Found at i:1099014 original size:22 final size:21
Alignment explanation
Indices: 1098989--1099030 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1098979 AGTAATTTTA
1098989 TTTTACTGAAAAATGCTTTGCT
1 TTTTA-TGAAAAATGCTTTGCT
* *
1099011 TTTTATGTAAAATGTTTTGC
1 TTTTATGAAAAATGCTTTGC
1099031 AAAATTATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (21 bp):
TTTTATGAAAAATGCTTTGCT
Found at i:1101888 original size:21 final size:20
Alignment explanation
Indices: 1101835--1101892 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 20
1101825 AAAAAGAATA
1101835 AATTAAAAA-AA-TTAAATT
1 AATTAAAAATAATTTAAATT
*
1101853 AATTAAAAATTATTTAAATT
1 AATTAAAAATAATTTAAATT
* *
1101873 GAATTGAAACTAATTTAAAT
1 -AATTAAAAATAATTTAAAT
1101893 ATTTAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 9 0.27
19 1 0.03
20 7 0.21
21 16 0.48
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (20 bp):
AATTAAAAATAATTTAAATT
Found at i:1105531 original size:44 final size:44
Alignment explanation
Indices: 1105468--1105557 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
1105458 TTATTGTCTT
1105468 TTTTAAGGGTTAAATTACTTTTTTGGGTTTGAACTTGGCTACCA
1 TTTTAAGGGTTAAATTACTTTTTTGGGTTTGAACTTGGCTACCA
*
1105512 TTTTAAGGGTTAAATTACTTTTTTGGGTTTGAACTTGGCTGCCA
1 TTTTAAGGGTTAAATTACTTTTTTGGGTTTGAACTTGGCTACCA
1105556 TT
1 TT
1105558 CTCATGTTGG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.47
Consensus pattern (44 bp):
TTTTAAGGGTTAAATTACTTTTTTGGGTTTGAACTTGGCTACCA
Found at i:1108480 original size:24 final size:24
Alignment explanation
Indices: 1108452--1108500 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1108442 TGGTTTTCAA
*
1108452 GATTATATATCCATAGTGAAGTGG
1 GATTATACATCCATAGTGAAGTGG
1108476 GATTATACATCCATAGTGAAGTGG
1 GATTATACATCCATAGTGAAGTGG
1108500 G
1 G
1108501 GTGGATTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.31
Consensus pattern (24 bp):
GATTATACATCCATAGTGAAGTGG
Found at i:1112017 original size:18 final size:18
Alignment explanation
Indices: 1111975--1112024 Score: 82
Period size: 18 Copynumber: 2.7 Consensus size: 18
1111965 TATTCTTCTA
*
1111975 TTTAAAAATTAATTTAAT
1 TTTAAACATTAATTTAAT
1111993 TTTAAACATTAATTTAAT
1 TTTAAACATTAATTTAAT
1112011 TTTAAACATGTAAT
1 TTTAAACAT-TAAT
1112025 GAGTCTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 26 0.87
19 4 0.13
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (18 bp):
TTTAAACATTAATTTAAT
Found at i:1112144 original size:41 final size:38
Alignment explanation
Indices: 1112097--1112207 Score: 112
Period size: 30 Copynumber: 3.1 Consensus size: 38
1112087 TTTGCTTTAC
1112097 TTGAATTTAAGCTCAAGCTGTTCAATTAGATAATTATT
1 TTGAATTTAAGCTCAAGCTGTTCAATTAGATAATTATT
* * *
1112135 TAATCGAATTTAAGCT-AATCT-TTC--TT-GCT--TTA-C
1 T--T-GAATTTAAGCTCAAGCTGTTCAATTAGATAATTATT
1112168 TTGAATTTAAGCTCAAGCTGTTCAATTAGATAATTATT
1 TTGAATTTAAGCTCAAGCTGTTCAATTAGATAATTATT
1112206 TT
1 TT
1112208 TTCACTAAAC
Statistics
Matches: 56, Mismatches: 6, Indels: 22
0.67 0.07 0.26
Matches are distributed among these distances:
30 11 0.20
31 5 0.09
32 3 0.05
33 1 0.02
34 5 0.09
35 2 0.04
36 2 0.04
37 5 0.09
38 3 0.05
39 3 0.05
40 5 0.09
41 11 0.20
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.44
Consensus pattern (38 bp):
TTGAATTTAAGCTCAAGCTGTTCAATTAGATAATTATT
Found at i:1113633 original size:185 final size:182
Alignment explanation
Indices: 1113315--1113684 Score: 503
Period size: 185 Copynumber: 2.0 Consensus size: 182
1113305 TCTTTGTATA
* * * * *
1113315 TTAGATTAAAGAGCAAATTAATATTTTCTGTTAAAAATTTTACCCTTATACTGTTAAAAGCTGGC
1 TTAGACTAAAGAGCAAACTAATATTTTCTGTCAAAAATTTTACACTTATACTGTTAAAAACTGGC
* *
1113380 ATAGCTAACAGAATAACTAAACAATAACACGTGGCATGCCACATGAACCTCATGCTGACGTACAG
66 ATAGCTAACAAAATAACTAAACAATAACACGTGACATGCCACATGAACCTCATGCTGACGTACAG
* * *
1113445 GGACCAATTTTTTATAGCAAAACTGGA-TGAATTTTTTAACAAAATAATCAAT
131 GGACCAATTTTTAACAGCAAAA-TGGATTGAATTTTTTAACAAAAGAATCAAT
* * *
1113497 TTAGACTAAAGAGCAAAACTAATATTTTCTGTCAAAATTTTTATTCATTTTTACTGTTAAAAACT
1 TTAGACTAAAGAGC-AAACTAATATTTTCTGTCAAAAATTTTA--CACTTATACTGTTAAAAACT
* * * *
1113562 GGCAT-GTCTAATAAAATAACTAAACAATGACACGTGACGTGCCACATGTACCTCATG-TAGACG
63 GGCATAG-CTAACAAAATAACTAAACAATAACACGTGACATGCCACATGAACCTCATGCT-GACG
*
1113625 TTCAGGGACCAATTTTTAACAGCAAAATGGATTGAATTTTTTAACAAAAGAATCAAT
126 TACAGGGACCAATTTTTAACAGCAAAATGGATTGAATTTTTTAACAAAAGAATCAAT
1113682 TTA
1 TTA
1113685 CTCTTTAATC
Statistics
Matches: 164, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
182 13 0.08
183 25 0.15
184 6 0.04
185 120 0.73
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (182 bp):
TTAGACTAAAGAGCAAACTAATATTTTCTGTCAAAAATTTTACACTTATACTGTTAAAAACTGGC
ATAGCTAACAAAATAACTAAACAATAACACGTGACATGCCACATGAACCTCATGCTGACGTACAG
GGACCAATTTTTAACAGCAAAATGGATTGAATTTTTTAACAAAAGAATCAAT
Found at i:1116526 original size:51 final size:52
Alignment explanation
Indices: 1116462--1116564 Score: 133
Period size: 51 Copynumber: 2.0 Consensus size: 52
1116452 AGCAGCCGAC
*
1116462 TGACTTGATTCCAAACTTCT-TCCAG-TAATTCCAACTTCTCTTC-TAGATTCAG
1 TGACTTGACTCCAAACTTCTCT-CAGAT-ATTCCAACTTCTCTTCTTA-ATTCAG
*
1116514 TGACTTG-CTCCAAACTTCTCTCAGATATTCCAACTTCTTTTCTTAATTCAG
1 TGACTTGACTCCAAACTTCTCTCAGATATTCCAACTTCTCTTCTTAATTCAG
1116565 CAGCCTGCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
51 35 0.76
52 11 0.24
ACGTcount: A:0.24, C:0.27, G:0.09, T:0.40
Consensus pattern (52 bp):
TGACTTGACTCCAAACTTCTCTCAGATATTCCAACTTCTCTTCTTAATTCAG
Found at i:1116574 original size:51 final size:51
Alignment explanation
Indices: 1116471--1116575 Score: 119
Period size: 51 Copynumber: 2.1 Consensus size: 51
1116461 CTGACTTGAT
* *
1116471 TCCAAACTTCTTCCAGTAATTCCAACTTCTCTTCTAGATTCAGTGACTTGC
1 TCCAAACTTCTTCCAGTAATTCCAACTTCTCTTCTAGATTCAGAGACCTGC
*
1116522 TCCAAACTTC-TCTCAG-ATATTCCAACTTCTTTTCTTA-ATTCAGCAG-CCTGC
1 TCCAAACTTCTTC-CAGTA-ATTCCAACTTCTCTTC-TAGATTCAG-AGACCTGC
1116573 TCC
1 TCC
1116576 GACCTCATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
50 3 0.06
51 41 0.87
52 3 0.06
ACGTcount: A:0.23, C:0.31, G:0.09, T:0.37
Consensus pattern (51 bp):
TCCAAACTTCTTCCAGTAATTCCAACTTCTCTTCTAGATTCAGAGACCTGC
Found at i:1131303 original size:13 final size:13
Alignment explanation
Indices: 1131285--1131311 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1131275 TTATTCATAA
1131285 AAATTAAGAATTT
1 AAATTAAGAATTT
1131298 AAATTAAGAATTT
1 AAATTAAGAATTT
1131311 A
1 A
1131312 GTCCAATTAT
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:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
AAATTAAGAATTT
Found at i:1135831 original size:15 final size:15
Alignment explanation
Indices: 1135811--1135842 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1135801 TCTTACTTTT
1135811 CAAAAAAAAAAAAAG
1 CAAAAAAAAAAAAAG
1135826 CAAAAAAAAAAAAAG
1 CAAAAAAAAAAAAAG
1135841 CA
1 CA
1135843 TACTTTTAAT
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:0.84, C:0.09, G:0.06, T:0.00
Consensus pattern (15 bp):
CAAAAAAAAAAAAAG
Found at i:1139205 original size:152 final size:152
Alignment explanation
Indices: 1138929--1139232 Score: 608
Period size: 152 Copynumber: 2.0 Consensus size: 152
1138919 CATTTTCGAT
1138929 GCGCTATTTTTGCTTTAGATTTTAAGTTCTCTGTTTTGAGAGACCATAAACTAAAGCGATCATGG
1 GCGCTATTTTTGCTTTAGATTTTAAGTTCTCTGTTTTGAGAGACCATAAACTAAAGCGATCATGG
1138994 AATCCGGGTTTATGGAAACATAGGGAACCACTCAGTCGATTCGATCAAGAAAGTGGCAAAAACCA
66 AATCCGGGTTTATGGAAACATAGGGAACCACTCAGTCGATTCGATCAAGAAAGTGGCAAAAACCA
1139059 GATTCTAGGTAAAAATTCCGAC
131 GATTCTAGGTAAAAATTCCGAC
1139081 GCGCTATTTTTGCTTTAGATTTTAAGTTCTCTGTTTTGAGAGACCATAAACTAAAGCGATCATGG
1 GCGCTATTTTTGCTTTAGATTTTAAGTTCTCTGTTTTGAGAGACCATAAACTAAAGCGATCATGG
1139146 AATCCGGGTTTATGGAAACATAGGGAACCACTCAGTCGATTCGATCAAGAAAGTGGCAAAAACCA
66 AATCCGGGTTTATGGAAACATAGGGAACCACTCAGTCGATTCGATCAAGAAAGTGGCAAAAACCA
1139211 GATTCTAGGTAAAAATTCCGAC
131 GATTCTAGGTAAAAATTCCGAC
1139233 ATTCTCACTC
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
152 152 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (152 bp):
GCGCTATTTTTGCTTTAGATTTTAAGTTCTCTGTTTTGAGAGACCATAAACTAAAGCGATCATGG
AATCCGGGTTTATGGAAACATAGGGAACCACTCAGTCGATTCGATCAAGAAAGTGGCAAAAACCA
GATTCTAGGTAAAAATTCCGAC
Found at i:1140876 original size:225 final size:225
Alignment explanation
Indices: 1140485--1140936 Score: 708
Period size: 225 Copynumber: 2.0 Consensus size: 225
1140475 CAGTCCTCGG
* * * * *
1140485 TTAAGCCAGTTCTATATCCTCCTAGTCTGCTGCCATCATTTGAAACATCATTTACGGCCCAGAAA
1 TTAAGCCAGTTCTATATCCTCCTAGTCCGCTGCCATCATTTAAAACATCATTCACAGCCCAAAAA
* *
1140550 CCATCTCCATCACCTAAAGGATTGACACCACCTAAACCAACCACACCGTCTCTGAAACCCTCTTC
66 CCATCTCCATCACCTAAAGGACTGACACCACCTAAACCAACCACACCGTCTCCGAAACCCTCTTC
*
1140615 ATCGTCTTTTAAGCCAAGTCCATCCCTTAAGCCAACTCTATCAGAACTAGGGAAAGGAAAGTACA
131 ATCGTCTTCTAAGCCAAGTCCATCCCTTAAGCCAACTCTATCAGAACTAGGGAAAGGAAAGTACA
*
1140680 AAACACTCAATCCAGAGGATACATTACCGA
196 AAACACTCAATCCAAAGGATACATTACCGA
* ** *
1140710 TTAAGCC-GATTCTATATCCTCCTAGTCCGCTTCCATCATTTAAAATGTCATTCACAGCCGAAAA
1 TTAAGCCAG-TTCTATATCCTCCTAGTCCGCTGCCATCATTTAAAACATCATTCACAGCCCAAAA
* *
1140774 ACCATCTCCATCACCTAAAGGACTGACACCACCTAAATCAACCACACCGTCTCCGAAACGCTCTT
65 ACCATCTCCATCACCTAAAGGACTGACACCACCTAAACCAACCACACCGTCTCCGAAACCCTCTT
*
1140839 CATCGTCTTCTAAGCCAAGTCCATCCCTTAAGCCAACTCTATCGGAACTAGGGAAAGGAAAGTAC
130 CATCGTCTTCTAAGCCAAGTCCATCCCTTAAGCCAACTCTATCAGAACTAGGGAAAGGAAAGTAC
* * **
1140904 AAAACAGTCGATCCAAAGGATATGTTACCGA
195 AAAACACTCAATCCAAAGGATACATTACCGA
1140935 TT
1 TT
1140937 TACATGATTC
Statistics
Matches: 206, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
224 1 0.00
225 205 1.00
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.24
Consensus pattern (225 bp):
TTAAGCCAGTTCTATATCCTCCTAGTCCGCTGCCATCATTTAAAACATCATTCACAGCCCAAAAA
CCATCTCCATCACCTAAAGGACTGACACCACCTAAACCAACCACACCGTCTCCGAAACCCTCTTC
ATCGTCTTCTAAGCCAAGTCCATCCCTTAAGCCAACTCTATCAGAACTAGGGAAAGGAAAGTACA
AAACACTCAATCCAAAGGATACATTACCGA
Found at i:1143975 original size:19 final size:17
Alignment explanation
Indices: 1143951--1143995 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 17
1143941 TAGTGTTTAT
1143951 ATTATTTATTTATAATATG
1 ATTATTTATTTAT-AT-TG
1143970 ATTATTAATATTTATATTG
1 ATTATT--TATTTATATTG
1143989 ATTATTT
1 ATTATTT
1143996 TATATCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 1 0.04
19 14 0.58
20 2 0.08
21 7 0.29
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
ATTATTTATTTATATTG
Found at i:1152101 original size:39 final size:38
Alignment explanation
Indices: 1152049--1152151 Score: 145
Period size: 39 Copynumber: 2.7 Consensus size: 38
1152039 ATAAATTCTA
* * * *
1152049 AAAATATGTTAGAATTTTTAAAATGTTGTAAAAAATAT
1 AAAATATATTAGAAATTTTAAAATATTGAAAAAAATAT
*
1152087 AAATATATATTAGAAATTGTAAAATATTGAAAAAAATAT
1 AAA-ATATATTAGAAATTTTAAAATATTGAAAAAAATAT
1152126 AAAA-ATATTAGAAATTTTAAAATATT
1 AAAATATATTAGAAATTTTAAAATATT
1152152 ATTTTTTAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
37 21 0.36
38 4 0.07
39 33 0.57
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (38 bp):
AAAATATATTAGAAATTTTAAAATATTGAAAAAAATAT
Found at i:1152147 original size:17 final size:17
Alignment explanation
Indices: 1152093--1152152 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
1152083 ATATAAATAT
*
1152093 ATATTAGAAATTGTAAA
1 ATATTAGAAATTTTAAA
* * *
1152110 ATATTGAAAAAAATATAAAA
1 ATATT---AGAAATTTTAAA
1152130 ATATTAGAAATTTTAAA
1 ATATTAGAAATTTTAAA
1152147 ATATTA
1 ATATTA
1152153 TTTTTTAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
17 20 0.61
20 13 0.39
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (17 bp):
ATATTAGAAATTTTAAA
Found at i:1152970 original size:2 final size:2
Alignment explanation
Indices: 1152963--1152993 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1152953 TTTAATGTAT
1152963 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1152994 GATAATGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1156996 original size:74 final size:75
Alignment explanation
Indices: 1156852--1157011 Score: 166
Period size: 74 Copynumber: 2.2 Consensus size: 75
1156842 GTTTGTTAAT
* * * * * *
1156852 ACTTAGATGGCTGCATATTTTCCTACGTGCCTACAAGGATGTGAAATGCAATAGTATATGGAGAA
1 ACTTAGATGGTTGCATACTTTCCTACATGCCTACAAGGATGTAAAATGCAATAATACATGGAGAA
*
1156917 GCATAATA-A
66 ACATAATATA
*** *
1156926 ACTTAGATGGTTGCATACTTTCCTACATTTGTACAAGGATG-AAAATTGCACTAATACATGTG-G
1 ACTTAGATGGTTGCATACTTTCCTACATGCCTACAAGGATGTAAAA-TGCAATAATACATG-GAG
*
1156989 AAACATAATATT
64 AAACATAATATA
1157001 ACTT-GATGGTT
1 ACTTAGATGGTT
1157012 TTCTATTCTT
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
73 3 0.04
74 63 0.89
75 5 0.07
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Consensus pattern (75 bp):
ACTTAGATGGTTGCATACTTTCCTACATGCCTACAAGGATGTAAAATGCAATAATACATGGAGAA
ACATAATATA
Found at i:1158525 original size:22 final size:22
Alignment explanation
Indices: 1158497--1158540 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1158487 GGTATGAGGC
1158497 TCAAAGGGTTTAGACAAAAAGA
1 TCAAAGGGTTTAGACAAAAAGA
1158519 TCAAAGGGTTTAGACAAAAAGA
1 TCAAAGGGTTTAGACAAAAAGA
1158541 AAAGTTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.23, T:0.18
Consensus pattern (22 bp):
TCAAAGGGTTTAGACAAAAAGA
Found at i:1160325 original size:6 final size:6
Alignment explanation
Indices: 1160314--1160338 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1160304 TTATAAAATT
1160314 ATATAA ATATAA ATATAA ATATAA A
1 ATATAA ATATAA ATATAA ATATAA A
1160339 ATATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:1163757 original size:7 final size:7
Alignment explanation
Indices: 1163745--1163771 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1163735 TTCGAAATAT
1163745 AAATTTC
1 AAATTTC
1163752 AAATTTC
1 AAATTTC
1163759 AAATTTC
1 AAATTTC
1163766 AAATTT
1 AAATTT
1163772 ATTTATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (7 bp):
AAATTTC
Found at i:1169992 original size:26 final size:28
Alignment explanation
Indices: 1169931--1169994 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 28
1169921 ACAGTTAATA
*
1169931 TAAATTATATAATTATTTTAATTATAAC
1 TAAATTTTATAATTATTTTAATTATAAC
*
1169959 TACA--TTATAATTATTTTAATTA-AAC
1 TAAATTTTATAATTATTTTAATTATAAC
1169984 -AAATTTTATAA
1 TAAATTTTATAA
1169995 AAATATATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 2 0.06
25 3 0.10
26 23 0.74
28 3 0.10
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (28 bp):
TAAATTTTATAATTATTTTAATTATAAC
Found at i:1175102 original size:32 final size:32
Alignment explanation
Indices: 1175063--1175133 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
1175053 TACGGATTAT
*
1175063 ACAACAAACACATATTTAAAACTCAAAACCCA
1 ACAACAAAAACATATTTAAAACTCAAAACCCA
1175095 ACAACAAAAACATATTTAAAACTCAAAACCCA
1 ACAACAAAAACATATTTAAAACTCAAAACCCA
1175127 ACAACAA
1 ACAACAA
1175134 TAATTATATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (32 bp):
ACAACAAAAACATATTTAAAACTCAAAACCCA
Found at i:1177209 original size:21 final size:20
Alignment explanation
Indices: 1177172--1177227 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
1177162 AATCGACATT
1177172 AAATTTTAGAATG-TTTAATTTA
1 AAATTTTA-AA-GATTTAA-TTA
1177194 AAATTTTAAAGATTTAATTA
1 AAATTTTAAAGATTTAATTA
*
1177214 ATATTTTAAA-ATTT
1 AAATTTTAAAGATTT
1177228 TTAAAGGGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 4 0.12
20 13 0.41
21 7 0.22
22 8 0.25
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
AAATTTTAAAGATTTAATTA
Found at i:1179765 original size:50 final size:50
Alignment explanation
Indices: 1179690--1180016 Score: 528
Period size: 50 Copynumber: 6.5 Consensus size: 50
1179680 CCATGGCAAC
* *
1179690 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
1179740 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1179790 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * * *
1179840 AAGTGATAAGTGATAGCTTCGACTACACTTATTTGATCAAGGATAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
1179890 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTAATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
1179940 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATGGC
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAAT-GA
* * *
1179991 AAGTAAAAAGTGGTAGCTTCGGCTAC
1 AAGTGATAAGTGATAGCTTCGGCTAC
1180017 CTGATCAATG
Statistics
Matches: 258, Mismatches: 18, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
50 235 0.91
51 23 0.09
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:1180034 original size:31 final size:31
Alignment explanation
Indices: 1179996--1180054 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
1179986 ATGGCAAGTA
1179996 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1180027 AAAAGTGGTAGCTTCGGCTACCTGATCA
1 AAAAGTGGTAGCTTCGGCTACCTGATCA
1180055 TCGGCTACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAAGTGGTAGCTTCGGCTACCTGATCAATG
Found at i:1180062 original size:46 final size:46
Alignment explanation
Indices: 1180009--1180100 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
1179999 AGTGGTAGCT
* * *
1180009 TCGGCTACCTGATCAATGAAAAGTGGTAGCTTCGGCTACCTGATCA
1 TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTAACTGATCA
* * *
1180055 TCGGCTACTTGATTAGTGAAAAATGGTAGCTCCGGCTAACTGATCA
1 TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTAACTGATCA
1180101 GTGAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (46 bp):
TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTAACTGATCA
Found at i:1180104 original size:31 final size:32
Alignment explanation
Indices: 1180056--1180123 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
1180046 ACCTGATCAT
* *
1180056 CGGCT-ACTTGATTAGTGAAAAATGGTAGCTC
1 CGGCTAACTTGATCAGTGAAAAATGATAGCTC
* *
1180087 CGGCTAAC-TGATCAGTGAATAATGATAGCTT
1 CGGCTAACTTGATCAGTGAAAAATGATAGCTC
1180118 CGGCTA
1 CGGCTA
1180124 CAAGTGACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (32 bp):
CGGCTAACTTGATCAGTGAAAAATGATAGCTC
Found at i:1182363 original size:52 final size:48
Alignment explanation
Indices: 1182322--1182475 Score: 179
Period size: 47 Copynumber: 3.2 Consensus size: 48
1182312 CTTCGGAGAA
*
1182322 ATGTGATATGTGCTTCCGTATAAGACCATATCCGGGATATGGCATCGG
1 ATGTGATATGTGCTTCCGTATAAGACCATATCTGGGATATGGCATCGG
* * * *
1182370 -TGTGATATGTGCTACTGTATAAGACCATATATGGGATATGGCATCAG
1 ATGTGATATGTGCTTCCGTATAAGACCATATCTGGGATATGGCATCGG
* * ** * *
1182417 -TGTGATATGTG-ATCCGTGTAAGACCATGGCTGGGTTATGGCCTCGG
1 ATGTGATATGTGCTTCCGTATAAGACCATATCTGGGATATGGCATCGG
1182463 TATGTGATATGTG
1 -ATGTGATATGTG
1182476 ACTGTTGTTT
Statistics
Matches: 89, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
46 25 0.28
47 53 0.60
48 11 0.12
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (48 bp):
ATGTGATATGTGCTTCCGTATAAGACCATATCTGGGATATGGCATCGG
Found at i:1183013 original size:13 final size:13
Alignment explanation
Indices: 1182995--1183023 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1182985 TTTTAACAAG
1182995 TTGCTTCCTACCT
1 TTGCTTCCTACCT
1183008 TTGCTTCCTACCT
1 TTGCTTCCTACCT
1183021 TTG
1 TTG
1183024 TTGACTTTTC
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:0.07, C:0.34, G:0.10, T:0.48
Consensus pattern (13 bp):
TTGCTTCCTACCT
Found at i:1184963 original size:21 final size:21
Alignment explanation
Indices: 1184937--1184977 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1184927 ATCTGCTCAA
* *
1184937 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1184958 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1184978 TCGCTTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1193244 original size:2 final size:2
Alignment explanation
Indices: 1193237--1193263 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1193227 GGTTAATTTG
1193237 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1193264 TGTCAATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1193744 original size:32 final size:32
Alignment explanation
Indices: 1193702--1193765 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1193692 TTTCAGGCGT
*
1193702 TTATAGACCAAATGAACCAACTATGGCCTTAA
1 TTATAAACCAAATGAACCAACTATGGCCTTAA
1193734 TTATAAACCAAATGAACCAACTATGGCCTTAA
1 TTATAAACCAAATGAACCAACTATGGCCTTAA
1193766 ATTTATATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (32 bp):
TTATAAACCAAATGAACCAACTATGGCCTTAA
Found at i:1194446 original size:31 final size:29
Alignment explanation
Indices: 1194409--1194509 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 29
1194399 ATTGGGATTT
1194409 TAATTAAAAAATTTAAAATTTTAAGAGACA
1 TAATTAAAAAATTTAAAATTTTAA-AGACA
* * **
1194439 TTAATTAAAATACTTAAAAAATTAAA-AGCA
1 -TAATTAAAAAATTTAAAATTTTAAAGA-CA
*
1194469 TAA-TAAGAAAATTTTAAAATTTTGAAAGATA
1 TAATTAA-AAAA-TTTAAAATTTT-AAAGACA
1194500 TAATTAAAAA
1 TAATTAAAAA
1194510 TTCCAAAGGA
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
28 3 0.05
29 7 0.13
30 11 0.20
31 30 0.55
32 4 0.07
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (29 bp):
TAATTAAAAAATTTAAAATTTTAAAGACA
Found at i:1195882 original size:31 final size:31
Alignment explanation
Indices: 1195825--1195883 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1195815 CTATGAAGTT
*
1195825 AAGTTCAAGTATCAATTTGAATAAAAAAGCC
1 AAGTTCAAGTATCAATTTGAACAAAAAAGCC
* *
1195856 AAGTTTAAGTATCTAA-TTGGACAAAAAA
1 AAGTTCAAGTATC-AATTTGAACAAAAAA
1195884 AGTATCAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 22 0.92
32 2 0.08
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (31 bp):
AAGTTCAAGTATCAATTTGAACAAAAAAGCC
Found at i:1199634 original size:14 final size:15
Alignment explanation
Indices: 1199617--1199647 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1199607 AAATATGTGG
1199617 ATGAAATA-ATAGAA
1 ATGAAATACATAGAA
1199631 ATGAAATACATAGAA
1 ATGAAATACATAGAA
1199646 AT
1 AT
1199648 TTGATATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.61, C:0.03, G:0.13, T:0.23
Consensus pattern (15 bp):
ATGAAATACATAGAA
Found at i:1213527 original size:21 final size:22
Alignment explanation
Indices: 1213489--1213532 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
1213479 GGAATATTTA
*
1213489 CAAAACCATTTAATTTGA-AAT
1 CAAAACCATTTAAATTGACAAT
1213510 CAAAACC-TATTAAATTGACAAT
1 CAAAACCAT-TTAAATTGACAAT
1213532 C
1 C
1213533 CAACTATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 15 0.75
22 4 0.20
ACGTcount: A:0.48, C:0.18, G:0.05, T:0.30
Consensus pattern (22 bp):
CAAAACCATTTAAATTGACAAT
Found at i:1215151 original size:43 final size:43
Alignment explanation
Indices: 1215102--1215190 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
1215092 TCATCAATTT
1215102 CAACAACATAAACAGACTCGGATAAGGAGAAAGAAAGAGAAAA
1 CAACAACATAAACAGACTCGGATAAGGAGAAAGAAAGAGAAAA
1215145 CAACAACATAAACAGACTCGGATAAGGAGAAAGAAAGAGAAAA
1 CAACAACATAAACAGACTCGGATAAGGAGAAAGAAAGAGAAAA
1215188 CAA
1 CAA
1215191 GGCCCTATGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.58, C:0.15, G:0.20, T:0.07
Consensus pattern (43 bp):
CAACAACATAAACAGACTCGGATAAGGAGAAAGAAAGAGAAAA
Found at i:1219766 original size:27 final size:27
Alignment explanation
Indices: 1219734--1219790 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
1219724 CGAACTCGAA
1219734 TCTATAATGCAATAATTATATTTGATG
1 TCTATAATGCAATAATTATATTTGATG
1219761 TCTATAATGCAATAATTATATTTGATG
1 TCTATAATGCAATAATTATATTTGATG
1219788 TCT
1 TCT
1219791 CTAAATTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.46
Consensus pattern (27 bp):
TCTATAATGCAATAATTATATTTGATG
Found at i:1229705 original size:19 final size:19
Alignment explanation
Indices: 1229681--1229723 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
1229671 ACATTTTTTT
1229681 ATAATAGGAGATAAAATTG
1 ATAATAGGAGATAAAATTG
1229700 ATAATAGGAGATAAAATTG
1 ATAATAGGAGATAAAATTG
1229719 ATAAT
1 ATAAT
1229724 TTGGTTTACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (19 bp):
ATAATAGGAGATAAAATTG
Found at i:1232646 original size:13 final size:13
Alignment explanation
Indices: 1232628--1232655 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1232618 AACATACAAG
1232628 TAAGAATACATAC
1 TAAGAATACATAC
1232641 TAAGAATACATAC
1 TAAGAATACATAC
1232654 TA
1 TA
1232656 CAATGATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.07, T:0.25
Consensus pattern (13 bp):
TAAGAATACATAC
Found at i:1235020 original size:6 final size:7
Alignment explanation
Indices: 1235003--1235028 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1234993 AGAGCATATA
1235003 AAAAAAT
1 AAAAAAT
1235010 AAAAAAT
1 AAAAAAT
1235017 AAAAAAT
1 AAAAAAT
1235024 AAAAA
1 AAAAA
1235029 GAAAGGATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:1238054 original size:29 final size:28
Alignment explanation
Indices: 1238022--1238084 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
1238012 TTAAAATCTA
1238022 AAAAGT-AATGAGACAAAATTCCTAAAAAT
1 AAAAGTAAAT-AGACAAAATT-CTAAAAAT
* *
1238051 AAAAGTAAATAGACTAAATTCTAAATAT
1 AAAAGTAAATAGACAAAATTCTAAAAAT
1238079 ACAAAG
1 A-AAAG
1238085 AGTTTAAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 8 0.27
29 19 0.63
30 3 0.10
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.22
Consensus pattern (28 bp):
AAAAGTAAATAGACAAAATTCTAAAAAT
Found at i:1238695 original size:14 final size:14
Alignment explanation
Indices: 1238659--1238715 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 14
1238649 AAATGATAAT
*
1238659 TTAAATATTTAAAA
1 TTAAATATTAAAAA
1238673 -TAAA-A-TAAAAA
1 TTAAATATTAAAAA
1238684 TTAAATATT-AAAA
1 TTAAATATTAAAAA
* *
1238697 TGGAAATATTAAAAG
1 T-TAAATATTAAAAA
1238712 TTAA
1 TTAA
1238716 TTCGCCAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
11 5 0.15
12 5 0.15
13 10 0.29
14 10 0.29
15 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.33
Consensus pattern (14 bp):
TTAAATATTAAAAA
Found at i:1239718 original size:5 final size:5
Alignment explanation
Indices: 1239701--1239736 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
1239691 TAAGCCTTCA
1239701 AAAAT ATAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1239737 TTGAATATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:1244205 original size:9 final size:9
Alignment explanation
Indices: 1244191--1244222 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1244181 ATCTTTGAAT
1244191 AATTTTTTA
1 AATTTTTTA
1244200 AATTTTTTA
1 AATTTTTTA
1244209 AA-TTTTTA
1 AATTTTTTA
1244217 AATTTT
1 AATTTT
1244223 AAAAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
AATTTTTTA
Found at i:1246951 original size:21 final size:20
Alignment explanation
Indices: 1246918--1246971 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
1246908 TAAAAAATAA
*
1246918 AAAATAAAT-TTAAAATATC
1 AAAATTAATATTAAAATATC
* *
1246937 AAAATTTTATATTAAAATTTC
1 AAAA-TTAATATTAAAATATC
*
1246958 CAAATTAATATTAA
1 AAAATTAATATTAA
1246972 CTAAAACAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.14
20 12 0.43
21 12 0.43
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAATTAATATTAAAATATC
Found at i:1248238 original size:26 final size:28
Alignment explanation
Indices: 1248189--1248241 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
1248179 GATAATCATA
1248189 ATTAATATATCAATAAATAAAATTTTAT
1 ATTAATATATCAATAAATAAAATTTTAT
* *
1248217 ATTAA-ATAT-AATAATTACAATTTTA
1 ATTAATATATCAATAAATAAAATTTTA
1248242 AAAGTATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 14 0.61
27 4 0.17
28 5 0.22
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (28 bp):
ATTAATATATCAATAAATAAAATTTTAT
Found at i:1251964 original size:20 final size:20
Alignment explanation
Indices: 1251926--1251964 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1251916 GTATATTATT
**
1251926 TTTATATTATGTAACCATAG
1 TTTATATTATACAACCATAG
*
1251946 TTTATATTATACAAGCATA
1 TTTATATTATACAACCATA
1251965 TATAATATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (20 bp):
TTTATATTATACAACCATAG
Found at i:1254290 original size:13 final size:13
Alignment explanation
Indices: 1254272--1254296 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1254262 TGTTGCTTAC
1254272 TACAGCTCTTTAT
1 TACAGCTCTTTAT
1254285 TACAGCTCTTTA
1 TACAGCTCTTTA
1254297 CCCATTGAGT
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:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (13 bp):
TACAGCTCTTTAT
Found at i:1254534 original size:3 final size:3
Alignment explanation
Indices: 1254526--1254564 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1254516 TGACCACCTT
1254526 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1254565 CGACTCCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1266144 original size:19 final size:20
Alignment explanation
Indices: 1266122--1266161 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1266112 TTTTACCCAA
1266122 AAAAAT-ATAGTTTAAGAAC
1 AAAAATAATAGTTTAAGAAC
*
1266141 AAAATTAATAGTTTAAGAAC
1 AAAAATAATAGTTTAAGAAC
1266161 A
1 A
1266162 TTTAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.28
Consensus pattern (20 bp):
AAAAATAATAGTTTAAGAAC
Found at i:1269525 original size:18 final size:18
Alignment explanation
Indices: 1269467--1269530 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
1269457 GTATTGTTAT
* *
1269467 TTTTTAATAAAATTATAAA
1 TTTTTAA-ATAATTTTAAA
* *
1269486 TTTTT-TATAACTTTTATGA
1 TTTTTAAATAA-TTTTA-AA
1269505 TTTTTAAATAATTTTAAA
1 TTTTTAAATAATTTTAAA
1269523 TTTTTAAA
1 TTTTTAAA
1269531 AAGGTTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
17 3 0.08
18 13 0.36
19 16 0.44
20 4 0.11
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTTTAAATAATTTTAAA
Found at i:1269538 original size:18 final size:18
Alignment explanation
Indices: 1269504--1269541 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1269494 AACTTTTATG
*
1269504 ATTTTTAAATAATTTTAA
1 ATTTTTAAATAAGTTTAA
1269522 ATTTTTAAA-AAGGTTTAA
1 ATTTTTAAATAA-GTTTAA
1269540 AT
1 AT
1269542 GATTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
ATTTTTAAATAAGTTTAA
Found at i:1270303 original size:15 final size:16
Alignment explanation
Indices: 1270273--1270311 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 16
1270263 TAATAAAAAT
1270273 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
1270290 ATAATTTA-TATTTTA
1 ATAATTTATTATTTTA
1270305 ATAATTT
1 ATAATTT
1270312 TTAAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 14 0.64
16 4 0.18
17 4 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:1271698 original size:19 final size:19
Alignment explanation
Indices: 1271662--1271698 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1271652 ATAATCAAAT
*
1271662 ATATATTATTGTTAAATAA
1 ATATATTATTGTCAAATAA
*
1271681 ATATATTATTGTCGAATA
1 ATATATTATTGTCAAATA
1271699 TCATTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (19 bp):
ATATATTATTGTCAAATAA
Found at i:1271737 original size:27 final size:27
Alignment explanation
Indices: 1271705--1271774 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 27
1271695 AATATCATTT
* *
1271705 TTTTTACATTTAAACTTTAGTTTTTTA-
1 TTTTTA-ATTTAAAATTTAGTTATTTAC
1271732 TTTTTAATTTAAAAATTTAGTTATTTAC
1 TTTTTAATTT-AAAATTTAGTTATTTAC
*
1271760 ATTTTAGATTTAAAA
1 TTTTTA-ATTTAAAA
1271775 ATAAAAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 4 0.11
27 20 0.54
28 9 0.24
29 4 0.11
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (27 bp):
TTTTTAATTTAAAATTTAGTTATTTAC
Found at i:1273534 original size:13 final size:13
Alignment explanation
Indices: 1273516--1273551 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1273506 TTTTTACCCA
1273516 TAATAATAATTAT
1 TAATAATAATTAT
1273529 TAATAATTAA-TAT
1 TAATAA-TAATTAT
1273542 TAATAATAAT
1 TAATAATAAT
1273552 AACTCTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.14
13 15 0.71
14 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATAATAATTAT
Found at i:1273543 original size:16 final size:17
Alignment explanation
Indices: 1273515--1273551 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1273505 ATTTTTACCC
*
1273515 ATAA-TAATAATTATTA
1 ATAATTAATAATTAATA
1273531 ATAATTAAT-ATTAATA
1 ATAATTAATAATTAATA
1273547 ATAAT
1 ATAAT
1273552 AACTCTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATTAATAATTAATA
Found at i:1273545 original size:10 final size:10
Alignment explanation
Indices: 1273516--1273553 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1273506 TTTTTACCCA
1273516 TAATAATAAT
1 TAATAATAAT
*
1273526 TATTAATAAT
1 TAATAATAAT
*
1273536 TAATATTAA-
1 TAATAATAAT
1273545 TAATAATAA
1 TAATAATAA
1273554 CTCTAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TAATAATAAT
Found at i:1274749 original size:14 final size:14
Alignment explanation
Indices: 1274730--1274760 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1274720 AGCACAATAT
*
1274730 TTTTATAGTTAGAG
1 TTTTATACTTAGAG
1274744 TTTTATACTTAGAG
1 TTTTATACTTAGAG
1274758 TTT
1 TTT
1274761 AAGAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.16, T:0.55
Consensus pattern (14 bp):
TTTTATACTTAGAG
Found at i:1277578 original size:30 final size:28
Alignment explanation
Indices: 1277535--1277590 Score: 94
Period size: 30 Copynumber: 1.9 Consensus size: 28
1277525 TGCAGCTTGG
1277535 TTATATATCCATGTGTGTTCTCCATTGA
1 TTATATATCCATGTGTGTTCTCCATTGA
1277563 TTATATAGTTCCATGTGTGTTCTCCATT
1 TTATATA--TCCATGTGTGTTCTCCATT
1277591 TCATCTGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 7 0.27
30 19 0.73
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (28 bp):
TTATATATCCATGTGTGTTCTCCATTGA
Found at i:1278863 original size:137 final size:138
Alignment explanation
Indices: 1278616--1278904 Score: 517
Period size: 137 Copynumber: 2.1 Consensus size: 138
1278606 CAAGTCAGCT
**
1278616 CAAGCCCATTCAGGTAACAGTGGTACTGGGCCAAAGCCCTTTTTCAGATTACAATAAACTAGGCC
1 CAAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTTCAGATTACAATAAACTAGGCC
1278681 TTAGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTA
66 TTAGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTA
1278746 AACATATG
131 AACATATG
* * *
1278754 CAAGCTCATTTGGGTAACAGTGGTACTGGGCCAGAGCCC-TTTTCAGATTACAATAAACTGGGCC
1 CAAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTTCAGATTACAATAAACTAGGCC
*
1278818 TTAGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCGGTA
66 TTAGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTA
1278883 AACATATG
131 AACATATG
1278891 CAAGCCCATTTGGG
1 CAAGCCCATTTGGG
1278905 GAGACTACTC
Statistics
Matches: 144, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
137 109 0.76
138 35 0.24
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (138 bp):
CAAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTTCAGATTACAATAAACTAGGCC
TTAGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTA
AACATATG
Found at i:1280703 original size:26 final size:26
Alignment explanation
Indices: 1280682--1280809 Score: 211
Period size: 26 Copynumber: 4.9 Consensus size: 26
1280672 TCTTATAATT
1280682 AAACATTTACCTAACCCATTATCATG
1 AAACATTTACCTAACCCATTATCATG
1280708 AAACATTTACCTAACCCATTATCATG
1 AAACATTTACCTAACCCATTATCATG
* *
1280734 GAACATTTACCTAACCTATTATCATG
1 AAACATTTACCTAACCCATTATCATG
*
1280760 AAACATTTACCGAACCCATTATCATG
1 AAACATTTACCTAACCCATTATCATG
* *
1280786 GAACATTTACCTAACCTATTATCA
1 AAACATTTACCTAACCCATTATCA
1280810 ATTTGTATCA
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 94 1.00
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.31
Consensus pattern (26 bp):
AAACATTTACCTAACCCATTATCATG
Found at i:1280761 original size:52 final size:52
Alignment explanation
Indices: 1280683--1280809 Score: 236
Period size: 52 Copynumber: 2.4 Consensus size: 52
1280673 CTTATAATTA
* *
1280683 AACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCATTATCATGG
1 AACATTTACCTAACCTATTATCATGAAACATTTACCGAACCCATTATCATGG
1280735 AACATTTACCTAACCTATTATCATGAAACATTTACCGAACCCATTATCATGG
1 AACATTTACCTAACCTATTATCATGAAACATTTACCGAACCCATTATCATGG
1280787 AACATTTACCTAACCTATTATCA
1 AACATTTACCTAACCTATTATCA
1280810 ATTTGTATCA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (52 bp):
AACATTTACCTAACCTATTATCATGAAACATTTACCGAACCCATTATCATGG
Found at i:1282032 original size:108 final size:104
Alignment explanation
Indices: 1281898--1282253 Score: 464
Period size: 108 Copynumber: 3.5 Consensus size: 104
1281888 AAATATTTTG
* *
1281898 TTTTCTTTAATTTTATTTTCAAATTACCTAATTAAATTAAATTATATTTAAAGTTTTATTTTAAA
1 TTTTATTTTATTTTATTTT-AAATTACCTAATTAAATTAAATTATATTTAAAGTTTTATTTTAAA
* *
1281963 TATTTTATTTTATTAGAATCACGGAAAATAATTTCAATATTTA
65 TATTTTATTTT-TTTGAATCACGAAAAATAATTTCAATA--TA
**
1282006 TTTTATTTTATTTTATTTTAACATTACAAAATTAAATTAAATTATATTTAAAGTTTTATTTTAAA
1 TTTTATTTTATTTTATTTTAA-ATTACCTAATTAAATTAAATTATATTTAAAGTTTTATTTTAAA
*
1282071 TATTTTATTTTTTTGAATCA-TAAAAATAATTTCAATAT-
65 TATTTTATTTTTTTGAATCACGAAAAATAATTTCAATATA
* * *
1282109 TTTTATTTTATTTTA----ACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTGTAAAT
1 TTTTATTTTATTTTATTTTAAATTACCTAATTAAATTAAATTATATTTAAAGTTTTATTTTAAAT
*
1282170 ATTTTATTTTTTTTTGAATCACGAAAAATAATTTTAATAT-
66 ATTTTA--TTTTTTTGAATCACGAAAAATAATTTCAATATA
*
1282210 TTTTATTTTATTTTA----AAATTACCTAATTAAATTAAATTTTATTT
1 TTTTATTTTATTTTATTTTAAATTACCTAATTAAATTAAATTATATTT
1282254 TCAAGTTCAC
Statistics
Matches: 228, Mismatches: 16, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
98 46 0.20
99 1 0.00
100 13 0.06
101 58 0.25
103 15 0.07
104 1 0.00
106 15 0.07
107 10 0.04
108 69 0.30
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (104 bp):
TTTTATTTTATTTTATTTTAAATTACCTAATTAAATTAAATTATATTTAAAGTTTTATTTTAAAT
ATTTTATTTTTTTGAATCACGAAAAATAATTTCAATATA
Found at i:1282152 original size:98 final size:100
Alignment explanation
Indices: 1282011--1282253 Score: 391
Period size: 98 Copynumber: 2.4 Consensus size: 100
1282001 ATTTATTTTA
** *
1282011 TTTTATTTTATTTTAACATTACAAAATTAAATTAAATTATATTTAAAGTTTTATTTTAAATATTT
1 TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTATATTTAAAGTTTTATTGTAAATATTT
*
1282076 TA-TTTTTTTGAATCA-TAAAAATAATTTCAATAT
66 TATTTTTTTTGAATCACGAAAAATAATTTCAATAT
*
1282109 TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTGTAAATATTT
1 TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTATATTTAAAGTTTTATTGTAAATATTT
*
1282174 TATTTTTTTTTGAATCACGAAAAATAATTTTAATAT
66 TA-TTTTTTTTGAATCACGAAAAATAATTTCAATAT
* *
1282210 TTTTATTTTATTTTAAAATTACCTAATTAAATTAAATTTTATTT
1 TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTATATTT
1282254 TCAAGTTCAC
Statistics
Matches: 134, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
98 63 0.47
100 13 0.10
101 58 0.43
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (100 bp):
TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTATATTTAAAGTTTTATTGTAAATATTT
TATTTTTTTTGAATCACGAAAAATAATTTCAATAT
Found at i:1282302 original size:16 final size:16
Alignment explanation
Indices: 1282281--1282739 Score: 133
Period size: 16 Copynumber: 29.0 Consensus size: 16
1282271 TCACATAATT
*
1282281 TACATAATTTACATAA
1 TACATAACTTACATAA
1282297 TACATAACTTACATAA
1 TACATAACTTACATAA
** *
1282313 TTTA-AAGTT-CA-AA
1 TACATAACTTACATAA
*
1282326 TTTCATAACTTACATAA
1 -TACATAACTTACATAA
*
1282343 TACTTAACTTACATAA
1 TACATAACTTACATAA
** **
1282359 TTTA-AAGAT-CA-AA
1 TACATAACTTACATAA
1282372 TTTA-ATAACTTACATAA
1 --TACATAACTTACATAA
1282389 TTTACATAACTTACATAA
1 --TACATAACTTACATAA
* *
1282407 TACTTTACTTACATAA
1 TACATAACTTACATAA
** * *
1282423 TTTAAAGATTTA-AT--
1 TACATA-ACTTACATAA
*
1282437 TTCATAACTTACATAA
1 TACATAACTTACATAA
1282453 TACATAACTTACATAA
1 TACATAACTTACATAA
** **
1282469 TTTA-AAGAT-CA-AA
1 TACATAACTTACATAA
1282482 TTTA-ATAACTTACATAA
1 --TACATAACTTACATAA
* *
1282499 TACTTGACTTACATAA
1 TACATAACTTACATAA
** **
1282515 TTTA-AAGGT-CA-AA
1 TACATAACTTACATAA
*
1282528 TTTCATAACTTACATAA
1 -TACATAACTTACATAA
1282545 TACATAACTTACATAA
1 TACATAACTTACATAA
** **
1282561 TTTA-AAGAT-CA-AA
1 TACATAACTTACATAA
*
1282574 TTTCATAACTTACATAA
1 -TACATAACTTACATAA
*
1282591 TTTAAATAACTTACATAA
1 --TACATAACTTACATAA
**
1282609 TA-ATTTAA-AGATCA-AA
1 TACA--TAACTTA-CATAA
* *
1282625 TTTCATAACTTACGTAA
1 -TACATAACTTACATAA
1282642 TACATAACTTACATAA
1 TACATAACTTACATAA
** **
1282658 TTTA-AAGAT-CA-AA
1 TACATAACTTACATAA
*
1282671 TTTCATAACTTACATAA
1 -TACATAACTTACATAA
1282688 TTTACATAACTTACATAA
1 --TACATAACTTACATAA
* * *
1282706 TACATAAATATATATCA
1 TACATAACT-TACATAA
1282723 TATCATAACTTACATAA
1 TA-CATAACTTACATAA
1282740 CTACTTATAA
Statistics
Matches: 322, Mismatches: 78, Indels: 85
0.66 0.16 0.18
Matches are distributed among these distances:
13 16 0.05
14 32 0.10
15 42 0.13
16 140 0.43
17 41 0.13
18 51 0.16
ACGTcount: A:0.46, C:0.14, G:0.02, T:0.37
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:1282345 original size:46 final size:46
Alignment explanation
Indices: 1282277--1282407 Score: 199
Period size: 46 Copynumber: 2.8 Consensus size: 46
1282267 CAACTCACAT
* *
1282277 AATTTACATAATTTACATAATACATAACTTACATAATTTAAAGTTCA
1 AATTT-CATAACTTACATAATACATAACTTACATAATTTAAAGATCA
*
1282324 AATTTCATAACTTACATAATACTTAACTTACATAATTTAAAGATCA
1 AATTTCATAACTTACATAATACATAACTTACATAATTTAAAGATCA
*
1282370 AATTTAATAACTTACATAATTTACATAACTTACATAAT
1 AATTTCATAACTTACATAA--TACATAACTTACATAAT
1282408 ACTTTACTTA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
46 56 0.73
47 5 0.06
48 16 0.21
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.38
Consensus pattern (46 bp):
AATTTCATAACTTACATAATACATAACTTACATAATTTAAAGATCA
Found at i:1282397 original size:64 final size:64
Alignment explanation
Indices: 1282324--1282469 Score: 235
Period size: 64 Copynumber: 2.3 Consensus size: 64
1282314 TTAAAGTTCA
1282324 AATTT-CATAACTTACATAATACTTAACTTACATAATTTAAAGATCAAATTTAATAACTTACAT
1 AATTTACATAACTTACATAATACTTAACTTACATAATTTAAAGATCAAATTTAATAACTTACAT
* ** *
1282387 AATTTACATAACTTACATAATACTTTACTTACATAATTTAAAGATTTAATTTCATAACTTACAT
1 AATTTACATAACTTACATAATACTTAACTTACATAATTTAAAGATCAAATTTAATAACTTACAT
1282451 AA--TACATAACTTACATAAT
1 AATTTACATAACTTACATAAT
1282470 TTAAAGATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
62 17 0.22
63 5 0.06
64 56 0.72
ACGTcount: A:0.45, C:0.14, G:0.01, T:0.39
Consensus pattern (64 bp):
AATTTACATAACTTACATAATACTTAACTTACATAATTTAAAGATCAAATTTAATAACTTACAT
Found at i:1282451 original size:46 final size:46
Alignment explanation
Indices: 1282387--1282706 Score: 478
Period size: 46 Copynumber: 6.8 Consensus size: 46
1282377 TAACTTACAT
* * **
1282387 AATTTACATAACTTACATAATACTTTACTTACATAATTTAAAGATTT
1 AATTT-CATAACTTACATAATACATAACTTACATAATTTAAAGATCA
1282434 AATTTCATAACTTACATAATACATAACTTACATAATTTAAAGATCA
1 AATTTCATAACTTACATAATACATAACTTACATAATTTAAAGATCA
* * * *
1282480 AATTTAATAACTTACATAATACTTGACTTACATAATTTAAAGGTCA
1 AATTTCATAACTTACATAATACATAACTTACATAATTTAAAGATCA
1282526 AATTTCATAACTTACATAATACATAACTTACATAATTTAAAGATCA
1 AATTTCATAACTTACATAATACATAACTTACATAATTTAAAGATCA
*
1282572 AATTTCATAACTTACATAATTTAAATAACTTACATAATAATTTAAAGATCA
1 AATTTCATAACTTACATAA--TACATAACTTAC---ATAATTTAAAGATCA
*
1282623 AATTTCATAACTTACGTAATACATAACTTACATAATTTAAAGATCA
1 AATTTCATAACTTACATAATACATAACTTACATAATTTAAAGATCA
1282669 AATTTCATAACTTACATAATTTACATAACTTACATAAT
1 AATTTCATAACTTACATAA--TACATAACTTACATAAT
1282707 ACATAAATAT
Statistics
Matches: 250, Mismatches: 16, Indels: 13
0.90 0.06 0.05
Matches are distributed among these distances:
46 173 0.69
47 5 0.02
48 28 0.11
49 11 0.04
51 33 0.13
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (46 bp):
AATTTCATAACTTACATAATACATAACTTACATAATTTAAAGATCA
Found at i:1282466 original size:110 final size:110
Alignment explanation
Indices: 1282268--1282515 Score: 394
Period size: 110 Copynumber: 2.3 Consensus size: 110
1282258 GTTCACTAGC
* *
1282268 AACTCACATAATTTACATAATTTACATAATACATAACTTACATAATTTAAAGTTCAAATTTCATA
1 AACTTACATAATTTACATAACTTACATAATACATAACTTACATAATTTAAAGTTCAAATTTCATA
*
1282333 ACTTACATAATACTTAACTTACATAATTTAAAGATCAAATTTAAT
66 ACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTAAT
* * *
1282378 AACTTACATAATTTACATAACTTACATAATACTTTACTTACATAATTTAAAGATT-TAATTTCAT
1 AACTTACATAATTTACATAACTTACATAATACATAACTTACATAATTTAAAG-TTCAAATTTCAT
1282442 AACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTAAT
65 AACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTAAT
* *
1282488 AACTTACATAA--TACTTGACTTACATAAT
1 AACTTACATAATTTACATAACTTACATAAT
1282516 TTAAAGGTCA
Statistics
Matches: 129, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
108 15 0.12
110 112 0.87
111 2 0.02
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.38
Consensus pattern (110 bp):
AACTTACATAATTTACATAACTTACATAATACATAACTTACATAATTTAAAGTTCAAATTTCATA
ACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTAAT
Found at i:1282581 original size:30 final size:30
Alignment explanation
Indices: 1282547--1282642 Score: 102
Period size: 30 Copynumber: 3.5 Consensus size: 30
1282537 TTACATAATA
1282547 CATAACTTACATAATTTAAAGATCAAATTT
1 CATAACTTACATAATTTAAAGATCAAATTT
1282577 CATAACTTACATAATTT-AA-AT--AA---
1 CATAACTTACATAATTTAAAGATCAAATTT
* *
1282600 C-TTACATA-ATAATTTAAAGATCAAATTT
1 CATAACTTACATAATTTAAAGATCAAATTT
*
1282628 CATAACTTACGTAAT
1 CATAACTTACATAAT
1282643 ACATAACTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
21 7 0.13
22 7 0.13
23 3 0.06
25 2 0.04
26 2 0.04
28 3 0.06
29 7 0.13
30 21 0.40
ACGTcount: A:0.47, C:0.14, G:0.03, T:0.36
Consensus pattern (30 bp):
CATAACTTACATAATTTAAAGATCAAATTT
Found at i:1282632 original size:21 final size:21
Alignment explanation
Indices: 1282608--1282678 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 21
1282598 AACTTACATA
1282608 ATAATTTAAAGATCAAATTTC
1 ATAATTTAAAGATCAAATTTC
* * *
1282629 ATAACTTACGTAATACAT-AACTTAC
1 ATAA-TT---TAA-AGATCAAATTTC
1282654 ATAATTTAAAGATCAAATTTC
1 ATAATTTAAAGATCAAATTTC
1282675 ATAA
1 ATAA
1282679 CTTACATAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
20 3 0.08
21 16 0.42
22 2 0.05
24 2 0.05
25 12 0.32
26 3 0.08
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (21 bp):
ATAATTTAAAGATCAAATTTC
Found at i:1282668 original size:97 final size:97
Alignment explanation
Indices: 1282277--1282707 Score: 454
Period size: 97 Copynumber: 4.4 Consensus size: 97
1282267 CAACTCACAT
* *
1282277 AATTTACATAATTTACATAA--TACATAACTTAC---ATAATTTAAAGTTCAAATTTCATAACTT
1 AATTT-CATAACTTACATAATTTACATAACTTACATAATAATTTAAAGATCAAATTTCATAACTT
*
1282337 ACATAATACTTAACTTACATAATTTAAAGATCA
65 ACATAATACATAACTTACATAATTTAAAGATCA
* * *** *
1282370 AATTTAATAACTTACATAATTTACATAACTTACATAATACTTTACTTA-CATAATTTAAAGATTT
1 AATTTCATAACTTACATAATTTACATAACTTACATAATAATTTAAAGATCA-AATTT---CA--T
* * *
1282434 AA-TTTCATAACTTACATAA--TACATAACTTACATA-ATTTA
60 AACTTACATAA--TACATAACTTACATAATTTA-A-AGA-TCA
** * * * *
1282473 AAGATCA-AATTTA-ATAACTTACATAATACTTGACTTACATAATTTAAAGGTCAAATTTCATAA
1 AATTTCATAACTTACATAATTTACAT-A-ACTT-ACATA-ATAATTTAAAGATCAAATTTCATAA
1282536 CTTACATAATACATAACTTACATAATTTAAAGATCA
62 CTTACATAATACATAACTTACATAATTTAAAGATCA
*
1282572 AATTTCATAACTTACATAATTTAAATAACTTACATAATAATTTAAAGATCAAATTTCATAACTTA
1 AATTTCATAACTTACATAATTTACATAACTTACATAATAATTTAAAGATCAAATTTCATAACTTA
*
1282637 CGTAATACATAACTTACATAATTTAAAGATCA
66 CATAATACATAACTTACATAATTTAAAGATCA
1282669 AATTTCATAACTTACATAATTTACATAACTTACATAATA
1 AATTTCATAACTTACATAATTTACATAACTTACATAATA
1282708 CATAAATATA
Statistics
Matches: 275, Mismatches: 36, Indels: 50
0.76 0.10 0.14
Matches are distributed among these distances:
92 12 0.04
93 5 0.02
94 12 0.04
96 2 0.01
97 109 0.40
98 4 0.01
99 19 0.07
100 12 0.04
101 53 0.19
102 12 0.04
103 17 0.06
104 4 0.01
105 12 0.04
106 2 0.01
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (97 bp):
AATTTCATAACTTACATAATTTACATAACTTACATAATAATTTAAAGATCAAATTTCATAACTTA
CATAATACATAACTTACATAATTTAAAGATCA
Found at i:1283727 original size:31 final size:31
Alignment explanation
Indices: 1283689--1283747 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1283679 TATTTGCTAC
*
1283689 ATTTGCTATATTTT-GTTGAATTTCATGTTAT
1 ATTTGCTAT-TTTTGGTTGAATTTAATGTTAT
*
1283720 ATTTGCTATTTTTGGTTGGATTTAATGT
1 ATTTGCTATTTTTGGTTGAATTTAATGT
1283748 AGGAAGGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.20, C:0.05, G:0.17, T:0.58
Consensus pattern (31 bp):
ATTTGCTATTTTTGGTTGAATTTAATGTTAT
Found at i:1286402 original size:27 final size:28
Alignment explanation
Indices: 1286372--1286427 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
1286362 TAAACACTCG
1286372 TAAATATAGTCAAAT-ATATATTATTGT
1 TAAATATAGTCAAATAATATATTATTGT
*
1286399 TAAATATAGTTAAATAAATATATTATTGT
1 TAAATATAGTCAAAT-AATATATTATTGT
1286428 CGATTATCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 14 0.54
29 12 0.46
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (28 bp):
TAAATATAGTCAAATAATATATTATTGT
Found at i:1288290 original size:13 final size:13
Alignment explanation
Indices: 1288272--1288307 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1288262 ATTTTACCCA
1288272 TAATAATAATTAT
1 TAATAATAATTAT
1288285 TAATAATTAA-TAT
1 TAATAA-TAATTAT
1288298 TAATAATAAT
1 TAATAATAAT
1288308 AACTCTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.14
13 15 0.71
14 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATAATAATTAT
Found at i:1288299 original size:16 final size:17
Alignment explanation
Indices: 1288271--1288307 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1288261 AATTTTACCC
*
1288271 ATAA-TAATAATTATTA
1 ATAATTAATAATTAATA
1288287 ATAATTAAT-ATTAATA
1 ATAATTAATAATTAATA
1288303 ATAAT
1 ATAAT
1288308 AACTCTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATTAATAATTAATA
Found at i:1288301 original size:10 final size:10
Alignment explanation
Indices: 1288272--1288309 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1288262 ATTTTACCCA
1288272 TAATAATAAT
1 TAATAATAAT
*
1288282 TATTAATAAT
1 TAATAATAAT
*
1288292 TAATATTAA-
1 TAATAATAAT
1288301 TAATAATAA
1 TAATAATAA
1288310 CTCTAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TAATAATAAT
Found at i:1294002 original size:30 final size:29
Alignment explanation
Indices: 1293929--1294003 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
1293919 TTGACGCTTC
* *
1293929 AACTTTTTCATATTTATACTTTAACCACT
1 AACTTTTTCATATTTACACTTAAACCACT
* * **
1293958 TACATGTTAAATATTTACACTTAAACCACAT
1 AAC-TTTTTCATATTTACACTTAAACCAC-T
1293989 AACTTTTTCATATTT
1 AACTTTTTCATATTT
1294004 TTTTATGATT
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
29 2 0.06
30 29 0.85
31 3 0.09
ACGTcount: A:0.35, C:0.19, G:0.01, T:0.45
Consensus pattern (29 bp):
AACTTTTTCATATTTACACTTAAACCACT
Found at i:1295473 original size:46 final size:44
Alignment explanation
Indices: 1295369--1295476 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
1295359 TGTCTTTGAC
** * * *
1295369 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
1295413 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
1295459 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
1295477 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:1302860 original size:46 final size:44
Alignment explanation
Indices: 1302756--1302863 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
1302746 TGTCTTTGAC
** * * *
1302756 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
1302800 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
1302846 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
1302864 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:1305005 original size:163 final size:164
Alignment explanation
Indices: 1304793--1305114 Score: 416
Period size: 163 Copynumber: 2.0 Consensus size: 164
1304783 TAATTCGAAT
** * *
1304793 GTGTCTTTTGGTTATTCACTATCGATTAGTTCAACTTGTTTTTGTTGTTGGCTATTATAATGTCA
1 GTGTCTTTTGGTTATTCACTATCGATTAGTTCAACTTGCGTTGGTTGTTGACTATTATAATGTCA
* * *
1304858 CTTCCATTTTTATATAATCAAGGACGAGCTTTAATGTT-ATCAGGCTCGACA-TTAGTGGTTGTT
66 CTTCCATCTTTATATAATCAAGGACGAGCTTTAATGTTGCT-AGACTCGACACTT-GTGGTTGTT
*
1304921 TGAGAGTATAGTCGCTCAAGGTTCAGGATTGGAAAC
129 TCAGAGTATAGTCGCTCAAGGTTCAGGATTGGAAAC
* * * *
1304957 GTGTCTTTTGGTTCTT-ACTCTTGATTGGTTCAACTTGCGTTGGTTGTTGACTATTATAATGTCA
1 GTGTCTTTTGGTTATTCACTATCGATTAGTTCAACTTGCGTTGGTTGTTGACTATTATAATGTCA
* * ** * *
1305021 TTTCTATCTTTATATTGTCAAGGACGAGCTTTGATGTTGCTAGACTCGATACTTGTGGTTGTTTC
66 CTTCCATCTTTATATAATCAAGGACGAGCTTTAATGTTGCTAGACTCGACACTTGTGGTTGTTTC
* * *
1305086 AGAGTGTAGTCGTTCAAGGTTTAGGATTG
131 AGAGTATAGTCGCTCAAGGTTCAGGATTG
1305115 AAAAGGTCTA
Statistics
Matches: 135, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
163 117 0.87
164 18 0.13
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.43
Consensus pattern (164 bp):
GTGTCTTTTGGTTATTCACTATCGATTAGTTCAACTTGCGTTGGTTGTTGACTATTATAATGTCA
CTTCCATCTTTATATAATCAAGGACGAGCTTTAATGTTGCTAGACTCGACACTTGTGGTTGTTTC
AGAGTATAGTCGCTCAAGGTTCAGGATTGGAAAC
Found at i:1311117 original size:20 final size:20
Alignment explanation
Indices: 1311081--1311118 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1311071 AGCTTTTAAT
1311081 AAAATATTTATTATAATTTA
1 AAAATATTTATTATAATTTA
*
1311101 AAAATCTTTCATT-TAATT
1 AAAATATTT-ATTATAATT
1311119 ATATTTAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATATTTATTATAATTTA
Found at i:1313675 original size:6 final size:7
Alignment explanation
Indices: 1313657--1313683 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1313647 AACCACTTTT
1313657 TAAAAAA
1 TAAAAAA
1313664 TAAAAAA
1 TAAAAAA
1313671 TAAAAAA
1 TAAAAAA
1313678 TAAAAA
1 TAAAAA
1313684 CCGCTATCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:1321229 original size:1 final size:1
Alignment explanation
Indices: 1321223--1321247 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1321213 TTGAACAACC
1321223 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
1321248 GAAGTGTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1325914 original size:141 final size:141
Alignment explanation
Indices: 1325660--1325939 Score: 420
Period size: 141 Copynumber: 2.0 Consensus size: 141
1325650 ATTTGATACC
* *** *
1325660 TTAAGCTAAGTTCATTAGAACTAGCCTAGAATTTCAAATTTTAGGCACGGCATAACCAGCAAATC
1 TTAAGCTAAGTTCATTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAACCAGCAAATC
* * *
1325725 AGTTCTTAACCTCTCATTCGCCATGACTCAATTTGATACCTTAAGCTAAGTTCAATCAGTTCAAG
66 AGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTCAAGCTAAGTTCAATCAGTTCAAC
1325790 TTCAATTAACT
131 TTCAATTAACT
* * *
1325801 TTAAGCTAA-TTCAGTTAAAACTAGCCTAGAGTTTCAAAAAATAGGCACTACATAGCCAAG-AAA
1 TTAAGCTAAGTTCA-TTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAACC-AGCAAA
*
1325864 TCAGTTCTTAACCTCTCATCCGCCATGATTCAATTTGATACCTCAAGCTAAGTTCAATCAGTTCA
64 TCAGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTCAAGCTAAGTTCAATCAGTTCA
1325929 ACTTCAATTAA
129 ACTTCAATTAA
1325940 AACTAGCTTA
Statistics
Matches: 125, Mismatches: 12, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
140 4 0.03
141 119 0.95
142 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (141 bp):
TTAAGCTAAGTTCATTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAACCAGCAAATC
AGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTCAAGCTAAGTTCAATCAGTTCAAC
TTCAATTAACT
Found at i:1326376 original size:19 final size:19
Alignment explanation
Indices: 1326352--1326396 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
1326342 GAATTGTGTA
1326352 GAAAAGAGATCATCCGGGT
1 GAAAAGAGATCATCCGGGT
1326371 GAAAAGAGATCATCCGGGT
1 GAAAAGAGATCATCCGGGT
1326390 GAAAAGA
1 GAAAAGA
1326397 AAGTGAATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.42, C:0.13, G:0.31, T:0.13
Consensus pattern (19 bp):
GAAAAGAGATCATCCGGGT
Found at i:1329432 original size:6 final size:6
Alignment explanation
Indices: 1329421--1329477 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
1329411 GCTCTAAACA
1329421 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1329469 ATACAT ATA
1 ATACAT ATA
1329478 TATGAAGGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:1333248 original size:2 final size:2
Alignment explanation
Indices: 1333241--1333275 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1333231 ATGAATTTGC
1333241 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1333276 AAGTTATCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1334262 original size:24 final size:24
Alignment explanation
Indices: 1334218--1334266 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
1334208 ACTATGAAAA
1334218 TAATAAAGGTTAAAATACAAACAC
1 TAATAAAGGTTAAAATACAAACAC
*
1334242 TAATAAAAGGTTGAAAT-CAAACAC
1 TAAT-AAAGGTTAAAATACAAACAC
1334266 T
1 T
1334267 TGACGGTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.22
Consensus pattern (24 bp):
TAATAAAGGTTAAAATACAAACAC
Found at i:1335728 original size:14 final size:15
Alignment explanation
Indices: 1335698--1335743 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1335688 TTAAAACTTG
*
1335698 AAAAATATAAAGATAA
1 AAAAATATAAA-CTAA
*
1335714 AAAAAT-TAAATTAA
1 AAAAATATAAACTAA
1335728 AAAAATATAAACTAA
1 AAAAATATAAACTAA
1335743 A
1 A
1335744 TTCGTAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 9 0.33
15 12 0.44
16 6 0.22
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (15 bp):
AAAAATATAAACTAA
Found at i:1336186 original size:2 final size:2
Alignment explanation
Indices: 1336179--1336212 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1336169 GTTTATTTGA
1336179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1336213 GAATTGGTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1338053 original size:13 final size:13
Alignment explanation
Indices: 1338030--1338067 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
1338020 TTAATAAAAA
1338030 TAAAAATTATATAT-
1 TAAAAA-TATA-ATC
1338044 TAAAAATATAATC
1 TAAAAATATAATC
1338057 TAAAAATATAA
1 TAAAAATATAA
1338068 ATACATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.09
13 15 0.65
14 6 0.26
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (13 bp):
TAAAAATATAATC
Found at i:1340196 original size:16 final size:15
Alignment explanation
Indices: 1340171--1340200 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1340161 AGAGTACTTG
1340171 AGAAAAGAAAAAAGA
1 AGAAAAGAAAAAAGA
1340186 AGAAGAAGAAAAAAG
1 AGAA-AAGAAAAAAG
1340201 GAACGCTCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAAAAAGA
Found at i:1343655 original size:14 final size:14
Alignment explanation
Indices: 1343601--1343655 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
1343591 ATGCCACACC
1343601 AATAAAATTA-ACAA
1 AATAAAATTATA-AA
*
1343615 AA-AAAATTCTAAA
1 AATAAAATTATAAA
* *
1343628 AATATAAGTATAAA
1 AATAAAATTATAAA
*
1343642 AATAAAATTTTAAA
1 AATAAAATTATAAA
1343656 TTTGTAAAGA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 10 0.31
14 22 0.69
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (14 bp):
AATAAAATTATAAA
Found at i:1350404 original size:18 final size:17
Alignment explanation
Indices: 1350369--1350401 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1350359 CTTTTTATTC
1350369 TTTTATTATTTCATTTA
1 TTTTATTATTTCATTTA
1350386 TTTTACTTATTT-ATTT
1 TTTTA-TTATTTCATTT
1350402 TATCATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTATTTCATTTA
Found at i:1359471 original size:6 final size:6
Alignment explanation
Indices: 1359462--1359486 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1359452 GCTGAAGCTA
1359462 GCAATG GCAATG GCAATG GCAATG G
1 GCAATG GCAATG GCAATG GCAATG G
1359487 TTGCTCCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (6 bp):
GCAATG
Found at i:1359890 original size:25 final size:25
Alignment explanation
Indices: 1359856--1359907 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1359846 TTAAAGTGTA
1359856 TTGTAAAGGTACCTCTATCTCTTTT
1 TTGTAAAGGTACCTCTATCTCTTTT
1359881 TTGTAAAGGTACCTCTATCTCTTTT
1 TTGTAAAGGTACCTCTATCTCTTTT
1359906 TT
1 TT
1359908 TTATGTCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (25 bp):
TTGTAAAGGTACCTCTATCTCTTTT
Found at i:1370315 original size:46 final size:48
Alignment explanation
Indices: 1370264--1370487 Score: 220
Period size: 47 Copynumber: 4.8 Consensus size: 48
1370254 ATGGTTGAGC
1370264 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T-G
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAACTAG
* * * *
1370311 -TCCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATGTAACTAGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACTA-G
* * * *
1370356 CATTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACTA-G
1370403 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC--G
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAACTAG
* *
1370451 -CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1370488 GCGGGTTACA
Statistics
Matches: 156, Mismatches: 12, Indels: 19
0.83 0.06 0.10
Matches are distributed among these distances:
42 2 0.01
43 5 0.03
45 3 0.02
46 63 0.40
47 73 0.47
48 3 0.02
50 4 0.03
51 3 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (48 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACTAG
Found at i:1370378 original size:47 final size:47
Alignment explanation
Indices: 1370262--1370433 Score: 228
Period size: 47 Copynumber: 3.7 Consensus size: 47
1370252 GGATGGTTGA
* * *
1370262 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAG
*
1370310 G--TCCGAACTCGTTGAGTTGAGTCTGAGTTCGTGAGATGTAACTAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAG
*
1370355 GCATTCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAG
1370402 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
1370434 ACTTATGGAT
Statistics
Matches: 112, Mismatches: 7, Indels: 11
0.86 0.05 0.08
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 28 0.25
47 73 0.65
48 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (47 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:1376163 original size:29 final size:26
Alignment explanation
Indices: 1376099--1376182 Score: 89
Period size: 29 Copynumber: 3.1 Consensus size: 26
1376089 TGAATTTGAA
1376099 TTTTTTTAATTTGGTA-TATAATTTTT
1 TTTTTTTAATTTGGTACTA-AATTTTT
* *
1376125 TTTATTTAATTTGATACTTAAATTTAATT
1 TTTTTTTAATTTGGTAC-TAAATTT--TT
*
1376154 TTTTTTTAATTTGGTACCTAAAATTTT
1 TTTTTTTAATTTGGTA-CTAAATTTTT
1376181 TT
1 TT
1376183 GGTGCCTAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
26 14 0.29
27 9 0.19
28 2 0.04
29 22 0.46
30 1 0.02
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (26 bp):
TTTTTTTAATTTGGTACTAAATTTTT
Found at i:1376713 original size:31 final size:31
Alignment explanation
Indices: 1376645--1376718 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
1376635 AAAAAAGATT
1376645 AGGTACTAAATTAAGAAAAAGAGTCAAGTTC
1 AGGTACTAAATTAAGAAAAAGAGTCAAGTTC
* * * * * *
1376676 AAGTACTAGATTAGGAAAACGTGTCAAGTTT
1 AGGTACTAAATTAAGAAAAAGAGTCAAGTTC
*
1376707 GGGTACTAAATT
1 AGGTACTAAATT
1376719 GAACCCAAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (31 bp):
AGGTACTAAATTAAGAAAAAGAGTCAAGTTC
Found at i:1376794 original size:8 final size:8
Alignment explanation
Indices: 1376781--1376823 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
1376771 ACTAAATGTC
*
1376781 ATAAATTT
1 ATAAATAT
1376789 ATAAATAT
1 ATAAATAT
*
1376797 ATATATAT
1 ATAAATAT
*
1376805 ATATATAT
1 ATAAATAT
*
1376813 ATATATAT
1 ATAAATAT
1376821 ATA
1 ATA
1376824 TATAAATTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
ATAAATAT
Found at i:1376800 original size:2 final size:2
Alignment explanation
Indices: 1376788--1376827 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1376778 GTCATAAATT
*
1376788 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1376828 AATTAGGTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1377174 original size:51 final size:51
Alignment explanation
Indices: 1377070--1377181 Score: 129
Period size: 51 Copynumber: 2.2 Consensus size: 51
1377060 CGTTGCGAGC
* * * * * **
1377070 TAAATTTGTT-AATTAAGATAAAATTGACATAATGTGTAAATATTGTGGGT
1 TAAATTTGTTAAATCAACATAAAATTAACAAAATGTGTAAATATTGAGCAT
*
1377120 TAAATTTGTTAAATCAACATAGAATTAACAAAATGTGTAAACT-TTGAGCAT
1 TAAATTTGTTAAATCAACATAAAATTAACAAAATGTGTAAA-TATTGAGCAT
1377171 TAAATTTGTTA
1 TAAATTTGTTA
1377182 TTATACTAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
50 10 0.19
51 41 0.79
52 1 0.02
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.38
Consensus pattern (51 bp):
TAAATTTGTTAAATCAACATAAAATTAACAAAATGTGTAAATATTGAGCAT
Found at i:1379351 original size:35 final size:35
Alignment explanation
Indices: 1379324--1379490 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
1379314 CATGGCAAAG
1379324 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1379359 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
*
1379394 TGTGAAATGTAGGTATGGTATTATTAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATT--ATCCATACTGAGC
** * * *
1379434 TAAGAAATGTAGGTATGGCATT-TCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATTAT-CCATACTGAGC
**
1379469 TGAAAAATGTAGGTATGGTATT
1 TGTGAAATGTAGGTATGGTATT
1379491 TCAATGAGGA
Statistics
Matches: 118, Mismatches: 8, Indels: 12
0.86 0.06 0.09
Matches are distributed among these distances:
34 1 0.01
35 82 0.69
37 3 0.03
38 4 0.03
40 28 0.24
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
Found at i:1379414 original size:40 final size:40
Alignment explanation
Indices: 1379335--1379451 Score: 140
Period size: 40 Copynumber: 3.0 Consensus size: 40
1379325 GTGAAATGTA
1379335 GGTATGGTATTATCCATACTGAGCTGTGAAA--T--GTA-
1 GGTATGGTATTATCCATACTGAGCTGTGAAATGTAGGTAT
1379370 GGTATGGTATTATCCATACTGAGCTGTGAAATGTAGGTAT
1 GGTATGGTATTATCCATACTGAGCTGTGAAATGTAGGTAT
* **
1379410 GGTAT--TATTAAATCCATACTGAGTTAAGAAATGTAGGTAT
1 GGTATGGTATT--ATCCATACTGAGCTGTGAAATGTAGGTAT
1379450 GG
1 GG
1379452 CATTTCCCAT
Statistics
Matches: 72, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
35 31 0.43
37 1 0.01
38 4 0.06
39 3 0.04
40 33 0.46
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (40 bp):
GGTATGGTATTATCCATACTGAGCTGTGAAATGTAGGTAT
Found at i:1379448 original size:75 final size:73
Alignment explanation
Indices: 1379324--1379490 Score: 207
Period size: 75 Copynumber: 2.3 Consensus size: 73
1379314 CATGGCAAAG
** *
1379324 TGTGAAATGTAGGTATGG---TATTATCCATACTGAGCTGTGAAATGTAGGTATGGTATTAT-CC
1 TGTGAAATGTAGGTATGGTATTATTATCCATACTGAGCTAAGAAATGTAGGTATGGCATT-TCCC
*
1379385 ATACTGAGC
65 ATACCGAGC
*
1379394 TGTGAAATGTAGGTATGGTATTATTAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATT--ATCCATACTGAGCTAAGAAATGTAGGTATGGCATTTCC
*
1379459 CATACCGAGT
64 CATACCGAGC
**
1379469 TGAAAAATGTAGGTATGGTATT
1 TGTGAAATGTAGGTATGGTATT
1379491 TCAATGAGGA
Statistics
Matches: 83, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
70 18 0.22
73 4 0.05
74 1 0.01
75 60 0.72
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34
Consensus pattern (73 bp):
TGTGAAATGTAGGTATGGTATTATTATCCATACTGAGCTAAGAAATGTAGGTATGGCATTTCCCA
TACCGAGC
Found at i:1381679 original size:30 final size:32
Alignment explanation
Indices: 1381626--1381685 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
1381616 TATTAGTCCT
1381626 TATATTTTACGAAAATTATAAATTT-AGTTTA
1 TATATTTTACGAAAATTATAAATTTCAGTTTA
*
1381657 TATATTTTTC-AAAATCTA-AAATTTCAGTT
1 TATATTTTACGAAAAT-TATAAATTTCAGTT
1381686 CTCAACAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (32 bp):
TATATTTTACGAAAATTATAAATTTCAGTTTA
Found at i:1382049 original size:31 final size:30
Alignment explanation
Indices: 1382014--1382072 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
1382004 GTATAAGGAT
1382014 TAAAATTAA-CAAATTTAAAAAATACAAAAAC
1 TAAAATTAATCAAA-TTAAAAAATA-AAAAAC
*
1382045 TAAAATTAATCAAATTAAAATATAAAAA
1 TAAAATTAATCAAATTAAAAAATAAAAA
1382073 TTAACCCACC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 4 0.15
31 18 0.69
32 4 0.15
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (30 bp):
TAAAATTAATCAAATTAAAAAATAAAAAAC
Found at i:1383794 original size:9 final size:9
Alignment explanation
Indices: 1383780--1383805 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1383770 CAAGTTAAAA
1383780 AAAAAAACC
1 AAAAAAACC
1383789 AAAAAAACC
1 AAAAAAACC
1383798 AAAAAAAC
1 AAAAAAAC
1383806 AACACCACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAACC
Found at i:1385996 original size:19 final size:19
Alignment explanation
Indices: 1385972--1386012 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1385962 GGAACTATTC
1385972 TTATTCTATTTGACTTTGA
1 TTATTCTATTTGACTTTGA
1385991 TTATTCTATTTGACTTTGA
1 TTATTCTATTTGACTTTGA
1386010 TTA
1 TTA
1386013 GAACAGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.59
Consensus pattern (19 bp):
TTATTCTATTTGACTTTGA
Found at i:1396531 original size:2 final size:2
Alignment explanation
Indices: 1396524--1396555 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1396514 TTATTATTAA
1396524 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1396556 TATGTATCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.