Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 4 of 318
Found at i:1034937 original size:20 final size:20
Alignment explanation
Indices: 1034912--1034961 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1034902 TGGCTTAAAA
1034912 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
1034932 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
1034949 GTGGTAGTGGATT
1 TTGGTAGTGGATT
1034962 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:1039576 original size:20 final size:20
Alignment explanation
Indices: 1039551--1039600 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1039541 TGGCTTAAAA
1039551 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
1039571 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
1039588 GTGGTAGTGGATT
1 TTGGTAGTGGATT
1039601 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:1047886 original size:27 final size:26
Alignment explanation
Indices: 1047844--1047914 Score: 65
Period size: 28 Copynumber: 2.6 Consensus size: 26
1047834 TACTTTGTGA
1047844 ATTATTTATCTT-AATTT-ATTTAACAT
1 ATTATTTAT-TTAAATTTGATTT-ACAT
* *
1047870 ATTATTTATTTAAAATTTGCTTTATAT
1 ATTATTTATTT-AAATTTGATTTACAT
1047897 ATTATTTTATTTCAAATT
1 ATTA-TTTATTT-AAATT
1047915 GTTTTATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
25 2 0.05
26 9 0.24
27 12 0.32
28 15 0.39
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (26 bp):
ATTATTTATTTAAATTTGATTTACAT
Found at i:1047920 original size:27 final size:28
Alignment explanation
Indices: 1047868--1047929 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
1047858 TTTATTTAAC
1047868 ATATTA-TTTATTTAAAATTTGCTTTAT
1 ATATTATTTTATTTAAAATTTGCTTTAT
* *
1047895 ATATTATTTTATTTCAAA-TTGTTTTAT
1 ATATTATTTTATTTAAAATTTGCTTTAT
*
1047922 ATTTTATT
1 ATATTATT
1047930 CATATTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 21 0.68
28 10 0.32
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (28 bp):
ATATTATTTTATTTAAAATTTGCTTTAT
Found at i:1061454 original size:11 final size:11
Alignment explanation
Indices: 1061431--1061463 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1061421 AGAAAAAAAA
1061431 AGAG-AGGGAAG
1 AGAGAAGGG-AG
1061442 AGAGAAGGGAG
1 AGAGAAGGGAG
1061453 AGAGAAGGGAG
1 AGAGAAGGGAG
1061464 GGGAATCCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (11 bp):
AGAGAAGGGAG
Found at i:1065106 original size:21 final size:21
Alignment explanation
Indices: 1065080--1065121 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1065070 CCTATAAATA
1065080 GACATAGTCTATTCCTCTTGT
1 GACATAGTCTATTCCTCTTGT
1065101 GACATAGTCTATTCCTCTTGT
1 GACATAGTCTATTCCTCTTGT
1065122 ATTGATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (21 bp):
GACATAGTCTATTCCTCTTGT
Found at i:1065227 original size:5 final size:5
Alignment explanation
Indices: 1065211--1065244 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
1065201 TTGTGTGTTC
*
1065211 TTTAT CTTTAT TTTAT TTTAT TTTAT TCTAT TTT
1 TTTAT -TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1065245 TCACAGAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:1069271 original size:72 final size:72
Alignment explanation
Indices: 1069154--1069301 Score: 260
Period size: 72 Copynumber: 2.1 Consensus size: 72
1069144 CAATTTCTTC
* *
1069154 CAAACTTGACATACTCCCCATCCACCTTGGTATGTCCCCAGAAAGCTCGTTATTGCTTAAATCCA
1 CAAACTTGACATACTCCCCATCCACCTTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCA
1069219 ATGTTGA
66 ATGTTGA
* *
1069226 CAAACTTGACATATTCTCCATCCACCTTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCA
1 CAAACTTGACATACTCCCCATCCACCTTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCA
1069291 ATGTTGA
66 ATGTTGA
1069298 CAAA
1 CAAA
1069302 AAGGAGCAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (72 bp):
CAAACTTGACATACTCCCCATCCACCTTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCA
ATGTTGA
Found at i:1074405 original size:14 final size:15
Alignment explanation
Indices: 1074386--1074422 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1074376 CAAAAATTGA
*
1074386 AAAATAATAC-TATT
1 AAAATAAAACTTATT
1074400 AAAATAAAACTTATT
1 AAAATAAAACTTATT
1074415 AAAATAAA
1 AAAATAAA
1074423 CACACATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATAAAACTTATT
Found at i:1075100 original size:5 final size:5
Alignment explanation
Indices: 1075090--1075118 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1075080 TATAATTTCA
1075090 TATAT TATAT TATAT TATAT TA-AT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT
1075119 ATTATCTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:1076625 original size:21 final size:22
Alignment explanation
Indices: 1076586--1076626 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1076576 TATTTTTTAC
1076586 AAAGGTTTTAATATCAATTAGA
1 AAAGGTTTTAATATCAATTAGA
* *
1076608 AAAGTTTTTATTAT-AATTA
1 AAAGGTTTTAATATCAATTA
1076627 TATTTTAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (22 bp):
AAAGGTTTTAATATCAATTAGA
Found at i:1079877 original size:15 final size:15
Alignment explanation
Indices: 1079857--1079889 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1079847 TGTACTCTGA
1079857 ATAAACTAAATCATC
1 ATAAACTAAATCATC
1079872 ATAAACTAAATCATC
1 ATAAACTAAATCATC
1079887 ATA
1 ATA
1079890 GGTCACAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (15 bp):
ATAAACTAAATCATC
Found at i:1084856 original size:18 final size:20
Alignment explanation
Indices: 1084812--1084850 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
1084802 TAACAATTTT
1084812 AGAGAAAGTTTGAGAGAAAA
1 AGAGAAAGTTTGAGAGAAAA
1084832 AGAGAAA-TTTGAGAGAAAA
1 AGAGAAAGTTTGAGAGAAAA
1084851 GTGAAAAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.15
Consensus pattern (20 bp):
AGAGAAAGTTTGAGAGAAAA
Found at i:1091174 original size:16 final size:16
Alignment explanation
Indices: 1091153--1091183 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1091143 ATAATACTTC
*
1091153 ATATTATGTTATTTAT
1 ATATTATGTAATTTAT
1091169 ATATTATGTAATTTA
1 ATATTATGTAATTTA
1091184 GAACACATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
ATATTATGTAATTTAT
Found at i:1102830 original size:13 final size:12
Alignment explanation
Indices: 1102772--1102834 Score: 51
Period size: 13 Copynumber: 5.2 Consensus size: 12
1102762 TAAACAATTC
1102772 AATAATATAAAT
1 AATAATATAAAT
1102784 AAT-ATA-AAATTT
1 AATAATATAAA--T
* *
1102796 AA-AATTTAATTT
1 AATAATATAA-AT
1102808 AATAATATAAAT
1 AATAATATAAAT
1102820 AATAGATATAAAT
1 AATA-ATATAAAT
1102833 AA
1 AA
1102835 AATTATTACT
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
10 3 0.08
11 3 0.08
12 16 0.40
13 18 0.45
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (12 bp):
AATAATATAAAT
Found at i:1103331 original size:18 final size:18
Alignment explanation
Indices: 1103308--1103344 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1103298 TATAGTTTGA
1103308 TATTTGAATTATTCGAAT
1 TATTTGAATTATTCGAAT
*
1103326 TATTTGAGTTATTCGAAT
1 TATTTGAATTATTCGAAT
1103344 T
1 T
1103345 CGAAAACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (18 bp):
TATTTGAATTATTCGAAT
Found at i:1106413 original size:22 final size:22
Alignment explanation
Indices: 1106384--1106451 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
1106374 TGCACAAACG
1106384 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* *
1106406 TACAGAGAGCAC-AGATGTGCTA
1 AACAGAGAGCACTA-AAGTGCTA
*
1106428 AACAGAGAGCACTTAACGTGCTA
1 AACAGAGAGCAC-TAAAGTGCTA
1106451 A
1 A
1106452 TAATAGTACA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.74
23 8 0.21
24 1 0.03
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:1107530 original size:7 final size:7
Alignment explanation
Indices: 1107520--1107553 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1107510 AAATCTCAAA
1107520 TTTTCTT
1 TTTTCTT
1107527 TTTTCTT
1 TTTTCTT
1107534 TTTTCTT
1 TTTTCTT
* *
1107541 TCTTCCT
1 TTTTCTT
1107548 TTTTCT
1 TTTTCT
1107554 CTATTTCGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTCTT
Found at i:1107609 original size:21 final size:21
Alignment explanation
Indices: 1107568--1107611 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1107558 TTCGTCCCTG
* **
1107568 CTATTCTGTTTGTTTTTTTTT
1 CTATTCTGTTTCTTTACTTTT
1107589 CTATTCTGTTTCTTTACTTTT
1 CTATTCTGTTTCTTTACTTTT
1107610 CT
1 CT
1107612 TATGTTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.07, C:0.16, G:0.07, T:0.70
Consensus pattern (21 bp):
CTATTCTGTTTCTTTACTTTT
Found at i:1107628 original size:7 final size:7
Alignment explanation
Indices: 1107618--1107685 Score: 50
Period size: 7 Copynumber: 9.4 Consensus size: 7
1107608 TTCTTATGTT
1107618 TTATATA
1 TTATATA
1107625 TTATACTA
1 TTATA-TA
1107633 -TATATA
1 TTATATA
*
1107639 ATATAATA
1 TTAT-ATA
*
1107647 TAATAATA
1 TTAT-ATA
*
1107655 TAATATA
1 TTATATA
1107662 TTATATA
1 TTATATA
1107669 TTA-ATA
1 TTATATA
*
1107675 CTTAAATA
1 -TTATATA
1107683 TTA
1 TTA
1107686 AGTTAATATA
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
6 5 0.09
7 30 0.57
8 18 0.34
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (7 bp):
TTATATA
Found at i:1107654 original size:13 final size:14
Alignment explanation
Indices: 1107619--1107662 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
1107609 TCTTATGTTT
* *
1107619 TATATATTATACTA
1 TATATAATATAATA
1107633 TATATAATATAATA
1 TATATAATATAATA
1107647 TA-ATAATATAATA
1 TATATAATATAATA
1107660 TAT
1 TAT
1107663 TATATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 13 0.48
14 14 0.52
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAATATAATA
Found at i:1115005 original size:46 final size:46
Alignment explanation
Indices: 1114938--1115064 Score: 218
Period size: 46 Copynumber: 2.8 Consensus size: 46
1114928 TGTAACCCGC
* ** *
1114938 CCATAAGTGAACTCGGACTCAACTCAACGAGCTTGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCAT
1114984 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCAT
1115030 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCG
1115065 GATGCCCAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCAT
Found at i:1126746 original size:29 final size:29
Alignment explanation
Indices: 1126714--1126774 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
1126704 TAAATTTATT
1126714 ATTATGTCAAAATTAAAAATTATCACGCC
1 ATTATGTCAAAATTAAAAATTATCACGCC
* *
1126743 ATTATGTCAAATTTAAAAATTATCACGTC
1 ATTATGTCAAAATTAAAAATTATCACGCC
1126772 ATT
1 ATT
1126775 TTTTCATCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.36
Consensus pattern (29 bp):
ATTATGTCAAAATTAAAAATTATCACGCC
Found at i:1134321 original size:2 final size:2
Alignment explanation
Indices: 1134314--1134344 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1134304 AAAATGAAGC
1134314 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1134345 ATCTTTAAGG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1139214 original size:14 final size:14
Alignment explanation
Indices: 1139195--1139233 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1139185 CCAGAAAAGT
1139195 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
1139209 AAATCATTTT-CTG
1 AAATCATTTTCCAG
1139222 AAAGTCATTTTC
1 AAA-TCATTTTC
1139234 AATAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:1145298 original size:44 final size:45
Alignment explanation
Indices: 1145250--1145338 Score: 137
Period size: 44 Copynumber: 2.0 Consensus size: 45
1145240 TAAATTTTAA
*
1145250 GATTCAAAAATTAAATTATTTAAA-TCTTAC-TTTTTAAGAATATG
1 GATTCAAAAATTAAATTACTTAAACT-TTACTTTTTTAAGAATATG
1145294 GATTCAAAAATTAAATTACTTAAACTTTACTTTTTTTAAGAATAT
1 GATTCAAAAATTAAATTACTTAAACTTTAC-TTTTTTAAGAATAT
1145339 AGAGTTAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
44 27 0.66
45 1 0.02
46 13 0.32
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.44
Consensus pattern (45 bp):
GATTCAAAAATTAAATTACTTAAACTTTACTTTTTTAAGAATATG
Found at i:1147764 original size:124 final size:124
Alignment explanation
Indices: 1147548--1148263 Score: 870
Period size: 124 Copynumber: 5.9 Consensus size: 124
1147538 AACACTAAAC
* * *
1147548 ATGAACTATAAAATAGACAT---G-A-AAAAAAATTGAATGAGCTAATTGTATTAATCGAATCTG
1 ATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCGGATCCG
* * *
1147608 ATGTGTAATTACTTTAAAAAGAAAATGTCTTTTAAAAAATTTGACTTGAAACCTTGAAT
66 ATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAATTTGACTTGAAACCTTGAAT
* *
1147667 ATGAACTACAAAATAGACATGAAGAATCAAAAAATTGAATGAGTTAATTGTATTAATCGGATCCG
1 ATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCGGATCCG
* *
1147732 ATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAAGTTGAATTGAAACCTTGAAT
66 ATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAATTTGACTTGAAACCTTGAAT
** * *
1147791 ATGAACTATAAAATAGACATGAAGAATGTAAAAATTGAATGAGTTAATTATATTAATCAGATCCG
1 ATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCGGATCCG
* * * *
1147856 ATATGTAATTACTTGAAAAAGAAAATGCCTTCTACAAGAA-TTGAATTGAAACCTTGAAT
66 ATATGTAATTACTTAAAAAAGAAAATGCCTTTTA-AAAAATTTGACTTGAAACCTTGAAT
* * * * *
1147915 ATAAACTATAAAATAGAC--G-TGAATAAAAAAATTGAATAAGTTAATTGTATTAATGGGATTCG
1 ATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCGGATCCG
* * *
1147977 ATATGTAATTAC-TAAAAAAGAAAATACC-TTTAAAAAAATTGACTTGAAACCTTGAAC
66 ATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAATTTGACTTGAAACCTTGAAT
* * * * *
1148034 ATAAACTATAAAATAGACATAAAGAATAAAAAAAATTAAATGAGTTAATTGTATTAATCAGATCT
1 ATGAACTATAAAATAGACATGAAGAAT-AAAAAAATTGAATGAGTTAATTGTATTAATCGGATCC
* * * *
1148099 GATATGTAATTACTT-AAAAAGAAAATGTCTTTT-AAAAATTTGACTTAAAAAACTTTAA-
65 GATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAATTTGACTT-GAAACCTTGAAT
* * * * * * *
1148157 AAGAACTATAAAATAAATATGAAGAATAAAAAAATTAAATAAGTTAATTATATTAATCGAATCCG
1 ATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCGGATCCG
* * *
1148222 ATATGAAAATT-CCTAAAAAAGAAAATG-CTTTTGGAAAAATTT
66 ATATG-TAATTACTTAAAAAAGAAAATGCCTTTT-AAAAAATTT
1148264 ACTGTATTCA
Statistics
Matches: 520, Mismatches: 59, Indels: 31
0.85 0.10 0.05
Matches are distributed among these distances:
118 4 0.01
119 57 0.11
120 14 0.03
121 47 0.09
122 51 0.10
123 107 0.21
124 236 0.45
125 4 0.01
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.30
Consensus pattern (124 bp):
ATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCGGATCCG
ATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAATTTGACTTGAAACCTTGAAT
Found at i:1155674 original size:41 final size:39
Alignment explanation
Indices: 1155629--1155706 Score: 88
Period size: 41 Copynumber: 1.9 Consensus size: 39
1155619 ATTTTCAAAA
1155629 TTATACATGAAT-TTTA-ATTTAATGTGTAATTTTATATAATT
1 TTATACAT-AATATTTAGATTTAAT-T-TAATTTT-TATAATT
* *
1155670 TTATATATAATATTTAGATTTGATTTAATTTTTATAA
1 TTATACATAATATTTAGATTTAATTTAATTTTTATAA
1155707 ATAACTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
39 5 0.15
40 10 0.30
41 12 0.36
42 6 0.18
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.55
Consensus pattern (39 bp):
TTATACATAATATTTAGATTTAATTTAATTTTTATAATT
Found at i:1157398 original size:16 final size:16
Alignment explanation
Indices: 1157379--1157427 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1157369 TTTAAATTTA
1157379 AAAAAATATAAAAATT
1 AAAAAATATAAAAATT
1157395 AAAAAATA-AATAAATT
1 AAAAAATATAA-AAATT
*
1157411 --AAAGTATAAAAATT
1 AAAAAATATAAAAATT
1157425 AAA
1 AAA
1157428 TTCATAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
14 10 0.36
15 4 0.14
16 14 0.50
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (16 bp):
AAAAAATATAAAAATT
Found at i:1157604 original size:18 final size:19
Alignment explanation
Indices: 1157572--1157607 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1157562 TAAAAAAGAC
*
1157572 AAGAGAAATACAAAAGTTG
1 AAGAGAAATAAAAAAGTTG
1157591 AAGAGAAA-AAAAAAGTT
1 AAGAGAAATAAAAAAGTT
1157608 AAAATATGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.64, C:0.03, G:0.19, T:0.14
Consensus pattern (19 bp):
AAGAGAAATAAAAAAGTTG
Found at i:1161564 original size:6 final size:6
Alignment explanation
Indices: 1161553--1161579 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1161543 AACGGTTATA
1161553 CCAGCT CCAGCT CCAGCT CCAGCT CCA
1 CCAGCT CCAGCT CCAGCT CCAGCT CCA
1161580 TGTTTTAATA
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:0.19, C:0.52, G:0.15, T:0.15
Consensus pattern (6 bp):
CCAGCT
Found at i:1164618 original size:51 final size:51
Alignment explanation
Indices: 1164539--1164793 Score: 350
Period size: 51 Copynumber: 5.0 Consensus size: 51
1164529 GATGCCGAAC
* * * *
1164539 CAGCAAGGCGGAAACATCGAATCTCAAACATACACTCAGCTACCACAACAG
1 CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCTACCACAACAG
* ** *
1164590 CAGCAAGGTGGTAACATCAAATCCCAAACATATACTCAACTACCACAACAG
1 CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCTACCACAACAG
* * * *
1164641 CAGCAAGGTGGAAACGTTGAATACCAAACATATACTCAGCTGCCACAACAA
1 CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCTACCACAACAG
* * *
1164692 CAGCAAGGAGGAAACATTGAATCCCAAACTTATACTCAGCTACAACAACAG
1 CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCTACCACAACAG
*
1164743 GAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCCT-CCACAACAG
1 CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAG-CTACCACAACAG
1164794 TACTTAATGG
Statistics
Matches: 178, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
51 176 0.99
52 2 0.01
ACGTcount: A:0.42, C:0.28, G:0.16, T:0.15
Consensus pattern (51 bp):
CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCTACCACAACAG
Found at i:1172589 original size:2 final size:2
Alignment explanation
Indices: 1172582--1172610 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1172572 AAGAAAGAAA
1172582 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1172611 ATGGTGGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1177086 original size:50 final size:51
Alignment explanation
Indices: 1177009--1177137 Score: 199
Period size: 50 Copynumber: 2.5 Consensus size: 51
1176999 GACCATGGCA
1177009 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGA-AAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAA-TG
*
1177060 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* * *
1177110 ACAAGTGAAAAGTGGTAGCTTCAGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
1177138 TTGATCAGTG
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
50 45 0.62
51 27 0.38
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:1177151 original size:31 final size:31
Alignment explanation
Indices: 1177113--1177261 Score: 228
Period size: 31 Copynumber: 4.8 Consensus size: 31
1177103 ACAAATGACA
* * *
1177113 AGTGAAAAGTGGTAGCTTCAGCTACTTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
*
1177144 AGTGAAAAGTGGTAGCTCCGGCTACCTAATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1177175 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1177206 AGTGAAAAGTGGTAG-TACCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCT-CCGGCTACCTGATC
* *
1177237 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTCCGGCTAC
1177262 AAGTGACAAG
Statistics
Matches: 109, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
30 1 0.01
31 107 0.98
32 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
Found at i:1177353 original size:47 final size:46
Alignment explanation
Indices: 1177284--1177492 Score: 201
Period size: 47 Copynumber: 4.5 Consensus size: 46
1177274 ATTTCCGTAC
* * * *
1177284 AAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACTGTAT
1 AAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATAC-GTGT
* * * * *
1177331 AAGACCATATCTGGGATATGGCATCAGTGAGATATGGGATTCGTGT
1 AAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATACGTGT
* *
1177377 AAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTACGTGT
1 AAGACCATAGCTGGGATATGGCATCG--GTGTGATATGTGA-TACGTGT
* * * * *
1177426 GAGACCATAGCTGGGCTATGGCATC-G-AT-ATATG-AATATGTGT
1 AAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATACGTGT
*
1177468 AAGACCATAGCTGGGCTATGGCATC
1 AAGACCATAGCTGGGATATGGCATC
1177493 ATTGTGTGAA
Statistics
Matches: 139, Mismatches: 20, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
42 30 0.22
43 1 0.01
44 5 0.04
45 1 0.01
46 26 0.19
47 36 0.26
48 10 0.07
49 30 0.22
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (46 bp):
AAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATACGTGT
Found at i:1177473 original size:42 final size:43
Alignment explanation
Indices: 1177373--1177536 Score: 172
Period size: 42 Copynumber: 3.7 Consensus size: 43
1177363 TATGGGATTC
*
1177373 GTGTAAGACCATAGCTGGGCTATGGCATCGATATGTGATATG-TGATT
1 GTGTAAGACCATAGCTGGGCTATGGCATCG--AT-T-ATATGAAGA-T
* *
1177420 ACGTGTGAGACCATAGCTGGGCTATGGCATCGA-TATATGAATAT
1 --GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
* *
1177464 GTGTAAGACCATAGCTGGGCTATGGCATC-ATTGTGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
* **
1177506 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGCTGGGCTATGGCATCGA
1177537 GAAAACGAAG
Statistics
Matches: 102, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
41 1 0.01
42 62 0.61
43 1 0.01
44 6 0.06
45 2 0.02
47 1 0.01
49 29 0.28
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.29
Consensus pattern (43 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
Found at i:1180110 original size:5 final size:5
Alignment explanation
Indices: 1180100--1180189 Score: 71
Period size: 5 Copynumber: 17.8 Consensus size: 5
1180090 AATTTCTCCT
1180100 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTCTT- TCTTTC -TTTC TATTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC T-TTTC TTTTC T-TTTC
* ** *
1180151 GTTTC TTCCC TGTTTC TTTTTC TTGT- TTTTC -TTTC TTTT
1 TTTTC TTTTC T-TTTC -TTTTC TTTTC TTTTC TTTTC TTTT
1180190 ATTTATTCTT
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
4 11 0.16
5 43 0.63
6 13 0.19
7 1 0.01
ACGTcount: A:0.01, C:0.21, G:0.03, T:0.74
Consensus pattern (5 bp):
TTTTC
Found at i:1180158 original size:26 final size:27
Alignment explanation
Indices: 1180106--1180189 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 27
1180096 TCCTTTTTCT
*
1180106 TTTCTTTTCTTTTCTTTTCTTTTCTTC
1 TTTCTTTTCTTTTCTTTTCGTTTCTTC
1180133 TTTC-TTTC-TTTCTATTTCGTTTCTTC
1 TTTCTTTTCTTTTCT-TTTCGTTTCTTC
* *
1180159 --CCTGTTTCTTTT-TCTT-GTTT-TTC
1 TTTCT-TTTCTTTTCTTTTCGTTTCTTC
1180182 TTTCTTTT
1 TTTCTTTT
1180190 ATTTATTCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
23 3 0.06
24 8 0.17
25 9 0.19
26 20 0.43
27 7 0.15
ACGTcount: A:0.01, C:0.21, G:0.04, T:0.74
Consensus pattern (27 bp):
TTTCTTTTCTTTTCTTTTCGTTTCTTC
Found at i:1180359 original size:3 final size:3
Alignment explanation
Indices: 1180353--1180377 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1180343 TTAATTGATG
1180353 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1180378 GTAAATATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1181194 original size:31 final size:31
Alignment explanation
Indices: 1181159--1181226 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
1181149 TAATTTGACC
1181159 ATTCTTTTAGTAGAGAGTAAAATACAATCTT
1 ATTCTTTTAGTAGAGAGTAAAATACAATCTT
1181190 ATTCTTTTAGTAGAGAGTAAAATACAATCTT
1 ATTCTTTTAGTAGAGAGTAAAATACAATCTT
1181221 ACTTCT
1 A-TTCT
1181227 AATATAAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 32 0.89
32 4 0.11
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (31 bp):
ATTCTTTTAGTAGAGAGTAAAATACAATCTT
Found at i:1184558 original size:19 final size:20
Alignment explanation
Indices: 1184534--1184572 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
1184524 TCCCATTATT
1184534 TATTTATTTTT-TGTTTTAA
1 TATTTATTTTTATGTTTTAA
1184553 TATTTATTTTTATGTTTTAA
1 TATTTATTTTTATGTTTTAA
1184573 ATGTATTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (20 bp):
TATTTATTTTTATGTTTTAA
Found at i:1184590 original size:25 final size:23
Alignment explanation
Indices: 1184534--1184598 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 23
1184524 TCCCATTATT
*
1184534 TATTTATTTTT-TGTTTT-AA--
1 TATTTATTTTTATATTTTAAATG
*
1184553 TATTTATTTTTATGTTTTAAATG
1 TATTTATTTTTATATTTTAAATG
1184576 TATTTGATTTATTATATTTTAAA
1 TATTT-ATTT-TTATATTTTAAA
1184599 GTTTTTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 11 0.28
20 6 0.15
21 2 0.05
23 5 0.13
24 4 0.10
25 11 0.28
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (23 bp):
TATTTATTTTTATATTTTAAATG
Found at i:1198646 original size:20 final size:21
Alignment explanation
Indices: 1198617--1198655 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1198607 ACTAAAGATA
1198617 TTTAAAAAATTTAC-TATTAT
1 TTTAAAAAATTTACATATTAT
*
1198637 TTTAATAAATTTACATATT
1 TTTAAAAAATTTACATATT
1198656 TAAATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAAAAAATTTACATATTAT
Found at i:1200153 original size:33 final size:33
Alignment explanation
Indices: 1200115--1200216 Score: 145
Period size: 33 Copynumber: 3.2 Consensus size: 33
1200105 AGATTAATTT
* *
1200115 ATATTTTATGTATCATTATATTAAATTATTTAA
1 ATATTTCATGTATCATTCTATTAAATTATTTAA
1200148 ATATTTCATGTATCATTCTATTAAATTATTTAA
1 ATATTTCATGTATCATTCTATTAAATTATTTAA
* * *
1200181 ATA--TCATTTACCATTCCATTAAATTATTTAA
1 ATATTTCATGTATCATTCTATTAAATTATTTAA
1200212 ATATT
1 ATATT
1200217 ATATAACTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
31 28 0.45
33 34 0.55
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (33 bp):
ATATTTCATGTATCATTCTATTAAATTATTTAA
Found at i:1200202 original size:31 final size:31
Alignment explanation
Indices: 1200134--1200215 Score: 119
Period size: 31 Copynumber: 2.6 Consensus size: 31
1200124 GTATCATTAT
* *
1200134 ATTAAATTATTTAAATATTTCATGTATCATTCT
1 ATTAAATTATTTAAATA--TCATGTACCATTCC
*
1200167 ATTAAATTATTTAAATATCATTTACCATTCC
1 ATTAAATTATTTAAATATCATGTACCATTCC
1200198 ATTAAATTATTTAAATAT
1 ATTAAATTATTTAAATAT
1200216 TATATAACTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 29 0.63
33 17 0.37
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.49
Consensus pattern (31 bp):
ATTAAATTATTTAAATATCATGTACCATTCC
Found at i:1209703 original size:50 final size:50
Alignment explanation
Indices: 1209628--1209804 Score: 248
Period size: 50 Copynumber: 3.5 Consensus size: 50
1209618 CCATGGAAAC
1209628 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * * *
1209678 AAGTGATAAGTAATAACTTCGGCTACACTTATCTGATTAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
1209728 AAGTGATAAGTGATAGCTTCGGTTACACTTATCTGATCAATGG-CAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAA-GGACAAATGA
* * * *
1209778 CAACTGAAAAGTGGTAGCTTCAGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
1209805 CTGATCAGTG
Statistics
Matches: 111, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
50 88 0.79
51 23 0.21
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:1209990 original size:31 final size:31
Alignment explanation
Indices: 1209782--1209983 Score: 314
Period size: 31 Copynumber: 6.5 Consensus size: 31
1209772 AAATGACAAC
1209782 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
1209813 TGAAAAGTGGTAGTTTCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* *
1209844 TGAAAAGTGGTAGCTTCTGCTACCTAATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
1209875 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* *
1209906 TGAAAAGTGGTAGCTCCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* **
1209937 TGAAAAATGGTAGCACCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
1209968 TGAATAGTGGTAGCTT
1 TGAAAAGTGGTAGCTT
1209984 TGGCTACAAG
Statistics
Matches: 157, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 157 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (31 bp):
TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
Found at i:1210001 original size:7 final size:7
Alignment explanation
Indices: 1209989--1210017 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1209979 AGCTTTGGCT
1209989 ACAAGTG
1 ACAAGTG
1209996 ACAAGTG
1 ACAAGTG
1210003 ACAAGTG
1 ACAAGTG
1210010 ACAAGTG
1 ACAAGTG
1210017 A
1 A
1210018 TTTCTGTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.28, T:0.14
Consensus pattern (7 bp):
ACAAGTG
Found at i:1213208 original size:32 final size:29
Alignment explanation
Indices: 1213149--1213210 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 29
1213139 TTCCAATTAC
*
1213149 TTAATTATTTTTTTCTTTAAAAGAATAAA
1 TTAATTATTTTTTTCTTTAAAAAAATAAA
1213178 TTAATT-TTTATTTTACTTTATAAATAAATAAA
1 TTAATTATTT-TTTT-CTTTA-AAA-AAATAAA
1213210 T
1 T
1213211 CTAAAAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 3 0.11
29 10 0.36
30 5 0.18
31 3 0.11
32 7 0.25
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (29 bp):
TTAATTATTTTTTTCTTTAAAAAAATAAA
Found at i:1214180 original size:48 final size:48
Alignment explanation
Indices: 1214109--1214206 Score: 160
Period size: 48 Copynumber: 2.0 Consensus size: 48
1214099 AGGCCTTTAC
**
1214109 CTTCAAACTCTATTCACTTTCATTCTCCATAACCCCCTGCTCTTTGTT
1 CTTCAAACTCTATTCACTTTCATTCTCCATAACCCCCAACTCTTTGTT
* *
1214157 CTTCAAACTCTCTTCACTTTCATTCTCCATAGCCCCCAACTCTTTGTT
1 CTTCAAACTCTATTCACTTTCATTCTCCATAACCCCCAACTCTTTGTT
1214205 CT
1 CT
1214207 AGCTGGGTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.18, C:0.37, G:0.04, T:0.41
Consensus pattern (48 bp):
CTTCAAACTCTATTCACTTTCATTCTCCATAACCCCCAACTCTTTGTT
Found at i:1214182 original size:24 final size:24
Alignment explanation
Indices: 1214109--1214182 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
1214099 AGGCCTTTAC
*
1214109 CTTCAAACTCTATTCACTTTCATT
1 CTTCAAACTCTCTTCACTTTCATT
* * * * * *
1214133 CTCCATAACCCCCTGCTCTTT-GTT
1 CTTCA-AACTCTCTTCACTTTCATT
1214157 CTTCAAACTCTCTTCACTTTCATT
1 CTTCAAACTCTCTTCACTTTCATT
1214181 CT
1 CT
1214183 CCATAGCCCC
Statistics
Matches: 35, Mismatches: 13, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
23 11 0.31
24 14 0.40
25 10 0.29
ACGTcount: A:0.19, C:0.35, G:0.03, T:0.43
Consensus pattern (24 bp):
CTTCAAACTCTCTTCACTTTCATT
Found at i:1226361 original size:22 final size:23
Alignment explanation
Indices: 1226331--1226374 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1226321 TTTTTACTTC
1226331 TTTAAACTTATATCCTG-ATTTT
1 TTTAAACTTATATCCTGTATTTT
*
1226353 TTTATACTTATATCCTGTATTT
1 TTTAAACTTATATCCTGTATTT
1226375 ATTACCATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.25, C:0.14, G:0.05, T:0.57
Consensus pattern (23 bp):
TTTAAACTTATATCCTGTATTTT
Found at i:1234785 original size:17 final size:18
Alignment explanation
Indices: 1234763--1234796 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1234753 TAAAAGGAAT
*
1234763 AATTATGAATT-TAAAAA
1 AATTATAAATTATAAAAA
1234780 AATTATAAATTATAAAA
1 AATTATAAATTATAAAA
1234797 CGAATCTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
AATTATAAATTATAAAAA
Found at i:1250019 original size:22 final size:20
Alignment explanation
Indices: 1249993--1250051 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 20
1249983 AGTTTATACA
*
1249993 TAATTTATATATTACAAATTT
1 TAATTTATATATTA-AAATCT
*
1250014 TCAATTTAAAATATTAAAATCT
1 T-AATTT-ATATATTAAAATCT
1250036 TAATTT-TATAGTTAAA
1 TAATTTATATA-TTAAA
1250052 TTATAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 3 0.09
20 5 0.16
21 6 0.19
22 11 0.34
23 7 0.22
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (20 bp):
TAATTTATATATTAAAATCT
Found at i:1251128 original size:11 final size:11
Alignment explanation
Indices: 1251112--1251136 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1251102 CGGGGAACAG
1251112 TTTTTTATTTT
1 TTTTTTATTTT
1251123 TTTTTTATTTT
1 TTTTTTATTTT
1251134 TTT
1 TTT
1251137 GAGGAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:1253487 original size:24 final size:25
Alignment explanation
Indices: 1253437--1253490 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
1253427 ATTATATACA
* *
1253437 AATAAATTTAACAAAAATAAAACAC
1 AATAAATTCAACAAAAAGAAAACAC
*
1253462 AATAAATTCAAC-ATAAGAAAACAC
1 AATAAATTCAACAAAAAGAAAACAC
1253486 AATAA
1 AATAA
1253491 CCAATCAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.67, C:0.13, G:0.02, T:0.19
Consensus pattern (25 bp):
AATAAATTCAACAAAAAGAAAACAC
Found at i:1254960 original size:39 final size:38
Alignment explanation
Indices: 1254917--1255005 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 38
1254907 ATATTTAATC
* * * *
1254917 AATAATTAAAATCTATT-AAAA-TTATTTATATTAGATTA
1 AATAATTAAAA--AATTAAAAATTTATTTATACTAAAATA
1254955 TAATAATTAAAAAATTAAAAATTTATTTATACTAAAATA
1 -AATAATTAAAAAATTAAAAATTTATTTATACTAAAATA
1254994 AATAATTAAAAA
1 AATAATTAAAAA
1255006 TATAAATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
37 3 0.07
38 16 0.36
39 25 0.57
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (38 bp):
AATAATTAAAAAATTAAAAATTTATTTATACTAAAATA
Found at i:1255010 original size:16 final size:18
Alignment explanation
Indices: 1254991--1255023 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1254981 TTATACTAAA
1254991 ATAAATA-AT-TAAAAAT
1 ATAAATATATATAAAAAT
1255007 ATAAATATATATAAAAA
1 ATAAATATATATAAAAA
1255024 AAAGCTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
ATAAATATATATAAAAAT
Found at i:1256440 original size:3 final size:3
Alignment explanation
Indices: 1256432--1256459 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1256422 TTATATTGAT
1256432 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1256460 GTAGTTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:1260234 original size:16 final size:16
Alignment explanation
Indices: 1260215--1260251 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1260205 TGGAAAGATG
1260215 GAAAACT-GAAGGGATA
1 GAAAACTAGAA-GGATA
1260231 GAAAACTAGAAGGATA
1 GAAAACTAGAAGGATA
1260247 GAAAA
1 GAAAA
1260252 TATAACTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.57, C:0.05, G:0.27, T:0.11
Consensus pattern (16 bp):
GAAAACTAGAAGGATA
Found at i:1264602 original size:75 final size:75
Alignment explanation
Indices: 1264481--1264621 Score: 196
Period size: 75 Copynumber: 1.9 Consensus size: 75
1264471 CCAGGCTATG
* *
1264481 CTCCTCCAAGGCCAAGTCCTCAAGCGCCACCACCAGGACCTCGTCATCCTCC-GAGTCCACCACA
1 CTCCTCCAAGGCCAAGTCCTCAAGCGCCACCACCAAGACCACGTCATCCTCCAG-GTCCACCACA
1264545 TGCTGAGCATC
65 TGCTGAGCATC
* * * *
1264556 CTCCTCCAAGGCCAAGT-CTCTATGTGCCACCACCAAGACCAGGTCATCCTCCAGGTCCACTACA
1 CTCCTCCAAGGCCAAGTCCTC-AAGCGCCACCACCAAGACCACGTCATCCTCCAGGTCCACCACA
1264620 TG
65 TG
1264622 AGCATCCTCC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
74 3 0.05
75 54 0.93
76 1 0.02
ACGTcount: A:0.23, C:0.42, G:0.17, T:0.18
Consensus pattern (75 bp):
CTCCTCCAAGGCCAAGTCCTCAAGCGCCACCACCAAGACCACGTCATCCTCCAGGTCCACCACAT
GCTGAGCATC
Found at i:1264642 original size:99 final size:99
Alignment explanation
Indices: 1264525--1264719 Score: 275
Period size: 99 Copynumber: 2.0 Consensus size: 99
1264515 AGGACCTCGT
* * * *
1264525 CATCCTCCGAGTCCACCACATGCTGAGCATCCTCCTCCAAGGCCA-AGTCTCTATGTGCCACCAC
1 CATCCTCCAAGTCCACCACATGCTGAGCATCCTCCTCCAAGGCCAGA-TCCCCATGCGCCACCAC
* *
1264589 CAAGACCAGGTCATCCTCCAGGTCCACTACATGAG
65 CAAGACCAGGTCATCCTCCAAGTCCACCACATGAG
* ***
1264624 CATCCTCCAAGTCCACCACATGTTGAGCATCCTCCTCCAAGGCCAGATCCCCATGCGCCACCGTT
1 CATCCTCCAAGTCCACCACATGCTGAGCATCCTCCTCCAAGGCCAGATCCCCATGCGCCACCACC
*
1264689 AGGACCAGGTCATCCTCCAAGTCCACCACAT
66 AAGACCAGGTCATCCTCCAAGTCCACCACAT
1264720 AATAATCATC
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 83 0.99
100 1 0.01
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.19
Consensus pattern (99 bp):
CATCCTCCAAGTCCACCACATGCTGAGCATCCTCCTCCAAGGCCAGATCCCCATGCGCCACCACC
AAGACCAGGTCATCCTCCAAGTCCACCACATGAG
Found at i:1264658 original size:27 final size:24
Alignment explanation
Indices: 1264600--1264645 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1264590 AAGACCAGGT
* *
1264600 CATCCTCCAGGTCCACTACATGAG
1 CATCCTCCAAGTCCACCACATGAG
1264624 CATCCTCCAAGTCCACCACATG
1 CATCCTCCAAGTCCACCACATG
1264646 TTGAGCATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.41, G:0.13, T:0.20
Consensus pattern (24 bp):
CATCCTCCAAGTCCACCACATGAG
Found at i:1264777 original size:93 final size:93
Alignment explanation
Indices: 1264653--1264983 Score: 319
Period size: 93 Copynumber: 3.6 Consensus size: 93
1264643 ATGTTGAGCA
* * ***
1264653 TCCTCCTCCAAGGCCAGATCCCCATGCGCCACCGTTAGGACCAGGTCATCCTCCAAGTCCACCAC
1 TCCTCCTCCAAGGCCAGGTCCCCATGTGCCACCACCAGGACCAGGTCATCCTCCAAGTCCACCAC
*
1264718 ATAATAATCATCTTCATCCAGACCATGC
66 ATAATAATCATCTTCATCCAGGCCATGC
* * * * * *
1264746 TCCTCCTCCAGGGCCAGGTCCCCATGTGCCACCACCAAGACCTGGACATCCTCCAAGTGCATCAC
1 TCCTCCTCCAAGGCCAGGTCCCCATGTGCCACCACCAGGACCAGGTCATCCTCCAAGTCCACCAC
**
1264811 ATGCTGAA-CAT-TCTCATCCAGGCCATGC
66 ATAAT-AATCATCT-TCATCCAGGCCATGC
* * * *
1264839 TCCTCCTCC-AGGACCAAGTCCCCATGCT-CCACCACCAGAACCAGGTCATCTTCCAAGTCAACC
1 TCCTCCTCCAAGG-CCAGGTCCCCATG-TGCCACCACCAGGACCAGGTCATCCTCCAAGTCCACC
** ** * * *
1264902 ACATCTTGGTCATCCTCATCCAGGCCACGG
64 ACATAATAATCATCTTCATCCAGGCCATGC
* ** * * *
1264932 TCCCCCTCCAAGGCCAGGTCCCCATGCACCACTACCAGGTCTAGGTCATCCT
1 TCCTCCTCCAAGGCCAGGTCCCCATGTGCCACCACCAGGACCAGGTCATCCT
1264984 TCTGAGCCAC
Statistics
Matches: 191, Mismatches: 39, Indels: 16
0.78 0.16 0.07
Matches are distributed among these distances:
92 3 0.02
93 182 0.95
94 6 0.03
ACGTcount: A:0.23, C:0.41, G:0.16, T:0.20
Consensus pattern (93 bp):
TCCTCCTCCAAGGCCAGGTCCCCATGTGCCACCACCAGGACCAGGTCATCCTCCAAGTCCACCAC
ATAATAATCATCTTCATCCAGGCCATGC
Found at i:1276235 original size:17 final size:19
Alignment explanation
Indices: 1276210--1276250 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
1276200 GCTAATAATT
*
1276210 TATTGTAATATT-ATA-TA
1 TATTTTAATATTAATAGTA
*
1276227 TATTTTAATTTTAATAGTA
1 TATTTTAATATTAATAGTA
1276246 TATTT
1 TATTT
1276251 AATTTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 10 0.50
18 3 0.15
19 7 0.35
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTTTAATATTAATAGTA
Found at i:1277390 original size:20 final size:21
Alignment explanation
Indices: 1277365--1277403 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1277355 TTGGTTTGAT
1277365 TTTTTTTATCT-AAATATAGA
1 TTTTTTTATCTGAAATATAGA
*
1277385 TTTTTTTATTTGAAATATA
1 TTTTTTTATCTGAAATATA
1277404 TTAATAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTTTTTATCTGAAATATAGA
Found at i:1282092 original size:58 final size:58
Alignment explanation
Indices: 1281989--1282101 Score: 136
Period size: 58 Copynumber: 1.9 Consensus size: 58
1281979 CAATTTGTTC
* * *
1281989 AAGCCTTAATATAGGTACAACTGCCAAATTCAAATATTAACTTGGAAAAAAAAAAGTT
1 AAGCCCTAATATAGGTACAACTGCCAAATTCAAAGACTAACTTGGAAAAAAAAAAGTT
* * * * * * *
1282047 AAGCCCTACTATAGGTACAATTGTCAAGTTCAGAGACTAATTTGGACAAAAAAAA
1 AAGCCCTAATATAGGTACAACTGCCAAATTCAAAGACTAACTTGGAAAAAAAAAA
1282102 TTCAAACCTT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
58 45 1.00
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (58 bp):
AAGCCCTAATATAGGTACAACTGCCAAATTCAAAGACTAACTTGGAAAAAAAAAAGTT
Found at i:1282427 original size:5 final size:5
Alignment explanation
Indices: 1282417--1282441 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1282407 AGTGAGAATT
1282417 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
1282442 AAAGAATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:1285311 original size:16 final size:18
Alignment explanation
Indices: 1285290--1285322 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1285280 TTATTTTAAA
1285290 TTTTTTC-AA-ATTTTTG
1 TTTTTTCTAATATTTTTG
1285306 TTTTTTCTAATATTTTT
1 TTTTTTCTAATATTTTT
1285323 TTTAGAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (18 bp):
TTTTTTCTAATATTTTTG
Found at i:1291358 original size:5 final size:5
Alignment explanation
Indices: 1291348--1291384 Score: 65
Period size: 5 Copynumber: 7.2 Consensus size: 5
1291338 ATGCGACAGC
1291348 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT CATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT -ATTTT A
1291385 AGTTCGGACA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:1297013 original size:24 final size:24
Alignment explanation
Indices: 1296965--1297014 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1296955 TTTAAATTAA
* *
1296965 TAAAAATAAATTTATATTTTGATT
1 TAAAAATAAATTTAGATTTTAATT
1296989 TAAAAATAAAATTTAGA-TTTAATT
1 TAAAAAT-AAATTTAGATTTTAATT
1297013 TA
1 TA
1297015 TTAAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
TAAAAATAAATTTAGATTTTAATT
Found at i:1306546 original size:10 final size:10
Alignment explanation
Indices: 1306533--1306588 Score: 64
Period size: 10 Copynumber: 5.8 Consensus size: 10
1306523 TTTTGATACA
1306533 TTTTATAAAT
1 TTTTATAAAT
1306543 TTTTACT--AT
1 TTTTA-TAAAT
*
1306552 TTTTATAAAA
1 TTTTATAAAT
*
1306562 TTTTA-CAAT
1 TTTTATAAAT
1306571 TTTTATAAAT
1 TTTTATAAAT
1306581 TTTTATAA
1 TTTTATAA
1306589 TTCTTAATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 1 0.03
9 14 0.37
10 22 0.58
11 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTTATAAAT
Found at i:1306555 original size:19 final size:19
Alignment explanation
Indices: 1306533--1306590 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 19
1306523 TTTTGATACA
*
1306533 TTTTATAAATTTTTACTAT
1 TTTTATAAATTTTTACAAT
*
1306552 TTTTATAAAATTTTACAAT
1 TTTTATAAATTTTTACAAT
*
1306571 TTTTATAAATTTTTATAAT
1 TTTTATAAATTTTTACAAT
1306590 T
1 T
1306591 CTTAATACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTATAAATTTTTACAAT
Found at i:1306564 original size:29 final size:28
Alignment explanation
Indices: 1306532--1306588 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
1306522 TTTTTGATAC
1306532 ATTTTATAAATTTTTACT-ATTTTTATAAA
1 ATTTTA-AAATTTTTA-TAATTTTTATAAA
*
1306561 ATTTTACAATTTTTATAAATTTTTATAA
1 ATTTTAAAATTTTTAT-AATTTTTATAA
1306589 TTCTTAATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 1 0.04
28 8 0.32
29 16 0.64
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (28 bp):
ATTTTAAAATTTTTATAATTTTTATAAA
Found at i:1315321 original size:15 final size:15
Alignment explanation
Indices: 1315296--1315339 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1315286 TAATTTTCTC
1315296 TAATTTAATTTAAATT
1 TAATTT-ATTTAAATT
* *
1315312 TAGTTTATTTAGATT
1 TAATTTATTTAAATT
*
1315327 TAATTTACTTAAA
1 TAATTTATTTAAA
1315340 ATACTTAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (15 bp):
TAATTTATTTAAATT
Found at i:1315587 original size:26 final size:22
Alignment explanation
Indices: 1315557--1315611 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 22
1315547 ATTGTGTAAA
*
1315557 TTTTAAAGTTTATATGTTATTTGATT
1 TTTTAAA-TTT-TAT-TTACTT-ATT
1315583 TTTTAAATTTTATTTACTTATT
1 TTTTAAATTTTATTTACTTATT
1315605 TTTTAAA
1 TTTTAAA
1315612 AAAAATAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 10 0.36
23 5 0.18
24 3 0.11
25 3 0.11
26 7 0.25
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (22 bp):
TTTTAAATTTTATTTACTTATT
Found at i:1324279 original size:30 final size:30
Alignment explanation
Indices: 1324205--1324281 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 30
1324195 ATTCAATTCG
* *
1324205 ATTCGAATTTTGAGTTAATCGAAACAAATT
1 ATTCGAATTTTGAGTCAATCGAAACAAATA
* *
1324235 ATTCGATTATTTTGAGTCAACTTG-AATAAATA
1 ATTCGA--ATTTTGAGTCAA-TCGAAACAAATA
1324267 ATTCGAATTTTGAGT
1 ATTCGAATTTTGAGT
1324282 TTCAGTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 15 0.38
32 23 0.57
33 2 0.05
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.40
Consensus pattern (30 bp):
ATTCGAATTTTGAGTCAATCGAAACAAATA
Found at i:1324431 original size:18 final size:17
Alignment explanation
Indices: 1324410--1324444 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1324400 AAAGCATTTT
1324410 AAATTCAAAATATTTATA
1 AAATTCAAAAT-TTTATA
*
1324428 AAATTCTAAATTTTATA
1 AAATTCAAAATTTTATA
1324445 TTTTTTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATTCAAAATTTTATA
Found at i:1327810 original size:21 final size:22
Alignment explanation
Indices: 1327784--1327830 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
1327774 CTCTGCTCAA
*
1327784 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
1327805 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
1327827 ACTC
1 ACTC
1327831 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:1331649 original size:22 final size:23
Alignment explanation
Indices: 1331619--1331662 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1331609 ATAGATACGC
*
1331619 GAATTTCC-ACCCAAACACACCA
1 GAATATCCAACCCAAACACACCA
1331641 GAATATCCAACCCAAACACACC
1 GAATATCCAACCCAAACACACC
1331663 CGGAATATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.43, C:0.41, G:0.05, T:0.11
Consensus pattern (23 bp):
GAATATCCAACCCAAACACACCA
Found at i:1332810 original size:18 final size:17
Alignment explanation
Indices: 1332775--1332807 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1332765 CTTTTTATTC
1332775 TTTTATTATTTCATTTA
1 TTTTATTATTTCATTTA
1332792 TTTTACTTATTT-ATTT
1 TTTTA-TTATTTCATTT
1332808 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:1334419 original size:30 final size:30
Alignment explanation
Indices: 1334385--1334442 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1334375 TCCGAGCCTT
*
1334385 GGGGTAAAAATGTAATTATGTAAAAGTTTA
1 GGGGTAAAAATGTAATTATGAAAAAGTTTA
* *
1334415 GGGGTAAAATTGTAATTTTGAAAAAGTT
1 GGGGTAAAAATGTAATTATGAAAAAGTT
1334443 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.34
Consensus pattern (30 bp):
GGGGTAAAAATGTAATTATGAAAAAGTTTA
Found at i:1334672 original size:13 final size:13
Alignment explanation
Indices: 1334654--1334685 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1334644 TTTCCAGCAA
1334654 TTATGAATTTATT
1 TTATGAATTTATT
1334667 TTATGAATTTATT
1 TTATGAATTTATT
*
1334680 TGATGA
1 TTATGA
1334686 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:1334893 original size:50 final size:50
Alignment explanation
Indices: 1334780--1335021 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
1334770 ATTTGGGTAA
* * *
1334780 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
1334836 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
1334886 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
1334936 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
1334986 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
1335022 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:1334969 original size:100 final size:103
Alignment explanation
Indices: 1334780--1335029 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
1334770 ATTTGGGTAA
1334780 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
1334845 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
1334886 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
1334948 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
1334986 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
1335030 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:1336569 original size:14 final size:13
Alignment explanation
Indices: 1336545--1336578 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1336535 ACCGTTTTAC
1336545 TATTATGTTGTTAT
1 TATT-TGTTGTTAT
1336559 TAGTTTGTTGTTAT
1 TA-TTTGTTGTTAT
1336573 TATTTG
1 TATTTG
1336579 GATATTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.21
14 13 0.68
15 2 0.11
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.65
Consensus pattern (13 bp):
TATTTGTTGTTAT
Found at i:1336738 original size:18 final size:20
Alignment explanation
Indices: 1336717--1336757 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
1336707 GAAATATTTA
*
1336717 TTTTGATGT-TTTTA-GTAT
1 TTTTGATGTATTATATGTAT
1336735 TTTTGATGTATTATATGTAT
1 TTTTGATGTATTATATGTAT
1336755 TTT
1 TTT
1336758 AAAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 4 0.20
20 7 0.35
ACGTcount: A:0.20, C:0.00, G:0.15, T:0.66
Consensus pattern (20 bp):
TTTTGATGTATTATATGTAT
Found at i:1336975 original size:23 final size:24
Alignment explanation
Indices: 1336932--1336976 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
1336922 AACAATAATT
1336932 TTTTGATAATTATTTTCTTTTTTC
1 TTTTGATAATTATTTTCTTTTTTC
*
1336956 TTTTG-TAA-TATTTTATTTTTT
1 TTTTGATAATTATTTTCTTTTTT
1336977 GTCGTGATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 3 0.15
24 5 0.25
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (24 bp):
TTTTGATAATTATTTTCTTTTTTC
Found at i:1356290 original size:18 final size:18
Alignment explanation
Indices: 1356259--1356339 Score: 72
Period size: 18 Copynumber: 4.5 Consensus size: 18
1356249 ATGGTGGGAG
* *
1356259 TGACGAAGAAGATGACGA
1 TGACGAAGATGATGATGA
* *
1356277 TGACGATGATGATGATGG
1 TGACGAAGATGATGATGA
*
1356295 GGACGAAGATGATGATGA
1 TGACGAAGATGATGATGA
* * * *
1356313 CGACGATGATGGTGAGGA
1 TGACGAAGATGATGATGA
*
1356331 TGAAGAAGA
1 TGACGAAGA
1356340 GGAGGACGAA
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.37, C:0.07, G:0.38, T:0.17
Consensus pattern (18 bp):
TGACGAAGATGATGATGA
Found at i:1356293 original size:15 final size:15
Alignment explanation
Indices: 1356269--1356333 Score: 58
Period size: 15 Copynumber: 4.1 Consensus size: 15
1356259 TGACGAAGAA
*
1356269 GATGACGATGACGAT
1 GATGATGATGACGAT
*
1356284 GATGATGATGGGGACGAA
1 GATGATGAT---GACGAT
*
1356302 GATGATGATGACGAC
1 GATGATGATGACGAT
* *
1356317 GATGATGGTGAGGAT
1 GATGATGATGACGAT
1356332 GA
1 GA
1356334 AGAAGAGGAG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
15 27 0.66
18 14 0.34
ACGTcount: A:0.32, C:0.08, G:0.40, T:0.20
Consensus pattern (15 bp):
GATGATGATGACGAT
Found at i:1356350 original size:15 final size:15
Alignment explanation
Indices: 1356326--1356360 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1356316 CGATGATGGT
*
1356326 GAGGATGAAGAAGAG
1 GAGGACGAAGAAGAG
*
1356341 GAGGACGAAGAAGAT
1 GAGGACGAAGAAGAG
1356356 GAGGA
1 GAGGA
1356361 TGATGAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.46, T:0.06
Consensus pattern (15 bp):
GAGGACGAAGAAGAG
Found at i:1367218 original size:18 final size:19
Alignment explanation
Indices: 1367195--1367232 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1367185 AAACTTGAAT
*
1367195 TTTGAAAACAAAA-TATAA
1 TTTGAAAAAAAAATTATAA
1367213 TTTGAAAAAAAAATTATAA
1 TTTGAAAAAAAAATTATAA
1367232 T
1 T
1367233 GAAAAAGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (19 bp):
TTTGAAAAAAAAATTATAA
Found at i:1367235 original size:17 final size:17
Alignment explanation
Indices: 1367196--1367238 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1367186 AACTTGAATT
*
1367196 TTGAAAACAAAATATAA
1 TTGAAAAAAAAATATAA
1367213 TTTGAAAAAAAAATTATAA
1 -TTGAAAAAAAAA-TATAA
1367232 -TGAAAAA
1 TTGAAAAA
1367239 GCTATATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 7 0.30
18 11 0.48
19 5 0.22
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (17 bp):
TTGAAAAAAAAATATAA
Found at i:1382708 original size:23 final size:22
Alignment explanation
Indices: 1382682--1382724 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1382672 ATTTTGATTA
1382682 TTAAATTATTTAAATTTTTTTAT
1 TTAAATTA-TTAAATTTTTTTAT
* *
1382705 TTAAGTTATTAGATTTTTTT
1 TTAAATTATTAAATTTTTTT
1382725 TAAATTTGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (22 bp):
TTAAATTATTAAATTTTTTTAT
Found at i:1389043 original size:22 final size:21
Alignment explanation
Indices: 1388994--1389044 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
1388984 TTTGAAATTC
1388994 ATTTTAAATATATATCATTAT
1 ATTTTAAATATATATCATTAT
* **
1389015 ATGTTTAAATTTATAATTGTTAT
1 AT-TTTAAATATAT-ATCATTAT
1389038 ATTTTAA
1 ATTTTAA
1389045 TGATATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 15 0.60
23 8 0.32
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (21 bp):
ATTTTAAATATATATCATTAT
Found at i:1389061 original size:31 final size:32
Alignment explanation
Indices: 1389026--1389093 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
1389016 TGTTTAAATT
1389026 TATAATTGTTATAT-TTTAATGAT-A-TTTAAAA
1 TATAATT-TTATATATTTAAT-ATAATTTTAAAA
1389057 TATAA-TTTATATATTTAATATAATTTTAAAA
1 TATAATTTTATATATTTAATATAATTTTAAAA
1389088 -ATAATT
1 TATAATT
1389094 AATATTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
29 8 0.24
30 12 0.36
31 13 0.39
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (32 bp):
TATAATTTTATATATTTAATATAATTTTAAAA
Found at i:1389092 original size:30 final size:29
Alignment explanation
Indices: 1389034--1389101 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
1389024 TTTATAATTG
1389034 TTATAT-TTTAATGATATTTAAAATATAA
1 TTATATATTTAATGATATTTAAAATATAA
1389062 TTTATATATTTAAT-ATAATTTTAAAA-ATAA
1 -TTATATATTTAATGAT-A-TTTAAAATATAA
1389092 TTA-ATATTTA
1 TTATATATTTA
1389102 TATCCATCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
28 7 0.19
29 11 0.31
30 11 0.31
31 7 0.19
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
TTATATATTTAATGATATTTAAAATATAA
Found at i:1403365 original size:61 final size:61
Alignment explanation
Indices: 1403283--1403412 Score: 147
Period size: 61 Copynumber: 2.1 Consensus size: 61
1403273 ACATATTCTA
* * * *
1403283 TCAATTT-GATCCAAATATAAAAAA-ATCAACAAATTTAGCCCTTAATATTTACAGAATTTG
1 TCAATTTAGATCCAAATATAAAAAATA-AAAAAAAATTAGCCCTTAATATTTACAAAATTTG
* * * * * *
1403343 TCATTTTAGATCCAATTCTAAAAAATAAAAAAAAATTGGCTCTTGATATTTACAAAATTTG
1 TCAATTTAGATCCAAATATAAAAAATAAAAAAAAATTAGCCCTTAATATTTACAAAATTTG
1403404 TCAATTTAG
1 TCAATTTAG
1403413 TCTTTAACTC
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
60 6 0.11
61 50 0.88
62 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (61 bp):
TCAATTTAGATCCAAATATAAAAAATAAAAAAAAATTAGCCCTTAATATTTACAAAATTTG
Found at i:1404556 original size:34 final size:34
Alignment explanation
Indices: 1404508--1404578 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
1404498 TGAGTACGTC
1404508 GTTTACTCAGTGCCACAATTCACAACTCAGTATG
1 GTTTACTCAGTGCCACAATTCACAACTCAGTATG
* *
1404542 GTTTTCTCAGTGCCACGATTCACAACTCAGTATG
1 GTTTACTCAGTGCCACAATTCACAACTCAGTATG
1404576 GTT
1 GTT
1404579 CTCCTCGTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (34 bp):
GTTTACTCAGTGCCACAATTCACAACTCAGTATG
Found at i:1404668 original size:34 final size:34
Alignment explanation
Indices: 1404590--1404742 Score: 218
Period size: 34 Copynumber: 4.5 Consensus size: 34
1404580 TCCTCGTGAA
* * *
1404590 AAATGCCATACCTACGTTTCATAACTCAGTATGG
1 AAATACCATACCTACGTATCATAACTCGGTATGG
1404624 AAAATACCATACCTACGTATCATAACTCGGTATGG
1 -AAATACCATACCTACGTATCATAACTCGGTATGG
* *
1404659 AAATACCATACCTACG-ATCATAGCTCGGTATAG
1 AAATACCATACCTACGTATCATAACTCGGTATGG
* * *
1404692 AATTACCATACCTACATATCATAGCTCGGTATGG
1 AAATACCATACCTACGTATCATAACTCGGTATGG
1404726 AAATACCATACCTACGT
1 AAATACCATACCTACGT
1404743 TTCACATTTT
Statistics
Matches: 107, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
33 29 0.27
34 47 0.44
35 31 0.29
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (34 bp):
AAATACCATACCTACGTATCATAACTCGGTATGG
Found at i:1404705 original size:67 final size:69
Alignment explanation
Indices: 1404590--1404742 Score: 220
Period size: 67 Copynumber: 2.2 Consensus size: 69
1404580 TCCTCGTGAA
* * * *
1404590 AAATGCCATACCTACGTTTCATAACTCAGTATGGAAAATACCATACCTACGTATCATAACTCGGT
1 AAATACCATACCTACGTATCATAACTCAGTATAGAAAATACCATACCTACATATCATAACTCGGT
1404655 ATGG
66 ATGG
* * * *
1404659 AAATACCATACCTACG-ATCATAGCTCGGTATAG-AATTACCATACCTACATATCATAGCTCGGT
1 AAATACCATACCTACGTATCATAACTCAGTATAGAAAATACCATACCTACATATCATAACTCGGT
1404722 ATGG
66 ATGG
1404726 AAATACCATACCTACGT
1 AAATACCATACCTACGT
1404743 TTCACATTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
67 47 0.63
68 13 0.17
69 15 0.20
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (69 bp):
AAATACCATACCTACGTATCATAACTCAGTATAGAAAATACCATACCTACATATCATAACTCGGT
ATGG
Found at i:1413389 original size:15 final size:15
Alignment explanation
Indices: 1413369--1413398 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1413359 CCGTAAGTAA
1413369 CTTAGCCATTTCTAT
1 CTTAGCCATTTCTAT
1413384 CTTAGCCATTTCTAT
1 CTTAGCCATTTCTAT
1413399 TTTCCTTAAC
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:0.20, C:0.27, G:0.07, T:0.47
Consensus pattern (15 bp):
CTTAGCCATTTCTAT
Found at i:1413659 original size:11 final size:10
Alignment explanation
Indices: 1413639--1413663 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1413629 CGTTCTAGAT
1413639 GGGGGTGGGG
1 GGGGGTGGGG
1413649 GGGGGTGGGG
1 GGGGGTGGGG
1413659 GGGGG
1 GGGGG
1413664 CTTATCCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.92, T:0.08
Consensus pattern (10 bp):
GGGGGTGGGG
Found at i:1414459 original size:12 final size:11
Alignment explanation
Indices: 1414437--1414462 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1414427 AACCTGCTTG
1414437 TTTTGTTTTTT
1 TTTTGTTTTTT
1414448 TTTTGTTTTTT
1 TTTTGTTTTTT
1414459 TTTT
1 TTTT
1414463 CTGTAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:1417638 original size:26 final size:28
Alignment explanation
Indices: 1417609--1417660 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
1417599 CTTAAAAATG
1417609 TAAAATAAATAATT-A-AATATATGATT
1 TAAAATAAATAATTAATAATATATGATT
* *
1417635 TAAAATTAATTATTAATAATATATGA
1 TAAAATAAATAATTAATAATATATGA
1417661 AATATATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
27 1 0.05
28 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (28 bp):
TAAAATAAATAATTAATAATATATGATT
Found at i:1418774 original size:14 final size:13
Alignment explanation
Indices: 1418749--1418773 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1418739 ATTCAATGAG
1418749 AATTAAAAAAAAT
1 AATTAAAAAAAAT
1418762 AATTAAAAAAAA
1 AATTAAAAAAAA
1418774 AACAGGCGCT
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AATTAAAAAAAAT
Found at i:1422838 original size:2 final size:2
Alignment explanation
Indices: 1422831--1422857 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1422821 GATTAGCCTT
1422831 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1422858 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1426011 original size:22 final size:22
Alignment explanation
Indices: 1425975--1426041 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
1425965 TGGTTGTACT
* * *
1425975 TTTTTGTATATTTAAAATTTAG
1 TTTTTCTATTTTTAAAATTTAA
1425997 TATTTT-TATTTTTAAAAATTTAA
1 T-TTTTCTATTTTT-AAAATTTAA
1426020 TTTTTCTAATTTTT-AAATTTAA
1 TTTTTCT-ATTTTTAAAATTTAA
1426042 AATTTCAGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
22 19 0.49
23 14 0.36
24 6 0.15
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.61
Consensus pattern (22 bp):
TTTTTCTATTTTTAAAATTTAA
Found at i:1432763 original size:17 final size:17
Alignment explanation
Indices: 1432719--1432766 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
1432709 AAATAATTTA
*
1432719 AAAATTATAAAAATATTC
1 AAAATT-TAAAAAAATTC
**
1432737 AAAAAATAAAAAAATTC
1 AAAATTTAAAAAAATTC
1432754 AAAATTTAAAAAA
1 AAAATTTAAAAAA
1432767 TTAAAAGTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAATTTAAAAAAATTC
Found at i:1432772 original size:7 final size:8
Alignment explanation
Indices: 1432716--1432772 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
1432706 GCCAAATAAT
*
1432716 TTAAAAAT
1 TTAAAAAA
1432724 TATAAAAATA
1 T-TAAAAA-A
1432734 TTCAAAAAA
1 TT-AAAAAA
*
1432743 TAAAAAAA
1 TTAAAAAA
* *
1432751 TTCAAAAT
1 TTAAAAAA
1432759 TTAAAAAA
1 TTAAAAAA
1432767 TTAAAA
1 TTAAAA
1432773 GTCCATAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
8 24 0.62
9 9 0.23
10 6 0.15
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (8 bp):
TTAAAAAA
Found at i:1437987 original size:31 final size:31
Alignment explanation
Indices: 1437952--1438013 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1437942 TACAATTTGA
* *
1437952 TCACTAAATTATTCAAAA-TTTTTCATTTAAG
1 TCACTAAACTATTAAAAAGTTTTT-ATTTAAG
1437983 TCACTAAACTATTAAAAAGTTTTTATTTAAG
1 TCACTAAACTATTAAAAAGTTTTTATTTAAG
1438014 CCATTGGACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (31 bp):
TCACTAAACTATTAAAAAGTTTTTATTTAAG
Found at i:1441209 original size:45 final size:45
Alignment explanation
Indices: 1441160--1441354 Score: 291
Period size: 45 Copynumber: 4.3 Consensus size: 45
1441150 TCGGCCACGG
* * * *
1441160 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
* *
1441205 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
* * * *
1441250 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAG
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
*
1441295 TGCTTCCTTAATTTGTTCCATAAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
1441340 TGCTTCCTTAATTTC
1 TGCTTCCTTAATTTC
1441355 ATGCTGTTCA
Statistics
Matches: 136, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 136 1.00
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (45 bp):
TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
Found at i:1441711 original size:20 final size:20
Alignment explanation
Indices: 1441686--1441740 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1441676 ACGAGTTAAA
* *
1441686 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
1441706 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
1441726 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
1441741 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:1444223 original size:68 final size:68
Alignment explanation
Indices: 1444057--1444254 Score: 371
Period size: 68 Copynumber: 2.9 Consensus size: 68
1444047 ATTTCTCTTT
1444057 TTTTTTATTTACGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGCAAAATTTTTTTT
1 TTTTTT-TTTACGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGCAAAATTTTTTTT
1444122 TTGA
65 TTGA
1444126 -TTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGCAAAATTTTTTTTT
1 TTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGCAAAATTTTTTTTT
1444190 TGA
66 TGA
*
1444193 TTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGATCGTAGGCAAAATTTTTT
1 TTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGCAAAATTTTTT
1444255 GATTTTTTTT
Statistics
Matches: 127, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
67 62 0.49
68 65 0.51
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.46
Consensus pattern (68 bp):
TTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGCAAAATTTTTTTTT
TGA
Found at i:1445078 original size:45 final size:45
Alignment explanation
Indices: 1444887--1445081 Score: 282
Period size: 45 Copynumber: 4.3 Consensus size: 45
1444877 TCGGCCATGG
* * * *
1444887 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
* *
1444932 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
* * * *
1444977 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAG
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
*
1445022 TGCTTCCTTAATTTGTTCCATAAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
*
1445067 TGCTTCTTTAATTTC
1 TGCTTCCTTAATTTC
1445082 ATGCCGTTCA
Statistics
Matches: 135, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 135 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (45 bp):
TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
Found at i:1445438 original size:20 final size:20
Alignment explanation
Indices: 1445413--1445467 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1445403 ACGAGTTAAA
* *
1445413 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
1445433 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
1445453 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
1445468 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:1445676 original size:39 final size:40
Alignment explanation
Indices: 1445633--1445744 Score: 104
Period size: 39 Copynumber: 2.8 Consensus size: 40
1445623 TCAGATAGTT
*
1445633 CGAAGTAATAGTTGACACCCAGTGTCTCATCG-GCCTAGC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
** * ** * *
1445672 CGAAGTAA-AGTTGGTACCGAGTACCTCATCGAATCTATC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
*
1445711 CGAAGAAATA-TAGTGACACCCAGTGTCTCATCGA
1 CGAAGTAATAGT--TGACACCCAGTGTCTCATCGA
1445745 CTCGAGGTTG
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
38 18 0.33
39 20 0.36
40 1 0.02
41 16 0.29
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.23
Consensus pattern (40 bp):
CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
Found at i:1447324 original size:5 final size:5
Alignment explanation
Indices: 1447306--1447336 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
1447296 TTTCTTTTAT
1447306 ATATA ATAATA ATATA ATATA ATATA ATATA
1 ATATA AT-ATA ATATA ATATA ATATA ATATA
1447337 CTTAATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:1448170 original size:50 final size:51
Alignment explanation
Indices: 1448093--1448221 Score: 190
Period size: 50 Copynumber: 2.5 Consensus size: 51
1448083 GACCATGGCA
*
1448093 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCCAGGA-AAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAA-TG
*
1448144 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* * *
1448194 ACAAGTGAAAAGTGGTAGCTTCAGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
1448222 CTGATCAGTG
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
50 44 0.62
51 27 0.38
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Done.